Disposable.

34 files changed, 5263 insertions, 3899 deletions

diff --git a/data/Pagoda-2.0.0-uobm1-test_queries.log b/data/Pagoda-2.0.0-uobm1-test_queries.log
new file mode 100644
index 0000000..42b338a
--- /dev/null
+++ b/data/Pagoda-2.0.0-uobm1-test_queries.log
@@ -0,0 +1,1158 @@
+The axiom: DataPropertyRange(<http://semantics.crl.ibm.com/univ-bench-dl.owl#firstName> xsd:string) is being ignored.
+The axiom: DataPropertyRange(<http://semantics.crl.ibm.com/univ-bench-dl.owl#lastName> xsd:string) is being ignored.
+The number of data property range axioms that are ignored: 2(186)
+XMLReader initialized using JAXP: org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser@5456afaa
+SimpleETL rewriting DONE
+additional ontology data is saved in /home/alessandro/Desktop/Pagoda_basic-version/PAGOdA/tmp2015-05-28T14:42:07.907/ABox.ttl.
+HermiT classification done: 0.108
+classification done and enriched lower bound rules.
+The number of rules: 238
+OntologyID: OntologyID(OntologyIRI(<http://semantics.crl.ibm.com/univ-bench-dl.owl>))
+ELHO fragment extracted ...
+Preprocessing ... checking satisfiability ...
+rl-lower-bound store after importing data: 257920 (257920 new)
+rl-lower-bound store finished importing data in 0.576 seconds.
+Prefix declared: prefix0:=http://semantics.crl.ibm.com/univ-bench-dl.owl#
+rl-lower-bound store after materialising lower program: 515592 (257672 new)
+rl-lower-bound store finished the materialisation of lower program in 0.557 seconds.
+The number of answers in the lower bound: 0
+The number of sameAs assertions in RL lower store: 102
+elho-lower-bound store after importing data: 257920 (257920 new)
+elho-lower-bound store finished importing data in 0.559 seconds.
+elho-lower-bound store after materialising saturate named individuals: 341262 (83342 new)
+elho-lower-bound store finished the materialisation of saturate named individuals in 0.173 seconds.
+elho-lower-bound store after materialising lower program: 557087 (215825 new)
+elho-lower-bound store finished the materialisation of lower program in 0.525 seconds.
+elho-lower-store finished its own materialisation in 0.579 seconds.
+Failed to find configuration: location-mapping.ttl;location-mapping.rdf;location-mapping.n3;etc/location-mapping.rdf;etc/location-mapping.n3;etc/location-mapping.ttl
+@Time to group individuals by equality: 0.062
+The number of answers in the lower bound: 0
+lazy-upper-bound store after importing data: 257920 (257920 new)
+lazy-upper-bound store finished importing data in 0.555 seconds.
+lazy-upper-bound store after materialising saturate named individuals: 341262 (83342 new)
+lazy-upper-bound store finished the materialisation of saturate named individuals in 0.18 seconds.
+lazy-upper-bound store is materialising multi-stage upper program ...
+Iteration 1:
+The lazy-upper-bound store is valid.
+lazy-upper-bound store after materialising datalog-rules: 550540 (209278 new)
+Time to materialise datalog-rules: 0.612
+Time to detect violations: 0.367
+Time to make the constraint being satisfied: 0.01 594 tuples for atLeast(1 <http://semantics.crl.ibm.com/univ-bench-dl.owl#like> <http://semantics.crl.ibm.com/univ-bench-dl.owl#SwimmingClass>)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#SwimmingLover>(X)
+tuple number: 594 before: 550540 after: 550540 (0 new) .
+Time to make the constraint being satisfied: 0.006 553 tuples for atLeast(1 <http://semantics.crl.ibm.com/univ-bench-dl.owl#like> <http://semantics.crl.ibm.com/univ-bench-dl.owl#BasketBallClass>)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#BasketBallLover>(X)
+tuple number: 553 before: 550540 after: 550540 (0 new) .
+Time to make the constraint being satisfied: 0.056 9627 tuples for <http://semantics.crl.ibm.com/univ-bench-dl.owl#NonScienceStudent>(X) v <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#concept_hasMajor_Science_exist>(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#Student>(X)
+tuple number: 0 before: 550540 after: 550540 (0 new) .
+Time to make the constraint being satisfied: 0.007 48 tuples for <http://semantics.crl.ibm.com/univ-bench-dl.owl#Man>(X) v <http://semantics.crl.ibm.com/univ-bench-dl.owl#Woman>(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#Person>(X)
+tuple number: 0 before: 550540 after: 550540 (0 new) .
+Time to make the constraint being satisfied: 0.004 331 tuples for atLeast(1 <http://semantics.crl.ibm.com/univ-bench-dl.owl#isCrazyAbout> <http://semantics.crl.ibm.com/univ-bench-dl.owl#SwimmingClass>)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#SwimmingFan>(X)
+tuple number: 331 before: 550540 after: 550540 (0 new) .
+Time to make the constraint being satisfied: 0.005 596 tuples for atLeast(1 <http://semantics.crl.ibm.com/univ-bench-dl.owl#like> <http://semantics.crl.ibm.com/univ-bench-dl.owl#BaseballClass>)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#BaseballLover>(X)
+tuple number: 596 before: 550540 after: 550540 (0 new) .
+Time to make the constraint being satisfied: 0.005 345 tuples for atLeast(1 <http://semantics.crl.ibm.com/univ-bench-dl.owl#isCrazyAbout> <http://semantics.crl.ibm.com/univ-bench-dl.owl#TennisClass>)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#TennisFan>(X)
+tuple number: 345 before: 550540 after: 550540 (0 new) .
+Time to make the constraint being satisfied: 0.052 43968 tuples for <http://semantics.crl.ibm.com/univ-bench-dl.owl#PeopleWithManyHobbies>(X) v [Y1 == Y2]@atMost(2 <http://semantics.crl.ibm.com/univ-bench-dl.owl#like> owl:Thing)(X) v [Y1 == Y3]@atMost(2 <http://semantics.crl.ibm.com/univ-bench-dl.owl#like> owl:Thing)(X) v [Y2 == Y3]@atMost(2 <http://semantics.crl.ibm.com/univ-bench-dl.owl#like> owl:Thing)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#like>(X,Y1), <http://semantics.crl.ibm.com/univ-bench-dl.owl#like>(X,Y2), <http://semantics.crl.ibm.com/univ-bench-dl.owl#like>(X,Y3)
+tuple number: 0 before: 550540 after: 550540 (0 new) .
+Time to make the constraint being satisfied: 0.008 1065 tuples for atLeast(1 <http://semantics.crl.ibm.com/univ-bench-dl.owl#worksFor> <http://semantics.crl.ibm.com/univ-bench-dl.owl#ResearchGroup>)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#ResearchAssistant>(X)
+tuple number: 1065 before: 550540 after: 550540 (0 new) .
+Time to make the constraint being satisfied: 0.004 478 tuples for atLeast(1 <http://semantics.crl.ibm.com/univ-bench-dl.owl#worksFor> <http://semantics.crl.ibm.com/univ-bench-dl.owl#Organization>)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#Employee>(X)
+tuple number: 478 before: 550540 after: 550540 (0 new) .
+Time to make the constraint being satisfied: 0.004 4 tuples for <http://semantics.crl.ibm.com/univ-bench-dl.owl#WomanCollege>(X) v <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#concept_hasStudent_Man_exist>(X) v <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#concept_hasStudent_UndergraduateStudent_neg_exist>(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#College>(X)
+tuple number: 0 before: 550540 after: 550540 (0 new) .
+Time to make the constraint being satisfied: 0.004 380 tuples for atLeast(1 <http://semantics.crl.ibm.com/univ-bench-dl.owl#like> <http://semantics.crl.ibm.com/univ-bench-dl.owl#Sports>)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#SportsLover>(X)
+tuple number: 380 before: 550540 after: 550540 (0 new) .
+Time to make the constraint being satisfied: 0.005 283 tuples for atLeast(1 <http://semantics.crl.ibm.com/univ-bench-dl.owl#isCrazyAbout> <http://semantics.crl.ibm.com/univ-bench-dl.owl#Sports>)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#SportsFan>(X)
+tuple number: 283 before: 550540 after: 550540 (0 new) .
+Time to make the constraint being satisfied: 0.004 361 tuples for atLeast(1 <http://semantics.crl.ibm.com/univ-bench-dl.owl#isCrazyAbout> <http://semantics.crl.ibm.com/univ-bench-dl.owl#BasketBallClass>)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#BasketBallFan>(X)
+tuple number: 361 before: 550540 after: 550540 (0 new) .
+Time to make the constraint being satisfied: 0.004 352 tuples for atLeast(1 <http://semantics.crl.ibm.com/univ-bench-dl.owl#isCrazyAbout> <http://semantics.crl.ibm.com/univ-bench-dl.owl#BaseballClass>)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#BaseballFan>(X)
+tuple number: 352 before: 550540 after: 550540 (0 new) .
+lazy-upper-bound store after adding facts for violations: 550540 (0 new)
+Time to add triples for violations: 0.283
+Iteration 2:
+The lazy-upper-bound store is valid.
+lazy-upper-bound store after materialising datalog-rules: 582920 (32380 new)
+Time to materialise datalog-rules: 0.057
+Time to detect violations: 0.233
+Time to make the constraint being satisfied: 0.007 3966 tuples for <http://semantics.crl.ibm.com/univ-bench-dl.owl#PeopleWithManyHobbies>(X) v [Y1 == Y2]@atMost(2 <http://semantics.crl.ibm.com/univ-bench-dl.owl#like> owl:Thing)(X) v [Y1 == Y3]@atMost(2 <http://semantics.crl.ibm.com/univ-bench-dl.owl#like> owl:Thing)(X) v [Y2 == Y3]@atMost(2 <http://semantics.crl.ibm.com/univ-bench-dl.owl#like> owl:Thing)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#like>(X,Y1), <http://semantics.crl.ibm.com/univ-bench-dl.owl#like>(X,Y2), <http://semantics.crl.ibm.com/univ-bench-dl.owl#like>(X,Y3)
+tuple number: 0 before: 582920 after: 582920 (0 new) .
+Time to make the constraint being satisfied: 0.015 1835 tuples for atLeast(3 <http://semantics.crl.ibm.com/univ-bench-dl.owl#like> owl:Thing)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#PeopleWithManyHobbies>(X)
+tuple number: 1835 before: 582920 after: 582920 (0 new) .
+lazy-upper-bound store after adding facts for violations: 582920 (0 new)
+Time to add triples for violations: 0.04
+Iteration 3:
+The lazy-upper-bound store is valid.
+lazy-upper-bound store after materialising datalog-rules: 594418 (11498 new)
+Time to materialise datalog-rules: 0.026
+Time to detect violations: 0.338
+Time to make the constraint being satisfied: 0.005 481 tuples for atLeast(3 <http://semantics.crl.ibm.com/univ-bench-dl.owl#like> owl:Thing)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#PeopleWithManyHobbies>(X)
+tuple number: 481 before: 594418 after: 594418 (0 new) .
+lazy-upper-bound store after adding facts for violations: 594418 (0 new)
+Time to add triples for violations: 0.017
+Iteration 4:
+The lazy-upper-bound store is valid.
+lazy-upper-bound store after materialising datalog-rules: 597304 (2886 new)
+Time to materialise datalog-rules: 0.016
+lazy-upper-bound store after materialising multi-stage upper program: 597304 (256042 new)
+lazy-upper-bound store is DONE for multi-stage materialising in 2.512 seconds.
+The lazy-upper-bound store is valid.
+There are no contradictions derived in the lazy upper bound materialisation.
+The ontology and dataset is satisfiable.
+time for satisfiability checking: 6.915
+tracking store after importing data: 257920 (257920 new)
+tracking store finished importing data in 0.589 seconds.
+tracking store after materialising saturate named individuals: 341262 (83342 new)
+tracking store finished the materialisation of saturate named individuals in 0.174 seconds.
+tracking store after materialising lower program: 557087 (215825 new)
+tracking store finished the materialisation of lower program in 0.532 seconds.
+tracking store is materialising multi-stage upper program ...
+Iteration 1:
+current store after materialising upper related rules: 646037 (88950 new)
+current store finished the materialisation of upper related rules in 0.513 seconds.
+gap query evaluted ...
+current store before importing gap tuples: 646037
+There are 126566 tuples in the gap between lower and upper bound materialisation.
+current store after importing gap tuples: 764044 (118007).
+current store finished importing gap tuples: 764044 in 0.372.
+tracking store after materialising datalog-rules: 764044 (206957 new)
+Time to materialise datalog-rules: 0.898
+Time to detect violations: 0.124
+Time to make the constraint being satisfied: 0.01 478 tuples for atLeast(1 <http://semantics.crl.ibm.com/univ-bench-dl.owl#like> <http://semantics.crl.ibm.com/univ-bench-dl.owl#SwimmingClass>)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#SwimmingLover>(X)
+tuple number: 478 before: 764044 after: 764044 (0 new) .
+Time to make the constraint being satisfied: 0.007 500 tuples for atLeast(1 <http://semantics.crl.ibm.com/univ-bench-dl.owl#like> <http://semantics.crl.ibm.com/univ-bench-dl.owl#BaseballClass>)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#BaseballLover>(X)
+tuple number: 500 before: 764044 after: 764044 (0 new) .
+Time to make the constraint being satisfied: 0.004 5 tuples for atLeast(1 <http://semantics.crl.ibm.com/univ-bench-dl.owl#hasStudent> <http://semantics.crl.ibm.com/univ-bench-dl.owl#UndergraduateStudent_neg>)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#College>(X)
+tuple number: 5 before: 764044 after: 764044 (0 new) .
+Time to make the constraint being satisfied: 0.005 295 tuples for atLeast(1 <http://semantics.crl.ibm.com/univ-bench-dl.owl#isCrazyAbout> <http://semantics.crl.ibm.com/univ-bench-dl.owl#TennisClass>)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#TennisFan>(X)
+tuple number: 295 before: 764044 after: 764044 (0 new) .
+Time to make the constraint being satisfied: 0.008 489 tuples for atLeast(1 <http://semantics.crl.ibm.com/univ-bench-dl.owl#like> <http://semantics.crl.ibm.com/univ-bench-dl.owl#BasketBallClass>)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#BasketBallLover>(X)
+tuple number: 489 before: 764044 after: 764044 (0 new) .
+Time to make the constraint being satisfied: 0.01 1065 tuples for atLeast(1 <http://semantics.crl.ibm.com/univ-bench-dl.owl#worksFor> <http://semantics.crl.ibm.com/univ-bench-dl.owl#ResearchGroup>)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#ResearchAssistant>(X)
+tuple number: 1065 before: 764044 after: 764044 (0 new) .
+Time to make the constraint being satisfied: 0.012 1543 tuples for atLeast(1 <http://semantics.crl.ibm.com/univ-bench-dl.owl#worksFor> <http://semantics.crl.ibm.com/univ-bench-dl.owl#Organization>)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#Employee>(X)
+tuple number: 1543 before: 764044 after: 764044 (0 new) .
+Time to make the constraint being satisfied: 0.048 9627 tuples for atLeast(1 <http://semantics.crl.ibm.com/univ-bench-dl.owl#hasMajor> <http://semantics.crl.ibm.com/univ-bench-dl.owl#Science>)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#Student>(X)
+tuple number: 9627 before: 764044 after: 764044 (0 new) .
+Time to make the constraint being satisfied: 0.012 1772 tuples for atLeast(1 <http://semantics.crl.ibm.com/univ-bench-dl.owl#like> <http://semantics.crl.ibm.com/univ-bench-dl.owl#Sports>)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#SportsLover>(X)
+tuple number: 1772 before: 764044 after: 764044 (0 new) .
+Time to make the constraint being satisfied: 0.01 1311 tuples for atLeast(1 <http://semantics.crl.ibm.com/univ-bench-dl.owl#isCrazyAbout> <http://semantics.crl.ibm.com/univ-bench-dl.owl#Sports>)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#SportsFan>(X)
+tuple number: 1311 before: 764044 after: 764044 (0 new) .
+Time to make the constraint being satisfied: 0.005 270 tuples for atLeast(1 <http://semantics.crl.ibm.com/univ-bench-dl.owl#isCrazyAbout> <http://semantics.crl.ibm.com/univ-bench-dl.owl#SwimmingClass>)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#SwimmingFan>(X)
+tuple number: 270 before: 764044 after: 764044 (0 new) .
+Time to make the constraint being satisfied: 0.004 4 tuples for atLeast(1 <http://semantics.crl.ibm.com/univ-bench-dl.owl#hasStudent> <http://semantics.crl.ibm.com/univ-bench-dl.owl#Man>)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#College>(X)
+tuple number: 4 before: 764044 after: 764044 (0 new) .
+Time to make the constraint being satisfied: 0.005 297 tuples for atLeast(1 <http://semantics.crl.ibm.com/univ-bench-dl.owl#isCrazyAbout> <http://semantics.crl.ibm.com/univ-bench-dl.owl#BasketBallClass>)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#BasketBallFan>(X)
+tuple number: 297 before: 764044 after: 764044 (0 new) .
+Time to make the constraint being satisfied: 0.012 1772 tuples for atLeast(1 <http://semantics.crl.ibm.com/univ-bench-dl.owl#like> owl:Thing)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#PeopleWithHobby>(X)
+tuple number: 1772 before: 764044 after: 764044 (0 new) .
+Time to make the constraint being satisfied: 0.006 290 tuples for atLeast(1 <http://semantics.crl.ibm.com/univ-bench-dl.owl#isCrazyAbout> <http://semantics.crl.ibm.com/univ-bench-dl.owl#BaseballClass>)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#BaseballFan>(X)
+tuple number: 290 before: 764044 after: 764044 (0 new) .
+Time to make the constraint being satisfied: 0.084 7041 tuples for atLeast(3 <http://semantics.crl.ibm.com/univ-bench-dl.owl#like> owl:Thing)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#PeopleWithManyHobbies>(X)
+tuple number: 7041 before: 764044 after: 764044 (0 new) .
+tracking store after adding facts for violations: 764044 (0 new)
+Time to add triples for violations: 0.38
+Iteration 2:
+current store after materialising upper related rules: 831557 (67513 new)
+current store finished the materialisation of upper related rules in 0.137 seconds.
+gap query evaluted ...
+current store before importing gap tuples: 831557
+There are 41367 tuples in the gap between lower and upper bound materialisation.
+current store after importing gap tuples: 867593 (36036).
+current store finished importing gap tuples: 867593 in 0.097.
+tracking store after materialising datalog-rules: 867593 (103549 new)
+Time to materialise datalog-rules: 0.245
+Time to detect violations: 0.134
+Time to make the constraint being satisfied: 0.005 2 tuples for atLeast(1 <http://semantics.crl.ibm.com/univ-bench-dl.owl#hasMajor> <http://semantics.crl.ibm.com/univ-bench-dl.owl#Science>)(X) :- <http://semantics.crl.ibm.com/univ-bench-dl.owl#Student>(X)
+tuple number: 2 before: 867593 after: 867593 (0 new) .
+tracking store after adding facts for violations: 867593 (0 new)
+Time to add triples for violations: 0.024
+Iteration 3:
+current store after materialising upper related rules: 867601 (8 new)
+current store finished the materialisation of upper related rules in 0.012 seconds.
+gap query evaluted ...
+current store before importing gap tuples: 867601
+There are 4 tuples in the gap between lower and upper bound materialisation.
+current store after importing gap tuples: 867605 (4).
+current store finished importing gap tuples: 867605 in 0.01.
+tracking store after materialising datalog-rules: 867605 (12 new)
+Time to materialise datalog-rules: 0.033
+tracking store after materialising multi-stage upper program: 867605 (310518 new)
+tracking store is DONE for multi-stage materialising in 1.91 seconds.
+The number of answers in the upper bound: 12782
+The number of answers in the upper bound: 0
+The number of answers in the upper bound: 14182
+The number of answers in the upper bound: 1
+The number of answers in the upper bound: 5
+The number of answers in the upper bound: 23
+There are 5 different bottom fragments.
+12782 triples are added into the store.
+Prefix declared: prefix1:=http://semantics.crl.ibm.com/univ-bench-dl-TBox.owl#
+14182 triples are added into the store.
+1 triples are added into the store.
+5 triples are added into the store.
+23 triples are added into the store.
+tracking store after materialising tracking program: 1441314 (573709 new)
+tracking store finished the materialisation of tracking program in 2.941 seconds.
+@Time to group individuals by equality: 0.018
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#Science> 10
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#Person> 0
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#ScienceStudent> 0
+class: <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#concept_hasStudent_Man_exist> 0
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#Organization> 5
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#College> 4
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#UndergraduateStudent> 0
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#Student> 9627
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#WomanCollege> 1
+class: <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#concept_hasMajor_Science_exist> 3153
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#Woman> 0
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#Man> 0
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#isMemberOf> 0
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#hasMember> 0
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#hasMajor> 3153
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#isStudentOf> 0
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#hasStudent> 0
+property: <http://www.w3.org/2002/07/owl#sameAs> 0
+ABox extraction Done
+TBox extraction Done
+Before adding bottom fragment:
+ABoxAxiomsCount = 15953, TBoxAxiomsCount = 24
+finish extracting axioms for bottom 0_1
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#Person> 48
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#Student> 9627
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#Organization> 5
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#WomanCollege> 1
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#Science> 0
+class: <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#concept_hasMajor_Science_exist> 0
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#UndergraduateStudent> 0
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#College> 4
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#Woman> 7211
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#Man> 6873
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#ScienceStudent> 0
+class: <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#concept_hasStudent_Man_exist> 19
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#hasStudent> 0
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#hasMember> 0
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#isMemberOf> 0
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#hasMajor> 0
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#isStudentOf> 0
+property: <http://www.w3.org/2002/07/owl#sameAs> 48
+ABox extraction Done
+TBox extraction Done
+Before adding bottom fragment:
+ABoxAxiomsCount = 23836, TBoxAxiomsCount = 24
+finish extracting axioms for bottom 0_2
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#WomanCollege> 1
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#Organization> 5
+class: <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#concept_hasMajor_Science_exist> 0
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#College> 4
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#Student> 9627
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#UndergraduateStudent> 0
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#Person> 0
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#ScienceStudent> 0
+class: <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#concept_hasStudent_Man_exist> 0
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#Woman> 0
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#Man> 0
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#Science> 0
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#hasMember> 0
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#isMemberOf> 0
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#hasMajor> 0
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#isStudentOf> 0
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#hasStudent> 0
+property: <http://www.w3.org/2002/07/owl#sameAs> 0
+ABox extraction Done
+TBox extraction Done
+Before adding bottom fragment:
+ABoxAxiomsCount = 9637, TBoxAxiomsCount = 23
+finish extracting axioms for bottom 0_3
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#College> 4
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#Student> 9627
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#Person> 0
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#Woman> 0
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#UndergraduateStudent> 0
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#WomanCollege> 1
+class: <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#concept_hasMajor_Science_exist> 0
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#Man> 0
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#ScienceStudent> 0
+class: <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#concept_hasStudent_Man_exist> 0
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#Organization> 5
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#Science> 0
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#hasStudent> 264
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#hasMember> 0
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#isMemberOf> 0
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#hasMajor> 0
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#isStudentOf> 0
+property: <http://www.w3.org/2002/07/owl#sameAs> 0
+ABox extraction Done
+TBox extraction Done
+Before adding bottom fragment:
+ABoxAxiomsCount = 9901, TBoxAxiomsCount = 24
+finish extracting axioms for bottom 0_4
+property: <http://www.w3.org/2002/07/owl#sameAs> 37
+ABox extraction Done
+TBox extraction Done
+Before adding bottom fragment:
+ABoxAxiomsCount = 37, TBoxAxiomsCount = 2
+finish extracting axioms for bottom 0_5
+The ontology is consistent!
+Preprocessing Done in 18.306 seconds.
+---------- start evaluating Query 1 ----------
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:UndergraduateStudent . ?x benchmark:takesCourse <http://www.Department0.University0.edu/Course0> }
+0.0
+The number of answers in the lower bound: 21
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:UndergraduateStudent . ?x benchmark:takesCourse <http://www.Department0.University0.edu/Course0> }
+0.005
+The number of answers returned by the upper bound: 21
+The number of answers in the upper bound: 21
+Difficulty of this query: UpperBound
+Total time to answer this query: 0.006
+The number of answer tuples: 21
+time for LowerBound: 0.001
+time for UpperBound: 0.005
+time for ELLowerBound: 0.0
+time for Fragment: 0.0
+time for FragmentRefinement: 0.0
+time for Summarisation: 0.0
+time for Dependency: 0.0
+time for FullReasoning: 0.0
+---------- start evaluating Query 2 ----------
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:Employee }
+0.001
+The number of answers in the lower bound: 2465
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:Employee }
+0.002
+The number of answers returned by the upper bound: 2465
+The number of answers in the upper bound: 2465
+Difficulty of this query: UpperBound
+Total time to answer this query: 0.009
+The number of answer tuples: 2465
+time for LowerBound: 0.007
+time for UpperBound: 0.002
+time for ELLowerBound: 0.0
+time for Fragment: 0.0
+time for FragmentRefinement: 0.0
+time for Summarisation: 0.0
+time for Dependency: 0.0
+time for FullReasoning: 0.0
+---------- start evaluating Query 3 ----------
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:Student . ?x benchmark:isMemberOf <http://www.Department0.University0.edu> }
+0.005
+The number of answers in the lower bound: 581
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:Student . ?x benchmark:isMemberOf <http://www.Department0.University0.edu> }
+0.009
+The number of answers returned by the upper bound: 581
+The number of answers in the upper bound: 581
+Difficulty of this query: UpperBound
+Total time to answer this query: 0.016
+The number of answer tuples: 581
+time for LowerBound: 0.007
+time for UpperBound: 0.009
+time for ELLowerBound: 0.0
+time for Fragment: 0.0
+time for FragmentRefinement: 0.0
+time for Summarisation: 0.0
+time for Dependency: 0.0
+time for FullReasoning: 0.0
+---------- start evaluating Query 4 ----------
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:Publication . ?x benchmark:publicationAuthor ?y . ?y rdf:type benchmark:Faculty . ?y benchmark:isMemberOf <http://www.Department0.University0.edu> }
+0.001
+The number of answers in the lower bound: 292
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:Publication . ?x benchmark:publicationAuthor ?y . ?y rdf:type benchmark:Faculty . ?y benchmark:isMemberOf <http://www.Department0.University0.edu> }
+0.006
+The number of answers returned by the upper bound: 292
+The number of answers in the upper bound: 292
+Difficulty of this query: UpperBound
+Total time to answer this query: 0.01
+The number of answer tuples: 292
+time for LowerBound: 0.003
+time for UpperBound: 0.007
+time for ELLowerBound: 0.0
+time for Fragment: 0.0
+time for FragmentRefinement: 0.0
+time for Summarisation: 0.0
+time for Dependency: 0.0
+time for FullReasoning: 0.0
+---------- start evaluating Query 5 ----------
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:ResearchGroup . ?x benchmark:subOrganizationOf <http://www.University0.edu> }
+0.001
+The number of answers in the lower bound: 235
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:ResearchGroup . ?x benchmark:subOrganizationOf <http://www.University0.edu> }
+0.003
+The number of answers returned by the upper bound: 235
+The number of answers in the upper bound: 235
+Difficulty of this query: UpperBound
+Total time to answer this query: 0.005
+The number of answer tuples: 235
+time for LowerBound: 0.002
+time for UpperBound: 0.003
+time for ELLowerBound: 0.0
+time for Fragment: 0.0
+time for FragmentRefinement: 0.0
+time for Summarisation: 0.0
+time for Dependency: 0.0
+time for FullReasoning: 0.0
+---------- start evaluating Query 6 ----------
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:Person . <http://www.University0.edu> benchmark:hasAlumnus ?x }
+0.006
+The number of answers in the lower bound: 991
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:Person . <http://www.University0.edu> benchmark:hasAlumnus ?x }
+0.007
+The number of answers returned by the upper bound: 991
+The number of answers in the upper bound: 991
+Difficulty of this query: UpperBound
+Total time to answer this query: 0.016
+The number of answer tuples: 991
+time for LowerBound: 0.008
+time for UpperBound: 0.008
+time for ELLowerBound: 0.0
+time for Fragment: 0.0
+time for FragmentRefinement: 0.0
+time for Summarisation: 0.0
+time for Dependency: 0.0
+time for FullReasoning: 0.0
+---------- start evaluating Query 7 ----------
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:Person . ?x benchmark:hasSameHomeTownWith <http://www.Department0.University0.edu/FullProfessor0> }
+0.0
+The number of answers in the lower bound: 0
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:Person . ?x benchmark:hasSameHomeTownWith <http://www.Department0.University0.edu/FullProfessor0> }
+0.001
+The number of answers in the upper bound: 0
+Difficulty of this query: UpperBound
+Total time to answer this query: 0.002
+The number of answer tuples: 0
+time for LowerBound: 0.001
+time for UpperBound: 0.001
+time for ELLowerBound: 0.0
+time for Fragment: 0.0
+time for FragmentRefinement: 0.0
+time for Summarisation: 0.0
+time for Dependency: 0.0
+time for FullReasoning: 0.0
+---------- start evaluating Query 8 ----------
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:SportsLover . <http://www.Department0.University0.edu> benchmark:hasMember ?x }
+0.0
+The number of answers in the lower bound: 376
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:SportsLover . <http://www.Department0.University0.edu> benchmark:hasMember ?x }
+0.002
+The number of answers returned by the upper bound: 376
+The number of answers in the upper bound: 376
+Difficulty of this query: UpperBound
+Total time to answer this query: 0.003
+The number of answer tuples: 376
+time for LowerBound: 0.001
+time for UpperBound: 0.002
+time for ELLowerBound: 0.0
+time for Fragment: 0.0
+time for FragmentRefinement: 0.0
+time for Summarisation: 0.0
+time for Dependency: 0.0
+time for FullReasoning: 0.0
+---------- start evaluating Query 9 ----------
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:GraduateCourse . ?x benchmark:isTaughtBy ?y . ?y rdf:type benchmark:SportsLover . ?y benchmark:isMemberOf ?z . ?z benchmark:subOrganizationOf <http://www.University0.edu> }
+0.002
+The number of answers in the lower bound: 747
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:GraduateCourse . ?x benchmark:isTaughtBy ?y . ?y rdf:type benchmark:SportsLover . ?y benchmark:isMemberOf ?z . ?z benchmark:subOrganizationOf <http://www.University0.edu> }
+0.004
+The number of answers returned by the upper bound: 747
+The number of answers in the upper bound: 747
+Difficulty of this query: UpperBound
+Total time to answer this query: 0.01
+The number of answer tuples: 747
+time for LowerBound: 0.005
+time for UpperBound: 0.005
+time for ELLowerBound: 0.0
+time for Fragment: 0.0
+time for FragmentRefinement: 0.0
+time for Summarisation: 0.0
+time for Dependency: 0.0
+time for FullReasoning: 0.0
+---------- start evaluating Query 10 ----------
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x benchmark:isFriendOf <http://www.Department0.University0.edu/FullProfessor0> }
+0.001
+The number of answers in the lower bound: 8
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x benchmark:isFriendOf <http://www.Department0.University0.edu/FullProfessor0> }
+0.002
+The number of answers returned by the upper bound: 8
+The number of answers in the upper bound: 8
+Difficulty of this query: UpperBound
+Total time to answer this query: 0.003
+The number of answer tuples: 8
+time for LowerBound: 0.001
+time for UpperBound: 0.002
+time for ELLowerBound: 0.0
+time for Fragment: 0.0
+time for FragmentRefinement: 0.0
+time for Summarisation: 0.0
+time for Dependency: 0.0
+time for FullReasoning: 0.0
+---------- start evaluating Query 11 ----------
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:Person . ?x benchmark:like ?y . ?z rdf:type benchmark:Chair . ?z benchmark:isHeadOf <http://www.Department0.University0.edu> . ?z benchmark:like ?y }
+0.003
+The number of answers in the lower bound: 2416
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:Person . ?x benchmark:like ?y . ?z rdf:type benchmark:Chair . ?z benchmark:isHeadOf <http://www.Department0.University0.edu> . ?z benchmark:like ?y }
+0.005
+The number of answers returned by the upper bound: 3886
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:Person . ?x benchmark:like ?y . ?z rdf:type benchmark:Chair . ?z benchmark:isHeadOf <http://www.Department0.University0.edu> . ?z benchmark:like ?y . ?y a <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#Original> . ?z a <http://www.cs.ox.ac.uk/PAGOdA/auxiliary#Original> }
+0.032
+The number of answers returned by the upper bound: 2416
+The number of answers in the upper bound: 2416
+Difficulty of this query: UpperBound
+Total time to answer this query: 0.04
+The number of answer tuples: 2416
+time for LowerBound: 0.008
+time for UpperBound: 0.032
+time for ELLowerBound: 0.0
+time for Fragment: 0.0
+time for FragmentRefinement: 0.0
+time for Summarisation: 0.0
+time for Dependency: 0.0
+time for FullReasoning: 0.0
+---------- start evaluating Query 12 ----------
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:Student . ?x benchmark:takesCourse ?y . ?y benchmark:isTaughtBy <http://www.Department0.University0.edu/FullProfessor0> }
+0.009
+The number of answers in the lower bound: 50
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:Student . ?x benchmark:takesCourse ?y . ?y benchmark:isTaughtBy <http://www.Department0.University0.edu/FullProfessor0> }
+0.011
+The number of answers returned by the upper bound: 50
+The number of answers in the upper bound: 50
+Difficulty of this query: UpperBound
+Total time to answer this query: 0.021
+The number of answer tuples: 50
+time for LowerBound: 0.01
+time for UpperBound: 0.011
+time for ELLowerBound: 0.0
+time for Fragment: 0.0
+time for FragmentRefinement: 0.0
+time for Summarisation: 0.0
+time for Dependency: 0.0
+time for FullReasoning: 0.0
+---------- start evaluating Query 13 ----------
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:PeopleWithHobby . ?x benchmark:isMemberOf <http://www.Department0.University0.edu> }
+0.004
+The number of answers in the lower bound: 416
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:PeopleWithHobby . ?x benchmark:isMemberOf <http://www.Department0.University0.edu> }
+0.005
+The number of answers returned by the upper bound: 416
+The number of answers in the upper bound: 416
+Difficulty of this query: UpperBound
+Total time to answer this query: 0.01
+The number of answer tuples: 416
+time for LowerBound: 0.005
+time for UpperBound: 0.005
+time for ELLowerBound: 0.0
+time for Fragment: 0.0
+time for FragmentRefinement: 0.0
+time for Summarisation: 0.0
+time for Dependency: 0.0
+time for FullReasoning: 0.0
+---------- start evaluating Query 14 ----------
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:Woman . ?x rdf:type benchmark:Student . ?x benchmark:isMemberOf ?y . ?y benchmark:subOrganizationOf <http://www.University0.edu> }
+0.012
+The number of answers in the lower bound: 6535
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:Woman . ?x rdf:type benchmark:Student . ?x benchmark:isMemberOf ?y . ?y benchmark:subOrganizationOf <http://www.University0.edu> }
+0.013
+The number of answers returned by the upper bound: 6535
+The number of answers in the upper bound: 6535
+Difficulty of this query: UpperBound
+Total time to answer this query: 0.039
+The number of answer tuples: 6535
+time for LowerBound: 0.024
+time for UpperBound: 0.015
+time for ELLowerBound: 0.0
+time for Fragment: 0.0
+time for FragmentRefinement: 0.0
+time for Summarisation: 0.0
+time for Dependency: 0.0
+time for FullReasoning: 0.0
+---------- start evaluating Query 15 ----------
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:PeopleWithManyHobbies . ?x benchmark:isMemberOf <http://www.Department0.University0.edu> }
+0.0
+The number of answers in the lower bound: 0
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:PeopleWithManyHobbies . ?x benchmark:isMemberOf <http://www.Department0.University0.edu> }
+0.003
+The number of answers in the upper bound: 112
+0.003
+The number of answers in the lower bound: 0
+112 triples are added into the store.
+tracking store after materialising tracking program: 1517657 (76343 new)
+tracking store finished the materialisation of tracking program in 0.749 seconds.
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#isTaughtBy> 19
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#isHeadOf> 1
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#isMemberOf> 111
+property: <http://www.w3.org/2002/07/owl#sameAs> 1
+ABox extraction Done
+TBox extraction Done
+Before adding bottom fragment:
+ABoxAxiomsCount = 132, TBoxAxiomsCount = 2
+None of bottom fragments is added for this query.
+ABox axioms: 132 TBox axioms: 2
+grouping individuals by its concepts
+The summary of ABox is consistent with the TBox.
+@TIME to check one tuple: 0.02
+@TIME to filter out non-answers by summarisation: 0.044
+Hermit was called 1 times.
+Hermit was called 0 times.
+Total time for full reasoner: 0.056
+Difficulty of this query: Summarisation
+Total time to answer this query: 0.936
+The number of answer tuples: 0
+time for LowerBound: 0.0
+time for UpperBound: 0.004
+time for ELLowerBound: 0.003
+time for Fragment: 0.873
+time for FragmentRefinement: 0.0
+time for Summarisation: 0.063
+time for Dependency: 0.0
+time for FullReasoning: 0.0
+---------- start evaluating Query 16 ----------
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:Publication . ?x benchmark:publicationAuthor _:y . _:y rdf:type benchmark:Faculty . _:y benchmark:isMemberOf <http://www.Department0.University0.edu> }
+0.002
+The number of answers in the lower bound: 292
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:Publication . ?x benchmark:publicationAuthor _:y . _:y rdf:type benchmark:Faculty . _:y benchmark:isMemberOf <http://www.Department0.University0.edu> }
+0.003
+The number of answers returned by the upper bound: 292
+The number of answers in the upper bound: 292
+Difficulty of this query: UpperBound
+Total time to answer this query: 0.006
+The number of answer tuples: 292
+time for LowerBound: 0.003
+time for UpperBound: 0.003
+time for ELLowerBound: 0.0
+time for Fragment: 0.0
+time for FragmentRefinement: 0.0
+time for Summarisation: 0.0
+time for Dependency: 0.0
+time for FullReasoning: 0.0
+---------- start evaluating Query 17 ----------
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:GraduateCourse . ?x benchmark:isTaughtBy _:y . _:y rdf:type benchmark:SportsLover . _:y benchmark:isMemberOf _:z . _:z benchmark:subOrganizationOf <http://www.University0.edu> }
+0.003
+The number of answers in the lower bound: 747
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:GraduateCourse . ?x benchmark:isTaughtBy _:y . _:y rdf:type benchmark:SportsLover . _:y benchmark:isMemberOf _:z . _:z benchmark:subOrganizationOf <http://www.University0.edu> }
+0.004
+The number of answers returned by the upper bound: 747
+The number of answers in the upper bound: 747
+Difficulty of this query: UpperBound
+Total time to answer this query: 0.009
+The number of answer tuples: 747
+time for LowerBound: 0.005
+time for UpperBound: 0.004
+time for ELLowerBound: 0.0
+time for Fragment: 0.0
+time for FragmentRefinement: 0.0
+time for Summarisation: 0.0
+time for Dependency: 0.0
+time for FullReasoning: 0.0
+---------- start evaluating Query 18 ----------
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:Person . ?x benchmark:like _:y . _:z rdf:type benchmark:Chair . _:z benchmark:isHeadOf <http://www.Department0.University0.edu> . _:z benchmark:like _:y }
+0.003
+The number of answers in the lower bound: 2416
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:Person . ?x benchmark:like _:y . _:z rdf:type benchmark:Chair . _:z benchmark:isHeadOf <http://www.Department0.University0.edu> . _:z benchmark:like _:y }
+0.006
+The number of answers returned by the upper bound: 3886
+The number of answers in the upper bound: 3886
+1.16
+The number of answers in the lower bound: 2416
+1470 triples are added into the store.
+tracking store after materialising tracking program: 1717999 (200342 new)
+tracking store finished the materialisation of tracking program in 3.166 seconds.
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#SwimmingFan> 675
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#PeopleWithHobby> 8813
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#Sports> 7
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#BasketBallClass> 1
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#SportsLover> 7881
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#Chair> 1
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#TennisClass> 1
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#BaseballFan> 687
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#SwimmingClass> 1
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#BaseballLover> 2281
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#SportsFan> 3489
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#BasketBallFan> 686
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#BaseballClass> 1
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#BasketBallLover> 2268
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#TennisFan> 699
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#SwimmingLover> 2178
+class: <http://semantics.crl.ibm.com/univ-bench-dl.owl#Person> 8787
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#like> 13770
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#isCrazyAbout> 3381
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#isHeadOf> 18
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#isTaughtBy> 1602
+property: <http://semantics.crl.ibm.com/univ-bench-dl.owl#love> 13770
+property: <http://www.w3.org/2002/07/owl#sameAs> 37
+ABox extraction Done
+TBox extraction Done
+Before adding bottom fragment:
+ABoxAxiomsCount = 71034, TBoxAxiomsCount = 30
+Part of bottom fragments is added for this query.
+ABox axioms: 71034 TBox axioms: 30
+grouping individuals by its concepts
+Prefix declared: prefix2:=http://www.Department4.University0.edu/
+The summary of ABox is consistent with the TBox.
+@TIME to check one tuple: 0.545
+@TIME to check one tuple: 0.129
+@TIME to check one tuple: 0.105
+@TIME to check one tuple: 0.09
+@TIME to check one tuple: 0.091
+@TIME to check one tuple: 0.091
+@TIME to check one tuple: 0.112
+@TIME to check one tuple: 0.087
+@TIME to check one tuple: 0.075
+@TIME to check one tuple: 0.071
+@TIME to check one tuple: 0.07
+@TIME to check one tuple: 0.07
+@TIME to check one tuple: 0.07
+@TIME to check one tuple: 0.073
+@TIME to check one tuple: 0.071
+@TIME to check one tuple: 0.864
+@TIME to check one tuple: 0.063
+@TIME to check one tuple: 0.063
+@TIME to check one tuple: 0.062
+@TIME to check one tuple: 0.063
+@TIME to check one tuple: 0.063
+@TIME to check one tuple: 0.064
+@TIME to check one tuple: 0.063
+@TIME to check one tuple: 0.063
+@TIME to check one tuple: 0.061
+@TIME to check one tuple: 0.094
+@TIME to check one tuple: 0.096
+@TIME to check one tuple: 0.065
+@TIME to check one tuple: 0.064
+@TIME to check one tuple: 0.064
+@TIME to check one tuple: 0.097
+@TIME to check one tuple: 0.1
+@TIME to check one tuple: 0.148
+@TIME to check one tuple: 0.1
+@TIME to check one tuple: 0.105
+@TIME to check one tuple: 0.074
+@TIME to check one tuple: 0.063
+@TIME to check one tuple: 0.094
+@TIME to check one tuple: 0.062
+@TIME to check one tuple: 0.064
+@TIME to check one tuple: 0.063
+@TIME to check one tuple: 0.063
+@TIME to check one tuple: 0.063
+@TIME to check one tuple: 0.062
+@TIME to check one tuple: 0.062
+@TIME to check one tuple: 0.061
+@TIME to check one tuple: 0.061
+@TIME to check one tuple: 0.061
+@TIME to check one tuple: 0.061
+@TIME to check one tuple: 0.063
+@TIME to check one tuple: 0.062
+@TIME to check one tuple: 0.063
+@TIME to filter out non-answers by summarisation: 6.698
+The number of answers to be checked with HermiT: 1460/1470
+(http://www.Department16.University0.edu/GraduateStudent74@http://semantics.crl.ibm.com/univ-bench-dl.owl#BaseballFan^http://semantics.crl.ibm.com/univ-bench-dl.owl#BaseballLover^http://semantics.crl.ibm.com/univ-bench-dl.owl#BasketBallFan^http://semantics.crl.ibm.com/univ-bench-dl.owl#BasketBallLover^http://semantics.crl.ibm.com/univ-bench-dl.owl#PeopleWithHobby^http://semantics.crl.ibm.com/univ-bench-dl.owl#Person^http://semantics.crl.ibm.com/univ-bench-dl.owl#SportsFan^http://semantics.crl.ibm.com/univ-bench-dl.owl#SportsLover^http://semantics.crl.ibm.com/univ-bench-dl.owl#TennisFan)
+(http://www.Department5.University0.edu/UndergraduateStudent359@http://semantics.crl.ibm.com/univ-bench-dl.owl#PeopleWithHobby^http://semantics.crl.ibm.com/univ-bench-dl.owl#Person^http://semantics.crl.ibm.com/univ-bench-dl.owl#SportsLover)
+The number of times to call homomorphism checker: 762299(645781,115809).
+Time to compute endomorphism relation: 2.32
+link: 2272
+@TIME to group individuals in the gap: 2.32
+The number of different groups: 853
+The number of individuals to be checked by Homomorphism checker: 1460
+Entrances: 98 Exists: 353
+start checking front ... <http://www.Department7.University0.edu/UndergraduateStudent70>
+@TIME to check one tuple: 24.128
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+start checking back ... <http://www.Department7.University0.edu/UndergraduateStudent505>
+start checking back ... <http://www.Department10.University0.edu/UndergraduateStudent52>
+start checking back ... <http://www.Department1.University0.edu/UndergraduateStudent513>
+start checking back ... <http://www.Department11.University0.edu/UndergraduateStudent184>
+start checking back ... <http://www.Department6.University0.edu/GraduateStudent148>
+start checking back ... <http://www.Department8.University0.edu/UndergraduateStudent471>
+start checking back ... <http://www.Department18.University0.edu/UndergraduateStudent205>
+start checking back ... <http://www.Department12.University0.edu/UndergraduateStudent186>
+start checking back ... <http://www.Department13.University0.edu/UndergraduateStudent470>
+start checking back ... <http://www.Department8.University0.edu/UndergraduateStudent404>
+start checking back ... <http://www.Department18.University0.edu/UndergraduateStudent308>
+start checking back ... <http://www.Department9.University0.edu/UndergraduateStudent142>
+start checking back ... <http://www.Department14.University0.edu/UndergraduateStudent283>
+start checking back ... <http://www.Department13.University0.edu/UndergraduateStudent530>
+start checking back ... <http://www.Department8.University0.edu/AssociateProfessor0>
+start checking back ... <http://www.Department5.University0.edu/Lecturer2>
+start checking back ... <http://www.Department16.University0.edu/AssociateProfessor4>
+start checking back ... <http://www.Department11.University0.edu/AssistantProfessor0>
+start checking back ... <http://www.Department16.University0.edu/AssistantProfessor5>
+start checking back ... <http://www.Department7.University0.edu/FullProfessor7>
+start checking back ... <http://www.Department11.University0.edu/FullProfessor5>
+start checking back ... <http://www.Department8.University0.edu/FullProfessor4>
+start checking back ... <http://www.Department18.University0.edu/UndergraduateStudent368>
+start checking back ... <http://www.Department11.University0.edu/UndergraduateStudent213>
+start checking back ... <http://www.Department16.University0.edu/GraduateStudent74>
+start checking back ... <http://www.Department5.University0.edu/UndergraduateStudent6>
+start checking back ... <http://www.Department9.University0.edu/UndergraduateStudent229>
+start checking back ... <http://www.Department16.University0.edu/other_staff4>
+start checking back ... <http://www.Department6.University0.edu/UndergraduateStudent319>
+start checking back ... <http://www.Department8.University0.edu/GraduateStudent156>
+start checking back ... <http://www.Department11.University0.edu/GraduateStudent32>
+start checking back ... <http://www.Department11.University0.edu/UndergraduateStudent370>
+start checking back ... <http://www.Department3.University0.edu/UndergraduateStudent145>
+start checking back ... <http://www.Department18.University0.edu/GraduateStudent103>
+start checking back ... <http://www.Department10.University0.edu/UndergraduateStudent412>
+start checking back ... <http://www.Department5.University0.edu/UndergraduateStudent286>
+start checking back ... <http://www.Department2.University0.edu/UndergraduateStudent316>
+start checking back ... <http://www.Department3.University0.edu/UndergraduateStudent171>
+start checking back ... <http://www.Department5.University0.edu/UndergraduateStudent492>
+start checking back ... <http://www.Department9.University0.edu/UndergraduateStudent133>
+start checking back ... <http://www.Department17.University0.edu/GraduateStudent55>
+start checking back ... <http://www.Department2.University0.edu/UndergraduateStudent209>
+start checking back ... <http://www.Department18.University0.edu/UndergraduateStudent59>
+start checking back ... <http://www.Department6.University0.edu/UndergraduateStudent12>
+start checking back ... <http://www.Department15.University0.edu/UndergraduateStudent128>
+start checking back ... <http://www.Department12.University0.edu/UndergraduateStudent556>
+start checking back ... <http://www.Department8.University0.edu/UndergraduateStudent427>
+start checking back ... <http://www.Department0.University0.edu/UndergraduateStudent301>
+start checking back ... <http://www.Department13.University0.edu/UndergraduateStudent511>
+start checking back ... <http://www.Department15.University0.edu/SystemsStaff11>
+start checking back ... <http://www.Department1.University0.edu/UndergraduateStudent6>
+start checking back ... <http://www.Department2.University0.edu/other_staff3>
+start checking back ... <http://www.Department5.University0.edu/GraduateStudent74>
+start checking back ... <http://www.Department1.University0.edu/GraduateStudent150>
+start checking back ... <http://www.Department18.University0.edu/GraduateStudent159>
+start checking back ... <http://www.Department5.University0.edu/GraduateStudent9>
+start checking back ... <http://www.Department11.University0.edu/UndergraduateStudent105>
+start checking back ... <http://www.Department6.University0.edu/GraduateStudent120>
+start checking back ... <http://www.Department9.University0.edu/GraduateStudent0>
+start checking back ... <http://www.Department12.University0.edu/UndergraduateStudent385>
+start checking back ... <http://www.Department13.University0.edu/UndergraduateStudent341>
+start checking back ... <http://www.Department8.University0.edu/UndergraduateStudent24>
+start checking back ... <http://www.Department1.University0.edu/GraduateStudent69>
+start checking back ... <http://www.Department10.University0.edu/GraduateStudent134>
+start checking back ... <http://www.Department3.University0.edu/UndergraduateStudent430>
+start checking back ... <http://www.Department18.University0.edu/UndergraduateStudent8>
+start checking back ... <http://www.Department5.University0.edu/GraduateStudent81>
+start checking back ... <http://www.Department12.University0.edu/UndergraduateStudent39>
+start checking back ... <http://www.Department15.University0.edu/UndergraduateStudent88>
+start checking back ... <http://www.Department7.University0.edu/UndergraduateStudent111>
+start checking back ... <http://www.Department15.University0.edu/AssociateProfessor7>
+start checking back ... <http://www.Department2.University0.edu/UndergraduateStudent241>
+start checking back ... <http://www.Department10.University0.edu/AssistantProfessor1>
+start checking back ... <http://www.Department13.University0.edu/UndergraduateStudent19>
+start checking back ... <http://www.Department3.University0.edu/UndergraduateStudent341>
+start checking back ... <http://www.Department8.University0.edu/UndergraduateStudent424>
+start checking back ... <http://www.Department6.University0.edu/UndergraduateStudent136>
+start checking back ... <http://www.Department7.University0.edu/UndergraduateStudent169>
+start checking back ... <http://www.Department15.University0.edu/GraduateStudent128>
+start checking back ... <http://www.Department8.University0.edu/UndergraduateStudent325>
+start checking back ... <http://www.Department10.University0.edu/UndergraduateStudent73>
+start checking back ... <http://www.Department12.University0.edu/GraduateStudent95>
+start checking back ... <http://www.Department5.University0.edu/AssistantProfessor2>
+start checking back ... <http://www.Department7.University0.edu/UndergraduateStudent415>
+start checking back ... <http://www.Department2.University0.edu/UndergraduateStudent114>
+start checking back ... <http://www.Department3.University0.edu/FullProfessor5>
+start checking back ... <http://www.Department9.University0.edu/UndergraduateStudent423>
+start checking back ... <http://www.Department3.University0.edu/UndergraduateStudent269>
+start checking back ... <http://www.Department12.University0.edu/GraduateStudent67>
+start checking back ... <http://www.Department4.University0.edu/ClericalStaff1>
+start checking back ... <http://www.Department6.University0.edu/UndergraduateStudent297>
+start checking back ... <http://www.Department13.University0.edu/UndergraduateStudent379>
+start checking back ... <http://www.Department18.University0.edu/GraduateStudent139>
+start checking back ... <http://www.Department17.University0.edu/UndergraduateStudent110>
+start checking back ... <http://www.Department11.University0.edu/GraduateStudent135>
+start checking back ... <http://www.Department2.University0.edu/GraduateStudent108>
+start checking back ... <http://www.Department2.University0.edu/UndergraduateStudent257>
+start checking back ... <http://www.Department13.University0.edu/UndergraduateStudent332>
+start checking back ... <http://www.Department14.University0.edu/UndergraduateStudent192>
+start checking back ... <http://www.Department2.University0.edu/UndergraduateStudent333>
+start checking back ... <http://www.Department10.University0.edu/other_staff8>
+start checking back ... <http://www.Department1.University0.edu/GraduateStudent154>
+start checking back ... <http://www.Department17.University0.edu/UndergraduateStudent400>
+start checking back ... <http://www.Department4.University0.edu/UndergraduateStudent73>
+start checking back ... <http://www.College0.University0.edu/woman_student203>
+start checking back ... <http://www.Department7.University0.edu/UndergraduateStudent116>
+start checking back ... <http://www.Department3.University0.edu/SystemsStaff14>
+start checking back ... <http://www.Department9.University0.edu/UndergraduateStudent65>
+start checking back ... <http://www.Department1.University0.edu/UndergraduateStudent482>
+start checking back ... <http://www.Department17.University0.edu/UndergraduateStudent324>
+start checking back ... <http://www.Department13.University0.edu/GraduateStudent24>
+start checking back ... <http://www.Department11.University0.edu/UndergraduateStudent67>
+start checking back ... <http://www.Department12.University0.edu/UndergraduateStudent404>
+start checking back ... <http://www.Department9.University0.edu/UndergraduateStudent138>
+start checking back ... <http://www.Department2.University0.edu/UndergraduateStudent42>
+start checking back ... <http://www.Department15.University0.edu/UndergraduateStudent127>
+start checking back ... <http://www.Department10.University0.edu/UndergraduateStudent164>
+start checking back ... <http://www.Department3.University0.edu/SameIndividual0>
+start checking back ... <http://www.Department17.University0.edu/SystemsStaff15>
+start checking back ... <http://www.Department6.University0.edu/UndergraduateStudent337>
+start checking back ... <http://www.Department3.University0.edu/GraduateStudent134>
+start checking back ... <http://www.Department1.University0.edu/UndergraduateStudent453>
+start checking back ... <http://www.Department5.University0.edu/UndergraduateStudent571>
+start checking back ... <http://www.Department2.University0.edu/UndergraduateStudent120>
+start checking back ... <http://www.Department1.University0.edu/AssociateProfessor12>
+start checking back ... <http://www.Department0.University0.edu/GraduateStudent4>
+start checking back ... <http://www.Department7.University0.edu/FullProfessor2>
+start checking back ... <http://www.Department14.University0.edu/AssociateProfessor1>
+start checking back ... <http://www.Department17.University0.edu/AssistantProfessor8>
+start checking back ... <http://www.Department18.University0.edu/GraduateStudent153>
+start checking back ... <http://www.Department11.University0.edu/other_staff8>
+start checking back ... <http://www.Department1.University0.edu/UndergraduateStudent35>
+start checking back ... <http://www.Department9.University0.edu/AssociateProfessor5>
+start checking back ... <http://www.Department8.University0.edu/UndergraduateStudent219>
+start checking back ... <http://www.Department14.University0.edu/UndergraduateStudent166>
+start checking back ... <http://www.Department8.University0.edu/SystemsStaff8>
+start checking back ... <http://www.Department6.University0.edu/FullProfessor5>
+start checking back ... <http://www.Department10.University0.edu/GraduateStudent161>
+start checking back ... <http://www.Department8.University0.edu/UndergraduateStudent94>
+start checking back ... <http://www.Department3.University0.edu/ClericalStaff0>
+start checking back ... <http://www.Department2.University0.edu/other_staff16>
+start checking back ... <http://www.Department16.University0.edu/UndergraduateStudent381>
+start checking back ... <http://www.Department2.University0.edu/GraduateStudent15>
+start checking back ... <http://www.Department1.University0.edu/GraduateStudent36>
+start checking back ... <http://www.Department12.University0.edu/UndergraduateStudent273>
+start checking back ... <http://www.Department10.University0.edu/UndergraduateStudent147>
+start checking back ... <http://www.Department10.University0.edu/other_staff0>
+start checking back ... <http://www.Department3.University0.edu/UndergraduateStudent94>
+start checking back ... <http://www.Department5.University0.edu/GraduateStudent164>
+start checking back ... <http://www.Department7.University0.edu/UndergraduateStudent293>
+start checking back ... <http://www.Department15.University0.edu/UndergraduateStudent269>
+start checking back ... <http://www.Department18.University0.edu/UndergraduateStudent514>
+start checking back ... <http://www.Department7.University0.edu/UndergraduateStudent51>
+start checking back ... <http://www.Department2.University0.edu/UndergraduateStudent127>
+start checking back ... <http://www.Department5.University0.edu/UndergraduateStudent306>
+start checking back ... <http://www.Department10.University0.edu/GraduateStudent112>
+start checking back ... <http://www.Department5.University0.edu/UndergraduateStudent322>
+start checking back ... <http://www.Department6.University0.edu/UndergraduateStudent282>
+start checking back ... <http://www.Department17.University0.edu/UndergraduateStudent498>
+start checking back ... <http://www.Department10.University0.edu/UndergraduateStudent417>
+start checking back ... <http://www.Department9.University0.edu/UndergraduateStudent86>
+start checking back ... <http://www.Department13.University0.edu/GraduateStudent43>
+start checking back ... <http://www.Department8.University0.edu/UndergraduateStudent358>
+start checking back ... <http://www.Department16.University0.edu/UndergraduateStudent277>
+start checking back ... <http://www.Department16.University0.edu/GraduateStudent85>
+start checking back ... <http://www.Department11.University0.edu/UndergraduateStudent10>
+start checking back ... <http://www.Department17.University0.edu/GraduateStudent42>
+The number of correct answers: 0
+Hermit was called 52 times.
+Hermit was called 1 times.
+Total time for full reasoner: 47.885
+Difficulty of this query: FullReasoning
+Total time to answer this query: 53.158
+The number of answer tuples: 2416
+time for LowerBound: 0.005
+time for UpperBound: 0.021
+time for ELLowerBound: 1.16
+time for Fragment: 4.037
+time for FragmentRefinement: 0.0
+time for Summarisation: 7.498
+time for Dependency: 0.0
+time for FullReasoning: 38.332
+---------- start evaluating Query 19 ----------
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:Student . ?x benchmark:takesCourse _:y . _:y benchmark:isTaughtBy <http://www.Department0.University0.edu/FullProfessor0> }
+0.009
+The number of answers in the lower bound: 50
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:Student . ?x benchmark:takesCourse _:y . _:y benchmark:isTaughtBy <http://www.Department0.University0.edu/FullProfessor0> }
+0.011
+The number of answers returned by the upper bound: 50
+The number of answers in the upper bound: 50
+Difficulty of this query: UpperBound
+Total time to answer this query: 0.021
+The number of answer tuples: 50
+time for LowerBound: 0.01
+time for UpperBound: 0.011
+time for ELLowerBound: 0.0
+time for Fragment: 0.0
+time for FragmentRefinement: 0.0
+time for Summarisation: 0.0
+time for Dependency: 0.0
+time for FullReasoning: 0.0
+---------- start evaluating Query 20 ----------
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:Woman . ?x rdf:type benchmark:Student . ?x benchmark:isMemberOf _:y . _:y benchmark:subOrganizationOf <http://www.University0.edu> }
+0.011
+The number of answers in the lower bound: 6535
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX benchmark: <http://semantics.crl.ibm.com/univ-bench-dl.owl#> SELECT distinct ?x WHERE { ?x rdf:type benchmark:Woman . ?x rdf:type benchmark:Student . ?x benchmark:isMemberOf _:y . _:y benchmark:subOrganizationOf <http://www.University0.edu> }
+0.013
+The number of answers returned by the upper bound: 6535
+The number of answers in the upper bound: 6535
+Difficulty of this query: UpperBound
+Total time to answer this query: 0.03
+The number of answer tuples: 6535
+time for LowerBound: 0.015
+time for UpperBound: 0.015
+time for ELLowerBound: 0.0
+time for Fragment: 0.0
+time for FragmentRefinement: 0.0
+time for Summarisation: 0.0
+time for Dependency: 0.0
+time for FullReasoning: 0.0
\ No newline at end of file
diff --git a/src/uk/ac/ox/cs/pagoda/approx/RLPlusOntology.java b/src/uk/ac/ox/cs/pagoda/approx/RLPlusOntology.java
index b92bceb..638a151 100644
--- a/src/uk/ac/ox/cs/pagoda/approx/RLPlusOntology.java
+++ b/src/uk/ac/ox/cs/pagoda/approx/RLPlusOntology.java
@@ -23,577 +23,585 @@ import java.util.regex.Pattern;
 
 public class RLPlusOntology implements KnowledgeBase {
 
-        private static final String DEFAULT_ONTOLOGY_FILE_EXTENSION = "owl";
-        private static final Pattern ONTOLOGY_ID_REGEX = Pattern.compile("ontologyid\\((?<id>[a-z0-9\\-]+)\\)");
-        OWLOntologyManager manager;
-        OWLDataFactory factory;
-        String ontologyIRI;
-        String corrFileName = null;
-        String outputPath, aBoxPath;
-        OWLOntology inputOntology = null;
-        OWLOntology tBox = null;
-        OWLOntology aBox = null;
-        OWLOntology restOntology = null;
-        OWLOntology outputOntology = null; //RL ontology
-        DLOntology dlOntology = null;
-        int rlCounter = 0;
-        LinkedList<Clause> clauses;
-        Map<OWLAxiom, OWLAxiom> correspondence;
-        BottomStrategy botStrategy;
-        Random random = new Random(19900114);
-        private Map<OWLClassExpression, Integer> subCounter = null;
-        private Map<OWLClass, OWLClass> atomic2negation = new HashMap<OWLClass, OWLClass>();
-
-        // FIXME multiple anonymous ontologies
-        @Override
-        public void load(OWLOntology ontology, uk.ac.ox.cs.pagoda.constraints.BottomStrategy bottomStrategy) {
-                if (bottomStrategy instanceof UnaryBottom)
-                        botStrategy = BottomStrategy.UNARY;
-                else if (bottomStrategy instanceof NullaryBottom)
-                        botStrategy = BottomStrategy.NULLARY;
-                else
-                        botStrategy = BottomStrategy.TOREMOVE;
-
-                if(corrFileName == null)
-                        corrFileName = "rlplus.crr";
-                manager = ontology.getOWLOntologyManager();
+    private static final String DEFAULT_ONTOLOGY_FILE_EXTENSION = "owl";
+    private static final Pattern ONTOLOGY_ID_REGEX = Pattern.compile("ontologyid\\((?<id>[a-z0-9\\-]+)\\)");
+    OWLOntologyManager manager;
+    OWLDataFactory factory;
+    String ontologyIRI;
+    String corrFileName = null;
+    String outputPath, aBoxPath;
+    OWLOntology inputOntology = null;
+    OWLOntology tBox = null;
+    OWLOntology aBox = null;
+    OWLOntology restOntology = null;
+    OWLOntology outputOntology = null; //RL ontology
+    DLOntology dlOntology = null;
+    int rlCounter = 0;
+    LinkedList<Clause> clauses;
+    Map<OWLAxiom, OWLAxiom> correspondence;
+    BottomStrategy botStrategy;
+    Random random = new Random(19900114);
+    private Map<OWLClassExpression, Integer> subCounter = null;
+    private Map<OWLClass, OWLClass> atomic2negation = new HashMap<OWLClass, OWLClass>();
+
+    // TODO don't know if it is correct
+    @Override
+    public void load(OWLOntology ontology, uk.ac.ox.cs.pagoda.constraints.BottomStrategy bottomStrategy) {
+        if(bottomStrategy instanceof UnaryBottom)
+            botStrategy = BottomStrategy.UNARY;
+        else if(bottomStrategy instanceof NullaryBottom)
+            botStrategy = BottomStrategy.NULLARY;
+        else
+            botStrategy = BottomStrategy.TOREMOVE;
+
+        if(corrFileName == null)
+            corrFileName = "rlplus.crr";
+        manager = ontology.getOWLOntologyManager();
 //              manager = OWLManager.createOWLOntologyManager();
-                factory = manager.getOWLDataFactory();
-                inputOntology = ontology;
-
-                try {
-                        IRI ontologyIri;
-                        if(ontology.isAnonymous()) {
-                                Matcher matcher = ONTOLOGY_ID_REGEX.matcher(ontology.getOntologyID().toString().toLowerCase());
-                                if(!matcher.matches()) throw new Error("Anonymous ontology without internal id");
-                                ontologyIri =
-                                                IRI.create("http://www.example.org/", matcher.group("id") + "." + DEFAULT_ONTOLOGY_FILE_EXTENSION);
-                        }
-                        else
-                                ontologyIri = inputOntology.getOntologyID().getOntologyIRI();
-
-                        String ontologyIriPrefix = ontologyIri.getNamespace();
-                        ontologyIRI = ontologyIri.toString();
-                        String ontologyIriFragment = ontologyIri.getFragment();
-                        String originalFileName = FilenameUtils.removeExtension(ontologyIriFragment);
-                        String originalExtension = FilenameUtils.getExtension(ontologyIriFragment);
-                        if(originalExtension.isEmpty()) originalExtension = DEFAULT_ONTOLOGY_FILE_EXTENSION;
-
-
-                        IRI rlOntologyIRI = IRI.create(ontologyIriPrefix, originalFileName + "-RL." + originalExtension);
-                        outputPath = Paths.get(Utility.getGlobalTempDirAbsolutePath(),
-                                                                   originalFileName + "-RL." + originalExtension).toString();
-                        IRI rlDocumentIRI = IRI.create("file://" + outputPath);
-                        outputOntology = manager.createOntology(rlOntologyIRI);
-                        manager.setOntologyDocumentIRI(outputOntology, rlDocumentIRI);
-
-                        String tBoxOntologyFragment = originalFileName + "-TBox." + originalExtension;
-                        IRI tBoxOntologyIRI = IRI.create(ontologyIriPrefix, tBoxOntologyFragment);
-                        IRI tBoxDocumentIRI =
-                                        IRI.create("file://" + Paths.get(Utility.getGlobalTempDirAbsolutePath(), tBoxOntologyFragment));
-
-                        String aBoxOntologyFragment = originalFileName + "-ABox." + originalExtension;
-                        IRI aBoxOntologyIRI = IRI.create(ontologyIriPrefix, aBoxOntologyFragment);
-                        aBoxPath = Paths.get(Utility.getGlobalTempDirAbsolutePath()) + aBoxOntologyFragment;
-                        IRI aBoxDocumentIRI =
-                                        IRI.create("file://" + Paths.get(Utility.getGlobalTempDirAbsolutePath(), aBoxOntologyFragment));
-
-                        tBox = manager.createOntology(tBoxOntologyIRI);
-                        aBox = manager.createOntology(aBoxOntologyIRI);
-                        manager.setOntologyDocumentIRI(tBox, tBoxDocumentIRI);
-                        manager.setOntologyDocumentIRI(aBox, aBoxDocumentIRI);
-
-                        FileOutputStream aBoxOut = new FileOutputStream(aBoxPath);
-                        manager.saveOntology(aBox, aBoxOut);
-                        aBoxOut.close();
-
-                        restOntology = manager.createOntology();
-                } catch(OWLOntologyCreationException | OWLOntologyStorageException | IOException e) {
-                        e.printStackTrace();
-                        System.exit(1);
-                }
-        }
-        
-        public OWLOntology getTBox() {
-                return tBox;
-        }
-        
-        public String getABoxPath() {
-                return aBoxPath;
-        }
-        
-        private void add2SubCounter(OWLClassExpression exp) {
-                Integer count = subCounter.get(exp);
-                if (count == null) count = 0;
-                ++count;
-                subCounter.put(exp, count);
-        }
-        
-        public void simplify() {
-                if(simplifyABox()) {
-                        save(aBox);
+        factory = manager.getOWLDataFactory();
+        inputOntology = ontology;
+
+        try {
+            IRI ontologyIri;
+            if(ontology.isAnonymous()) {
+                Matcher matcher = ONTOLOGY_ID_REGEX.matcher(ontology.getOntologyID().toString().toLowerCase());
+                if(!matcher.matches()) throw new Error("Anonymous ontology without internal id");
+                ontologyIri =
+                        IRI.create("http://www.example.org/", matcher.group("id") + "." + DEFAULT_ONTOLOGY_FILE_EXTENSION);
+            }
+            else
+                ontologyIri = inputOntology.getOntologyID().getOntologyIRI();
+
+            String ontologyIriPrefix = ontologyIri.getNamespace();
+            ontologyIRI = ontologyIri.toString();
+            String ontologyIriFragment = ontologyIri.getFragment();
+            String originalFileName = FilenameUtils.removeExtension(ontologyIriFragment);
+            String originalExtension = FilenameUtils.getExtension(ontologyIriFragment);
+            if(originalExtension.isEmpty()) originalExtension = DEFAULT_ONTOLOGY_FILE_EXTENSION;
+
+
+            IRI rlOntologyIRI = IRI.create(ontologyIriPrefix, originalFileName + "-RL." + originalExtension);
+            outputPath = Paths.get(Utility.getGlobalTempDirAbsolutePath(),
+                                   originalFileName + "-RL." + originalExtension).toString();
+            IRI rlDocumentIRI = IRI.create("file://" + outputPath);
+            outputOntology = manager.createOntology(rlOntologyIRI);
+            manager.setOntologyDocumentIRI(outputOntology, rlDocumentIRI);
+
+            String tBoxOntologyFragment = originalFileName + "-TBox." + originalExtension;
+            IRI tBoxOntologyIRI = IRI.create(ontologyIriPrefix, tBoxOntologyFragment);
+            IRI tBoxDocumentIRI =
+                    IRI.create("file://" + Paths.get(Utility.getGlobalTempDirAbsolutePath(), tBoxOntologyFragment));
+
+            String aBoxOntologyFragment = originalFileName + "-ABox." + originalExtension;
+            IRI aBoxOntologyIRI = IRI.create(ontologyIriPrefix, aBoxOntologyFragment);
+            aBoxPath = Paths.get(Utility.getGlobalTempDirAbsolutePath(), aBoxOntologyFragment).toString();
+            IRI aBoxDocumentIRI =
+                    IRI.create("file://" + Paths.get(Utility.getGlobalTempDirAbsolutePath(), aBoxOntologyFragment));
+
+            tBox = manager.createOntology(tBoxOntologyIRI);
+            aBox = manager.createOntology(aBoxOntologyIRI);
+            manager.setOntologyDocumentIRI(tBox, tBoxDocumentIRI);
+            manager.setOntologyDocumentIRI(aBox, aBoxDocumentIRI);
+
+            FileOutputStream aBoxOut = new FileOutputStream(aBoxPath);
+            manager.saveOntology(aBox, aBoxOut);
+            aBoxOut.close();
+
+            restOntology = manager.createOntology();
+        } catch(OWLOntologyCreationException | OWLOntologyStorageException | IOException e) {
+            e.printStackTrace();
+            System.exit(1);
+        }
+    }
+
+    public OWLOntology getTBox() {
+        return tBox;
+    }
+
+    public String getABoxPath() {
+        return aBoxPath;
+    }
+
+    public void simplify() {
+        if(simplifyABox()) {
+            save(aBox);
 //                      save(tBox);
-                } else
-                        tBox = inputOntology;
-        }
+        }
+        else
+            tBox = inputOntology;
+    }
 
-        @Override
-        public void transform() {
-                simplify();
-                filter();
-                clausify();
+    @Override
+    public void transform() {
+        simplify();
+        filter();
+        clausify();
 
-                subCounter = new HashMap<OWLClassExpression, Integer>();
-                clauses = new LinkedList<Clause>();
-                Clausifier clausifier = Clausifier.getInstance(restOntology);
+        subCounter = new HashMap<OWLClassExpression, Integer>();
+        clauses = new LinkedList<Clause>();
+        Clausifier clausifier = Clausifier.getInstance(restOntology);
 
-                for (DLClause c: dlOntology.getDLClauses()) {
-                        Clause clause = new Clause(clausifier, c);
-                        clauses.add(clause);
+        for(DLClause c : dlOntology.getDLClauses()) {
+            Clause clause = new Clause(clausifier, c);
+            clauses.add(clause);
 
                         /*
-                         * count the expressions in the left
+             * count the expressions in the left
                          */
-                        for (OWLClassExpression exp: clause.getSubClasses()) {
-                                if(exp instanceof OWLClass)
-                                        add2SubCounter(exp);
-                                else if (exp instanceof OWLObjectSomeValuesFrom) {
-                                        OWLObjectSomeValuesFrom someValue = (OWLObjectSomeValuesFrom)exp;
-                                        add2SubCounter(factory.getOWLObjectSomeValuesFrom(someValue.getProperty(), factory.getOWLThing()));
-                                        add2SubCounter(someValue.getFiller());
-                                }
-                                else if (exp instanceof OWLObjectMinCardinality) {
-                                        OWLObjectMinCardinality minCard = (OWLObjectMinCardinality)exp;
-                                        add2SubCounter(factory.getOWLObjectSomeValuesFrom(minCard.getProperty(), factory.getOWLThing()));
-                                        add2SubCounter(minCard.getFiller());
-                                } else
-                                        Utility.logError("strange class expression: " + exp);
-
-                        }
-                }
-
-                correspondence = new HashMap<OWLAxiom, OWLAxiom>();
-                Set<OWLAxiom> addedAxioms = new HashSet<OWLAxiom>();
-                OWLClassExpression subExp;
-                for (Clause clause: clauses) {
-                        subExp = uk.ac.ox.cs.pagoda.owl.OWLHelper.getSimplifiedConjunction(factory, clause.getSubClasses());
-                        addedAxioms.clear();
-                        for (OWLClassExpression exp: getDisjunctionApprox0(clause.getSuperClasses())) {
-                                addedAxioms.add(factory.getOWLSubClassOfAxiom(subExp, transform(exp, addedAxioms)));
-                                for(OWLAxiom a : addedAxioms)
-                                        addAxiom2output(a, factory.getOWLSubClassOfAxiom(subExp,
-                                                        OWLHelper.getSimplifiedDisjunction(factory, clause.getSuperClasses())));
-                        }
-                }
-
-                subCounter.clear();
-        }
-        
-        @Override
-        public void save() {
-                if (corrFileName != null)
-                        save(correspondence, corrFileName);
-                save(outputOntology);
-        }
-
-        private void save(Map<OWLAxiom, OWLAxiom> map, String corrFileName) {
-                if (corrFileName == null) return ;
-                ObjectOutput output;
-                try {
-                        output = new ObjectOutputStream(new BufferedOutputStream(new FileOutputStream(corrFileName)));
-                        output.writeObject(map);
-                        output.close();
-                } catch (IOException e) {
-                        e.printStackTrace();
-                }
-        }
-
-        protected void save(OWLOntology onto) {
-                try {
-                        onto.getOWLOntologyManager().saveOntology(onto);
-                } catch (OWLOntologyStorageException e) {
-                        e.printStackTrace();
-                }
-        }
-
-        /*
-         * treat disjunction as conjunction
-         */
-        private Set<OWLClassExpression> getDisjunctionApprox0(Set<OWLClassExpression> superClasses) {
-                return superClasses;
-        }
-        
-        /*
-         * choose one simple class disjunct
-         */
-        @SuppressWarnings("unused")
-        private Set<OWLClassExpression> getDisjunctionApprox1(Set<OWLClassExpression> superClasses) {
-                if(superClasses.isEmpty() || superClasses.size() == 1)
-                        return superClasses;
-
-                OWLClassExpression rep = null;
-                int min = Integer.MAX_VALUE, o;
-                for(OWLClassExpression exp : superClasses)
-                        if(exp instanceof OWLClass && (o = getOccurrence(exp)) < min) {
-                                min = o;
-                                rep = exp;
-                        }
-
-                if(rep == null) rep = superClasses.iterator().next();
-
-                return Collections.singleton(rep);
-        }
-
-        /*
-         * randomly choose a class expression to represent this disjunction
-         */
-        @SuppressWarnings("unused")
-        private Set<OWLClassExpression> getDisjunctionApprox2(Set<OWLClassExpression> superClasses) {
-                if(superClasses.isEmpty() || superClasses.size() == 1)
-                        return superClasses;
-
-                int index = random.nextInt() % superClasses.size();
-                if (index < 0) index += superClasses.size();
-
-                int i = 0;
-                for(OWLClassExpression exp : superClasses)
-                        if (i++ == index)
-                                return Collections.singleton(exp);
-                return null;
-        }
-        
-        /*
-         * choose the one that appears least in the l.h.s.
-         */
-        @SuppressWarnings("unused")
-        private Set<OWLClassExpression> getDisjunctionApprox3(Set<OWLClassExpression> superClasses) {
-                if(superClasses.isEmpty() || superClasses.size() == 1)
-                        return superClasses;
-
-                OWLClassExpression rep = null, exp1;
-                int occurrence = Integer.MAX_VALUE, o;
-                for (OWLClassExpression exp: superClasses) {
-                        o = 0;
-                        exp1 = exp;
-                        if (exp instanceof OWLObjectMinCardinality) {
-                                OWLObjectMinCardinality minCard = (OWLObjectMinCardinality)exp;
-                                if (minCard.getCardinality() == 1)
-                                        exp1 = factory.getOWLObjectSomeValuesFrom(minCard.getProperty(), minCard.getFiller());
-                        }
-
-                        if (!subCounter.containsKey(exp1) || (o = subCounter.get(exp1)) < occurrence) {
-                                rep = exp;
-                                occurrence = o;
-                        }
-                }
-
-                return Collections.singleton(rep);
-        }
-
-        private int getOccurrence(OWLClassExpression exp) {
-                if (!subCounter.containsKey(exp))
-                        return 0;
-                return subCounter.get(exp);
-        }
-
-        @SuppressWarnings("unused")
-        private Set<OWLClassExpression> getDisjunctionApprox4(Set<OWLClassExpression> superClasses) {
-                if(superClasses.isEmpty() || superClasses.size() == 1)
-                        return superClasses;
-
-                OWLClassExpression rep = null;
-                int occurrence = Integer.MAX_VALUE, o;
-                for (OWLClassExpression exp: superClasses) {
-                        o = 0;
-                        if (exp instanceof OWLObjectMinCardinality) {
-                                OWLObjectMinCardinality minCard = (OWLObjectMinCardinality)exp;
-                                if (minCard.getCardinality() == 1) {
-                                        o = getOccurrence((factory.getOWLObjectSomeValuesFrom(minCard.getProperty(), factory.getOWLThing())));
-                                        o += getOccurrence(minCard.getFiller());
+            for(OWLClassExpression exp : clause.getSubClasses()) {
+                if(exp instanceof OWLClass)
+                    add2SubCounter(exp);
+                else if(exp instanceof OWLObjectSomeValuesFrom) {
+                    OWLObjectSomeValuesFrom someValue = (OWLObjectSomeValuesFrom) exp;
+                    add2SubCounter(factory.getOWLObjectSomeValuesFrom(someValue.getProperty(), factory.getOWLThing()));
+                    add2SubCounter(someValue.getFiller());
+                }
+                else if(exp instanceof OWLObjectMinCardinality) {
+                    OWLObjectMinCardinality minCard = (OWLObjectMinCardinality) exp;
+                    add2SubCounter(factory.getOWLObjectSomeValuesFrom(minCard.getProperty(), factory.getOWLThing()));
+                    add2SubCounter(minCard.getFiller());
+                }
+                else
+                    Utility.logError("strange class expression: " + exp);
+
+            }
+        }
+
+        correspondence = new HashMap<OWLAxiom, OWLAxiom>();
+        Set<OWLAxiom> addedAxioms = new HashSet<OWLAxiom>();
+        OWLClassExpression subExp;
+        for(Clause clause : clauses) {
+            subExp = uk.ac.ox.cs.pagoda.owl.OWLHelper.getSimplifiedConjunction(factory, clause.getSubClasses());
+            addedAxioms.clear();
+            for(OWLClassExpression exp : getDisjunctionApprox0(clause.getSuperClasses())) {
+                addedAxioms.add(factory.getOWLSubClassOfAxiom(subExp, transform(exp, addedAxioms)));
+                for(OWLAxiom a : addedAxioms)
+                    addAxiom2output(a, factory.getOWLSubClassOfAxiom(subExp,
+                                                                     OWLHelper.getSimplifiedDisjunction(factory, clause.getSuperClasses())));
+            }
+        }
+
+        subCounter.clear();
+    }
+
+    @Override
+    public void save() {
+        if(corrFileName != null)
+            save(correspondence, corrFileName);
+        save(outputOntology);
+    }
+
+    public OWLOntologyManager getOWLOntologyManager() {
+        return inputOntology.getOWLOntologyManager();
+    }
+
+    public String getOntologyIRI() {
+        return ontologyIRI;
+    }
+
+    public OWLOntology getOutputOntology() {
+        return outputOntology;
+    }
+
+    @Override
+    public String getOutputPath() {
+        return outputPath;
+    }
+
+    @Override
+    public String getDirectory() {
+        return outputPath.substring(0, outputPath.lastIndexOf(Utility.FILE_SEPARATOR));
+    }
+
+    public void setCorrespondenceFileLoc(String path) {
+        corrFileName = path;
+    }
+
+    private void add2SubCounter(OWLClassExpression exp) {
+        Integer count = subCounter.get(exp);
+        if(count == null) count = 0;
+        ++count;
+        subCounter.put(exp, count);
+    }
+
+    private void save(Map<OWLAxiom, OWLAxiom> map, String corrFileName) {
+        if(corrFileName == null) return;
+        ObjectOutput output;
+        try {
+            output = new ObjectOutputStream(new BufferedOutputStream(new FileOutputStream(corrFileName)));
+            output.writeObject(map);
+            output.close();
+        } catch(IOException e) {
+            e.printStackTrace();
+        }
+    }
+
+    protected void save(OWLOntology onto) {
+        try {
+            onto.getOWLOntologyManager().saveOntology(onto);
+        } catch(OWLOntologyStorageException e) {
+            e.printStackTrace();
+        }
+    }
+
+    /*
+     * treat disjunction as conjunction
+     */
+    private Set<OWLClassExpression> getDisjunctionApprox0(Set<OWLClassExpression> superClasses) {
+        return superClasses;
+    }
+
+    /*
+     * choose one simple class disjunct
+     */
+    @SuppressWarnings("unused")
+    private Set<OWLClassExpression> getDisjunctionApprox1(Set<OWLClassExpression> superClasses) {
+        if(superClasses.isEmpty() || superClasses.size() == 1)
+            return superClasses;
+
+        OWLClassExpression rep = null;
+        int min = Integer.MAX_VALUE, o;
+        for(OWLClassExpression exp : superClasses)
+            if(exp instanceof OWLClass && (o = getOccurrence(exp)) < min) {
+                min = o;
+                rep = exp;
+            }
+
+        if(rep == null) rep = superClasses.iterator().next();
+
+        return Collections.singleton(rep);
+    }
+
+    /*
+     * randomly choose a class expression to represent this disjunction
+     */
+    @SuppressWarnings("unused")
+    private Set<OWLClassExpression> getDisjunctionApprox2(Set<OWLClassExpression> superClasses) {
+        if(superClasses.isEmpty() || superClasses.size() == 1)
+            return superClasses;
+
+        int index = random.nextInt() % superClasses.size();
+        if(index < 0) index += superClasses.size();
+
+        int i = 0;
+        for(OWLClassExpression exp : superClasses)
+            if(i++ == index)
+                return Collections.singleton(exp);
+        return null;
+    }
+
+    /*
+     * choose the one that appears least in the l.h.s.
+     */
+    @SuppressWarnings("unused")
+    private Set<OWLClassExpression> getDisjunctionApprox3(Set<OWLClassExpression> superClasses) {
+        if(superClasses.isEmpty() || superClasses.size() == 1)
+            return superClasses;
+
+        OWLClassExpression rep = null, exp1;
+        int occurrence = Integer.MAX_VALUE, o;
+        for(OWLClassExpression exp : superClasses) {
+            o = 0;
+            exp1 = exp;
+            if(exp instanceof OWLObjectMinCardinality) {
+                OWLObjectMinCardinality minCard = (OWLObjectMinCardinality) exp;
+                if(minCard.getCardinality() == 1)
+                    exp1 = factory.getOWLObjectSomeValuesFrom(minCard.getProperty(), minCard.getFiller());
+            }
+
+            if(!subCounter.containsKey(exp1) || (o = subCounter.get(exp1)) < occurrence) {
+                rep = exp;
+                occurrence = o;
+            }
+        }
+
+        return Collections.singleton(rep);
+    }
+
+    private int getOccurrence(OWLClassExpression exp) {
+        if(!subCounter.containsKey(exp))
+            return 0;
+        return subCounter.get(exp);
+    }
+
+    @SuppressWarnings("unused")
+    private Set<OWLClassExpression> getDisjunctionApprox4(Set<OWLClassExpression> superClasses) {
+        if(superClasses.isEmpty() || superClasses.size() == 1)
+            return superClasses;
+
+        OWLClassExpression rep = null;
+        int occurrence = Integer.MAX_VALUE, o;
+        for(OWLClassExpression exp : superClasses) {
+            o = 0;
+            if(exp instanceof OWLObjectMinCardinality) {
+                OWLObjectMinCardinality minCard = (OWLObjectMinCardinality) exp;
+                if(minCard.getCardinality() == 1) {
+                    o =
+                            getOccurrence((factory.getOWLObjectSomeValuesFrom(minCard.getProperty(), factory.getOWLThing())));
+                    o += getOccurrence(minCard.getFiller());
 //                                      if (o < o1) o = o1;
-                                }
-                        } else
-                                o = getOccurrence(exp);
-
-                        if (o < occurrence || o == occurrence && !(rep instanceof OWLClass)) {
-                                rep = exp;
-                                occurrence = o;
-                        }
-                }
-
-                return Collections.singleton(rep);
-        }
-
-        private boolean simplifyABox() {
-                boolean flag = false;
-                Map<OWLClassExpression, OWLClass> complex2atomic= new HashMap<OWLClassExpression, OWLClass>();
-
-                OWLDatatype anyURI = factory.getOWLDatatype(IRI.create(Namespace.XSD_NS + "anyURI"));
-                OWLObjectProperty sameAs = factory.getOWLObjectProperty(IRI.create(Namespace.EQUALITY));
-                OWLObjectProperty differentFrom = factory.getOWLObjectProperty(IRI.create(Namespace.INEQUALITY));
-
-                for (OWLOntology imported: inputOntology.getImportsClosure())
-                        for (OWLAxiom axiom: imported.getAxioms()) {
-                                if (axiom instanceof OWLClassAssertionAxiom) {
-                                        flag = true;
-                                        OWLClassAssertionAxiom assertion = (OWLClassAssertionAxiom)axiom;
-                                        OWLClassExpression clsExp = assertion.getClassExpression();
-                                        OWLClass cls;
-                                        if (clsExp instanceof OWLClass) {
-                                                if (((OWLClass) clsExp).toStringID().startsWith("owl:"))
-                                                        manager.addAxiom(tBox, axiom);
-                                                else manager.addAxiom(aBox, axiom);
-                                        }
-                                        else {
-                                                if ((cls = complex2atomic.get(clsExp)) == null) {
-                                                        complex2atomic.put(clsExp, cls = getNewConcept(tBox, rlCounter++));
-                                                        manager.addAxiom(tBox, factory.getOWLSubClassOfAxiom(cls, clsExp));
-                                                }
-                                                manager.addAxiom(aBox, factory.getOWLClassAssertionAxiom(cls, assertion.getIndividual()));
-                                        }
-                                }
-                                else if (axiom instanceof OWLObjectPropertyAssertionAxiom || axiom instanceof OWLDataPropertyAssertionAxiom || axiom instanceof OWLAnnotationAssertionAxiom) {
-                                        if(axiom.getDataPropertiesInSignature().contains(anyURI)) continue;
-                                        flag = true;
-                                        manager.addAxiom(aBox, axiom);
-                                }
-                                else if (axiom instanceof OWLSameIndividualAxiom) {
-                                        OWLIndividual firstIndividual = null, previousIndividual = null, lastIndividual = null;
-                                        for (OWLIndividual next: ((OWLSameIndividualAxiom) axiom).getIndividuals()) {
-                                                if(firstIndividual == null) firstIndividual = previousIndividual = next;
-                                                else
-                                                        manager.addAxiom(aBox, factory.getOWLObjectPropertyAssertionAxiom(sameAs, previousIndividual, next));
-                                                previousIndividual = lastIndividual = next;
-                                        }
-                                        manager.addAxiom(aBox, factory.getOWLObjectPropertyAssertionAxiom(sameAs, lastIndividual, firstIndividual));
-                                }
-                                else if (axiom instanceof OWLDifferentIndividualsAxiom) {
-                                        int index1 = 0, index2;
-                                        for (OWLIndividual individual1: ((OWLDifferentIndividualsAxiom) axiom).getIndividuals()) {
-                                                ++index1;
-                                                index2 = 0;
-                                                for (OWLIndividual individual2: ((OWLDifferentIndividualsAxiom) axiom).getIndividuals()) {
-                                                        if (index2++ < index1) {
-                                                                manager.addAxiom(aBox, factory.getOWLObjectPropertyAssertionAxiom(differentFrom, individual1, individual2));
-                                                        } else break;
-                                                }
-                                        }
-                                } else
-                                        manager.addAxiom(tBox, axiom);
-                        }
-
-                return flag;
-        }
-
-        private void filter() {
-                OWL2RLProfile profile = new OWL2RLProfile();
-                OWLProfileReport report = profile.checkOntology(tBox);
-                Set<OWLAxiom> rlAxioms = tBox.getAxioms();
-                OWLAxiom axiom;
-
-                for (OWLProfileViolation violation: report.getViolations()) {
-                        manager.addAxiom(restOntology, axiom = violation.getAxiom());
-                        rlAxioms.remove(axiom);
-                }
-
-                for (Iterator<OWLAxiom> iter = rlAxioms.iterator(); iter.hasNext(); )
-                        addAxiom2output(iter.next(), null);
-        }
-        
-        private void clausify() {
-                Configuration conf = new Configuration();
-                OWLClausification clausifier = new OWLClausification(conf);
-                dlOntology = (DLOntology)clausifier.preprocessAndClausify(restOntology, null)[1];
-                clausifier = null;
-        }
-        
-        protected void addAxiom2output(OWLAxiom axiom, OWLAxiom correspondingAxiom) {
-                manager.addAxiom(outputOntology, axiom);
-                if (correspondingAxiom != null)
-                        correspondence.put(axiom, correspondingAxiom);
-        }
-
-        private OWLClassExpression transform(OWLClassExpression exp, Set<OWLAxiom> addedAxioms) {
-                if (exp instanceof OWLClass) 
-                        return exp;
-                
-                if (exp instanceof OWLObjectHasValue) 
-                        return exp;
-                
-                if (exp instanceof OWLObjectSomeValuesFrom) {
-                        OWLObjectSomeValuesFrom someValueExp = (OWLObjectSomeValuesFrom)exp;
-                        
-                        OWLClassExpression tExp = someValueExp.getFiller();
-                        if (tExp.equals(factory.getOWLThing()))
-                                exp = factory.getOWLObjectMinCardinality(1, someValueExp.getProperty());
-                        else 
-                                exp = factory.getOWLObjectMinCardinality(1, someValueExp.getProperty(), someValueExp.getFiller());
-                }
-                
-                if (exp instanceof OWLObjectMinCardinality) {
-                        OWLObjectMinCardinality minExp = (OWLObjectMinCardinality)exp;
-                        OWLObjectPropertyExpression r;
-
-                        if (minExp.getFiller().equals(factory.getOWLThing())) {
-                                r = minExp.getProperty();
-                        }
-                        //TODO to be restored ... 
-                        //else if ((r = exists2role.get(someValueExp)) == null) {
-                                // deal with r' \subseteq r & range(r') \subseteq C
-                        else {
-                                r = getNewRole(outputOntology, rlCounter);
-                                addedAxioms.add(factory.getOWLSubObjectPropertyOfAxiom(r, minExp.getProperty()));
-                                OWLClassExpression tExp = minExp.getFiller();
-                                if (!(tExp instanceof OWLObjectComplementOf)) {
-                                        if (tExp.equals(factory.getOWLThing())); 
-                                        else 
-                                                addedAxioms.add(factory.getOWLObjectPropertyRangeAxiom(r, tExp));
-                                }
-                                else if (botStrategy != BottomStrategy.TOREMOVE) {
-                                                OWLClass cls = (OWLClass) tExp.getComplementNNF();
-                                                OWLClass neg;
-                                                if ((neg = atomic2negation.get(cls)) == null) {
-                                                        neg = getNewConcept(outputOntology, rlCounter);
-                                                        addedAxioms.add(factory.getOWLDisjointClassesAxiom(neg, cls));
-                                                        atomic2negation.put(cls, neg);
-                                                }
-                                                addedAxioms.add(factory.getOWLObjectPropertyRangeAxiom(r, neg));
-                                        }
+                }
+            }
+            else
+                o = getOccurrence(exp);
+
+            if(o < occurrence || o == occurrence && !(rep instanceof OWLClass)) {
+                rep = exp;
+                occurrence = o;
+            }
+        }
+
+        return Collections.singleton(rep);
+    }
+
+    private boolean simplifyABox() {
+        boolean flag = false;
+        Map<OWLClassExpression, OWLClass> complex2atomic = new HashMap<OWLClassExpression, OWLClass>();
+
+        OWLDatatype anyURI = factory.getOWLDatatype(IRI.create(Namespace.XSD_NS + "anyURI"));
+        OWLObjectProperty sameAs = factory.getOWLObjectProperty(IRI.create(Namespace.EQUALITY));
+        OWLObjectProperty differentFrom = factory.getOWLObjectProperty(IRI.create(Namespace.INEQUALITY));
+
+        for(OWLOntology imported : inputOntology.getImportsClosure())
+            for(OWLAxiom axiom : imported.getAxioms()) {
+                if(axiom instanceof OWLClassAssertionAxiom) {
+                    flag = true;
+                    OWLClassAssertionAxiom assertion = (OWLClassAssertionAxiom) axiom;
+                    OWLClassExpression clsExp = assertion.getClassExpression();
+                    OWLClass cls;
+                    if(clsExp instanceof OWLClass) {
+                        if(((OWLClass) clsExp).toStringID().startsWith("owl:"))
+                            manager.addAxiom(tBox, axiom);
+                        else manager.addAxiom(aBox, axiom);
+                    }
+                    else {
+                        if((cls = complex2atomic.get(clsExp)) == null) {
+                            complex2atomic.put(clsExp, cls = getNewConcept(tBox, rlCounter++));
+                            manager.addAxiom(tBox, factory.getOWLSubClassOfAxiom(cls, clsExp));
+                        }
+                        manager.addAxiom(aBox, factory.getOWLClassAssertionAxiom(cls, assertion.getIndividual()));
+                    }
+                }
+                else if(axiom instanceof OWLObjectPropertyAssertionAxiom || axiom instanceof OWLDataPropertyAssertionAxiom || axiom instanceof OWLAnnotationAssertionAxiom) {
+                    if(axiom.getDataPropertiesInSignature().contains(anyURI)) continue;
+                    flag = true;
+                    manager.addAxiom(aBox, axiom);
+                }
+                else if(axiom instanceof OWLSameIndividualAxiom) {
+                    OWLIndividual firstIndividual = null, previousIndividual = null, lastIndividual = null;
+                    for(OWLIndividual next : ((OWLSameIndividualAxiom) axiom).getIndividuals()) {
+                        if(firstIndividual == null) firstIndividual = previousIndividual = next;
+                        else
+                            manager.addAxiom(aBox, factory.getOWLObjectPropertyAssertionAxiom(sameAs, previousIndividual, next));
+                        previousIndividual = lastIndividual = next;
+                    }
+                    manager.addAxiom(aBox, factory.getOWLObjectPropertyAssertionAxiom(sameAs, lastIndividual, firstIndividual));
+                }
+                else if(axiom instanceof OWLDifferentIndividualsAxiom) {
+                    int index1 = 0, index2;
+                    for(OWLIndividual individual1 : ((OWLDifferentIndividualsAxiom) axiom).getIndividuals()) {
+                        ++index1;
+                        index2 = 0;
+                        for(OWLIndividual individual2 : ((OWLDifferentIndividualsAxiom) axiom).getIndividuals()) {
+                            if(index2++ < index1) {
+                                manager.addAxiom(aBox, factory.getOWLObjectPropertyAssertionAxiom(differentFrom, individual1, individual2));
+                            }
+                            else break;
+                        }
+                    }
+                }
+                else
+                    manager.addAxiom(tBox, axiom);
+            }
+
+        return flag;
+    }
+
+    private void filter() {
+        OWL2RLProfile profile = new OWL2RLProfile();
+        OWLProfileReport report = profile.checkOntology(tBox);
+        Set<OWLAxiom> rlAxioms = tBox.getAxioms();
+        OWLAxiom axiom;
+
+        for(OWLProfileViolation violation : report.getViolations()) {
+            manager.addAxiom(restOntology, axiom = violation.getAxiom());
+            rlAxioms.remove(axiom);
+        }
+
+        for(Iterator<OWLAxiom> iter = rlAxioms.iterator(); iter.hasNext(); )
+            addAxiom2output(iter.next(), null);
+    }
+
+    private void clausify() {
+        Configuration conf = new Configuration();
+        OWLClausification clausifier = new OWLClausification(conf);
+        dlOntology = (DLOntology) clausifier.preprocessAndClausify(restOntology, null)[1];
+        clausifier = null;
+    }
+
+    protected void addAxiom2output(OWLAxiom axiom, OWLAxiom correspondingAxiom) {
+        manager.addAxiom(outputOntology, axiom);
+        if(correspondingAxiom != null)
+            correspondence.put(axiom, correspondingAxiom);
+    }
+
+    private OWLClassExpression transform(OWLClassExpression exp, Set<OWLAxiom> addedAxioms) {
+        if(exp instanceof OWLClass)
+            return exp;
+
+        if(exp instanceof OWLObjectHasValue)
+            return exp;
+
+        if(exp instanceof OWLObjectSomeValuesFrom) {
+            OWLObjectSomeValuesFrom someValueExp = (OWLObjectSomeValuesFrom) exp;
+
+            OWLClassExpression tExp = someValueExp.getFiller();
+            if(tExp.equals(factory.getOWLThing()))
+                exp = factory.getOWLObjectMinCardinality(1, someValueExp.getProperty());
+            else
+                exp = factory.getOWLObjectMinCardinality(1, someValueExp.getProperty(), someValueExp.getFiller());
+        }
+
+        if(exp instanceof OWLObjectMinCardinality) {
+            OWLObjectMinCardinality minExp = (OWLObjectMinCardinality) exp;
+            OWLObjectPropertyExpression r;
+
+            if(minExp.getFiller().equals(factory.getOWLThing())) {
+                r = minExp.getProperty();
+            }
+            //TODO to be restored ...
+            //else if ((r = exists2role.get(someValueExp)) == null) {
+            // deal with r' \subseteq r & range(r') \subseteq C
+            else {
+                r = getNewRole(outputOntology, rlCounter);
+                addedAxioms.add(factory.getOWLSubObjectPropertyOfAxiom(r, minExp.getProperty()));
+                OWLClassExpression tExp = minExp.getFiller();
+                if(!(tExp instanceof OWLObjectComplementOf)) {
+                    if(tExp.equals(factory.getOWLThing())) ;
+                    else
+                        addedAxioms.add(factory.getOWLObjectPropertyRangeAxiom(r, tExp));
+                }
+                else if(botStrategy != BottomStrategy.TOREMOVE) {
+                    OWLClass cls = (OWLClass) tExp.getComplementNNF();
+                    OWLClass neg;
+                    if((neg = atomic2negation.get(cls)) == null) {
+                        neg = getNewConcept(outputOntology, rlCounter);
+                        addedAxioms.add(factory.getOWLDisjointClassesAxiom(neg, cls));
+                        atomic2negation.put(cls, neg);
+                    }
+                    addedAxioms.add(factory.getOWLObjectPropertyRangeAxiom(r, neg));
+                }
 //                              exists2role.put(someValueExp, (OWLObjectProperty) r);
-                        }
-                        
-                        // deal with r'(x,c)
-                        Set<OWLClassExpression> ret = new HashSet<OWLClassExpression>();
-                        int num = minExp.getCardinality();
-                        
-                        Set<OWLNamedIndividual> cs = new HashSet<OWLNamedIndividual>();
-                        OWLNamedIndividual c;
-                        for (int i = 0; i < num; ++i) {
-                                c = getNewIndividual(outputOntology, rlCounter++);
-                                ret.add(factory.getOWLObjectHasValue(r, c));
-                                cs.add(c);
-                        }
-                        
-                        if (botStrategy != BottomStrategy.TOREMOVE && cs.size() > 1) {
-                                addedAxioms.add(factory.getOWLDifferentIndividualsAxiom(cs));
-                        }
-                        
-                        return OWLHelper.getSimplifiedConjunction(factory, ret);
-                }
-                
-                if (exp instanceof OWLObjectMaxCardinality) {
-                        OWLObjectMaxCardinality maxExp = (OWLObjectMaxCardinality)exp;
-                        OWLClassExpression tExp = maxExp.getFiller();
-                        int card = maxExp.getCardinality() >= 1 ? 1 : 0;
-                        if (!(tExp instanceof OWLObjectComplementOf))
-                                return factory.getOWLObjectMaxCardinality(card, maxExp.getProperty(), tExp);
-                        else {
-                                Utility.logDebug("oh, to be tested ... ");
-                                OWLClassExpression tExp1 = factory.getOWLObjectAllValuesFrom(maxExp.getProperty(), tExp.getComplementNNF());
-                                if (card == 0)
-                                        return tExp1;
-                                else {
-                                        OWLClassExpression tExp2 = factory.getOWLObjectMaxCardinality(1, maxExp.getProperty());
-                                        return factory.getOWLObjectIntersectionOf(tExp1, tExp2);
-                                }
-                        }
-                }
-                
-                if (exp instanceof OWLObjectAllValuesFrom) 
-                        return exp;
-                
-                if (exp instanceof OWLObjectOneOf) 
-                        if (((OWLObjectOneOf) exp).getIndividuals().size() == 1)
-                                return exp;
-                        else 
-                                return null;
-                        
-                if (exp instanceof OWLDataHasValue)
-                        return exp;
-                
-                //TODO overapproximation - dealing with OWLDataMinCardinality
-                        
-                if (exp instanceof OWLDataSomeValuesFrom) {
-                        return exp;
-                }
-                
-                if (exp instanceof OWLDataMinCardinality) {
-                        return exp;
-                }
-                
-                if (exp instanceof OWLDataMaxCardinality) {
-                        return exp;
-                }
-                        
-                
-                Set<OWLClassExpression> exps = exp.asConjunctSet();
-                if (exps.size() == 1 && exps.iterator().next() == exp) {
-                        Utility.logError(exp, "error in transform of Ontology~~~~");
-                }
-                Set<OWLClassExpression> nexps = new HashSet<OWLClassExpression>();
-                OWLClassExpression ne;
-                boolean changes = false;
-                for (OWLClassExpression e: exps) {
-                        ne = transform(e, addedAxioms);
-                        if (ne != e) changes = true;
-                        nexps.add(ne);
-                }
-                if (changes) 
-                        return OWLHelper.getSimplifiedConjunction(factory, nexps);
-                else 
-                        return exp;
-        }
-        
-        protected OWLNamedIndividual getNewIndividual(OWLOntology onto, int number) {
-                OWLOntologyManager manager = onto.getOWLOntologyManager();
-                OWLDataFactory factory = manager.getOWLDataFactory();
-                OWLNamedIndividual newIndividual = factory.getOWLNamedIndividual(IRI.create(Namespace.PAGODA_ANONY + "NI" + number));
-                manager.addAxiom(onto, factory.getOWLDeclarationAxiom(newIndividual)); 
-                return newIndividual;                           
-        }
-
-        protected OWLObjectProperty getNewRole(OWLOntology onto, int number) {
-                OWLOntologyManager manager = onto.getOWLOntologyManager();
-                OWLDataFactory factory = manager.getOWLDataFactory();
-                OWLObjectProperty newProperty = factory.getOWLObjectProperty(IRI.create(Namespace.PAGODA_AUX + "NR" + number));
-                manager.addAxiom(onto, factory.getOWLDeclarationAxiom(newProperty)); 
-                return newProperty; 
-        }
-
-        private OWLClass getNewConcept(OWLOntology onto, int number) {
-                OWLOntologyManager manager = onto.getOWLOntologyManager();
-                OWLDataFactory factory = manager.getOWLDataFactory(); 
-                OWLClass newClass = factory.getOWLClass(IRI.create(Namespace.PAGODA_AUX + "NC" + number));
-                manager.addAxiom(onto, factory.getOWLDeclarationAxiom(newClass)); 
-                return newClass; 
-        }
-
-        public OWLOntologyManager getOWLOntologyManager() {
-                return inputOntology.getOWLOntologyManager();
-        }
-
-        public String getOntologyIRI() {
-                return ontologyIRI; 
-        }
-        
-        public OWLOntology getOutputOntology() {
-                return outputOntology;
-        }
-
-        @Override
-        public String getOutputPath() {
-                return outputPath;
-        }
-
-        @Override
-        public String getDirectory() {
-                return outputPath.substring(0, outputPath.lastIndexOf(Utility.FILE_SEPARATOR));
-        }
-
-        public void setCorrespondenceFileLoc(String path) {
-                corrFileName = path; 
-        }
-        
-        private enum BottomStrategy { TOREMOVE, NULLARY, UNARY }
+            }
+
+            // deal with r'(x,c)
+            Set<OWLClassExpression> ret = new HashSet<OWLClassExpression>();
+            int num = minExp.getCardinality();
+
+            Set<OWLNamedIndividual> cs = new HashSet<OWLNamedIndividual>();
+            OWLNamedIndividual c;
+            for(int i = 0; i < num; ++i) {
+                c = getNewIndividual(outputOntology, rlCounter++);
+                ret.add(factory.getOWLObjectHasValue(r, c));
+                cs.add(c);
+            }
+
+            if(botStrategy != BottomStrategy.TOREMOVE && cs.size() > 1) {
+                addedAxioms.add(factory.getOWLDifferentIndividualsAxiom(cs));
+            }
+
+            return OWLHelper.getSimplifiedConjunction(factory, ret);
+        }
+
+        if(exp instanceof OWLObjectMaxCardinality) {
+            OWLObjectMaxCardinality maxExp = (OWLObjectMaxCardinality) exp;
+            OWLClassExpression tExp = maxExp.getFiller();
+            int card = maxExp.getCardinality() >= 1 ? 1 : 0;
+            if(!(tExp instanceof OWLObjectComplementOf))
+                return factory.getOWLObjectMaxCardinality(card, maxExp.getProperty(), tExp);
+            else {
+                Utility.logDebug("oh, to be tested ... ");
+                OWLClassExpression tExp1 =
+                        factory.getOWLObjectAllValuesFrom(maxExp.getProperty(), tExp.getComplementNNF());
+                if(card == 0)
+                    return tExp1;
+                else {
+                    OWLClassExpression tExp2 = factory.getOWLObjectMaxCardinality(1, maxExp.getProperty());
+                    return factory.getOWLObjectIntersectionOf(tExp1, tExp2);
+                }
+            }
+        }
+
+        if(exp instanceof OWLObjectAllValuesFrom)
+            return exp;
+
+        if(exp instanceof OWLObjectOneOf)
+            if(((OWLObjectOneOf) exp).getIndividuals().size() == 1)
+                return exp;
+            else
+                return null;
+
+        if(exp instanceof OWLDataHasValue)
+            return exp;
+
+        //TODO overapproximation - dealing with OWLDataMinCardinality
+
+        if(exp instanceof OWLDataSomeValuesFrom) {
+            return exp;
+        }
+
+        if(exp instanceof OWLDataMinCardinality) {
+            return exp;
+        }
+
+        if(exp instanceof OWLDataMaxCardinality) {
+            return exp;
+        }
+
+
+        Set<OWLClassExpression> exps = exp.asConjunctSet();
+        if(exps.size() == 1 && exps.iterator().next() == exp) {
+            Utility.logError(exp, "error in transform of Ontology~~~~");
+        }
+        Set<OWLClassExpression> nexps = new HashSet<OWLClassExpression>();
+        OWLClassExpression ne;
+        boolean changes = false;
+        for(OWLClassExpression e : exps) {
+            ne = transform(e, addedAxioms);
+            if(ne != e) changes = true;
+            nexps.add(ne);
+        }
+        if(changes)
+            return OWLHelper.getSimplifiedConjunction(factory, nexps);
+        else
+            return exp;
+    }
+
+    protected OWLNamedIndividual getNewIndividual(OWLOntology onto, int number) {
+        OWLOntologyManager manager = onto.getOWLOntologyManager();
+        OWLDataFactory factory = manager.getOWLDataFactory();
+        OWLNamedIndividual newIndividual =
+                factory.getOWLNamedIndividual(IRI.create(Namespace.PAGODA_ANONY + "NI" + number));
+        manager.addAxiom(onto, factory.getOWLDeclarationAxiom(newIndividual));
+        return newIndividual;
+    }
+
+    protected OWLObjectProperty getNewRole(OWLOntology onto, int number) {
+        OWLOntologyManager manager = onto.getOWLOntologyManager();
+        OWLDataFactory factory = manager.getOWLDataFactory();
+        OWLObjectProperty newProperty = factory.getOWLObjectProperty(IRI.create(Namespace.PAGODA_AUX + "NR" + number));
+        manager.addAxiom(onto, factory.getOWLDeclarationAxiom(newProperty));
+        return newProperty;
+    }
+
+    private OWLClass getNewConcept(OWLOntology onto, int number) {
+        OWLOntologyManager manager = onto.getOWLOntologyManager();
+        OWLDataFactory factory = manager.getOWLDataFactory();
+        OWLClass newClass = factory.getOWLClass(IRI.create(Namespace.PAGODA_AUX + "NC" + number));
+        manager.addAxiom(onto, factory.getOWLDeclarationAxiom(newClass));
+        return newClass;
+    }
+
+    private enum BottomStrategy {TOREMOVE, NULLARY, UNARY}
 }
 
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java b/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java
index 50996d0..b708bee 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java
+++ b/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java
@@ -11,161 +11,173 @@ import uk.ac.ox.cs.pagoda.rules.DatalogProgram;
 import uk.ac.ox.cs.pagoda.rules.Program;
 import uk.ac.ox.cs.pagoda.util.Timer;
 import uk.ac.ox.cs.pagoda.util.Utility;
+import uk.ac.ox.cs.pagoda.util.disposable.DisposedException;
 
 import java.util.Collection;
 
 public class MultiStageQueryEngine extends StageQueryEngine {
 
-        public MultiStageQueryEngine(String name, boolean checkValidity) {
-                super(name, checkValidity);
-        }
-
-        /**
-         * c-chase
-         */
-        @Override
-        public void materialiseFoldedly(DatalogProgram dProgram, GapByStore4ID gap) {
-                materialise("lower program", dProgram.getLower().toString());
-                Program generalProgram = dProgram.getGeneral(); 
-                FoldedApplication program = new FoldedApplication(generalProgram, dProgram.getUpperBottomStrategy()); 
-                Treatment treatment = new Pick4NegativeConceptNaive(this, program); 
-                materialise(program, treatment, gap); 
-        }
-        
-        /**
-         * c-chase^f
-         */
-        @Override
-        public int materialiseRestrictedly(DatalogProgram dProgram, GapByStore4ID gap) {
-                if (gap != null)
-                        materialise("lower program", dProgram.getLower().toString());
-                
-                Program generalProgram = dProgram.getGeneral();
-                RestrictedApplication program = new RestrictedApplication(generalProgram, dProgram.getUpperBottomStrategy());
-                Treatment treatment = new Pick4NegativeConceptNaive(this, program);
-                int ret = materialise(program, treatment, gap);
-                treatment.dispose(); // does nothing
-                return ret; 
-        }
-        
-        public int materialise4SpecificQuery(Program generalProgram, QueryRecord record, BottomStrategy upperBottom) {
-                RestrictedApplication program = new RestrictedApplication(generalProgram, upperBottom);
-                Treatment treatment = new Pick4NegativeConceptQuerySpecific(this, program, record);
-                int ret = materialise(program, treatment, null);
-                treatment.dispose();
-                return ret; 
-        }
-
-        /**
-         * delta-chase
-         */
-        @Override
-        public int materialiseSkolemly(DatalogProgram dProgram, GapByStore4ID gap) {
-                materialise("lower program", dProgram.getLower().toString());
-                Program generalProgram = dProgram.getGeneral();
-                LimitedSkolemisationApplication program = new LimitedSkolemisationApplication(generalProgram, dProgram.getUpperBottomStrategy());
-                Treatment treatment = new Pick4NegativeConceptNaive(this, program);
-                return materialise(program, treatment, gap);
-        }
-        
-        private int materialise(MultiStageUpperProgram program, Treatment treatment, GapByStore4ID gap) {
-                if (gap != null) 
-                        treatment.addAdditionalGapTuples(); 
-                String programName = "multi-stage upper program"; 
-                Utility.logInfo(name + " store is materialising " + programName +  " ..."); 
-                Timer t = new Timer();
-                
-                String datalogProgram = program.getDatalogRuleText();
-                long tripleCountBeforeMat = 0;
-                
-                // TODO to be removed ... 
+    public MultiStageQueryEngine(String name, boolean checkValidity) {
+        super(name, checkValidity);
+    }
+
+    /**
+     * c-chase
+     */
+    @Override
+    public void materialiseFoldedly(DatalogProgram dProgram, GapByStore4ID gap) {
+        if(isDisposed()) throw new DisposedException();
+
+        materialise("lower program", dProgram.getLower().toString());
+        Program generalProgram = dProgram.getGeneral();
+        FoldedApplication program = new FoldedApplication(generalProgram, dProgram.getUpperBottomStrategy());
+        Treatment treatment = new Pick4NegativeConceptNaive(this, program);
+        materialise(program, treatment, gap);
+    }
+
+    /**
+     * c-chase^f
+     */
+    @Override
+    public int materialiseRestrictedly(DatalogProgram dProgram, GapByStore4ID gap) {
+        if(isDisposed()) throw new DisposedException();
+
+        if(gap != null)
+            materialise("lower program", dProgram.getLower().toString());
+
+        Program generalProgram = dProgram.getGeneral();
+        RestrictedApplication program = new RestrictedApplication(generalProgram, dProgram.getUpperBottomStrategy());
+        Treatment treatment = new Pick4NegativeConceptNaive(this, program);
+        int ret = materialise(program, treatment, gap);
+        treatment.dispose(); // does nothing
+        return ret;
+    }
+
+    public int materialise4SpecificQuery(Program generalProgram, QueryRecord record, BottomStrategy upperBottom) {
+        if(isDisposed()) throw new DisposedException();
+
+        RestrictedApplication program = new RestrictedApplication(generalProgram, upperBottom);
+        Treatment treatment = new Pick4NegativeConceptQuerySpecific(this, program, record);
+        int ret = materialise(program, treatment, null);
+        treatment.dispose();
+        return ret;
+    }
+
+    /**
+     * delta-chase
+     */
+    @Override
+    public int materialiseSkolemly(DatalogProgram dProgram, GapByStore4ID gap) {
+        if(isDisposed()) throw new DisposedException();
+
+        materialise("lower program", dProgram.getLower().toString());
+        Program generalProgram = dProgram.getGeneral();
+        LimitedSkolemisationApplication program =
+                new LimitedSkolemisationApplication(generalProgram, dProgram.getUpperBottomStrategy());
+        Treatment treatment = new Pick4NegativeConceptNaive(this, program);
+        return materialise(program, treatment, gap);
+    }
+
+    private int materialise(MultiStageUpperProgram program, Treatment treatment, GapByStore4ID gap) {
+        if(gap != null)
+            treatment.addAdditionalGapTuples();
+        String programName = "multi-stage upper program";
+        Utility.logInfo(name + " store is materialising " + programName + " ...");
+        Timer t = new Timer();
+
+        String datalogProgram = program.getDatalogRuleText();
+        long tripleCountBeforeMat = 0;
+
+        // TODO to be removed ...
 //              if (gap == null)
 //                      program.save("output/multi.dlog");
 
-                Collection<Violation> violations;
-                int iteration = 0;
-                Timer subTimer = new Timer();
-                boolean incrementally;
-                try {
-                        while (true) {
-                                long oldTripleCount = store.getTriplesCount();
-                                
-                                subTimer.reset();
-                                Utility.logInfo("Iteration " + ++iteration + ": ");
-                                
-                                incrementally = (iteration != 1);
-                                
-                                if (!incrementally) 
-                                        tripleCountBeforeMat = oldTripleCount; 
-                                
-                                if (gap != null) {
-                                        try {
-                                                gap.compile(incrementally ? null : datalogProgram);
-                                                gap.addBackTo();
-                                        } finally {
-                                                gap.clear();
-                                        }
-                                }
-                                else {
-                                        if (!incrementally)  {
+        Collection<Violation> violations;
+        int iteration = 0;
+        Timer subTimer = new Timer();
+        boolean incrementally;
+        try {
+            while(true) {
+                long oldTripleCount = store.getTriplesCount();
+
+                subTimer.reset();
+                Utility.logInfo("Iteration " + ++iteration + ": ");
+
+                incrementally = (iteration != 1);
+
+                if(!incrementally)
+                    tripleCountBeforeMat = oldTripleCount;
+
+                if(gap != null) {
+                    try {
+                        gap.compile(incrementally ? null : datalogProgram);
+                        gap.addBackTo();
+                    } finally {
+                        gap.clear();
+                    }
+                }
+                else {
+                    if(!incrementally) {
 //                                              store.addRules(new String[] {datalogProgram});
-                                                store.importRules(datalogProgram);
-                                        }
-                                        store.applyReasoning(incrementally);
-                                }
-                                
+                        store.importRules(datalogProgram);
+                    }
+                    store.applyReasoning(incrementally);
+                }
+
 //                              Utility.logInfo("The number of sameAs assertions in the current store: " + getSameAsNumber());
-                                
-                                if (!isValid()) {
-                                        if (iteration == 1) {
-                                                Utility.logInfo("The ontology is inconsistent.");
-                                                return -1; 
-                                        }
-                                        Utility.logInfo(name + " store FAILED for multi-stage materialisation in " + t.duration() + " seconds.");
-                                        return 0; 
-                                }
-                                else validMaterialisation = null; 
-                                
-                                long tripleCount = store.getTriplesCount(); 
-                                Utility.logDebug(name + " store after materialising datalog-rules: " + tripleCount + " (" + (tripleCount - oldTripleCount) + " new)");
-                                Utility.logDebug("Time to materialise datalog-rules: " + subTimer.duration()); 
-                                
-                                subTimer.reset(); 
-                                if ((violations = program.isIntegrated(this, incrementally)) == null || violations.size() == 0) {
-                                        store.clearRulesAndMakeFactsExplicit();
-                                        Utility.logInfo(name + " store after materialising " + programName + ": " + tripleCount + " (" + (tripleCount - tripleCountBeforeMat) + " new)");
-                                        Utility.logInfo(name + " store is DONE for multi-stage materialising in " + t.duration() + " seconds.");
-                                        return isValid() ? 1 : 0;
-                                }
-                                Utility.logDebug("Time to detect violations: " + subTimer.duration()); 
-
-                                store.makeFactsExplicit();
-                                subTimer.reset(); 
-                                oldTripleCount = store.getTriplesCount(); 
-                                for (Violation v : violations) {
-
-                                        Utility.logDebug("Dealing with violation: " + v.constraint);
-                                        Utility.logDebug("Number of violation tuples: " + v.size());
-
-                                        Timer localTimer = new Timer(); 
-                                        int number = v.size(); 
-                                        long vOldCounter = store.getTriplesCount();  
-                                        if (!treatment.makeSatisfied(v)) {
-                                                validMaterialisation = false;
-                                                Utility.logInfo(name + " store FAILED for multi-stage materialisation in " + t.duration() + " seconds."); 
-                                                return 0; 
-                                        }
-                                        Utility.logDebug("Time to make the constraint being satisfied: " + localTimer.duration());
-                                        Utility.logDebug("Triples in the store: before=" + vOldCounter + ", after=" + store.getTriplesCount() + ", new=" + (store.getTriplesCount() - vOldCounter));
-                                }
-                                Utility.logDebug(name + " store after adding facts for violations: " + (tripleCount = store.getTriplesCount()) + " (" + (tripleCount - oldTripleCount) + " new)");
-                                Utility.logDebug("Time to add triples for violations: " + subTimer.duration()); 
-                        }
-                } catch (JRDFStoreException e) {
-                        e.printStackTrace();
-                } 
-                return 0; 
-        }
-                        
+
+                if(!isValid()) {
+                    if(iteration == 1) {
+                        Utility.logInfo("The ontology is inconsistent.");
+                        return -1;
+                    }
+                    Utility.logInfo(name + " store FAILED for multi-stage materialisation in " + t.duration() + " seconds.");
+                    return 0;
+                }
+                else validMaterialisation = null;
+
+                long tripleCount = store.getTriplesCount();
+                Utility.logDebug(name + " store after materialising datalog-rules: " + tripleCount + " (" + (tripleCount - oldTripleCount) + " new)");
+                Utility.logDebug("Time to materialise datalog-rules: " + subTimer.duration());
+
+                subTimer.reset();
+                if((violations = program.isIntegrated(this, incrementally)) == null || violations.size() == 0) {
+                    store.clearRulesAndMakeFactsExplicit();
+                    Utility.logInfo(name + " store after materialising " + programName + ": " + tripleCount + " (" + (tripleCount - tripleCountBeforeMat) + " new)");
+                    Utility.logInfo(name + " store is DONE for multi-stage materialising in " + t.duration() + " seconds.");
+                    return isValid() ? 1 : 0;
+                }
+                Utility.logDebug("Time to detect violations: " + subTimer.duration());
+
+                store.makeFactsExplicit();
+                subTimer.reset();
+                oldTripleCount = store.getTriplesCount();
+                for(Violation v : violations) {
+
+                    Utility.logDebug("Dealing with violation: " + v.constraint);
+                    Utility.logDebug("Number of violation tuples: " + v.size());
+
+                    Timer localTimer = new Timer();
+                    int number = v.size();
+                    long vOldCounter = store.getTriplesCount();
+                    if(!treatment.makeSatisfied(v)) {
+                        validMaterialisation = false;
+                        Utility.logInfo(name + " store FAILED for multi-stage materialisation in " + t.duration() + " seconds.");
+                        return 0;
+                    }
+                    Utility.logDebug("Time to make the constraint being satisfied: " + localTimer.duration());
+                    Utility.logDebug("Triples in the store: before=" + vOldCounter + ", after=" + store.getTriplesCount() + ", new=" + (store
+                            .getTriplesCount() - vOldCounter));
+                }
+                Utility.logDebug(name + " store after adding facts for violations: " + (tripleCount =
+                        store.getTriplesCount()) + " (" + (tripleCount - oldTripleCount) + " new)");
+                Utility.logDebug("Time to add triples for violations: " + subTimer.duration());
+            }
+        } catch(JRDFStoreException e) {
+            e.printStackTrace();
+        }
+        return 0;
+    }
+
 }
 
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/StageQueryEngine.java b/src/uk/ac/ox/cs/pagoda/multistage/StageQueryEngine.java
index e652f66..c8776fe 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/StageQueryEngine.java
+++ b/src/uk/ac/ox/cs/pagoda/multistage/StageQueryEngine.java
@@ -23,10 +23,6 @@ public abstract class StageQueryEngine extends BasicQueryEngine {
 
         public abstract int materialiseSkolemly(DatalogProgram dProgram, GapByStore4ID gap);
 
-        public void dispose() {
-                super.dispose();
-        }
-
         public boolean isValid() {
                 if (!checkValidity) return true; 
                 if (validMaterialisation != null) return validMaterialisation; 
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConcept.java b/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConcept.java
index 00e7e2b..687fa4a 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConcept.java
+++ b/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConcept.java
@@ -14,194 +14,193 @@ import uk.ac.ox.cs.pagoda.reasoner.light.RDFoxTripleManager;
 import uk.ac.ox.cs.pagoda.util.Namespace;
 import uk.ac.ox.cs.pagoda.util.SparqlHelper;
 import uk.ac.ox.cs.pagoda.util.Utility;
+import uk.ac.ox.cs.pagoda.util.disposable.DisposedException;
 import uk.ac.ox.cs.pagoda.util.tuples.Tuple;
 import uk.ac.ox.cs.pagoda.util.tuples.TupleBuilder;
 
 import java.util.*;
 
-public abstract class Pick4NegativeConcept implements Treatment {
-
-        public Set<Atom> addedGroundAtoms = new HashSet<Atom>();
-        MultiStageQueryEngine engine;
-        MultiStageUpperProgram program;
-        RDFoxTripleManager tripleManager;
-        PredicateDependency dependencyGraph;
-        boolean addGap = false;
-        
-        public Pick4NegativeConcept(MultiStageQueryEngine store, MultiStageUpperProgram multiProgram) {
-                this.engine = store;
-                this.program = multiProgram;
-                this.tripleManager = new RDFoxTripleManager(store.getDataStore(), true);
-        }
-
-        void addTripleByID(Atom atom, Atom gapAtom, Map<Variable, Integer> assignment) {
-                int[] newTuple = tripleManager.getInstance(atom, assignment);
-                tripleManager.addTripleByID(newTuple);
-                if (addGap)
-                        tripleManager.addTripleByID(tripleManager.getInstance(gapAtom, assignment));
-        }
-
-        protected boolean makeSatisfied(Violation violation, Comparator<Atom> comp) {
-                LinkedList<AnswerTupleID> tuples = violation.getTuples();
-                DLClause constraint = violation.getConstraint();
-                Map<Variable, Integer> assignment = new HashMap<Variable, Integer>();
-                
-                if (constraint.getHeadLength() > 1) {
-                        Atom[] orderedAtoms = Arrays.copyOf(constraint.getHeadAtoms(), constraint.getHeadLength());
-                        Arrays.sort(orderedAtoms, comp);
-        
-                        Set<AnswerTupleID> negTuples = new HashSet<AnswerTupleID>(); 
-                        String negativeQuery; 
-                        String[] subVars; 
-                        for (Atom headAtom: orderedAtoms) {
-                                Atom negativeAtom = MultiStageUpperProgram.getNegativeAtom(headAtom); 
-                                if (negativeAtom == null) continue; 
-                                negativeQuery = SparqlHelper.getSPARQLQuery(new Atom[] { negativeAtom }, 
-                                                subVars = MultiStageUpperProgram.getVarSubset(violation.getVariables(), headAtom));
-                                negTuples.clear();
-                                Atom gapHeadAtom = addGap ? getGapAtom(headAtom) : null; 
-                                TupleIterator negAnswers = null; 
-                                try {
-                                        negAnswers = engine.internal_evaluateNotExpanded(negativeQuery); 
-                                        for (long multi = negAnswers.open(); multi != 0; multi = negAnswers.getNext()) 
-                                                negTuples.add(new AnswerTupleID(negAnswers)); 
-                                } catch (JRDFStoreException e) {
-                                        e.printStackTrace();
-                                } finally {
-                                        if (negAnswers != null) negAnswers.dispose();
-                                }
-
-                                if (!tuples.isEmpty())
+public abstract class Pick4NegativeConcept extends Treatment {
+
+    public Set<Atom> addedGroundAtoms = new HashSet<Atom>();
+    MultiStageQueryEngine engine;
+    MultiStageUpperProgram program;
+    RDFoxTripleManager tripleManager;
+    PredicateDependency dependencyGraph;
+    boolean addGap = false;
+
+    public Pick4NegativeConcept(MultiStageQueryEngine store, MultiStageUpperProgram multiProgram) {
+        this.engine = store;
+        this.program = multiProgram;
+        this.tripleManager = new RDFoxTripleManager(store.getDataStore(), true);
+    }
+
+    @Override
+    public void addAdditionalGapTuples() {
+        if(isDisposed()) throw new DisposedException();
+        addGap = true;
+    }
+
+    void addTripleByID(Atom atom, Atom gapAtom, Map<Variable, Integer> assignment) {
+        if(isDisposed()) throw new DisposedException();
+        int[] newTuple = tripleManager.getInstance(atom, assignment);
+        tripleManager.addTripleByID(newTuple);
+        if(addGap)
+            tripleManager.addTripleByID(tripleManager.getInstance(gapAtom, assignment));
+    }
+
+    protected boolean makeSatisfied(Violation violation, Comparator<Atom> comp) {
+        LinkedList<AnswerTupleID> tuples = violation.getTuples();
+        DLClause constraint = violation.getConstraint();
+        Map<Variable, Integer> assignment = new HashMap<Variable, Integer>();
+
+        if(constraint.getHeadLength() > 1) {
+            Atom[] orderedAtoms = Arrays.copyOf(constraint.getHeadAtoms(), constraint.getHeadLength());
+            Arrays.sort(orderedAtoms, comp);
+
+            Set<AnswerTupleID> negTuples = new HashSet<AnswerTupleID>();
+            String negativeQuery;
+            String[] subVars;
+            for(Atom headAtom : orderedAtoms) {
+                Atom negativeAtom = MultiStageUpperProgram.getNegativeAtom(headAtom);
+                if(negativeAtom == null) continue;
+                negativeQuery = SparqlHelper.getSPARQLQuery(new Atom[]{negativeAtom},
+                                                            subVars =
+                                                                    MultiStageUpperProgram.getVarSubset(violation.getVariables(), headAtom));
+                negTuples.clear();
+                Atom gapHeadAtom = addGap ? getGapAtom(headAtom) : null;
+                TupleIterator negAnswers = null;
+                try {
+                    negAnswers = engine.internal_evaluateNotExpanded(negativeQuery);
+                    for(long multi = negAnswers.open(); multi != 0; multi = negAnswers.getNext())
+                        negTuples.add(new AnswerTupleID(negAnswers));
+                } catch(JRDFStoreException e) {
+                    e.printStackTrace();
+                } finally {
+                    if(negAnswers != null) negAnswers.dispose();
+                }
+
+                if(!tuples.isEmpty())
 //                                      program.addUpdatedPredicates(dependencyGraph.getDependence(headAtom.getDLPredicate()));
-                                        program.addUpdatedPredicate(headAtom.getDLPredicate());
-
-                                Comparator<AnswerTupleID> tComp = new TupleComparator(subVars); 
-                                Collections.sort(tuples, tComp);
-                                
-                                AnswerTupleID lastAdded = null; 
-                                
-                                for (Iterator<AnswerTupleID> iter = tuples.iterator(); iter.hasNext(); ) {
-
-                                        AnswerTupleID tuple = iter.next();
-                                        if (!negTuples.contains(MultiStageUpperProgram.project(tuple, violation.getVariables(), subVars))) {
-                                                if (lastAdded == null || tComp.compare(lastAdded, tuple) != 0) {
-                                                        lastAdded = tuple; 
-                                                        tuple.getAssignment(violation.getVariables(), assignment);
-                                                        addTripleByID(headAtom, gapHeadAtom, assignment);
-                                                }
-                                                iter.remove();
-                                        }
-                                }
+                    program.addUpdatedPredicate(headAtom.getDLPredicate());
+
+                Comparator<AnswerTupleID> tComp = new TupleComparator(subVars);
+                Collections.sort(tuples, tComp);
+
+                AnswerTupleID lastAdded = null;
+
+                for(Iterator<AnswerTupleID> iter = tuples.iterator(); iter.hasNext(); ) {
+
+                    AnswerTupleID tuple = iter.next();
+                    if(!negTuples.contains(MultiStageUpperProgram.project(tuple, violation.getVariables(), subVars))) {
+                        if(lastAdded == null || tComp.compare(lastAdded, tuple) != 0) {
+                            lastAdded = tuple;
+                            tuple.getAssignment(violation.getVariables(), assignment);
+                            addTripleByID(headAtom, gapHeadAtom, assignment);
+                        }
+                        iter.remove();
+                    }
+                }
 //                              tuples.reset();
-                                
-                                if (tuples.isEmpty()) 
-                                        return true; 
-                        }
-                        if (!tuples.isEmpty()) return false;
-                }
-                else {
-                        Set<Atom> headAtoms = new HashSet<Atom>();
-
-                        ArrayList<Tuple<Individual>> violationTuples = new ArrayList<>(violation.getTuples().size());
-                        for (int i = 0; i < violation.getTuples().size(); i++) {
-                                AnswerTupleID answerTupleID = violation.getTuples().get(i);
-                                TupleBuilder<Individual> tupleBuilder = new TupleBuilder<>();
-                                for (int j = 0; j < answerTupleID.getArity(); j++) {
-                                        String rawTerm = tripleManager.getRawTerm(answerTupleID.getTerm(j));
-                                        Individual individual = Individual.create(rawTerm.substring(1, rawTerm.length()-1));
-                                        tupleBuilder.append(individual);
-                                }
-                                violationTuples.add(tupleBuilder.build());
-                        }
-
-                        for (DLClause clause : program.convertExist(constraint, violation.getClause(), violationTuples)) {
-
-                                if (!DLClauseHelper.hasSubsetBodyAtoms(clause, constraint)) {
-                                        Utility.logError("There might be an error here... Cannot happen!!!");
-                                        throw new Error("This condition should not happen!!!");
-                                }
-
-                                Atom tHeadAtom = clause.getHeadAtom(0);
-                                Atom tGapHeadAtom = addGap ? getGapAtom(tHeadAtom) : null;
-                                if (DLClauseHelper.isGround(tHeadAtom)) {
-                                        if (!addedGroundAtoms.contains(tHeadAtom)) {
-                                                program.addUpdatedPredicate(tHeadAtom.getDLPredicate());
-                                                addTripleByID(tHeadAtom, tGapHeadAtom, null);
-                                                addedGroundAtoms.add(tHeadAtom);
-                                        }
-                                } else headAtoms.add(tHeadAtom);
-                        }
-                        if (!tuples.isEmpty())
-                                for (Atom atom: headAtoms)
-                                        program.addUpdatedPredicate(atom.getDLPredicate()); 
-
-                        for (AnswerTupleID tuple: tuples) { 
-                                tuple.getAssignment(violation.getVariables(), assignment); 
-                                for (Atom atom: headAtoms) {
-                                        addTripleByID(atom, getGapAtom(atom), assignment);
-                                }
-                        }
-                }
-                
-                assignment.clear(); 
-                return true;
-        }
-        
-        private Atom getGapAtom(Atom atom) {
-                if (!addGap) return null; 
-                String gapPredicate = GapTupleIterator.getGapPredicate(getPredicateIRI(atom.getDLPredicate()));
-                Atom gapAtom = atom.getArity() == 1 ? Atom.create(AtomicConcept.create(gapPredicate), atom.getArgument(0)) : 
-                        Atom.create(AtomicRole.create(gapPredicate), atom.getArgument(0), atom.getArgument(1)); 
-                return gapAtom;
-        }
-
-        private String getPredicateIRI(DLPredicate dlPredicate) {
-                if (dlPredicate instanceof Equality || dlPredicate instanceof AnnotatedEquality)
-                        return Namespace.EQUALITY; 
-                if (dlPredicate instanceof Inequality)
-                        return Namespace.INEQUALITY; 
-                if (dlPredicate instanceof AtomicConcept)
-                        return ((AtomicConcept) dlPredicate).getIRI(); 
-                if (dlPredicate instanceof AtomicRole)
-                        return ((AtomicRole) dlPredicate).getIRI(); 
-                return null; 
-        }
-
-        @Override
-        public void dispose() {
-//              tripleManager.outputAddedInstance();
-//              addedGroundAtoms.clear();
-        }
-
-        @Override
-        public void addAdditionalGapTuples() {
-                addGap = true; 
-        }
-        
+
+                if(tuples.isEmpty())
+                    return true;
+            }
+            if(!tuples.isEmpty()) return false;
+        }
+        else {
+            Set<Atom> headAtoms = new HashSet<Atom>();
+
+            ArrayList<Tuple<Individual>> violationTuples = new ArrayList<>(violation.getTuples().size());
+            for(int i = 0; i < violation.getTuples().size(); i++) {
+                AnswerTupleID answerTupleID = violation.getTuples().get(i);
+                TupleBuilder<Individual> tupleBuilder = new TupleBuilder<>();
+                for(int j = 0; j < answerTupleID.getArity(); j++) {
+                    String rawTerm = tripleManager.getRawTerm(answerTupleID.getTerm(j));
+                    Individual individual = Individual.create(rawTerm.substring(1, rawTerm.length() - 1));
+                    tupleBuilder.append(individual);
+                }
+                violationTuples.add(tupleBuilder.build());
+            }
+
+            for(DLClause clause : program.convertExist(constraint, violation.getClause(), violationTuples)) {
+
+                if(!DLClauseHelper.hasSubsetBodyAtoms(clause, constraint)) {
+                    Utility.logError("There might be an error here... Cannot happen!!!");
+                    throw new Error("This condition should not happen!!!");
+                }
+
+                Atom tHeadAtom = clause.getHeadAtom(0);
+                Atom tGapHeadAtom = addGap ? getGapAtom(tHeadAtom) : null;
+                if(DLClauseHelper.isGround(tHeadAtom)) {
+                    if(!addedGroundAtoms.contains(tHeadAtom)) {
+                        program.addUpdatedPredicate(tHeadAtom.getDLPredicate());
+                        addTripleByID(tHeadAtom, tGapHeadAtom, null);
+                        addedGroundAtoms.add(tHeadAtom);
+                    }
+                }
+                else headAtoms.add(tHeadAtom);
+            }
+            if(!tuples.isEmpty())
+                for(Atom atom : headAtoms)
+                    program.addUpdatedPredicate(atom.getDLPredicate());
+
+            for(AnswerTupleID tuple : tuples) {
+                tuple.getAssignment(violation.getVariables(), assignment);
+                for(Atom atom : headAtoms) {
+                    addTripleByID(atom, getGapAtom(atom), assignment);
+                }
+            }
+        }
+
+        assignment.clear();
+        return true;
+    }
+
+    private Atom getGapAtom(Atom atom) {
+        if(!addGap) return null;
+        String gapPredicate = GapTupleIterator.getGapPredicate(getPredicateIRI(atom.getDLPredicate()));
+        Atom gapAtom = atom.getArity() == 1 ? Atom.create(AtomicConcept.create(gapPredicate), atom.getArgument(0)) :
+                Atom.create(AtomicRole.create(gapPredicate), atom.getArgument(0), atom.getArgument(1));
+        return gapAtom;
+    }
+
+    private String getPredicateIRI(DLPredicate dlPredicate) {
+        if(dlPredicate instanceof Equality || dlPredicate instanceof AnnotatedEquality)
+            return Namespace.EQUALITY;
+        if(dlPredicate instanceof Inequality)
+            return Namespace.INEQUALITY;
+        if(dlPredicate instanceof AtomicConcept)
+            return ((AtomicConcept) dlPredicate).getIRI();
+        if(dlPredicate instanceof AtomicRole)
+            return ((AtomicRole) dlPredicate).getIRI();
+        return null;
+    }
+
 }
 
 class TupleComparator implements Comparator<AnswerTupleID> {
 
-        int[] validIndexes; 
-        
-        public TupleComparator(String[] validTerms) {
-                int num = 0; 
-                for (int i = 0; i < validTerms.length; ++i)
-                        if (validTerms[i] != null) 
-                                ++num; 
-                validIndexes = new int[num]; 
-                for (int i = 0, j = 0; i < validTerms.length; ++i)
-                        if (validTerms[i] != null)
-                                validIndexes[j++] = i; 
-        }
-        
-        @Override
-        public int compare(AnswerTupleID o1, AnswerTupleID o2) {
-                int delta = 0; 
-                for (int i = 0; i < validIndexes.length; ++i)
-                        if ((delta = o1.getTerm(validIndexes[i]) - o2.getTerm(validIndexes[i])) != 0) 
-                                return delta;
-                return 0; 
-        }
-        
+    int[] validIndexes;
+
+    public TupleComparator(String[] validTerms) {
+        int num = 0;
+        for(int i = 0; i < validTerms.length; ++i)
+            if(validTerms[i] != null)
+                ++num;
+        validIndexes = new int[num];
+        for(int i = 0, j = 0; i < validTerms.length; ++i)
+            if(validTerms[i] != null)
+                validIndexes[j++] = i;
+    }
+
+    @Override
+    public int compare(AnswerTupleID o1, AnswerTupleID o2) {
+        int delta = 0;
+        for(int i = 0; i < validIndexes.length; ++i)
+            if((delta = o1.getTerm(validIndexes[i]) - o2.getTerm(validIndexes[i])) != 0)
+                return delta;
+        return 0;
+    }
+
 }
\ No newline at end of file
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConceptNaive.java b/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConceptNaive.java
index b0c5d46..af190fc 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConceptNaive.java
+++ b/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConceptNaive.java
@@ -1,25 +1,25 @@
 package uk.ac.ox.cs.pagoda.multistage.treatement;
 
+import uk.ac.ox.cs.JRDFox.JRDFStoreException;
 import uk.ac.ox.cs.pagoda.constraints.PredicateDependency;
 import uk.ac.ox.cs.pagoda.multistage.MultiStageQueryEngine;
 import uk.ac.ox.cs.pagoda.multistage.MultiStageUpperProgram;
 import uk.ac.ox.cs.pagoda.multistage.Violation;
-
-import uk.ac.ox.cs.JRDFox.JRDFStoreException;
+import uk.ac.ox.cs.pagoda.util.disposable.DisposedException;
 
 public class Pick4NegativeConceptNaive extends Pick4NegativeConcept {
 
+        SimpleComparator comp = new SimpleComparator();
+        
         public Pick4NegativeConceptNaive(MultiStageQueryEngine store, MultiStageUpperProgram multiProgram) {
                 super(store, multiProgram);
-                dependencyGraph = new PredicateDependency(multiProgram.getClauses()); 
+                dependencyGraph = new PredicateDependency(multiProgram.getClauses());
         }
         
-        SimpleComparator comp = new SimpleComparator(); 
-        
         @Override
         public boolean makeSatisfied(Violation violation) throws JRDFStoreException {
+                if(isDisposed()) throw new DisposedException();
                 return makeSatisfied(violation, comp);
         }
-
 }
 
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConceptQuerySpecific.java b/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConceptQuerySpecific.java
index 10aa22f..20b4376 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConceptQuerySpecific.java
+++ b/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConceptQuerySpecific.java
@@ -11,77 +11,81 @@ import uk.ac.ox.cs.pagoda.multistage.Violation;
 import uk.ac.ox.cs.pagoda.query.QueryRecord;
 import uk.ac.ox.cs.pagoda.rules.approximators.OverApproxExist;
 import uk.ac.ox.cs.pagoda.util.Namespace;
+import uk.ac.ox.cs.pagoda.util.disposable.DisposedException;
 
 import java.util.Comparator;
 import java.util.Set;
 
 public class Pick4NegativeConceptQuerySpecific extends Pick4NegativeConcept {
 
-        QueryRecord record;
-        Comparator<Atom> comp; 
-        Normalisation norm; 
-        
-        public Pick4NegativeConceptQuerySpecific(MultiStageQueryEngine multiStageQueryEngine, RestrictedApplication program, QueryRecord record) {
-                super(multiStageQueryEngine, program);
-                this.record = record;
-                norm = program.getNormalisation(); 
-                dependencyGraph = new PredicateDependency(record.getRelevantClauses()); 
-                comp = new DisjunctComparator(new SimpleComparator());
-        }
-
-        @Override
-        public boolean makeSatisfied(Violation violation) throws JRDFStoreException {
-                return makeSatisfied(violation, comp);
-        }
-
-        class DisjunctComparator implements Comparator<Atom> {
-
-//              Map<DLPredicate, Integer> dist = new HashMap<DLPredicate, Integer>();
-                Comparator<Atom> m_reference;  
-                Set<DLPredicate> dsts; 
-                
-                public DisjunctComparator(Comparator<Atom> referenceComp) {
-                        m_reference = referenceComp; 
-                        dsts = dependencyGraph.collectPredicate(DLClauseHelper.getQuery(record.getQueryText(), null).getBodyAtoms()); 
-                }
-                
-                @Override
-                public int compare(Atom arg0, Atom arg1) {
-                        int dist0 = getDistance(arg0.getDLPredicate()); 
-                        int dist1 = getDistance(arg1.getDLPredicate()); 
-                        int ret = dist1 - dist0;
-                        if (ret != 0) return ret; 
-                        
-                        return - m_reference.compare(arg0, arg1); 
-                }
-
-                private int getDistance(DLPredicate p) {
-                        if (p instanceof Equality || p instanceof AnnotatedEquality) 
-                                return -1;
-                        if (p instanceof Inequality)
-                                p = AtomicRole.create(Namespace.INEQUALITY); 
-
-                        AtLeastConcept alc; 
-                        if (p instanceof AtomicConcept)
-                                if ((alc = norm.getRightAtLeastConcept((AtomicConcept) p)) != null) {
-                                        AtomicRole r = alc.getOnRole() instanceof AtomicRole ? 
-                                                        (AtomicRole) alc.getOnRole() : 
-                                                                ((InverseRole) alc.getOnRole()).getInverseOf(); 
-                                        AtomicConcept c = alc.getToConcept() instanceof AtomicConcept ? 
-                                                        (AtomicConcept) alc.getToConcept() : 
-                                                                OverApproxExist.getNegationConcept(((AtomicNegationConcept) alc.getToConcept()).getNegatedAtomicConcept()); 
-                                        
-                                        if (c.equals(AtomicConcept.THING))
-                                                return dependencyGraph.distance(dsts, r); 
-                                        else 
-                                                return dependencyGraph.distance(dsts, r, c); 
-                                } else if ((alc = norm.getLeftAtLeastConcept((AtomicConcept) p)) != null) {
-                                        return 2; 
-                                }
-                        
-                        return dependencyGraph.distance(dsts, p);
-                }
-                
-        }
+    QueryRecord record;
+    Comparator<Atom> comp;
+    Normalisation norm;
+
+    public Pick4NegativeConceptQuerySpecific(MultiStageQueryEngine multiStageQueryEngine, RestrictedApplication program, QueryRecord record) {
+        super(multiStageQueryEngine, program);
+        this.record = record;
+        norm = program.getNormalisation();
+        dependencyGraph = new PredicateDependency(record.getRelevantClauses());
+        comp = new DisjunctComparator(new SimpleComparator());
+    }
+
+    @Override
+    public boolean makeSatisfied(Violation violation) throws JRDFStoreException {
+        if(isDisposed()) throw new DisposedException();
+        return makeSatisfied(violation, comp);
+    }
+
+    class DisjunctComparator implements Comparator<Atom> {
+
+        //              Map<DLPredicate, Integer> dist = new HashMap<DLPredicate, Integer>();
+        Comparator<Atom> m_reference;
+        Set<DLPredicate> dsts;
+
+        public DisjunctComparator(Comparator<Atom> referenceComp) {
+            m_reference = referenceComp;
+            dsts = dependencyGraph.collectPredicate(DLClauseHelper.getQuery(record.getQueryText(), null)
+                                                                  .getBodyAtoms());
+        }
+
+        @Override
+        public int compare(Atom arg0, Atom arg1) {
+            int dist0 = getDistance(arg0.getDLPredicate());
+            int dist1 = getDistance(arg1.getDLPredicate());
+            int ret = dist1 - dist0;
+            if(ret != 0) return ret;
+
+            return -m_reference.compare(arg0, arg1);
+        }
+
+        private int getDistance(DLPredicate p) {
+            if(p instanceof Equality || p instanceof AnnotatedEquality)
+                return -1;
+            if(p instanceof Inequality)
+                p = AtomicRole.create(Namespace.INEQUALITY);
+
+            AtLeastConcept alc;
+            if(p instanceof AtomicConcept)
+                if((alc = norm.getRightAtLeastConcept((AtomicConcept) p)) != null) {
+                    AtomicRole r = alc.getOnRole() instanceof AtomicRole ?
+                            (AtomicRole) alc.getOnRole() :
+                            ((InverseRole) alc.getOnRole()).getInverseOf();
+                    AtomicConcept c = alc.getToConcept() instanceof AtomicConcept ?
+                            (AtomicConcept) alc.getToConcept() :
+                            OverApproxExist.getNegationConcept(((AtomicNegationConcept) alc.getToConcept()).getNegatedAtomicConcept());
+
+                    if(c.equals(AtomicConcept.THING))
+                        return dependencyGraph.distance(dsts, r);
+                    else
+                        return dependencyGraph.distance(dsts, r, c);
+                }
+                else if((alc = norm.getLeftAtLeastConcept((AtomicConcept) p)) != null) {
+                    return 2;
+                }
+
+            return dependencyGraph.distance(dsts, p);
+        }
+
+    }
 
 }
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/treatement/SkolemTreatment.java b/src/uk/ac/ox/cs/pagoda/multistage/treatement/SkolemTreatment.java
deleted file mode 100644
index 7a92b79..0000000
--- a/src/uk/ac/ox/cs/pagoda/multistage/treatement/SkolemTreatment.java
+++ /dev/null
@@ -1,33 +0,0 @@
-package uk.ac.ox.cs.pagoda.multistage.treatement;
-
-import uk.ac.ox.cs.JRDFox.JRDFStoreException;
-import uk.ac.ox.cs.pagoda.multistage.FoldedApplication;
-import uk.ac.ox.cs.pagoda.multistage.MultiStageQueryEngine;
-import uk.ac.ox.cs.pagoda.multistage.Violation;
-
-// TODO should I implement something like this?
-public class SkolemTreatment implements Treatment {
-
-        public SkolemTreatment(MultiStageQueryEngine multiStageQueryEngine,     FoldedApplication program) {
-                // TODO Auto-generated constructor stub
-        }
-
-        @Override
-        public boolean makeSatisfied(Violation violation) throws JRDFStoreException {
-                // TODO Auto-generated method stub
-                return false;
-        }
-
-        @Override
-        public void dispose() {
-                // TODO Auto-generated method stub
-
-        }
-
-        @Override
-        public void addAdditionalGapTuples() {
-                // TODO Auto-generated method stub
-
-        }
-
-}
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/treatement/Treatment.java b/src/uk/ac/ox/cs/pagoda/multistage/treatement/Treatment.java
index 686379a..cb81af0 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/treatement/Treatment.java
+++ b/src/uk/ac/ox/cs/pagoda/multistage/treatement/Treatment.java
@@ -1,14 +1,12 @@
 package uk.ac.ox.cs.pagoda.multistage.treatement;
 
-import uk.ac.ox.cs.pagoda.multistage.Violation;
-
 import uk.ac.ox.cs.JRDFox.JRDFStoreException;
+import uk.ac.ox.cs.pagoda.multistage.Violation;
+import uk.ac.ox.cs.pagoda.util.disposable.Disposable;
 
-public interface Treatment {
+public abstract class Treatment extends Disposable {
 
-        public boolean makeSatisfied(Violation violation) throws JRDFStoreException;  
-        
-        public void dispose();
+    public abstract boolean makeSatisfied(Violation violation) throws JRDFStoreException;
 
-        public void addAdditionalGapTuples(); 
+    public abstract void addAdditionalGapTuples();
 }
diff --git a/src/uk/ac/ox/cs/pagoda/query/AnswerTuple.java b/src/uk/ac/ox/cs/pagoda/query/AnswerTuple.java
index cb2b0a3..78aced1 100644
--- a/src/uk/ac/ox/cs/pagoda/query/AnswerTuple.java
+++ b/src/uk/ac/ox/cs/pagoda/query/AnswerTuple.java
@@ -172,7 +172,7 @@ public class AnswerTuple {
                                                 String lexicalForm = matcher.group("lexicalForm");
                                                 String dataTypeIRI = matcher.group("dataType");
                                                 Datatype dataType;
-                                                if (dataTypeIRI.isEmpty()) dataType = Datatype.RDF_PLAIN_LITERAL;
+                                                if(dataTypeIRI == null || dataTypeIRI.isEmpty()) dataType = Datatype.RDF_PLAIN_LITERAL;
                                                 else dataType = uk.ac.ox.cs.JRDFox.model.Datatype.value(dataTypeIRI);
                                                 terms[i] = uk.ac.ox.cs.JRDFox.model.Literal.create(lexicalForm, dataType);
                                         }
diff --git a/src/uk/ac/ox/cs/pagoda/query/AnswerTuples.java b/src/uk/ac/ox/cs/pagoda/query/AnswerTuples.java
index e1e5302..81efed0 100644
--- a/src/uk/ac/ox/cs/pagoda/query/AnswerTuples.java
+++ b/src/uk/ac/ox/cs/pagoda/query/AnswerTuples.java
@@ -1,23 +1,22 @@
 package uk.ac.ox.cs.pagoda.query;
 
-public interface AnswerTuples {
-        
-        public void reset(); 
-        
-        public boolean isValid();
-        
-        public int getArity();  
-        
-        public String[] getAnswerVariables(); 
-        
-        public void moveNext(); 
-        
-        public void dispose(); 
-        
-        public AnswerTuple getTuple(); 
-        
-        public boolean contains(AnswerTuple t);
-        
-        public void remove(); 
+import uk.ac.ox.cs.pagoda.util.disposable.Disposable;
 
+public abstract class AnswerTuples extends Disposable {
+
+    public abstract void reset();
+
+    public abstract boolean isValid();
+
+    public abstract int getArity();
+
+    public abstract String[] getAnswerVariables();
+
+    public abstract void moveNext();
+
+    public abstract AnswerTuple getTuple();
+
+    public abstract boolean contains(AnswerTuple t);
+
+    public abstract void remove();
 }
diff --git a/src/uk/ac/ox/cs/pagoda/query/AnswerTuplesImp.java b/src/uk/ac/ox/cs/pagoda/query/AnswerTuplesImp.java
index 3e0f320..fd3fb1f 100644
--- a/src/uk/ac/ox/cs/pagoda/query/AnswerTuplesImp.java
+++ b/src/uk/ac/ox/cs/pagoda/query/AnswerTuplesImp.java
@@ -3,7 +3,7 @@ package uk.ac.ox.cs.pagoda.query;
 import java.util.Iterator;
 import java.util.Set;
 
-public class AnswerTuplesImp implements AnswerTuples {
+public class AnswerTuplesImp extends AnswerTuples {
 
         int m_index; 
         Iterator<AnswerTuple> m_iter;
@@ -54,9 +54,6 @@ public class AnswerTuplesImp implements AnswerTuples {
         }
 
         @Override
-        public void dispose() {}
-
-        @Override
         public void reset() {
                 if (m_answers1 == null || m_answers1.isEmpty()) {
                         m_index = 2;
diff --git a/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java b/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
index 1f81a78..742b7da 100644
--- a/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
+++ b/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
@@ -11,6 +11,8 @@ import uk.ac.ox.cs.pagoda.util.ConjunctiveQueryHelper;
 import uk.ac.ox.cs.pagoda.util.Namespace;
 import uk.ac.ox.cs.pagoda.util.PagodaProperties;
 import uk.ac.ox.cs.pagoda.util.Utility;
+import uk.ac.ox.cs.pagoda.util.disposable.Disposable;
+import uk.ac.ox.cs.pagoda.util.disposable.DisposedException;
 import uk.ac.ox.cs.pagoda.util.tuples.Tuple;
 import uk.ac.ox.cs.pagoda.util.tuples.TupleBuilder;
 
@@ -18,162 +20,180 @@ import java.io.*;
 import java.lang.reflect.Type;
 import java.util.*;
 
-public class QueryRecord {
-        
-        public static final String botQueryText = "SELECT ?X WHERE { ?X <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Nothing> }";
-        public static final String SEPARATOR = "----------------------------------------";
-        private static final String RDF_TYPE = "a"; //"rdf:type"; //RDF.type.toString();
-        boolean processed = false;
-        String stringQueryID = null;
-        OWLOntology relevantOntology = null;
-        Set<DLClause> relevantClauses = new HashSet<DLClause>();
-        double[] timer;
-        int subID;
-        DLClause queryClause = null;
-        int queryID = -1;
-        Set<AnswerTuple> soundAnswerTuples = new HashSet<AnswerTuple>();
-        private Step difficulty;
-        private String queryText;
-        private String[][] answerVariables = null;
-        private Set<AnswerTuple> gapAnswerTuples = null;
-        private QueryManager m_manager;
-
-        private QueryRecord() {
-        }
+public class QueryRecord extends Disposable {
+
+    public static final String botQueryText =
+            "SELECT ?X WHERE { ?X <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Nothing> }";
+    public static final String SEPARATOR = "----------------------------------------";
+    private static final String RDF_TYPE = "a"; //"rdf:type"; //RDF.type.toString();
+    boolean processed = false;
+    String stringQueryID = null;
+    OWLOntology relevantOntology = null;
+    Set<DLClause> relevantClauses = new HashSet<DLClause>();
+    double[] timer;
+    int subID;
+    DLClause queryClause = null;
+    int queryID = -1;
+    Set<AnswerTuple> soundAnswerTuples = new HashSet<AnswerTuple>();
+    private Step difficulty;
+    private String queryText;
+    private String[][] answerVariables = null;
+    private Set<AnswerTuple> gapAnswerTuples = null;
+    private QueryManager m_manager;
+
+    private QueryRecord() {
+    }
 
 //      private boolean containsAuxPredicate(String str) {
 //              return  str.contains(Namespace.PAGODA_AUX) || str.contains("_AUX") || str.contains("owl#Nothing") ||
 //                              str.contains("internal:def"); 
 //      }
 
-        public QueryRecord(QueryManager manager, String text, int id, int subID) {
-                m_manager = manager;
-                resetInfo(text, id, subID);
-                resetTimer();
-        }
-
-        public static Collection<String> collectQueryTexts(Collection<QueryRecord> queryRecords) {
-                Collection<String> texts = new LinkedList<String>();
-                for(QueryRecord record : queryRecords)
-                        texts.add(record.queryText);
-                return texts;
-        }
-
-        public void resetInfo(String text, int id, int subid) {
-                queryID = id;
-                subID = subid;
-                stringQueryID = id + (subID == 0 ? "" : "_" + subID);
-                m_manager.remove(queryText);
-                m_manager.put(text, this);
-                queryClause = null;
-                answerVariables = ConjunctiveQueryHelper.getAnswerVariables(text);
-                queryText = text; // .replace("_:", "?");
-        }
-
-        public void resetTimer() {
-                int length = Step.values().length;
-                timer = new double[length];
-                for(int i = 0; i < length; ++i) timer[i] = 0;
-        }
-
-        public AnswerTuples getAnswers() {
-                if(isProcessed())
-                        return getLowerBoundAnswers();
-
-                return getUpperBoundAnswers();
-        }
-
-        public AnswerTuples getLowerBoundAnswers() {
-                return new AnswerTuplesImp(answerVariables[0], soundAnswerTuples);
-        }
-
-        public AnswerTuples getUpperBoundAnswers() {
-                return new AnswerTuplesImp(answerVariables[0], soundAnswerTuples, gapAnswerTuples);
-        }
-
-        public boolean updateLowerBoundAnswers(AnswerTuples answerTuples) {
-                if(answerTuples == null) return false;
-                boolean update = false;
-                for(AnswerTuple tuple; answerTuples.isValid(); answerTuples.moveNext()) {
-                        tuple = answerTuples.getTuple();
-                        if(!soundAnswerTuples.contains(tuple) && (gapAnswerTuples == null || gapAnswerTuples.contains(tuple))) {
-                                soundAnswerTuples.add(tuple);
-                                if(gapAnswerTuples != null)
-                                        gapAnswerTuples.remove(tuple);
-                                update = true;
-                        }
-                }
-
-                if(soundAnswerTuples.isEmpty())
-                        Utility.logInfo("Lower bound answers empty");
-                else if(update)
-                        Utility.logInfo("Lower bound answers updated: " + soundAnswerTuples.size());
-                else
-                        Utility.logInfo("Lower bound answers unchanged");
-
-                return update;
-        }
-
-        public boolean updateUpperBoundAnswers(AnswerTuples answerTuples) {
-                return updateUpperBoundAnswers(answerTuples, false);
-        }
-
-        public boolean updateUpperBoundAnswers(AnswerTuples answerTuples, boolean toCheckAux) {
-                if(!(answerTuples instanceof RDFoxAnswerTuples)) {
-                        String msg = "The upper bound must be computed by RDFox!";
-                        Utility.logError(msg);
-                        throw new IllegalArgumentException(msg);
-                }
-
-                RDFoxAnswerTuples rdfoxAnswerTuples = (RDFoxAnswerTuples) answerTuples;
-
-                Set<AnswerTuple> candidateGapAnswerTuples = new HashSet<AnswerTuple>();
-                AnswerTuple tuple;
-                for(; rdfoxAnswerTuples.isValid(); rdfoxAnswerTuples.moveNext()) {
-                        tuple = rdfoxAnswerTuples.getTuple();
-                        if(isBottom() || !tuple.hasAnonymousIndividual())
-                                if((!toCheckAux || !tuple.hasAuxPredicate()) && !soundAnswerTuples.contains(tuple))
-                                        candidateGapAnswerTuples.add(tuple);
-                }
-
-                /*** START: debugging ***/
-                if(PagodaProperties.isDebuggingMode()) {
-                        if(rdfoxAnswerTuples.getArity() != getAnswerVariables().length)
-                                throw new IllegalArgumentException(
-                                                "The arity of answers (" + rdfoxAnswerTuples.getArity() + ") " +
-                                                                "is different from the number of answer variables (" +
-                                                                getAnswerVariables().length + ")");
-
-                        Set<AnswerTuple> namedAnswerTuples = new HashSet<>();
-                        rdfoxAnswerTuples.reset();
-                        for(; rdfoxAnswerTuples.isValid(); rdfoxAnswerTuples.moveNext()) {
-                                tuple = rdfoxAnswerTuples.getTuple();
+    public QueryRecord(QueryManager manager, String text, int id, int subID) {
+        m_manager = manager;
+        resetInfo(text, id, subID);
+        resetTimer();
+    }
+
+    public static Collection<String> collectQueryTexts(Collection<QueryRecord> queryRecords) {
+        Collection<String> texts = new LinkedList<String>();
+        for(QueryRecord record : queryRecords)
+            texts.add(record.queryText);
+        return texts;
+    }
+
+    public void resetInfo(String text, int id, int subid) {
+        if(isDisposed()) throw new DisposedException();
+
+        queryID = id;
+        subID = subid;
+        stringQueryID = id + (subID == 0 ? "" : "_" + subID);
+        m_manager.remove(queryText);
+        m_manager.put(text, this);
+        queryClause = null;
+        answerVariables = ConjunctiveQueryHelper.getAnswerVariables(text);
+        queryText = text; // .replace("_:", "?");
+    }
+
+    public void resetTimer() {
+        if(isDisposed()) throw new DisposedException();
+
+        int length = Step.values().length;
+        timer = new double[length];
+        for(int i = 0; i < length; ++i) timer[i] = 0;
+    }
+
+    public AnswerTuples getAnswers() {
+        if(isDisposed()) throw new DisposedException();
+
+        if(isProcessed())
+            return getLowerBoundAnswers();
+
+        return getUpperBoundAnswers();
+    }
+
+    public AnswerTuples getLowerBoundAnswers() {
+        if(isDisposed()) throw new DisposedException();
+
+        return new AnswerTuplesImp(answerVariables[0], soundAnswerTuples);
+    }
+
+    public AnswerTuples getUpperBoundAnswers() {
+        if(isDisposed()) throw new DisposedException();
+
+        return new AnswerTuplesImp(answerVariables[0], soundAnswerTuples, gapAnswerTuples);
+    }
+
+    public boolean updateLowerBoundAnswers(AnswerTuples answerTuples) {
+        if(isDisposed()) throw new DisposedException();
+
+        if(answerTuples == null) return false;
+        boolean update = false;
+        for(AnswerTuple tuple; answerTuples.isValid(); answerTuples.moveNext()) {
+            tuple = answerTuples.getTuple();
+            if(!soundAnswerTuples.contains(tuple) && (gapAnswerTuples == null || gapAnswerTuples.contains(tuple))) {
+                soundAnswerTuples.add(tuple);
+                if(gapAnswerTuples != null)
+                    gapAnswerTuples.remove(tuple);
+                update = true;
+            }
+        }
+
+        if(soundAnswerTuples.isEmpty())
+            Utility.logInfo("Lower bound answers empty");
+        else if(update)
+            Utility.logInfo("Lower bound answers updated: " + soundAnswerTuples.size());
+        else
+            Utility.logInfo("Lower bound answers unchanged");
+
+        return update;
+    }
+
+    public boolean updateUpperBoundAnswers(AnswerTuples answerTuples) {
+        if(isDisposed()) throw new DisposedException();
+
+        return updateUpperBoundAnswers(answerTuples, false);
+    }
+
+    public boolean updateUpperBoundAnswers(AnswerTuples answerTuples, boolean toCheckAux) {
+        if(isDisposed()) throw new DisposedException();
+
+        if(!(answerTuples instanceof RDFoxAnswerTuples)) {
+            String msg = "The upper bound must be computed by RDFox!";
+            Utility.logError(msg);
+            throw new IllegalArgumentException(msg);
+        }
+
+        RDFoxAnswerTuples rdfoxAnswerTuples = (RDFoxAnswerTuples) answerTuples;
+
+        Set<AnswerTuple> candidateGapAnswerTuples = new HashSet<AnswerTuple>();
+        AnswerTuple tuple;
+        for(; rdfoxAnswerTuples.isValid(); rdfoxAnswerTuples.moveNext()) {
+            tuple = rdfoxAnswerTuples.getTuple();
+            if(isBottom() || !tuple.hasAnonymousIndividual())
+                if((!toCheckAux || !tuple.hasAuxPredicate()) && !soundAnswerTuples.contains(tuple))
+                    candidateGapAnswerTuples.add(tuple);
+        }
+
+        /*** START: debugging ***/
+        if(PagodaProperties.isDebuggingMode()) {
+            if(rdfoxAnswerTuples.getArity() != getAnswerVariables().length)
+                throw new IllegalArgumentException(
+                        "The arity of answers (" + rdfoxAnswerTuples.getArity() + ") " +
+                                "is different from the number of answer variables (" +
+                                getAnswerVariables().length + ")");
+
+            Set<AnswerTuple> namedAnswerTuples = new HashSet<>();
+            rdfoxAnswerTuples.reset();
+            for(; rdfoxAnswerTuples.isValid(); rdfoxAnswerTuples.moveNext()) {
+                tuple = rdfoxAnswerTuples.getTuple();
 //                              if(isBottom() || !tuple.hasAnonymousIndividual()) {
-                                namedAnswerTuples.add(tuple);
+                namedAnswerTuples.add(tuple);
 //                              }
-                        }
-                        HashSet<AnswerTuple> difference = new HashSet<>(soundAnswerTuples);
-                        difference.removeAll(namedAnswerTuples);
-                        if(!difference.isEmpty())
-                                throw new IllegalArgumentException("The upper bound does not contain the lower bound! Missing answers: " + difference
-                                                .size());
-                }
-                /*** END: debugging ***/
-
-                boolean update;
-                if(gapAnswerTuples == null) {
-                        gapAnswerTuples = candidateGapAnswerTuples;
-                        update = true;
-                } else {
-                        update = gapAnswerTuples.retainAll(candidateGapAnswerTuples);
-                }
-
-                if(update)
-                        Utility.logInfo("Upper bound answers updated: " + getNumberOfAnswers());
-                else
-                        Utility.logInfo("Upper bound answers unchanged");
-
-                return update;
+            }
+            HashSet<AnswerTuple> difference = new HashSet<>(soundAnswerTuples);
+            difference.removeAll(namedAnswerTuples);
+            if(!difference.isEmpty())
+                throw new IllegalArgumentException("The upper bound does not contain the lower bound! Missing answers: " + difference
+                        .size());
+        }
+        /*** END: debugging ***/
+
+        boolean update;
+        if(gapAnswerTuples == null) {
+            gapAnswerTuples = candidateGapAnswerTuples;
+            update = true;
+        }
+        else {
+            update = gapAnswerTuples.retainAll(candidateGapAnswerTuples);
+        }
+
+        if(update)
+            Utility.logInfo("Upper bound answers updated: " + getNumberOfAnswers());
+        else
+            Utility.logInfo("Upper bound answers unchanged");
+
+        return update;
 
 //              boolean update = false;
 //              for(Iterator<AnswerTuple> iter = gapAnswerTuples.iterator(); iter.hasNext(); ) {
@@ -183,96 +203,116 @@ public class QueryRecord {
 //                              update = true;
 //                      }
 //              }
-        }
-
-        public int getNumberOfAnswers() {
-                return soundAnswerTuples.size() + gapAnswerTuples.size();
-        }
-
-        public void markAsProcessed() {
-                processed = true;
-        }
-
-        public boolean isProcessed() {
-                if(gapAnswerTuples != null && gapAnswerTuples.isEmpty()) processed = true;
-                return processed;
-        }
-
-        public String[] getDistinguishedVariables() {
-                return answerVariables[1];
-        }
-
-        public String[] getAnswerVariables() {
-                return answerVariables[0];
-        }
-
-        public String[][] getVariables() {
-                return answerVariables;
-        }
-        
-        public String getQueryText() {
-                return queryText;
-        }
-        
-        public String getQueryID() {
-                return stringQueryID;
-        }
-
-        public AnswerTuples getGapAnswers() {
-                return new AnswerTuplesImp(answerVariables[0], gapAnswerTuples);
-        }
-
-        public String toString() {
-                return queryText;
-        }
-
-        public void outputAnswers(BufferedWriter writer) throws IOException {
-
-                int answerCounter = soundAnswerTuples.size();
-                if(!isProcessed()) answerCounter += gapAnswerTuples.size();
-
-                Utility.logInfo("The number of answer tuples: " + answerCounter);
-
-                if (writer != null) {
-                        writer.write("-------------- Query " + queryID + " ---------------------");
-                        writer.newLine();
-                        writer.write(queryText);
-                        writer.newLine();
-                        StringBuilder space = new StringBuilder();
-                        int arity = getArity(), varSpace = 0;
-                        for (int i = 0; i < arity; ++i)
-                                varSpace += answerVariables[0][i].length();
-                        for (int i = 0; i < (SEPARATOR.length() - varSpace) / (arity + 1); ++i)
-                                space.append(" ");
-                        for (int i = 0; i < getArity(); ++i) {
-                                writer.write(space.toString());
-                                writer.write(answerVariables[0][i]);
-                        }
-                        writer.newLine();
-                        writer.write(SEPARATOR);
-                        writer.newLine();
-                        for (AnswerTuple tuple: soundAnswerTuples) {
-                                writer.write(tuple.toString());
-                                writer.newLine();
-                        }
-                        if(!isProcessed())
-                                for (AnswerTuple tuple: gapAnswerTuples) {
-                                        writer.write("*");
-                                        writer.write(tuple.toString());
-                                        writer.newLine();
-                                }
+    }
+
+    public int getNumberOfAnswers() {
+        if(isDisposed()) throw new DisposedException();
+
+        return soundAnswerTuples.size() + gapAnswerTuples.size();
+    }
+
+    public void markAsProcessed() {
+        processed = true;
+    }
+
+    public boolean isProcessed() {
+        if(isDisposed()) throw new DisposedException();
+
+        if(gapAnswerTuples != null && gapAnswerTuples.isEmpty()) processed = true;
+        return processed;
+    }
+
+    public String[] getDistinguishedVariables() {
+        if(isDisposed()) throw new DisposedException();
+
+        return answerVariables[1];
+    }
+
+    public String[] getAnswerVariables() {
+        if(isDisposed()) throw new DisposedException();
+
+        return answerVariables[0];
+    }
+
+    public String[][] getVariables() {
+        if(isDisposed()) throw new DisposedException();
+
+        return answerVariables;
+    }
+
+    public String getQueryText() {
+        if(isDisposed()) throw new DisposedException();
+
+        return queryText;
+    }
+
+    public String getQueryID() {
+        if(isDisposed()) throw new DisposedException();
+
+        return stringQueryID;
+    }
+
+    public AnswerTuples getGapAnswers() {
+        if(isDisposed()) throw new DisposedException();
+
+        return new AnswerTuplesImp(answerVariables[0], gapAnswerTuples);
+    }
+
+    public String toString() {
+        if(isDisposed()) throw new DisposedException();
+
+        return queryText;
+    }
+
+    public void outputAnswers(BufferedWriter writer) throws IOException {
+        if(isDisposed()) throw new DisposedException();
+
+        int answerCounter = soundAnswerTuples.size();
+        if(!isProcessed()) answerCounter += gapAnswerTuples.size();
+
+        Utility.logInfo("The number of answer tuples: " + answerCounter);
+
+        if(writer != null) {
+            writer.write("-------------- Query " + queryID + " ---------------------");
+            writer.newLine();
+            writer.write(queryText);
+            writer.newLine();
+            StringBuilder space = new StringBuilder();
+            int arity = getArity(), varSpace = 0;
+            for(int i = 0; i < arity; ++i)
+                varSpace += answerVariables[0][i].length();
+            for(int i = 0; i < (SEPARATOR.length() - varSpace) / (arity + 1); ++i)
+                space.append(" ");
+            for(int i = 0; i < getArity(); ++i) {
+                writer.write(space.toString());
+                writer.write(answerVariables[0][i]);
+            }
+            writer.newLine();
+            writer.write(SEPARATOR);
+            writer.newLine();
+            for(AnswerTuple tuple : soundAnswerTuples) {
+                writer.write(tuple.toString());
+                writer.newLine();
+            }
+            if(!isProcessed())
+                for(AnswerTuple tuple : gapAnswerTuples) {
+                    writer.write("*");
+                    writer.write(tuple.toString());
+                    writer.newLine();
+                }
 //                      writer.write(SEPARATOR);
-                        writer.newLine();
-                }
+            writer.newLine();
+        }
 
-        }
+    }
 
-        public void outputAnswerStatistics() {
+    public void outputAnswerStatistics() {
+        if(isDisposed()) throw new DisposedException();
 
-                int answerCounter = soundAnswerTuples.size();
-                if(!isProcessed()) answerCounter += gapAnswerTuples.size();
+        int answerCounter = soundAnswerTuples.size();
+        if(!isProcessed()) answerCounter += gapAnswerTuples.size();
 
-                Utility.logInfo("The number of answer tuples: " + answerCounter);
+        Utility.logInfo("The number of answer tuples: " + answerCounter);
 //              if (jsonAnswers != null) {
 //                      JSONObject jsonAnswer = new JSONObject();
 //
@@ -297,407 +337,476 @@ public class QueryRecord {
 //
 //                      jsonAnswers.put(Integer.toString(queryID), jsonAnswer);
 //              }
-        }
-
-        public void outputTimes() {
-                for (Step step: Step.values()) {
-                        Utility.logDebug("time for " + step + ": " + timer[step.ordinal()]);
-                }
-        }
-
-        public String outputSoundAnswerTuple() {
-                StringBuilder builder = new StringBuilder();
-                for (AnswerTuple tuple: soundAnswerTuples)
-                        builder.append(tuple.toString()).append(Utility.LINE_SEPARATOR);
-                return builder.toString();
-        }
-
-        public String outputGapAnswerTuple() {
-                StringBuilder builder = new StringBuilder();
-                for(AnswerTuple tuple : gapAnswerTuples)
-                        builder.append(tuple.toString()).append(Utility.LINE_SEPARATOR);
-                return builder.toString();
-        }
-
-        public Step getDifficulty() {
-                return difficulty;
-        }
-
-        public void setDifficulty(Step step) {
-                this.difficulty = step;
-        }
-
-        public OWLOntology getRelevantOntology() {
-                return relevantOntology;
-        }
-
-        public void setRelevantOntology(OWLOntology knowledgebase) {
-                relevantOntology = knowledgebase;
-        }
-
-        public void saveRelevantOntology(String filename) {
-                if(relevantOntology == null) return;
-                OWLOntologyManager manager = relevantOntology.getOWLOntologyManager();
-                try {
-                        FileOutputStream outputStream = new FileOutputStream(filename);
-                        manager.saveOntology(relevantOntology, outputStream);
-                        outputStream.close();
-                } catch (OWLOntologyStorageException e) {
-                        e.printStackTrace();
-                } catch (FileNotFoundException e) {
-                        e.printStackTrace();
-                } catch (IOException e) {
-                        e.printStackTrace();
-                }
-        }
-
-        public void saveRelevantClause() {
-                if(relevantClauses == null) return;
-                GeneralProgram p = new GeneralProgram(relevantClauses, relevantOntology);
-                p.save();
-        }
-
-        public void removeUpperBoundAnswers(Collection<AnswerTuple> answers) {
-                for (AnswerTuple answer: answers) {
+    }
+
+    public void outputTimes() {
+        if(isDisposed()) throw new DisposedException();
+
+        for(Step step : Step.values()) {
+            Utility.logDebug("time for " + step + ": " + timer[step.ordinal()]);
+        }
+    }
+
+    public String outputSoundAnswerTuple() {
+        if(isDisposed()) throw new DisposedException();
+
+        StringBuilder builder = new StringBuilder();
+        for(AnswerTuple tuple : soundAnswerTuples)
+            builder.append(tuple.toString()).append(Utility.LINE_SEPARATOR);
+        return builder.toString();
+    }
+
+    public String outputGapAnswerTuple() {
+        if(isDisposed()) throw new DisposedException();
+
+        StringBuilder builder = new StringBuilder();
+        for(AnswerTuple tuple : gapAnswerTuples)
+            builder.append(tuple.toString()).append(Utility.LINE_SEPARATOR);
+        return builder.toString();
+    }
+
+    public Step getDifficulty() {
+        if(isDisposed()) throw new DisposedException();
+
+        return difficulty;
+    }
+
+    public void setDifficulty(Step step) {
+        if(isDisposed()) throw new DisposedException();
+
+        this.difficulty = step;
+    }
+
+    public OWLOntology getRelevantOntology() {
+        if(isDisposed()) throw new DisposedException();
+
+        return relevantOntology;
+    }
+
+    public void setRelevantOntology(OWLOntology knowledgebase) {
+        if(isDisposed()) throw new DisposedException();
+
+        relevantOntology = knowledgebase;
+    }
+
+    public void saveRelevantOntology(String filename) {
+        if(isDisposed()) throw new DisposedException();
+
+        if(relevantOntology == null) return;
+        OWLOntologyManager manager = relevantOntology.getOWLOntologyManager();
+        try {
+            FileOutputStream outputStream = new FileOutputStream(filename);
+            manager.saveOntology(relevantOntology, outputStream);
+            outputStream.close();
+        } catch(OWLOntologyStorageException e) {
+            e.printStackTrace();
+        } catch(FileNotFoundException e) {
+            e.printStackTrace();
+        } catch(IOException e) {
+            e.printStackTrace();
+        }
+    }
+
+    public void saveRelevantClause() {
+        if(isDisposed()) throw new DisposedException();
+
+        if(relevantClauses == null) return;
+        GeneralProgram p = new GeneralProgram(relevantClauses, relevantOntology);
+        p.save();
+    }
+
+    public void removeUpperBoundAnswers(Collection<AnswerTuple> answers) {
+        if(isDisposed()) throw new DisposedException();
+
+        for(AnswerTuple answer : answers) {
 //                      if (soundAnswerTuples.contains(answer))
 //                              Utility.logError("The answer (" + answer + ") cannot be removed, because it is in the lower bound.");
-                        if (!gapAnswerTuples.contains(answer))
-                                Utility.logError("The answer (" + answer + ") cannot be removed, because it is not in the upper bound.");
-                        gapAnswerTuples.remove(answer);
-                }
-        }
-
-        public void addLowerBoundAnswers(Collection<AnswerTuple> answers) {
-                for (AnswerTuple answer: answers) {
-                        if (!gapAnswerTuples.contains(answer))
-                                Utility.logError("The answer (" + answer + ") cannot be added, because it is not in the upper bound.");
-                        gapAnswerTuples.remove(answer);
-
-                        answer = AnswerTuple.getInstance(answer, answerVariables[0].length);
+            if(!gapAnswerTuples.contains(answer))
+                Utility.logError("The answer (" + answer + ") cannot be removed, because it is not in the upper bound.");
+            gapAnswerTuples.remove(answer);
+        }
+    }
+
+    public void addLowerBoundAnswers(Collection<AnswerTuple> answers) {
+        if(isDisposed()) throw new DisposedException();
+
+        for(AnswerTuple answer : answers) {
+            if(!gapAnswerTuples.contains(answer))
+                Utility.logError("The answer (" + answer + ") cannot be added, because it is not in the upper bound.");
+            gapAnswerTuples.remove(answer);
+
+            answer = AnswerTuple.getInstance(answer, answerVariables[0].length);
 //                      if (soundAnswerTuples.contains(answer))
 //                              Utility.logError("The answer (" + answer + ") cannot be added, because it is in the lower bound.");
-                        soundAnswerTuples.add(answer);
-                }
-        }
-
-        public int getNoOfSoundAnswers() {
-                return soundAnswerTuples.size();
-        }
-
-        public void addProcessingTime(Step step, double time) {
-                timer[step.ordinal()] += time;
-        }
-
-        public int getArity() {
-                return answerVariables[0].length;
-        }
-
-        public void addRelevantClauses(DLClause clause) {
-                relevantClauses.add(clause);
-        }
-
-        public Set<DLClause> getRelevantClauses() {
-                return relevantClauses;
-        }
-
-        public void clearClauses() {
-                relevantClauses.clear();
-        }
-
-        public boolean isHorn() {
-                for (DLClause clause: relevantClauses)
-                        if (clause.getHeadLength() > 1)
-                                return false;
-                return true;
-        }
-
-        public void saveABoxInTurtle(String filename) {
-                try {
-                        BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(filename)));
-                        OWLIndividual a, b;
-                        StringBuilder builder = new StringBuilder();
-                        for (OWLAxiom axiom: relevantOntology.getABoxAxioms(true)) {
-                                if (axiom instanceof OWLClassAssertionAxiom) {
-                                        OWLClassAssertionAxiom classAssertion = (OWLClassAssertionAxiom) axiom;
-                                        OWLClass c = (OWLClass) classAssertion.getClassExpression();
-                                        a = classAssertion.getIndividual();
-                                        builder.append(a.toString())
-                                                   .append(" <")
-                                                   .append(Namespace.RDF_TYPE)
-                                                   .append("> ")
-                                                   .append(c.toString());
-                                }
-                                else if (axiom instanceof OWLObjectPropertyAssertionAxiom) {
-                                        OWLObjectPropertyAssertionAxiom propertyAssertion = (OWLObjectPropertyAssertionAxiom) axiom;
-                                        OWLObjectProperty p = (OWLObjectProperty) propertyAssertion.getProperty();
-                                        a = propertyAssertion.getSubject();
-                                        b = propertyAssertion.getObject();
-                                        builder.append(a.toString()).append(" ").append(p.toString()).append(" ").append(b.toString());
-                                }
-                                else if (axiom instanceof OWLDataPropertyAssertionAxiom) {
-                                        OWLDataPropertyAssertionAxiom propertyAssertion = (OWLDataPropertyAssertionAxiom) axiom;
-                                        OWLDataProperty p = (OWLDataProperty) propertyAssertion.getProperty();
-                                        a = propertyAssertion.getSubject();
-                                        OWLLiteral l = propertyAssertion.getObject();
-                                        builder.append(a.toString()).append(" ").append(p.toString()).append(" ").append(l.toString());
-                                }
-
-                                writer.write(builder.toString());
-                                writer.write(" .");
-                                writer.newLine();
-                                builder.setLength(0);
-                        }
-                        writer.close();
-                } catch (IOException e) {
-                        e.printStackTrace();
-                } finally {
-
-                }
-        }
-        
-        public void updateSubID() {
-                ++subID;
-                stringQueryID = String.valueOf(queryID) + "_" + subID;
-        }
-
-        public DLClause getClause() {
-                if (queryClause != null)
-                        return queryClause;
-                return queryClause = DLClauseHelper.getQuery(queryText, null);
-        }
-
-        public boolean isBottom() {
-                return queryID == 0;
-        }
-
-        public int getNoOfCompleteAnswers() {
-                return soundAnswerTuples.size() + gapAnswerTuples.size();
-        }
-
-        public int getSubID() {
-                return subID;
-        }
-
-        public boolean hasSameGapAnswers(QueryRecord that) {
-                return gapAnswerTuples.containsAll(that.gapAnswerTuples) && that.gapAnswerTuples.containsAll(gapAnswerTuples);
-        }
-
-        public void dispose() {
-                m_manager.remove(queryText);
-                if(gapAnswerTuples != null) gapAnswerTuples = null;
-                if(soundAnswerTuples != null) soundAnswerTuples = null;
-                if (relevantClauses != null) relevantClauses.clear();
-                if (relevantOntology != null)
-                        relevantOntology.getOWLOntologyManager().removeOntology(relevantOntology);
-                answerVariables = null;
-        }
-
-        public boolean canBeEncodedIntoAtom() {
-                // FIXME
-                return true;
+            soundAnswerTuples.add(answer);
+        }
+    }
+
+    public int getNoOfSoundAnswers() {
+        if(isDisposed()) throw new DisposedException();
+
+        return soundAnswerTuples.size();
+    }
+
+    public void addProcessingTime(Step step, double time) {
+        if(isDisposed()) throw new DisposedException();
+
+        timer[step.ordinal()] += time;
+    }
+
+    public int getArity() {
+        if(isDisposed()) throw new DisposedException();
+
+        return answerVariables[0].length;
+    }
+
+    public void addRelevantClauses(DLClause clause) {
+        if(isDisposed()) throw new DisposedException();
+
+        relevantClauses.add(clause);
+    }
+
+    public Set<DLClause> getRelevantClauses() {
+        if(isDisposed()) throw new DisposedException();
+
+        return relevantClauses;
+    }
+
+    public void clearClauses() {
+        if(isDisposed()) throw new DisposedException();
+
+        relevantClauses.clear();
+    }
+
+    public boolean isHorn() {
+        if(isDisposed()) throw new DisposedException();
+
+        for(DLClause clause : relevantClauses)
+            if(clause.getHeadLength() > 1)
+                return false;
+        return true;
+    }
+
+    public void saveABoxInTurtle(String filename) {
+        if(isDisposed()) throw new DisposedException();
+
+        try {
+            BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(filename)));
+            OWLIndividual a, b;
+            StringBuilder builder = new StringBuilder();
+            for(OWLAxiom axiom : relevantOntology.getABoxAxioms(true)) {
+                if(axiom instanceof OWLClassAssertionAxiom) {
+                    OWLClassAssertionAxiom classAssertion = (OWLClassAssertionAxiom) axiom;
+                    OWLClass c = (OWLClass) classAssertion.getClassExpression();
+                    a = classAssertion.getIndividual();
+                    builder.append(a.toString())
+                           .append(" <")
+                           .append(Namespace.RDF_TYPE)
+                           .append("> ")
+                           .append(c.toString());
+                }
+                else if(axiom instanceof OWLObjectPropertyAssertionAxiom) {
+                    OWLObjectPropertyAssertionAxiom propertyAssertion = (OWLObjectPropertyAssertionAxiom) axiom;
+                    OWLObjectProperty p = (OWLObjectProperty) propertyAssertion.getProperty();
+                    a = propertyAssertion.getSubject();
+                    b = propertyAssertion.getObject();
+                    builder.append(a.toString()).append(" ").append(p.toString()).append(" ").append(b.toString());
+                }
+                else if(axiom instanceof OWLDataPropertyAssertionAxiom) {
+                    OWLDataPropertyAssertionAxiom propertyAssertion = (OWLDataPropertyAssertionAxiom) axiom;
+                    OWLDataProperty p = (OWLDataProperty) propertyAssertion.getProperty();
+                    a = propertyAssertion.getSubject();
+                    OWLLiteral l = propertyAssertion.getObject();
+                    builder.append(a.toString()).append(" ").append(p.toString()).append(" ").append(l.toString());
+                }
+
+                writer.write(builder.toString());
+                writer.write(" .");
+                writer.newLine();
+                builder.setLength(0);
+            }
+            writer.close();
+        } catch(IOException e) {
+            e.printStackTrace();
+        } finally {
+
+        }
+    }
+
+    public void updateSubID() {
+        if(isDisposed()) throw new DisposedException();
+
+        ++subID;
+        stringQueryID = String.valueOf(queryID) + "_" + subID;
+    }
+
+    public DLClause getClause() {
+        if(isDisposed()) throw new DisposedException();
+
+        if(queryClause != null)
+            return queryClause;
+        return queryClause = DLClauseHelper.getQuery(queryText, null);
+    }
+
+    public boolean isBottom() {
+        if(isDisposed()) throw new DisposedException();
+
+        return queryID == 0;
+    }
+
+    public int getNoOfCompleteAnswers() {
+        if(isDisposed()) throw new DisposedException();
+
+        return soundAnswerTuples.size() + gapAnswerTuples.size();
+    }
+
+    public int getSubID() {
+        if(isDisposed()) throw new DisposedException();
+
+        return subID;
+    }
+
+    public boolean hasSameGapAnswers(QueryRecord that) {
+        if(isDisposed()) throw new DisposedException();
+
+        return gapAnswerTuples.containsAll(that.gapAnswerTuples) && that.gapAnswerTuples.containsAll(gapAnswerTuples);
+    }
+
+    @Override
+    public void dispose() {
+        super.dispose();
+        m_manager.remove(queryText);
+        if(gapAnswerTuples != null) gapAnswerTuples = null;
+        if(soundAnswerTuples != null) soundAnswerTuples = null;
+        if(relevantClauses != null) relevantClauses.clear();
+        if(relevantOntology != null)
+            relevantOntology.getOWLOntologyManager().removeOntology(relevantOntology);
+        answerVariables = null;
+    }
+
+    public boolean canBeEncodedIntoAtom() {
+        if(isDisposed()) throw new DisposedException();
+
+        // FIXME
+        return true;
 //              return false;
-        }
-
-        public boolean isPredicate(AnswerTuple a, int i) {
-                Atom[] atoms = getClause().getBodyAtoms();
-                Variable v = Variable.create(answerVariables[1][i]);
-                String iri;
-                for(Atom atom : atoms) {
-                        DLPredicate p = atom.getDLPredicate();
-                        if (p instanceof AtomicConcept) {
-                                if(((AtomicConcept) p).getIRI().equals(v.toString())) return true;
-                        }
-                        else if (p instanceof AtomicRole) {
-                                iri = ((AtomicRole) p).getIRI();
-                                if (iri.equals(v.toString())) return true;
-                                if(iri.startsWith("?"))
-                                        iri = a.getGroundTerm(i).toString();
-                                if(iri.equals(Namespace.RDF_TYPE) && atom.getArgument(1).equals(v)) return true;
-                        }
-                }
-                return false;
-        }
-
-        // TODO remove fully extended query
-        public Tuple<String> getExtendedQueryText() {
+    }
+
+    public boolean isPredicate(AnswerTuple a, int i) {
+        if(isDisposed()) throw new DisposedException();
+
+        Atom[] atoms = getClause().getBodyAtoms();
+        Variable v = Variable.create(answerVariables[1][i]);
+        String iri;
+        for(Atom atom : atoms) {
+            DLPredicate p = atom.getDLPredicate();
+            if(p instanceof AtomicConcept) {
+                if(((AtomicConcept) p).getIRI().equals(v.toString())) return true;
+            }
+            else if(p instanceof AtomicRole) {
+                iri = ((AtomicRole) p).getIRI();
+                if(iri.equals(v.toString())) return true;
+                if(iri.startsWith("?"))
+                    iri = a.getGroundTerm(i).toString();
+                if(iri.equals(Namespace.RDF_TYPE) && atom.getArgument(1).equals(v)) return true;
+            }
+        }
+        return false;
+    }
+
+    // TODO remove fully extended query
+    public Tuple<String> getExtendedQueryText() {
+        if(isDisposed()) throw new DisposedException();
+
 //              String[] ret = new String[2];s
-                int index = queryText.toUpperCase().indexOf(" WHERE");
-                String extendedSelect = queryText.substring(0, index);
-                String extendedWhere= queryText.substring(index + 1), fullyExtendedWhere = queryText.substring(index + 1);
-
-                String sub, obj;
-                Map<String, Set<String>> links = new HashMap<String, Set<String>>();
-                Set<String> list;
-                for (Atom atom: getClause().getBodyAtoms())
-                        if (atom.getDLPredicate() instanceof AtomicRole && atom.getArgument(0) instanceof Variable && atom.getArgument(1) instanceof Variable) {
-                                sub = atom.getArgumentVariable(0).getName();
-                                obj = atom.getArgumentVariable(1).getName();
-                                if((list = links.get(sub)) == null)
-                                        links.put(sub, list = new HashSet<String>());
-                                list.add(obj);
-                                if((list = links.get(obj)) == null)
-                                        links.put(obj, list = new HashSet<String>());
-                                list.add(sub);
-                        }
-
-                StringBuilder extra = new StringBuilder(), fullyExtra = new StringBuilder();
+        int index = queryText.toUpperCase().indexOf(" WHERE");
+        String extendedSelect = queryText.substring(0, index);
+        String extendedWhere = queryText.substring(index + 1), fullyExtendedWhere = queryText.substring(index + 1);
+
+        String sub, obj;
+        Map<String, Set<String>> links = new HashMap<String, Set<String>>();
+        Set<String> list;
+        for(Atom atom : getClause().getBodyAtoms())
+            if(atom.getDLPredicate() instanceof AtomicRole && atom.getArgument(0) instanceof Variable && atom.getArgument(1) instanceof Variable) {
+                sub = atom.getArgumentVariable(0).getName();
+                obj = atom.getArgumentVariable(1).getName();
+                if((list = links.get(sub)) == null)
+                    links.put(sub, list = new HashSet<String>());
+                list.add(obj);
+                if((list = links.get(obj)) == null)
+                    links.put(obj, list = new HashSet<String>());
+                list.add(sub);
+            }
+
+        StringBuilder extra = new StringBuilder(), fullyExtra = new StringBuilder();
 //              if (answerVariables[0] != answerVariables[1]) {
-                        for (int i = answerVariables[0].length; i < answerVariables[1].length; ++i) {
+        for(int i = answerVariables[0].length; i < answerVariables[1].length; ++i) {
 //                      for (int i = 0; i < answerVariables[1].length; ++i) {
-                                fullyExtra.append(" . ?")
-                                                  .append(answerVariables[1][i])
-                                                  .append(" " + RDF_TYPE + " <")
-                                                  .append(Namespace.PAGODA_ORIGINAL)
-                                                  .append(">");
-                                if ((list = links.get(answerVariables[1][i])) == null || list.size() < 2) ;
-                                else {
-                                        extra.append(" . ?")
-                                                 .append(answerVariables[1][i])
-                                                 .append(" " + RDF_TYPE + " <")
-                                                 .append(Namespace.PAGODA_ORIGINAL)
-                                                 .append(">");
-                                }
-                        }
-
-                if(extra.length() > 0) {
-                        extra.append(" }");
-                                extendedWhere = extendedWhere.replace(" }", extendedWhere.contains(". }") ? extra.substring(2) : extra.toString());
-                        }
-
-                if(fullyExtra.length() > 0) {
-                        fullyExtra.append(" }");
-                                fullyExtendedWhere = fullyExtendedWhere.replace(" }", fullyExtendedWhere.contains(". }") ? fullyExtra.substring(2) : fullyExtra.toString());
-                        }
+            fullyExtra.append(" . ?")
+                      .append(answerVariables[1][i])
+                      .append(" " + RDF_TYPE + " <")
+                      .append(Namespace.PAGODA_ORIGINAL)
+                      .append(">");
+            if((list = links.get(answerVariables[1][i])) == null || list.size() < 2) ;
+            else {
+                extra.append(" . ?")
+                     .append(answerVariables[1][i])
+                     .append(" " + RDF_TYPE + " <")
+                     .append(Namespace.PAGODA_ORIGINAL)
+                     .append(">");
+            }
+        }
+
+        if(extra.length() > 0) {
+            extra.append(" }");
+            extendedWhere =
+                    extendedWhere.replace(" }", extendedWhere.contains(". }") ? extra.substring(2) : extra.toString());
+        }
+
+        if(fullyExtra.length() > 0) {
+            fullyExtra.append(" }");
+            fullyExtendedWhere =
+                    fullyExtendedWhere.replace(" }", fullyExtendedWhere.contains(". }") ? fullyExtra.substring(2) : fullyExtra
+                            .toString());
+        }
 //              }
 
-                TupleBuilder result = new TupleBuilder();
-                result.append(extendedSelect + " " + fullyExtendedWhere);
-
-                extra.setLength(0);
-                if (answerVariables[0] != answerVariables[1]) {
-                        for (int i = answerVariables[0].length; i < answerVariables[1].length; ++i)
-                                extra.append(" ?").append(answerVariables[1][i]);
-                        extendedSelect = extendedSelect + extra.toString();
-                }
-                result.append(extendedSelect + " " + extendedWhere);
-
-                return result.build();
-        }
-
-        public boolean hasNonAnsDistinguishedVariables() {
-                return answerVariables[1].length > answerVariables[0].length;
-        }
-
-        /**
-         * Two <tt>QueryRecords</tt> are equal iff
-         * they have the same <tt>queryText</tt>,
-         * <tt>soundAnswerTuples</tt>.
-         */
-        @Override
-        public boolean equals(Object o) {
-                if(!o.getClass().equals(getClass())) return false;
-                QueryRecord that = (QueryRecord) o;
-                return this.queryText.equals(that.queryText)
-                                && soundAnswerTuples.equals(that.soundAnswerTuples);
-        }
-
-        @Override
-        public int hashCode() {
-                return Objects.hash(queryText, soundAnswerTuples);
-        }
-
-        public enum Step {
-                LOWER_BOUND,
-                UPPER_BOUND,
-                SIMPLE_UPPER_BOUND,
-                LAZY_UPPER_BOUND,
-                L_SKOLEM_UPPER_BOUND,
-                EL_LOWER_BOUND,
-                FRAGMENT,
-                FRAGMENT_REFINEMENT,
-                SUMMARISATION,
-                DEPENDENCY,
-                FULL_REASONING
-        }
-
-        /**
-         * A Json serializer, which considers the main attributes.
-         */
-        public static class QueryRecordSerializer implements JsonSerializer<QueryRecord> {
-                public JsonElement serialize(QueryRecord src, Type typeOfSrc, JsonSerializationContext context) {
-                        Gson gson = new GsonBuilder().setPrettyPrinting().create();
-                        JsonObject object = new JsonObject();
-                        object.addProperty("queryID", src.queryID);
-                        object.addProperty("queryText", src.queryText);
+        TupleBuilder result = new TupleBuilder();
+        result.append(extendedSelect + " " + fullyExtendedWhere);
+
+        extra.setLength(0);
+        if(answerVariables[0] != answerVariables[1]) {
+            for(int i = answerVariables[0].length; i < answerVariables[1].length; ++i)
+                extra.append(" ?").append(answerVariables[1][i]);
+            extendedSelect = extendedSelect + extra.toString();
+        }
+        result.append(extendedSelect + " " + extendedWhere);
+
+        return result.build();
+    }
+
+    public boolean hasNonAnsDistinguishedVariables() {
+        if(isDisposed()) throw new DisposedException();
+
+        return answerVariables[1].length > answerVariables[0].length;
+    }
+
+    /**
+     * Two <tt>QueryRecords</tt> are equal iff
+     * they have the same <tt>queryText</tt>,
+     * <tt>soundAnswerTuples</tt>.
+     */
+    @Override
+    public boolean equals(Object o) {
+        if(isDisposed()) throw new DisposedException();
+
+        if(!o.getClass().equals(getClass())) return false;
+        QueryRecord that = (QueryRecord) o;
+        return this.queryText.equals(that.queryText)
+                && soundAnswerTuples.equals(that.soundAnswerTuples);
+    }
+
+    @Override
+    public int hashCode() {
+        if(isDisposed()) throw new DisposedException();
+
+        return Objects.hash(queryText, soundAnswerTuples);
+    }
+
+    public enum Step {
+        LOWER_BOUND,
+        UPPER_BOUND,
+        SIMPLE_UPPER_BOUND,
+        LAZY_UPPER_BOUND,
+        L_SKOLEM_UPPER_BOUND,
+        EL_LOWER_BOUND,
+        FRAGMENT,
+        FRAGMENT_REFINEMENT,
+        SUMMARISATION,
+        DEPENDENCY,
+        FULL_REASONING
+    }
+
+    /**
+     * A Json serializer, which considers the main attributes.
+     */
+    public static class QueryRecordSerializer implements JsonSerializer<QueryRecord> {
+        public JsonElement serialize(QueryRecord src, Type typeOfSrc, JsonSerializationContext context) {
+            Gson gson = new GsonBuilder().setPrettyPrinting().create();
+            JsonObject object = new JsonObject();
+            object.addProperty("queryID", src.queryID);
+            object.addProperty("queryText", src.queryText);
 //                      object.addProperty("difficulty", src.difficulty != null ? src.difficulty.toString() : "");
 
-                        object.add("answerVariables", context.serialize(src.getAnswerVariables()));
-                        object.add("answers", context.serialize(src.soundAnswerTuples));
+            object.add("answerVariables", context.serialize(src.getAnswerVariables()));
+            object.add("answers", context.serialize(src.soundAnswerTuples));
 //                      object.add("gapAnswers", context.serialize(src.gapAnswerTuples));
 
-                        return object;
-                }
-        }
-
-        /**
-         * A Json deserializer, compliant to the output of the serializer defined above.
-         */
-        public static class QueryRecordDeserializer implements JsonDeserializer<QueryRecord> {
-                public QueryRecord deserialize(JsonElement json, Type typeOfT, JsonDeserializationContext context)
-                                throws JsonParseException {
-
-                        QueryRecord record = new QueryRecord();
-                        JsonObject object = json.getAsJsonObject();
-                        record.queryID = object.getAsJsonPrimitive("queryID").getAsInt();
-                        record.queryText = object.getAsJsonPrimitive("queryText").getAsString();
+            return object;
+        }
+    }
+
+    /**
+     * A Json deserializer, compliant to the output of the serializer defined above.
+     */
+    public static class QueryRecordDeserializer implements JsonDeserializer<QueryRecord> {
+        public QueryRecord deserialize(JsonElement json, Type typeOfT, JsonDeserializationContext context)
+                throws JsonParseException {
+
+            QueryRecord record = new QueryRecord();
+            JsonObject object = json.getAsJsonObject();
+            record.queryID = object.getAsJsonPrimitive("queryID").getAsInt();
+            record.queryText = object.getAsJsonPrimitive("queryText").getAsString();
 //                      record.difficulty = Step.valueOf(object.getAsJsonPrimitive("difficulty").getAsString());
 
-                        JsonArray answerVariablesJson = object.getAsJsonArray("answerVariables");
-                        record.answerVariables = new String[2][];
-                        record.answerVariables[0] = new String[answerVariablesJson.size()];
-                        for(int i = 0; i < answerVariablesJson.size(); i++)
-                                record.answerVariables[0][i] = answerVariablesJson.get(i).getAsString();
+            JsonArray answerVariablesJson = object.getAsJsonArray("answerVariables");
+            record.answerVariables = new String[2][];
+            record.answerVariables[0] = new String[answerVariablesJson.size()];
+            for(int i = 0; i < answerVariablesJson.size(); i++)
+                record.answerVariables[0][i] = answerVariablesJson.get(i).getAsString();
 
-                        record.soundAnswerTuples = new HashSet<>();
+            record.soundAnswerTuples = new HashSet<>();
 //                      record.gapAnswerTuples = new HashSet<>();
-                        Type type = new TypeToken<AnswerTuple>() { }.getType();
-                        for (JsonElement answer : object.getAsJsonArray("answers")) {
-                                record.soundAnswerTuples.add(context.deserialize(answer, type));
-                        }
+            Type type = new TypeToken<AnswerTuple>() {
+            }.getType();
+            for(JsonElement answer : object.getAsJsonArray("answers")) {
+                record.soundAnswerTuples.add(context.deserialize(answer, type));
+            }
 //                      for (JsonElement answer : object.getAsJsonArray("gapAnswers")) {
 //                              record.soundAnswerTuples.add(context.deserialize(answer, type));
 //                      }
 
-                        return record;
-                }
-        }
-
-        /**
-         * Provides an instance (singleton) of Gson, having a specific configuration.
-         * */
-        public static class GsonCreator {
-
-                private static Gson gson;
-
-                private GsonCreator() {}
-
-                public static Gson getInstance() {
-                        if(gson == null) {
-                                gson = new GsonBuilder()
-                                                .registerTypeAdapter(AnswerTuple.class, new AnswerTuple.AnswerTupleSerializer())
-                                                .registerTypeAdapter(QueryRecord.class, new QueryRecord.QueryRecordSerializer())
-                                                .registerTypeAdapter(QueryRecord.class, new QueryRecord.QueryRecordDeserializer())
-                                                .registerTypeAdapter(AnswerTuple.class, new AnswerTuple.AnswerTupleDeserializer())
-                                                .disableHtmlEscaping()
-                                                .setPrettyPrinting()
-                                                .create();
-                        }
-                        return gson;
-                }
+            return record;
+        }
+    }
+
+    /**
+     * Provides an instance (singleton) of Gson, having a specific configuration.
+     */
+    public static class GsonCreator {
+
+        private static Gson gson;
+
+        private GsonCreator() {
+        }
+
+        public static Gson getInstance() {
+            if(gson == null) {
+                gson = new GsonBuilder()
+                        .registerTypeAdapter(AnswerTuple.class, new AnswerTuple.AnswerTupleSerializer())
+                        .registerTypeAdapter(QueryRecord.class, new QueryRecord.QueryRecordSerializer())
+                        .registerTypeAdapter(QueryRecord.class, new QueryRecord.QueryRecordDeserializer())
+                        .registerTypeAdapter(AnswerTuple.class, new AnswerTuple.AnswerTupleDeserializer())
+                        .disableHtmlEscaping()
+                        .setPrettyPrinting()
+                        .create();
+            }
+            return gson;
+        }
 
 //              public static void dispose() {
 //                      gson = null;
 //              }
 
-        }
+    }
 }
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java b/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
index ef9338a..b4a1775 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
@@ -22,10 +22,11 @@ import uk.ac.ox.cs.pagoda.tracking.QueryTracker;
 import uk.ac.ox.cs.pagoda.tracking.TrackingRuleEncoder;
 import uk.ac.ox.cs.pagoda.util.Timer;
 import uk.ac.ox.cs.pagoda.util.Utility;
+import uk.ac.ox.cs.pagoda.util.disposable.Disposable;
 
 import java.util.LinkedList;
 
-public class ConsistencyManager {
+public class ConsistencyManager extends Disposable {
 
         protected MyQueryReasoner m_reasoner;
         protected QueryManager m_queryManager;  
@@ -40,7 +41,109 @@ public class ConsistencyManager {
                 m_reasoner = reasoner;
                 m_queryManager = reasoner.getQueryManager();
         }
-        
+
+        @Override
+        public void dispose() {
+                super.dispose();
+                fullQueryRecord.dispose();
+        }
+
+        public void extractBottomFragment() {
+                if(fragmentExtracted) return;
+                fragmentExtracted = true;
+
+                UpperDatalogProgram upperProgram = m_reasoner.program.getUpper();
+                int number = upperProgram.getBottomNumber();
+
+                if(number <= 1) {
+                        botQueryRecords = new QueryRecord[]{fullQueryRecord};
+                }
+                else {
+                        QueryRecord[] tempQueryRecords = new QueryRecord[number - 1];
+                        QueryRecord record;
+                        for(int i = 0; i < number - 1; ++i) {
+                                tempQueryRecords[i] = record =
+                                                m_queryManager.create(QueryRecord.botQueryText.replace("Nothing", "Nothing" + (i + 1)), 0, i + 1);
+                                AnswerTuples iter = null;
+                                try {
+                                        iter = m_reasoner.trackingStore.evaluate(record.getQueryText(), record.getAnswerVariables());
+                                        record.updateUpperBoundAnswers(iter);
+                                } finally {
+                                        if(iter != null) iter.dispose();
+                                        iter = null;
+                                }
+                        }
+
+                        int bottomNumber = 0;
+                        int[] group = new int[number - 1];
+                        for(int i = 0; i < number - 1; ++i) group[i] = i;
+                        for(int i = 0; i < number - 1; ++i)
+                                if(tempQueryRecords[i].isProcessed()) tempQueryRecords[i].dispose();
+                                else if(group[i] == i) {
+                                        ++bottomNumber;
+                                        record = tempQueryRecords[i];
+                                        for(int j = i + 1; j < number - 1; ++j)
+                                                if(record.hasSameGapAnswers(tempQueryRecords[j]))
+                                                        group[j] = i;
+                                }
+
+                        Utility.logInfo("There are " + bottomNumber + " different bottom fragments.");
+                        toAddClauses = new LinkedList<DLClause>();
+                        int bottomCounter = 0;
+                        botQueryRecords = new QueryRecord[bottomNumber];
+                        Variable X = Variable.create("X");
+                        for(int i = 0; i < number - 1; ++i)
+                                if(!tempQueryRecords[i].isDisposed() && !tempQueryRecords[i].isProcessed())
+                                        if(group[i] == i) {
+                                                botQueryRecords[bottomCounter] = record = tempQueryRecords[i];
+                                                record.resetInfo(QueryRecord.botQueryText.replace("Nothing", "Nothing_final" + (++bottomCounter)), 0,
+                                                                                 group[i] = bottomCounter);
+                                                toAddClauses.add(
+                                                                DLClause.create(
+                                                                                new Atom[]{Atom.create(AtomicConcept.create(AtomicConcept.NOTHING.getIRI() + "_final" + bottomCounter), X)},
+                                                                                new Atom[]{Atom.create(AtomicConcept.create(AtomicConcept.NOTHING.getIRI() + (i + 1)), X)}));
+                                        }
+                                        else {
+                                                toAddClauses.add(
+                                                                DLClause.create(
+                                                                                new Atom[]{Atom.create(AtomicConcept.create(AtomicConcept.NOTHING.getIRI() + "_final" + group[group[i]]), X)},
+                                                                                new Atom[]{Atom.create(AtomicConcept.create(AtomicConcept.NOTHING.getIRI() + (i + 1)), X)}));
+                                                tempQueryRecords[i].dispose();
+                                        }
+
+                        upperProgram.updateDependencyGraph(toAddClauses);
+                }
+
+                String[] programs = collectTrackingProgramAndImport();
+                if(programs.length == 0)
+                        return;
+
+                DataStore store = m_reasoner.trackingStore.getDataStore();
+                long oldTripleCount, tripleCount;
+                try {
+                        Timer t1 = new Timer();
+                        oldTripleCount = store.getTriplesCount();
+                        for(String program : programs)
+                                store.importRules(program, UpdateType.ScheduleForAddition);
+                        store.applyReasoning(true);
+                        tripleCount = store.getTriplesCount();
+
+                        Utility.logInfo("tracking store after materialising tracking program: " + tripleCount + " (" + (tripleCount - oldTripleCount) + " new)",
+                                                        "tracking store finished the materialisation of tracking program in " + t1.duration() + " seconds.");
+
+                        extractAxioms();
+                        store.clearRulesAndMakeFactsExplicit();
+                } catch(JRDFStoreException e) {
+                        e.printStackTrace();
+                } catch(OWLOntologyCreationException e) {
+                        e.printStackTrace();
+                }
+        }
+
+        public QueryRecord[] getQueryRecords() {
+                return botQueryRecords;
+        }
+
         boolean checkRLLowerBound() {
                 fullQueryRecord = m_queryManager.create(QueryRecord.botQueryText, 0);
                 AnswerTuples iter = null;
@@ -59,9 +162,22 @@ public class ConsistencyManager {
                 return true;
         }
 
+//      protected boolean unsatisfiability(double duration) {
+//              fullQueryRecord.dispose();
+//              Utility.logDebug("The ontology and dataset is unsatisfiable.");
+//              return false;
+//      }
+
+//      protected boolean satisfiability(double duration) {
+//              fullQueryRecord.dispose();
+//              Utility.logDebug("The ontology and dataset is satisfiable.");
+//              return true;
+//      }
+
         boolean checkELLowerBound() {
-                fullQueryRecord.updateLowerBoundAnswers(m_reasoner.elLowerStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables()));
-                if (fullQueryRecord.getNoOfSoundAnswers() > 0) {
+                fullQueryRecord.updateLowerBoundAnswers(m_reasoner.elLowerStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord
+                                .getAnswerVariables()));
+                if(fullQueryRecord.getNoOfSoundAnswers() > 0) {
                         Utility.logInfo("Answers to bottom in the lower bound: ", fullQueryRecord.outputSoundAnswerTuple());
                         return true;
                 }
@@ -69,39 +185,22 @@ public class ConsistencyManager {
         }
 
         boolean checkUpper(BasicQueryEngine upperStore) {
-                if (upperStore != null) {
+                if(upperStore != null) {
                         AnswerTuples tuples = null;
                         try {
                                 tuples = upperStore.evaluate(fullQueryRecord.getQueryText(), fullQueryRecord.getAnswerVariables());
-                                if (!tuples.isValid()) {
-                                        Utility.logInfo("There are no contradictions derived in "+ upperStore.getName() +" materialisation.");
+                                if(!tuples.isValid()) {
+                                        Utility.logInfo("There are no contradictions derived in " + upperStore.getName() + " materialisation.");
                                         Utility.logDebug("The ontology and dataset is satisfiable.");
                                         return true;
                                 }
-                        }
-                        finally {
-                                if (tuples != null) tuples.dispose();
+                        } finally {
+                                if(tuples != null) tuples.dispose();
                         }
                 }
                 return false;
         }
 
-        void dispose() {
-                fullQueryRecord.dispose();
-        }
-
-//      protected boolean unsatisfiability(double duration) {
-//              fullQueryRecord.dispose();
-//              Utility.logDebug("The ontology and dataset is unsatisfiable.");
-//              return false;
-//      }
-
-//      protected boolean satisfiability(double duration) {
-//              fullQueryRecord.dispose();
-//              Utility.logDebug("The ontology and dataset is satisfiable.");
-//              return true;
-//      }
-
         boolean check() {
 //              if (!checkRLLowerBound()) return false;
 //              if (!checkELLowerBound()) return false;
@@ -148,148 +247,54 @@ public class ConsistencyManager {
                 return true;
         }
 
-        public void extractBottomFragment() {
-                if (fragmentExtracted) return ;
-                fragmentExtracted = true;
-                
-                UpperDatalogProgram upperProgram = m_reasoner.program.getUpper(); 
-                int number = upperProgram.getBottomNumber();
-                
-                if (number <= 1) {
-                        botQueryRecords = new QueryRecord[] { fullQueryRecord }; 
-                }
-                else {
-                        QueryRecord[] tempQueryRecords = new QueryRecord[number - 1];
-                        QueryRecord record; 
-                        for (int i = 0; i < number - 1; ++i) {
-                                tempQueryRecords[i] = record = m_queryManager.create(QueryRecord.botQueryText.replace("Nothing", "Nothing" + (i + 1)), 0, i + 1);
-                                AnswerTuples iter = null; 
-                                try {
-                                        iter = m_reasoner.trackingStore.evaluate(record.getQueryText(), record.getAnswerVariables());
-                                        record.updateUpperBoundAnswers(iter); 
-                                } finally {
-                                        if (iter != null) iter.dispose();
-                                        iter = null; 
-                                }
-                        }
-                        
-                        int bottomNumber = 0; 
-                        int[] group = new int[number - 1]; 
-                        for (int i = 0; i < number - 1; ++i) group[i] = i; 
-                        for (int i = 0; i < number - 1; ++i)
-                                if(tempQueryRecords[i].isProcessed()) tempQueryRecords[i].dispose();
-                                else if (group[i] == i) {
-                                        ++bottomNumber; 
-                                        record = tempQueryRecords[i]; 
-                                        for (int j = i + 1; j < number - 1; ++j)
-                                                if (record.hasSameGapAnswers(tempQueryRecords[j]))
-                                                        group[j] = i; 
-                                }
-                        
-                        Utility.logInfo("There are " + bottomNumber + " different bottom fragments."); 
-                        toAddClauses = new LinkedList<DLClause>(); 
-                        int bottomCounter = 0;
-                        botQueryRecords = new QueryRecord[bottomNumber];
-                        Variable X = Variable.create("X"); 
-                        for (int i = 0; i < number - 1; ++i)
-                                if(!tempQueryRecords[i].isProcessed())
-                                        if (group[i] == i) {
-                                                botQueryRecords[bottomCounter] = record = tempQueryRecords[i];
-                                                record.resetInfo(QueryRecord.botQueryText.replace("Nothing", "Nothing_final" + (++bottomCounter)), 0, group[i] = bottomCounter);
-                                                toAddClauses.add(
-                                                                DLClause.create(
-                                                                                new Atom[] {Atom.create(AtomicConcept.create(AtomicConcept.NOTHING.getIRI() + "_final" + bottomCounter), X)}, 
-                                                                                new Atom[] {Atom.create(AtomicConcept.create(AtomicConcept.NOTHING.getIRI() + (i + 1)), X)}));
-                                        }
-                                        else {
-                                                toAddClauses.add(
-                                                                DLClause.create(
-                                                                                new Atom[] {Atom.create(AtomicConcept.create(AtomicConcept.NOTHING.getIRI() + "_final" + group[group[i]]), X)}, 
-                                                                                new Atom[] {Atom.create(AtomicConcept.create(AtomicConcept.NOTHING.getIRI() + (i + 1)), X)}));
-                                                tempQueryRecords[i].dispose();
-                                        }
-                        
-                        upperProgram.updateDependencyGraph(toAddClauses); 
-                }
-                
-                String[] programs = collectTrackingProgramAndImport();
-                if (programs.length == 0)
-                        return ; 
-                
-                DataStore store = m_reasoner.trackingStore.getDataStore(); 
-                long oldTripleCount, tripleCount;
-                try {
-                        Timer t1 = new Timer();
-                        oldTripleCount = store.getTriplesCount();
-                        for (String program: programs) 
-                                store.importRules(program, UpdateType.ScheduleForAddition);
-                        store.applyReasoning(true);
-                        tripleCount = store.getTriplesCount(); 
-                        
-                        Utility.logInfo("tracking store after materialising tracking program: " + tripleCount + " (" + (tripleCount - oldTripleCount) + " new)", 
-                                        "tracking store finished the materialisation of tracking program in " + t1.duration() + " seconds.");
-                        
-                        extractAxioms();
-                        store.clearRulesAndMakeFactsExplicit();
-                } catch (JRDFStoreException e) {
-                        e.printStackTrace();
-                } catch (OWLOntologyCreationException e) {
-                        e.printStackTrace();
-                }
-        }
-        
         private void extractAxioms4Full() throws OWLOntologyCreationException {
-                OWLOntologyManager manager = m_reasoner.encoder.getProgram().getOntology().getOWLOntologyManager(); 
+                OWLOntologyManager manager = m_reasoner.encoder.getProgram().getOntology().getOWLOntologyManager();
                 OWLOntology fullOntology = manager.createOntology();
                 for (QueryRecord record: botQueryRecords) {
                         for (DLClause clause: record.getRelevantClauses()) {
                                 fullQueryRecord.addRelevantClauses(clause);
                         }
-                        manager.addAxioms(fullOntology, record.getRelevantOntology().getAxioms()); 
+                        manager.addAxioms(fullOntology, record.getRelevantOntology().getAxioms());
                 }
                 fullQueryRecord.setRelevantOntology(fullOntology);
         }
 
         private void extractAxioms() throws OWLOntologyCreationException {
-                OWLOntologyManager manager = m_reasoner.encoder.getProgram().getOntology().getOWLOntologyManager(); 
+                OWLOntologyManager manager = m_reasoner.encoder.getProgram().getOntology().getOWLOntologyManager();
                 for (QueryRecord record: botQueryRecords) {
                         record.setRelevantOntology(manager.createOntology());
-                        QueryTracker tracker = new QueryTracker(m_reasoner.encoder, m_reasoner.rlLowerStore, record); 
+                        QueryTracker tracker = new QueryTracker(m_reasoner.encoder, m_reasoner.rlLowerStore, record);
                         m_reasoner.encoder.setCurrentQuery(record);
                         tracker.extractAxioms(m_reasoner.trackingStore);
 //                      record.saveRelevantClause();
 //                      record.saveRelevantOntology("bottom" + record.getQueryID() + ".owl");
                         Utility.logInfo("finish extracting axioms for bottom " + record.getQueryID());
-                }                       
+                }
         }
 
         private String[] collectTrackingProgramAndImport() {
-                String[] programs = new String[botQueryRecords.length]; 
+                String[] programs = new String[botQueryRecords.length];
                 TrackingRuleEncoder encoder = m_reasoner.encoder;
-                
+
                 StringBuilder builder;
-                LinkedList<DLClause> currentClauses = new LinkedList<DLClause>(); 
-                
+                LinkedList<DLClause> currentClauses = new LinkedList<DLClause>();
+
                 for (int i = 0; i < botQueryRecords.length; ++i) {
                         encoder.setCurrentQuery(botQueryRecords[i]);
                         builder = new StringBuilder(encoder.getTrackingProgram());
 //                      encoder.saveTrackingRules("tracking_bottom" + (i + 1) + ".dlog");
-                        
+
                         for (DLClause clause: toAddClauses)
                                 if (clause.getHeadAtom(0).getDLPredicate().toString().contains("_final" + (i + 1)))
-                                        currentClauses.add(clause); 
-                        
+                                        currentClauses.add(clause);
+
                         builder.append(DLClauseHelper.toString(currentClauses));
-                        programs[i] = builder.toString(); 
-                        
+                        programs[i] = builder.toString();
+
                         currentClauses.clear();
                 }
-                
-                return programs; 
-        }
 
-        public QueryRecord[] getQueryRecords() {
-                return botQueryRecords; 
+                return programs;
         }
 
 
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java
index f5a8093..0a151bc 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java
@@ -10,86 +10,92 @@ import uk.ac.ox.cs.pagoda.reasoner.light.KarmaQueryEngine;
 import uk.ac.ox.cs.pagoda.rules.LowerDatalogProgram;
 import uk.ac.ox.cs.pagoda.util.Timer;
 import uk.ac.ox.cs.pagoda.util.Utility;
+import uk.ac.ox.cs.pagoda.util.disposable.DisposedException;
 
 class ELHOQueryReasoner extends QueryReasoner {
 
-        LowerDatalogProgram program; 
-        
-        OWLOntology elho_ontology; 
-        KarmaQueryEngine elLowerStore = null; 
-
-        private Timer t = new Timer(); 
-        
-        public ELHOQueryReasoner() {
-                elLowerStore = new KarmaQueryEngine("el");
-        }
-        
-        @Override
-        public void evaluate(QueryRecord queryRecord) {
-                AnswerTuples elAnswer = null;
-                t.reset(); 
-                try {
-                        elAnswer = elLowerStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
-                        queryRecord.updateLowerBoundAnswers(elAnswer); 
-                } finally {
-                        if (elAnswer != null) elAnswer.dispose();
-                }
-                queryRecord.addProcessingTime(Step.EL_LOWER_BOUND, t.duration());
-
-                queryRecord.setDifficulty(Step.EL_LOWER_BOUND);
-                queryRecord.markAsProcessed();
-        }
-
-        @Override
-        public void evaluateUpper(QueryRecord queryRecord) {
-                evaluate(queryRecord); 
-        }
-
-        @Override
-        public void dispose() {
-                if (elLowerStore != null) elLowerStore.dispose();
-                super.dispose();
-        }
-
-        @Override
-        public void loadOntology(OWLOntology ontology) {
-                program = new LowerDatalogProgram(properties.getToClassify()); 
-                program.load(ontology, new UnaryBottom());
-                program.transform();
-                
-                importData(program.getAdditionalDataFile());
-                
-                elho_ontology = new ELHOProfile().getFragment(ontology);
-                elLowerStore.processOntology(elho_ontology);
-        }
-
-        @Override
-        public boolean preprocess() {
-                elLowerStore.importRDFData("data", importedData.toString()); 
-                String rlLowerProgramText = program.toString();
+    LowerDatalogProgram program;
+
+    OWLOntology elho_ontology;
+    KarmaQueryEngine elLowerStore = null;
+
+    private Timer t = new Timer();
+
+    public ELHOQueryReasoner() {
+        elLowerStore = new KarmaQueryEngine("el");
+    }
+
+    @Override
+    public void evaluate(QueryRecord queryRecord) {
+        if(isDisposed()) throw new DisposedException();
+        AnswerTuples elAnswer = null;
+        t.reset();
+        try {
+            elAnswer = elLowerStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
+            queryRecord.updateLowerBoundAnswers(elAnswer);
+        } finally {
+            if(elAnswer != null) elAnswer.dispose();
+        }
+        queryRecord.addProcessingTime(Step.EL_LOWER_BOUND, t.duration());
+
+        queryRecord.setDifficulty(Step.EL_LOWER_BOUND);
+        queryRecord.markAsProcessed();
+    }
+
+    @Override
+    public void evaluateUpper(QueryRecord queryRecord) {
+        if(isDisposed()) throw new DisposedException();
+        evaluate(queryRecord);
+    }
+
+    @Override
+    public void dispose() {
+        super.dispose();
+        if(elLowerStore != null) elLowerStore.dispose();
+    }
+
+    @Override
+    public void loadOntology(OWLOntology ontology) {
+        if(isDisposed()) throw new DisposedException();
+        program = new LowerDatalogProgram(properties.getToClassify());
+        program.load(ontology, new UnaryBottom());
+        program.transform();
+
+        importData(program.getAdditionalDataFile());
+
+        elho_ontology = new ELHOProfile().getFragment(ontology);
+        elLowerStore.processOntology(elho_ontology);
+    }
+
+    @Override
+    public boolean preprocess() {
+        if(isDisposed()) throw new DisposedException();
+        elLowerStore.importRDFData("data", importedData.toString());
+        String rlLowerProgramText = program.toString();
 //              program.save();
-                elLowerStore.materialise("lower program", rlLowerProgramText);
-                elLowerStore.initialiseKarma(); 
-                
-                if (!isConsistent()) {
-                        Utility.logDebug("The dataset is not consistent with the ontology."); 
-                        return false; 
-                }
-                return true; 
-        }
-
-        @Override
-        public boolean isConsistent() {
-                String[] X = new String[] {"X"}; 
-                AnswerTuples ans = null;
-                try {
-                        ans = elLowerStore.evaluate(QueryRecord.botQueryText, X); 
-                        if (ans.isValid()) return false; 
-                } finally {
-                        if (ans != null) ans.dispose();
-                }
-                
-                return true;
-        }
+        elLowerStore.materialise("lower program", rlLowerProgramText);
+        elLowerStore.initialiseKarma();
+
+        if(!isConsistent()) {
+            Utility.logDebug("The dataset is not consistent with the ontology.");
+            return false;
+        }
+        return true;
+    }
+
+    @Override
+    public boolean isConsistent() {
+        if(isDisposed()) throw new DisposedException();
+        String[] X = new String[]{"X"};
+        AnswerTuples ans = null;
+        try {
+            ans = elLowerStore.evaluate(QueryRecord.botQueryText, X);
+            if(ans.isValid()) return false;
+        } finally {
+            if(ans != null) ans.dispose();
+        }
+
+        return true;
+    }
 
 }
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
index c74ea58..771190e 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
@@ -13,181 +13,187 @@ import uk.ac.ox.cs.pagoda.reasoner.light.KarmaQueryEngine;
 import uk.ac.ox.cs.pagoda.rules.DatalogProgram;
 import uk.ac.ox.cs.pagoda.util.Timer;
 import uk.ac.ox.cs.pagoda.util.Utility;
+import uk.ac.ox.cs.pagoda.util.disposable.DisposedException;
 
 class ELHOUQueryReasoner extends QueryReasoner {
 
-        DatalogProgram program; 
-        
-        BasicQueryEngine rlLowerStore; 
-        BasicQueryEngine rlUpperStore; 
-        
-        OWLOntology elho_ontology; 
-        KarmaQueryEngine elLowerStore = null; 
-        
-        boolean multiStageTag, equalityTag;
-        String originalMarkProgram;
-        private Timer t = new Timer();
-
-        public ELHOUQueryReasoner(boolean multiStageTag, boolean considerEqualities) {
-                this.multiStageTag = multiStageTag;
-                this.equalityTag = considerEqualities;
-                rlLowerStore = new BasicQueryEngine("rl-lower-bound");
-                elLowerStore = new KarmaQueryEngine("el-lower-bound");
-
-                if(!multiStageTag)
-                        rlUpperStore = new BasicQueryEngine("rl-upper-bound");
-                else
-                        rlUpperStore = new MultiStageQueryEngine("rl-upper-bound", false);
-        }
-
-        @Override
-        public void evaluate(QueryRecord queryRecord) {
-                AnswerTuples rlAnswer = null;
-                t.reset();
-                try {
-                        rlAnswer = rlLowerStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
-                        queryRecord.updateLowerBoundAnswers(rlAnswer);
-                } finally {
-                        if(rlAnswer != null) rlAnswer.dispose();
-                }
-                queryRecord.addProcessingTime(Step.LOWER_BOUND, t.duration());
-
-                String extendedQueryText = queryRecord.getExtendedQueryText().get(0);
-                String[] toQuery = queryRecord.getQueryText().equals(extendedQueryText) ?
-                                new String[]{queryRecord.getQueryText()} :
-                                new String[] {queryRecord.getQueryText(), extendedQueryText};
-
-                for (String queryText: toQuery) {
-                        rlAnswer = null;
-                        t.reset();
-                        try {
-                                rlAnswer = rlUpperStore.evaluate(queryText, queryRecord.getAnswerVariables());
-                                queryRecord.updateUpperBoundAnswers(rlAnswer);
-                        } finally {
-                                if(rlAnswer != null) rlAnswer.dispose();
-                        }
-                        queryRecord.addProcessingTime(Step.UPPER_BOUND, t.duration());
-
-                        if(queryRecord.isProcessed()) {
-                                queryRecord.setDifficulty(Step.UPPER_BOUND);
-                                return;
-                        }
-                }
-
-                AnswerTuples elAnswer = null;
-                t.reset();
-                try {
-                        elAnswer =
-                                        elLowerStore.evaluate(extendedQueryText, queryRecord.getAnswerVariables(), queryRecord.getLowerBoundAnswers());
-                        queryRecord.updateLowerBoundAnswers(elAnswer);
-                } finally {
-                        if (elAnswer != null) elAnswer.dispose();
-                }
-                queryRecord.addProcessingTime(Step.EL_LOWER_BOUND, t.duration());
-        }
-
-        @Override
-        public void evaluateUpper(QueryRecord queryRecord) {
-                AnswerTuples rlAnswer = null;
-                try {
-                        rlAnswer = rlUpperStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
-                        queryRecord.updateUpperBoundAnswers(rlAnswer, true);
-                } finally {
-                        if(rlAnswer != null) rlAnswer.dispose();
-                }
-        }
-
-        @Override
-        public void dispose() {
-                if (elLowerStore != null) elLowerStore.dispose();
-                if(rlUpperStore != null) rlUpperStore.dispose();
-                super.dispose();
-        }
-
-        @Override
-        public void loadOntology(OWLOntology o) {
-                if (!equalityTag) {
-                        EqualitiesEliminator eliminator = new EqualitiesEliminator(o);
-                        o = eliminator.getOutputOntology();
-                        eliminator.save();
-                }
-
-                OWLOntology ontology = o;
-                program = new DatalogProgram(ontology, properties.getToClassify());
-
-                importData(program.getAdditionalDataFile());
-
-                elho_ontology = new ELHOProfile().getFragment(ontology);
-                elLowerStore.processOntology(elho_ontology);
-                originalMarkProgram = OWLHelper.getOriginalMarkProgram(ontology);
-        }
-
-        @Override
-        public boolean preprocess() {
-                String name = "data", datafile = importedData.toString(); 
-
-                String lowername = "lower program";
-                String rlLowerProgramText = program.getLower().toString();
-                
-                rlUpperStore.importRDFData(name, datafile);
-                rlUpperStore.materialise("saturate named individuals", originalMarkProgram);
-                
-                int flag = rlUpperStore.materialiseRestrictedly(program, null); 
-                if (flag != 1) {
-                        if (flag == -1) return false;           
-                        rlUpperStore.dispose();
-                        
-                        if (!multiStageTag) 
-                                rlUpperStore = new BasicQueryEngine("rl-upper-bound"); 
-                        else  
-                                rlUpperStore = new MultiStageQueryEngine("rl-upper-bound", false); 
-                        rlUpperStore.importRDFData(name, datafile);
-                        rlUpperStore.materialise("saturate named individuals", originalMarkProgram);
-                        rlUpperStore.materialiseFoldedly(program, null); 
-                }
-                Utility.logInfo("upper store ready.");
-                
-                rlLowerStore.importRDFData(name, datafile);
-                rlLowerStore.materialise(lowername, rlLowerProgramText);
-                Utility.logInfo("lower store ready.");
-                
-                elLowerStore.importRDFData(name, datafile);
-                elLowerStore.materialise("saturate named individuals", originalMarkProgram);
-                elLowerStore.materialise(lowername, rlLowerProgramText);
-                
-                elLowerStore.initialiseKarma(); 
-                Utility.logInfo("EL lower store ready.");
-                
-                if (!isConsistent()) {
-                        Utility.logInfo("The dataset is not consistent with the ontology."); 
-                        return false;
-                }
-                Utility.logInfo("The dataset is consistent.");
-                return true; 
-        }
-
-        @Override
-        public boolean isConsistent() {
-                Utility.logInfo("Start checking consistency... ");
-                String[] X = new String[] {"X"}; 
-                AnswerTuples ans = null; 
-                try {
-                        ans = rlUpperStore.evaluate(QueryRecord.botQueryText, X);
-                        if (!ans.isValid()) return true; 
-                } finally {
-                        if (ans != null) ans.dispose();
-                }
-
-                ans = null; 
-                try {
-                        ans = elLowerStore.evaluate(QueryRecord.botQueryText, X);
-                        if (ans.isValid()) return false; 
-                } finally {
-                        if (ans != null) ans.dispose();
-                }
-                
-                Utility.logDebug("The consistency of the data has not been determined yet.");
-                return true; 
-        }
+    DatalogProgram program;
+
+    BasicQueryEngine rlLowerStore;
+    BasicQueryEngine rlUpperStore;
+
+    OWLOntology elho_ontology;
+    KarmaQueryEngine elLowerStore = null;
+
+    boolean multiStageTag, equalityTag;
+    String originalMarkProgram;
+    private Timer t = new Timer();
+
+    public ELHOUQueryReasoner(boolean multiStageTag, boolean considerEqualities) {
+        this.multiStageTag = multiStageTag;
+        this.equalityTag = considerEqualities;
+        rlLowerStore = new BasicQueryEngine("rl-lower-bound");
+        elLowerStore = new KarmaQueryEngine("el-lower-bound");
+
+        if(!multiStageTag)
+            rlUpperStore = new BasicQueryEngine("rl-upper-bound");
+        else
+            rlUpperStore = new MultiStageQueryEngine("rl-upper-bound", false);
+    }
+
+    @Override
+    public void evaluate(QueryRecord queryRecord) {
+        if(isDisposed()) throw new DisposedException();
+        AnswerTuples rlAnswer = null;
+        t.reset();
+        try {
+            rlAnswer = rlLowerStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
+            queryRecord.updateLowerBoundAnswers(rlAnswer);
+        } finally {
+            if(rlAnswer != null) rlAnswer.dispose();
+        }
+        queryRecord.addProcessingTime(Step.LOWER_BOUND, t.duration());
+
+        String extendedQueryText = queryRecord.getExtendedQueryText().get(0);
+        String[] toQuery = queryRecord.getQueryText().equals(extendedQueryText) ?
+                new String[]{queryRecord.getQueryText()} :
+                new String[]{queryRecord.getQueryText(), extendedQueryText};
+
+        for(String queryText : toQuery) {
+            rlAnswer = null;
+            t.reset();
+            try {
+                rlAnswer = rlUpperStore.evaluate(queryText, queryRecord.getAnswerVariables());
+                queryRecord.updateUpperBoundAnswers(rlAnswer);
+            } finally {
+                if(rlAnswer != null) rlAnswer.dispose();
+            }
+            queryRecord.addProcessingTime(Step.UPPER_BOUND, t.duration());
+
+            if(queryRecord.isProcessed()) {
+                queryRecord.setDifficulty(Step.UPPER_BOUND);
+                return;
+            }
+        }
+
+        AnswerTuples elAnswer = null;
+        t.reset();
+        try {
+            elAnswer =
+                    elLowerStore.evaluate(extendedQueryText, queryRecord.getAnswerVariables(), queryRecord.getLowerBoundAnswers());
+            queryRecord.updateLowerBoundAnswers(elAnswer);
+        } finally {
+            if(elAnswer != null) elAnswer.dispose();
+        }
+        queryRecord.addProcessingTime(Step.EL_LOWER_BOUND, t.duration());
+    }
+
+    @Override
+    public void evaluateUpper(QueryRecord queryRecord) {
+        if(isDisposed()) throw new DisposedException();
+        AnswerTuples rlAnswer = null;
+        try {
+            rlAnswer = rlUpperStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
+            queryRecord.updateUpperBoundAnswers(rlAnswer, true);
+        } finally {
+            if(rlAnswer != null) rlAnswer.dispose();
+        }
+    }
+
+    @Override
+    public void dispose() {
+        super.dispose();
+        if(elLowerStore != null) elLowerStore.dispose();
+        if(rlUpperStore != null) rlUpperStore.dispose();
+    }
+
+    @Override
+    public void loadOntology(OWLOntology o) {
+        if(isDisposed()) throw new DisposedException();
+        if(!equalityTag) {
+            EqualitiesEliminator eliminator = new EqualitiesEliminator(o);
+            o = eliminator.getOutputOntology();
+            eliminator.save();
+        }
+
+        OWLOntology ontology = o;
+        program = new DatalogProgram(ontology, properties.getToClassify());
+
+        importData(program.getAdditionalDataFile());
+
+        elho_ontology = new ELHOProfile().getFragment(ontology);
+        elLowerStore.processOntology(elho_ontology);
+        originalMarkProgram = OWLHelper.getOriginalMarkProgram(ontology);
+    }
+
+    @Override
+    public boolean preprocess() {
+        if(isDisposed()) throw new DisposedException();
+        String name = "data", datafile = importedData.toString();
+
+        String lowername = "lower program";
+        String rlLowerProgramText = program.getLower().toString();
+
+        rlUpperStore.importRDFData(name, datafile);
+        rlUpperStore.materialise("saturate named individuals", originalMarkProgram);
+
+        int flag = rlUpperStore.materialiseRestrictedly(program, null);
+        if(flag != 1) {
+            if(flag == -1) return false;
+            rlUpperStore.dispose();
+
+            if(!multiStageTag)
+                rlUpperStore = new BasicQueryEngine("rl-upper-bound");
+            else
+                rlUpperStore = new MultiStageQueryEngine("rl-upper-bound", false);
+            rlUpperStore.importRDFData(name, datafile);
+            rlUpperStore.materialise("saturate named individuals", originalMarkProgram);
+            rlUpperStore.materialiseFoldedly(program, null);
+        }
+        Utility.logInfo("upper store ready.");
+
+        rlLowerStore.importRDFData(name, datafile);
+        rlLowerStore.materialise(lowername, rlLowerProgramText);
+        Utility.logInfo("lower store ready.");
+
+        elLowerStore.importRDFData(name, datafile);
+        elLowerStore.materialise("saturate named individuals", originalMarkProgram);
+        elLowerStore.materialise(lowername, rlLowerProgramText);
+
+        elLowerStore.initialiseKarma();
+        Utility.logInfo("EL lower store ready.");
+
+        if(!isConsistent()) {
+            Utility.logInfo("The dataset is not consistent with the ontology.");
+            return false;
+        }
+        Utility.logInfo("The dataset is consistent.");
+        return true;
+    }
+
+    @Override
+    public boolean isConsistent() {
+        if(isDisposed()) throw new DisposedException();
+        Utility.logInfo("Start checking consistency... ");
+        String[] X = new String[]{"X"};
+        AnswerTuples ans = null;
+        try {
+            ans = rlUpperStore.evaluate(QueryRecord.botQueryText, X);
+            if(!ans.isValid()) return true;
+        } finally {
+            if(ans != null) ans.dispose();
+        }
+
+        ans = null;
+        try {
+            ans = elLowerStore.evaluate(QueryRecord.botQueryText, X);
+            if(ans.isValid()) return false;
+        } finally {
+            if(ans != null) ans.dispose();
+        }
+
+        Utility.logDebug("The consistency of the data has not been determined yet.");
+        return true;
+    }
 
 }
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java
index d1856c9..78b9a0b 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java
@@ -10,6 +10,7 @@ import uk.ac.ox.cs.pagoda.query.*;
 import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine;
 import uk.ac.ox.cs.pagoda.rules.DatalogProgram;
 import uk.ac.ox.cs.pagoda.util.Utility;
+import uk.ac.ox.cs.pagoda.util.disposable.DisposedException;
 
 import java.io.File;
 import java.io.IOException;
@@ -17,100 +18,105 @@ import java.util.HashSet;
 import java.util.Set;
 
 class HermiTReasoner extends QueryReasoner {
-        
-        Reasoner hermit;
-        
-        BasicQueryEngine upperStore = null;
-        
-        OWLOntology onto;
-        OWLDataFactory factory; 
-        
-        String importedOntologyPath = null;
-
-        QueryRoller roller;
-        boolean toCheckSatisfiability;  
-        
-        public HermiTReasoner(boolean toCheckSatisfiability) {
-                this.toCheckSatisfiability = toCheckSatisfiability;  
-        }
-
-        @Override
-        public void loadOntology(OWLOntology ontology) {
-                onto = ontology; 
-        }
-
-        @Override
-        public boolean preprocess() {
-                OWLOntology tbox = onto;
-                try {
-                        onto = OWLHelper.getImportedOntology(tbox, importedData.toString().split(ImportDataFileSeparator));
-                        importedOntologyPath = OWLHelper.getOntologyPath(onto);
-                } catch(OWLOntologyCreationException | OWLOntologyStorageException | IOException e) {
-                        e.printStackTrace();
-                }
-                
-                DatalogProgram datalogProgram = new DatalogProgram(tbox, false);
-                importData(datalogProgram.getAdditionalDataFile()); 
-                upperStore = new MultiStageQueryEngine("rl-upper", false);
-                upperStore.importRDFData("data", importedData.toString());
-                GapByStore4ID gap = new GapByStore4ID(upperStore); 
-                upperStore.materialiseFoldedly(datalogProgram, gap);
-                gap.clear();
-
-                factory = onto.getOWLOntologyManager().getOWLDataFactory();
-                roller = new QueryRoller(factory);
-                
-                hermit = new Reasoner(onto);
-                return isConsistent();
-        }
-
-        @Override
-        public boolean isConsistent() {
-                if (toCheckSatisfiability)
-                        return hermit.isConsistent(); 
-                return true; 
-        }
-
-        @Override
-        public void evaluate(QueryRecord record) {
-                String[] disVars = record.getDistinguishedVariables();
-                Set<OWLNamedIndividual> individuals = onto.getIndividualsInSignature(true); 
-                if (disVars.length == 1) {
-                        OWLClassExpression clsExp = roller.rollUp(record.getClause(), record.getAnswerVariables()[0]);
-                        Set<AnswerTuple> answers = new HashSet<AnswerTuple>(); 
-                        for (OWLNamedIndividual individual: individuals) {
-                                Utility.logDebug("checking ... " + individual);
-                                if (hermit.isEntailed(factory.getOWLClassAssertionAxiom(clsExp, individual))) {
-                                        answers.add(new AnswerTuple(new Individual[] {Individual.create(individual.toStringID())})); 
-                                }
-                        }
-                        record.updateLowerBoundAnswers(new AnswerTuplesImp(record.getAnswerVariables(), answers));              
-                        record.markAsProcessed();
-                }
-                else {
-                        // FIXME join here
-                        record.markAsProcessed(); 
-                }
-        }
-
-        @Override
-        public void evaluateUpper(QueryRecord record) {
-                AnswerTuples rlAnswer = null; 
-                try {
-                        rlAnswer = upperStore.evaluate(record.getQueryText(), record.getAnswerVariables());
-                        record.updateUpperBoundAnswers(rlAnswer, true); 
-                } finally {
-                        if (rlAnswer != null) rlAnswer.dispose();
-                }
-        }
-
-        @Override
-        public void dispose() {
-                if (importedOntologyPath != null) {
-                        File tmp = new File(importedOntologyPath);
-                        if (tmp.exists()) tmp.delete(); 
-                }
-                super.dispose();
-        }
+
+    Reasoner hermit;
+
+    BasicQueryEngine upperStore = null;
+
+    OWLOntology onto;
+    OWLDataFactory factory;
+
+    String importedOntologyPath = null;
+
+    QueryRoller roller;
+    boolean toCheckSatisfiability;
+
+    public HermiTReasoner(boolean toCheckSatisfiability) {
+        this.toCheckSatisfiability = toCheckSatisfiability;
+    }
+
+    @Override
+    public void loadOntology(OWLOntology ontology) {
+        if(isDisposed()) throw new DisposedException();
+        onto = ontology;
+    }
+
+    @Override
+    public boolean preprocess() {
+        if(isDisposed()) throw new DisposedException();
+        OWLOntology tbox = onto;
+        try {
+            onto = OWLHelper.getImportedOntology(tbox, importedData.toString().split(ImportDataFileSeparator));
+            importedOntologyPath = OWLHelper.getOntologyPath(onto);
+        } catch(OWLOntologyCreationException | OWLOntologyStorageException | IOException e) {
+            e.printStackTrace();
+        }
+
+        DatalogProgram datalogProgram = new DatalogProgram(tbox, false);
+        importData(datalogProgram.getAdditionalDataFile());
+        upperStore = new MultiStageQueryEngine("rl-upper", false);
+        upperStore.importRDFData("data", importedData.toString());
+        GapByStore4ID gap = new GapByStore4ID(upperStore);
+        upperStore.materialiseFoldedly(datalogProgram, gap);
+        gap.clear();
+
+        factory = onto.getOWLOntologyManager().getOWLDataFactory();
+        roller = new QueryRoller(factory);
+
+        hermit = new Reasoner(onto);
+        return isConsistent();
+    }
+
+    @Override
+    public boolean isConsistent() {
+        if(isDisposed()) throw new DisposedException();
+        if(toCheckSatisfiability)
+            return hermit.isConsistent();
+        return true;
+    }
+
+    @Override
+    public void evaluate(QueryRecord record) {
+        if(isDisposed()) throw new DisposedException();
+        String[] disVars = record.getDistinguishedVariables();
+        Set<OWLNamedIndividual> individuals = onto.getIndividualsInSignature(true);
+        if(disVars.length == 1) {
+            OWLClassExpression clsExp = roller.rollUp(record.getClause(), record.getAnswerVariables()[0]);
+            Set<AnswerTuple> answers = new HashSet<AnswerTuple>();
+            for(OWLNamedIndividual individual : individuals) {
+                Utility.logDebug("checking ... " + individual);
+                if(hermit.isEntailed(factory.getOWLClassAssertionAxiom(clsExp, individual))) {
+                    answers.add(new AnswerTuple(new Individual[]{Individual.create(individual.toStringID())}));
+                }
+            }
+            record.updateLowerBoundAnswers(new AnswerTuplesImp(record.getAnswerVariables(), answers));
+            record.markAsProcessed();
+        }
+        else {
+            // FIXME join here
+            record.markAsProcessed();
+        }
+    }
+
+    @Override
+    public void evaluateUpper(QueryRecord record) {
+        if(isDisposed()) throw new DisposedException();
+        AnswerTuples rlAnswer = null;
+        try {
+            rlAnswer = upperStore.evaluate(record.getQueryText(), record.getAnswerVariables());
+            record.updateUpperBoundAnswers(rlAnswer, true);
+        } finally {
+            if(rlAnswer != null) rlAnswer.dispose();
+        }
+    }
+
+    @Override
+    public void dispose() {
+        super.dispose();
+        if(importedOntologyPath != null) {
+            File tmp = new File(importedOntologyPath);
+            if(tmp.exists()) tmp.delete();
+        }
+    }
 
 }
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
index 618fb70..8445713 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
@@ -21,362 +21,364 @@ import uk.ac.ox.cs.pagoda.tracking.TrackingRuleEncoderDisjVar1;
 import uk.ac.ox.cs.pagoda.tracking.TrackingRuleEncoderWithGap;
 import uk.ac.ox.cs.pagoda.util.Timer;
 import uk.ac.ox.cs.pagoda.util.Utility;
+import uk.ac.ox.cs.pagoda.util.disposable.DisposedException;
 import uk.ac.ox.cs.pagoda.util.tuples.Tuple;
 
 import java.util.Collection;
 
 class MyQueryReasoner extends QueryReasoner {
 
-        OWLOntology ontology;
-        DatalogProgram program;
-
-//      String additonalDataFile; 
-        BasicQueryEngine rlLowerStore = null;
-        BasicQueryEngine lazyUpperStore = null;
-        //      BasicQueryEngine limitedSkolemUpperStore;
-        OWLOntology elho_ontology;
-//      boolean[] namedIndividuals_lazyUpper; 
-        KarmaQueryEngine elLowerStore = null;
-        BasicQueryEngine trackingStore = null;
-        //      boolean[] namedIndividuals_tracking;
-        TrackingRuleEncoder encoder;
-        private boolean equalityTag;
-        private boolean multiStageTag;
-        private Timer t = new Timer();
-        private Collection<String> predicatesWithGap = null;
-        private SatisfiabilityStatus satisfiable;
-        private ConsistencyManager consistency = new ConsistencyManager(this);
-        private boolean useUpperStores = false;
-        public MyQueryReasoner() {
-                setup(true, true);
-        }
-        public MyQueryReasoner(boolean multiStageTag, boolean considerEqualities) {
-                setup(multiStageTag, considerEqualities);
-        }
-
-        private BasicQueryEngine getUpperStore(String name, boolean checkValidity) {
-                if (multiStageTag)
-                        return new MultiStageQueryEngine(name, checkValidity);
-//                      return new TwoStageQueryEngine(name, checkValidity);
-                else
-                        return new BasicQueryEngine(name);
-        }
-
-        public void setup(boolean multiStageTag, boolean considerEqualities) {
-                satisfiable = SatisfiabilityStatus.UNCHECKED;
-                this.multiStageTag = multiStageTag;
-                this.equalityTag = considerEqualities;
-
-                rlLowerStore = new BasicQueryEngine("rl-lower-bound");
-                elLowerStore = new KarmaQueryEngine("elho-lower-bound");
-
-                trackingStore = getUpperStore("tracking", false);
-        }
-        
-        protected void internal_importDataFile(String name, String datafile) {
-//              addDataFile(datafile);
-                rlLowerStore.importRDFData(name, datafile);
-                if (lazyUpperStore != null)
-                        lazyUpperStore.importRDFData(name, datafile);
-                elLowerStore.importRDFData(name, datafile);
-                trackingStore.importRDFData(name, datafile);
-        }
-
-        @Override
-        public void loadOntology(OWLOntology o) {
-                if(!equalityTag) {
-                        EqualitiesEliminator eliminator = new EqualitiesEliminator(o);
-                        o = eliminator.getOutputOntology();
-                        eliminator.save();
-                }
-
-                ontology = o;
-                program = new DatalogProgram(ontology, properties.getToClassify());
+    OWLOntology ontology;
+    DatalogProgram program;
+
+    //  String additonalDataFile;
+    BasicQueryEngine rlLowerStore = null;
+    BasicQueryEngine lazyUpperStore = null;
+    MultiStageQueryEngine limitedSkolemUpperStore;
+    OWLOntology elho_ontology;
+    //  boolean[] namedIndividuals_lazyUpper;
+    KarmaQueryEngine elLowerStore = null;
+    BasicQueryEngine trackingStore = null;
+    //  boolean[] namedIndividuals_tracking;
+    TrackingRuleEncoder encoder;
+    private boolean equalityTag;
+    private boolean multiStageTag;
+    private Timer t = new Timer();
+    private Collection<String> predicatesWithGap = null;
+    private SatisfiabilityStatus satisfiable;
+    private ConsistencyManager consistency = new ConsistencyManager(this);
+    private boolean useUpperStores = false;
+
+    public MyQueryReasoner() {
+        setup(true, true);
+    }
+
+    public MyQueryReasoner(boolean multiStageTag, boolean considerEqualities) {
+        setup(multiStageTag, considerEqualities);
+    }
+
+    public void setup(boolean multiStageTag, boolean considerEqualities) {
+        if(isDisposed()) throw new DisposedException();
+        satisfiable = SatisfiabilityStatus.UNCHECKED;
+        this.multiStageTag = multiStageTag;
+        this.equalityTag = considerEqualities;
+
+        rlLowerStore = new BasicQueryEngine("rl-lower-bound");
+        elLowerStore = new KarmaQueryEngine("elho-lower-bound");
+
+        trackingStore = getUpperStore("tracking", false);
+    }
+
+    @Override
+    public void loadOntology(OWLOntology o) {
+        if(isDisposed()) throw new DisposedException();
+        if(!equalityTag) {
+            EqualitiesEliminator eliminator = new EqualitiesEliminator(o);
+            o = eliminator.getOutputOntology();
+            eliminator.save();
+        }
+
+        ontology = o;
+        program = new DatalogProgram(ontology, properties.getToClassify());
 //              program.getLower().save();
 //              program.getUpper().save();
 //              program.getGeneral().save();
 
-                useUpperStores = multiStageTag && !program.getGeneral().isHorn();
-                if(useUpperStores) {
-                        lazyUpperStore = getUpperStore("lazy-upper-bound", true);
-//                      limitedSkolemUpperStore = getUpperStore("limited-skolem-upper-bound", true);
-                }
+        useUpperStores = multiStageTag && !program.getGeneral().isHorn();
+        if(useUpperStores) {
+            lazyUpperStore = getUpperStore("lazy-upper-bound", true);
+            limitedSkolemUpperStore = new MultiStageQueryEngine("limited-skolem-upper-bound", true);
+        }
 
-                importData(program.getAdditionalDataFile());
+        importData(program.getAdditionalDataFile());
 
-                elho_ontology = new ELHOProfile().getFragment(ontology);
-                elLowerStore.processOntology(elho_ontology);
-        }
+        elho_ontology = new ELHOProfile().getFragment(ontology);
+        elLowerStore.processOntology(elho_ontology);
+    }
 
-        public Collection<String> getPredicatesWithGap() {
-                return predicatesWithGap;
-        }
+    public Collection<String> getPredicatesWithGap() {
+        if(isDisposed()) throw new DisposedException();
+        return predicatesWithGap;
+    }
 
-        @Override
-        public boolean preprocess() {
-                t.reset();
-                Utility.logInfo("Preprocessing... checking satisfiability... ");
+    @Override
+    public boolean preprocess() {
+        if(isDisposed()) throw new DisposedException();
+        t.reset();
+        Utility.logInfo("Preprocessing... checking satisfiability... ");
 
-                String name = "data", datafile = importedData.toString();
-                rlLowerStore.importRDFData(name, datafile);
-                rlLowerStore.materialise("lower program", program.getLower().toString());
+        String name = "data", datafile = importedData.toString();
+        rlLowerStore.importRDFData(name, datafile);
+        rlLowerStore.materialise("lower program", program.getLower().toString());
 //              program.getLower().save();
-                if(!consistency.checkRLLowerBound()) return false;
-                Utility.logInfo("The number of sameAs assertions in RL lower store: " + rlLowerStore.getSameAsNumber());
-
-                String originalMarkProgram = OWLHelper.getOriginalMarkProgram(ontology);
-
-                elLowerStore.importRDFData(name, datafile);
-                elLowerStore.materialise("saturate named individuals", originalMarkProgram);
-                elLowerStore.materialise("lower program", program.getLower().toString());
-                elLowerStore.initialiseKarma();
-                if(!consistency.checkELLowerBound()) return false;
-
-                if(lazyUpperStore != null) {
-                        lazyUpperStore.importRDFData(name, datafile);
-                        lazyUpperStore.materialise("saturate named individuals", originalMarkProgram);
-                        int tag = lazyUpperStore.materialiseRestrictedly(program, null);
-                        if(tag != 1) {
-                                lazyUpperStore.dispose();
-                                lazyUpperStore = null;
-                        }
-                        if(tag == -1) return false;
-                }
-                if(consistency.checkUpper(lazyUpperStore)) {
-                        satisfiable = SatisfiabilityStatus.SATISFIABLE;
-                        Utility.logInfo("time for satisfiability checking: " + t.duration());
-                }
-
-//              if(limitedSkolemUpperStore != null) {
-//                      limitedSkolemUpperStore.importRDFData(name, datafile);
-//                      limitedSkolemUpperStore.materialise("saturate named individuals", originalMarkProgram);
-//                      int tag = limitedSkolemUpperStore.materialiseSkolemly(program, null);
-//                      if(tag != 1) {
-//                              limitedSkolemUpperStore.dispose();
-//                              limitedSkolemUpperStore = null;
-//                      }
-//                      if(tag == -1) return false;
-//              }
-//              if(satisfiable == SatisfiabilityStatus.UNCHECKED && consistency.checkUpper(limitedSkolemUpperStore)) {
-//                      satisfiable = SatisfiabilityStatus.SATISFIABLE;
-//                      Utility.logInfo("time for satisfiability checking: " + t.duration());
-//              }
-
-                trackingStore.importRDFData(name, datafile);
-                trackingStore.materialise("saturate named individuals", originalMarkProgram);
+        if(!consistency.checkRLLowerBound()) return false;
+        Utility.logInfo("The number of sameAs assertions in RL lower store: " + rlLowerStore.getSameAsNumber());
+
+        String originalMarkProgram = OWLHelper.getOriginalMarkProgram(ontology);
+
+        elLowerStore.importRDFData(name, datafile);
+        elLowerStore.materialise("saturate named individuals", originalMarkProgram);
+        elLowerStore.materialise("lower program", program.getLower().toString());
+        elLowerStore.initialiseKarma();
+        if(!consistency.checkELLowerBound()) return false;
+
+        if(lazyUpperStore != null) {
+            lazyUpperStore.importRDFData(name, datafile);
+            lazyUpperStore.materialise("saturate named individuals", originalMarkProgram);
+            int tag = lazyUpperStore.materialiseRestrictedly(program, null);
+            if(tag != 1) {
+                lazyUpperStore.dispose();
+                lazyUpperStore = null;
+            }
+            if(tag == -1) return false;
+        }
+        if(consistency.checkUpper(lazyUpperStore)) {
+            satisfiable = SatisfiabilityStatus.SATISFIABLE;
+            Utility.logInfo("time for satisfiability checking: " + t.duration());
+        }
+
+        if(limitedSkolemUpperStore != null) {
+            limitedSkolemUpperStore.importRDFData(name, datafile);
+            limitedSkolemUpperStore.materialise("saturate named individuals", originalMarkProgram);
+            int tag = limitedSkolemUpperStore.materialiseSkolemly(program, null);
+            if(tag != 1) {
+                limitedSkolemUpperStore.dispose();
+                limitedSkolemUpperStore = null;
+            }
+            if(tag == -1) return false;
+        }
+        if(satisfiable == SatisfiabilityStatus.UNCHECKED && consistency.checkUpper(limitedSkolemUpperStore)) {
+            satisfiable = SatisfiabilityStatus.SATISFIABLE;
+            Utility.logInfo("time for satisfiability checking: " + t.duration());
+        }
+
+        trackingStore.importRDFData(name, datafile);
+        trackingStore.materialise("saturate named individuals", originalMarkProgram);
 
 //              materialiseFullUpper();
-//              GapByStore4ID gap = new GapByStore4ID(trackingStore); 
-                GapByStore4ID gap = new GapByStore4ID2(trackingStore, rlLowerStore);
-                trackingStore.materialiseFoldedly(program, gap);
-                predicatesWithGap = gap.getPredicatesWithGap();
-                gap.clear();
-
-                if(program.getGeneral().isHorn())
-                        encoder = new TrackingRuleEncoderWithGap(program.getUpper(), trackingStore);
-                else
-                        encoder = new TrackingRuleEncoderDisjVar1(program.getUpper(), trackingStore);
+//              GapByStore4ID gap = new GapByStore4ID(trackingStore);
+        GapByStore4ID gap = new GapByStore4ID2(trackingStore, rlLowerStore);
+        trackingStore.materialiseFoldedly(program, gap);
+        predicatesWithGap = gap.getPredicatesWithGap();
+        gap.clear();
+
+        if(program.getGeneral().isHorn())
+            encoder = new TrackingRuleEncoderWithGap(program.getUpper(), trackingStore);
+        else
+            encoder = new TrackingRuleEncoderDisjVar1(program.getUpper(), trackingStore);
 //                      encoder = new TrackingRuleEncoderDisj1(program.getUpper(), trackingStore);
 //                      encoder = new TrackingRuleEncoderDisjVar2(program.getUpper(), trackingStore);
 //                      encoder = new TrackingRuleEncoderDisj2(program.getUpper(), trackingStore);
 
-                program.deleteABoxTurtleFile();
-
-                if(!isConsistent())
-                        return false;
-
-                consistency.extractBottomFragment();
-                consistency.dispose();
-
-                return true;
-        }
-        
-        @Override
-        public boolean isConsistent() {
-                if(satisfiable == SatisfiabilityStatus.UNCHECKED) {
-                        satisfiable = consistency.check() ? SatisfiabilityStatus.SATISFIABLE : SatisfiabilityStatus.UNSATISFIABLE;
-                        Utility.logInfo("time for satisfiability checking: " + t.duration());
-                }
-                return satisfiable == SatisfiabilityStatus.SATISFIABLE;
-        }
-
-        /**
-         * It deals with blanks nodes differently from variables
-         * according to SPARQL semantics for OWL2 Entailment Regime.
-         * <p>
-         * In particular variables are matched only against named individuals,
-         * and blank nodes against named and anonymous individuals.
-         */
-        private boolean queryUpperStore(BasicQueryEngine upperStore, QueryRecord queryRecord,
-                                                                        Tuple<String> extendedQuery, Step step) {
-
-                if(queryRecord.hasNonAnsDistinguishedVariables())
-                        queryUpperBound(upperStore, queryRecord, extendedQuery.get(0), queryRecord.getAnswerVariables());
-                else
-                        queryUpperBound(upperStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables());
-
-                queryRecord.addProcessingTime(step, t.duration());
-                if(queryRecord.isProcessed()) {
-                        queryRecord.setDifficulty(step);
-                        return true;
-                }
-                return false;
-        }
-
-        /**
-         * Returns the part of the ontology relevant for Hermit, while computing the bound answers.
-         * */
-        private boolean queryBounds(QueryRecord queryRecord) {
-                AnswerTuples rlAnswer = null, elAnswer = null;
-
-                t.reset();
-                try {
-                        rlAnswer = rlLowerStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
-                        Utility.logDebug(t.duration());
-                        queryRecord.updateLowerBoundAnswers(rlAnswer);
-                } finally {
-                        if (rlAnswer != null) rlAnswer.dispose();
-                }
-                queryRecord.addProcessingTime(Step.LOWER_BOUND, t.duration());
-
-                t.reset();
-
-                Tuple<String> extendedQueryTexts = queryRecord.getExtendedQueryText();
-
-                Utility.logDebug("Tracking store");
-                if(queryUpperStore(trackingStore, queryRecord, extendedQueryTexts, Step.SIMPLE_UPPER_BOUND))
-                        return true;
-
-                if(!queryRecord.isBottom()) {
-                        Utility.logDebug("Lazy store");
-                        if(lazyUpperStore != null && queryUpperStore(lazyUpperStore, queryRecord, extendedQueryTexts, Step.LAZY_UPPER_BOUND))
-                                return true;
+        if(!isConsistent())
+            return false;
+
+        consistency.extractBottomFragment();
+        consistency.dispose();
+
+        program.dispose();
+
+        return true;
+    }
+
+    @Override
+    public boolean isConsistent() {
+        if(isDisposed()) throw new DisposedException();
+        if(satisfiable == SatisfiabilityStatus.UNCHECKED) {
+            satisfiable = consistency.check() ? SatisfiabilityStatus.SATISFIABLE : SatisfiabilityStatus.UNSATISFIABLE;
+            Utility.logInfo("time for satisfiability checking: " + t.duration());
+        }
+        return satisfiable == SatisfiabilityStatus.SATISFIABLE;
+    }
+
+    @Override
+    public void evaluate(QueryRecord queryRecord) {
+        if(isDisposed()) throw new DisposedException();
+        if(queryBounds(queryRecord))
+            return;
+
+        OWLOntology relevantOntologySubset = extractRelevantOntologySubset(queryRecord);
+
+        int aBoxCount = relevantOntologySubset.getABoxAxioms(true).size();
+        Utility.logInfo("Relevant ontology subset: ABox_axioms=" + aBoxCount + " TBox_axioms=" + (relevantOntologySubset
+                .getAxiomCount() - aBoxCount));
+//              queryRecord.saveRelevantOntology("fragment_query" + queryRecord.getQueryID() + ".owl");
+
+        if(querySkolemisedRelevantSubset(relevantOntologySubset, queryRecord))
+            return;
+
+        Timer t = new Timer();
+        Checker summarisedChecker = new HermitSummaryFilter(queryRecord, properties.getToCallHermiT());
+        summarisedChecker.check(queryRecord.getGapAnswers());
+        summarisedChecker.dispose();
+        Utility.logDebug("Total time for full reasoner: " + t.duration());
+        queryRecord.markAsProcessed();
+        Utility.logDebug("Difficulty of this query: " + queryRecord.getDifficulty());
+    }
+
+    @Override
+    public void evaluateUpper(QueryRecord queryRecord) {
+        if(isDisposed()) throw new DisposedException();
+        // TODO add new upper store
+        AnswerTuples rlAnswer = null;
+        boolean useFull = queryRecord.isBottom() || lazyUpperStore == null;
+        try {
+            rlAnswer =
+                    (useFull ? trackingStore : lazyUpperStore).evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
+            queryRecord.updateUpperBoundAnswers(rlAnswer, true);
+        } finally {
+            if(rlAnswer != null) rlAnswer.dispose();
+        }
+    }
+
+    @Override
+    public void dispose() {
+        super.dispose();
+
+        if(encoder != null) encoder.dispose();
+        if(rlLowerStore != null) rlLowerStore.dispose();
+        if(lazyUpperStore != null) lazyUpperStore.dispose();
+        if(elLowerStore != null) elLowerStore.dispose();
+        if(trackingStore != null) trackingStore.dispose();
+        if(limitedSkolemUpperStore != null) limitedSkolemUpperStore.dispose();
+
+    }
+
+    private BasicQueryEngine getUpperStore(String name, boolean checkValidity) {
+        if(multiStageTag)
+            return new MultiStageQueryEngine(name, checkValidity);
+//                      return new TwoStageQueryEngine(name, checkValidity);
+        else
+            return new BasicQueryEngine(name);
+    }
+
+    protected void internal_importDataFile(String name, String datafile) {
+//              addDataFile(datafile);
+        rlLowerStore.importRDFData(name, datafile);
+        if(lazyUpperStore != null)
+            lazyUpperStore.importRDFData(name, datafile);
+        elLowerStore.importRDFData(name, datafile);
+        trackingStore.importRDFData(name, datafile);
+    }
+
+    /**
+     * It deals with blanks nodes differently from variables
+     * according to SPARQL semantics for OWL2 Entailment Regime.
+     * <p>
+     * In particular variables are matched only against named individuals,
+     * and blank nodes against named and anonymous individuals.
+     */
+    private boolean queryUpperStore(BasicQueryEngine upperStore, QueryRecord queryRecord,
+                                    Tuple<String> extendedQuery, Step step) {
+
+        if(queryRecord.hasNonAnsDistinguishedVariables())
+            queryUpperBound(upperStore, queryRecord, extendedQuery.get(0), queryRecord.getAnswerVariables());
+        else
+            queryUpperBound(upperStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables());
+
+        queryRecord.addProcessingTime(step, t.duration());
+        if(queryRecord.isProcessed()) {
+            queryRecord.setDifficulty(step);
+            return true;
+        }
+        return false;
+    }
+
+    /**
+     * Returns the part of the ontology relevant for Hermit, while computing the bound answers.
+     */
+    private boolean queryBounds(QueryRecord queryRecord) {
+        AnswerTuples rlAnswer = null, elAnswer = null;
+
+        t.reset();
+        try {
+            rlAnswer = rlLowerStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
+            Utility.logDebug(t.duration());
+            queryRecord.updateLowerBoundAnswers(rlAnswer);
+        } finally {
+            if(rlAnswer != null) rlAnswer.dispose();
+        }
+        queryRecord.addProcessingTime(Step.LOWER_BOUND, t.duration());
+
+        t.reset();
+
+        Tuple<String> extendedQueryTexts = queryRecord.getExtendedQueryText();
+
+        Utility.logDebug("Tracking store");
+        if(queryUpperStore(trackingStore, queryRecord, extendedQueryTexts, Step.SIMPLE_UPPER_BOUND))
+            return true;
+
+        if(!queryRecord.isBottom()) {
+            Utility.logDebug("Lazy store");
+            if(lazyUpperStore != null && queryUpperStore(lazyUpperStore, queryRecord, extendedQueryTexts, Step.LAZY_UPPER_BOUND))
+                return true;
 //                      Utility.logDebug("Skolem store");
 //                      if(limitedSkolemUpperStore != null && queryUpperStore(limitedSkolemUpperStore, queryRecord, extendedQueryTexts, Step.L_SKOLEM_UPPER_BOUND))
 //                              return null;
-                }
-
-                t.reset();
-                try {
-                        elAnswer = elLowerStore.evaluate(extendedQueryTexts.get(0),
-                                                                                         queryRecord.getAnswerVariables(),
-                                                                                         queryRecord.getLowerBoundAnswers());
-                        Utility.logDebug(t.duration());
-                        queryRecord.updateLowerBoundAnswers(elAnswer);
-                } finally {
-                        if (elAnswer != null) elAnswer.dispose();
-                }
-                queryRecord.addProcessingTime(Step.EL_LOWER_BOUND, t.duration());
-
-                if(queryRecord.isProcessed()) {
-                        queryRecord.setDifficulty(Step.EL_LOWER_BOUND);
-                        return true;
-                }
-
-                return false;
-        }
-
-        private OWLOntology extractRelevantOntologySubset(QueryRecord queryRecord) {
-                t.reset();
-
-                QueryTracker tracker = new QueryTracker(encoder, rlLowerStore, queryRecord);
-                OWLOntology relevantOntologySubset = tracker.extract(trackingStore, consistency.getQueryRecords(), true);
-
-                queryRecord.addProcessingTime(Step.FRAGMENT, t.duration());
-
-                return relevantOntologySubset;
-        }
-
-        private void queryUpperBound(BasicQueryEngine upperStore, QueryRecord queryRecord, String queryText, String[] answerVariables) {
-                AnswerTuples rlAnswer = null;
-                try {
-                        Utility.logDebug(queryText);
-                        rlAnswer = upperStore.evaluate(queryText, answerVariables);
-                        Utility.logDebug(t.duration());
-                        queryRecord.updateUpperBoundAnswers(rlAnswer);
-                } finally {
-                        if(rlAnswer != null) rlAnswer.dispose();
-                }
-        }
-
-        @Override
-        public void evaluate(QueryRecord queryRecord) {
-                if(queryBounds(queryRecord))
-                        return;
-
-                OWLOntology relevantOntologySubset = extractRelevantOntologySubset(queryRecord);
-
-                int aBoxCount = relevantOntologySubset.getABoxAxioms(true).size();
-                Utility.logInfo("Relevant ontology subset: ABox_axioms=" + aBoxCount + " TBox_axioms=" + (relevantOntologySubset
-                                .getAxiomCount() - aBoxCount));
-//              queryRecord.saveRelevantOntology("fragment_query" + queryRecord.getQueryID() + ".owl");
-
-                if(querySkolemisedRelevantSubset(relevantOntologySubset, queryRecord))
-                        return;
-
-                Timer t = new Timer();
-                Checker summarisedChecker = new HermitSummaryFilter(queryRecord, properties.getToCallHermiT());
-                summarisedChecker.check(queryRecord.getGapAnswers());
-                summarisedChecker.dispose();
-                Utility.logDebug("Total time for full reasoner: " + t.duration());
-                queryRecord.markAsProcessed();
-                Utility.logDebug("Difficulty of this query: " + queryRecord.getDifficulty());
-        }
-
-        private boolean querySkolemisedRelevantSubset(OWLOntology relevantSubset, QueryRecord queryRecord) {
-                MultiStageQueryEngine relevantStore =
-                                new MultiStageQueryEngine("Relevant-store", true); // checkValidity is true
-                DatalogProgram relevantProgram = new DatalogProgram(relevantSubset, false); // toClassify is false
-
-//        relevantStore.importRDFData("data", importedData.toString()); // 2 answers more
-                relevantStore.importDataFromABoxOf(relevantSubset);
-
-                int materialisationResult = relevantStore.materialiseSkolemly(relevantProgram, null);
-                if(materialisationResult != 1)
-                        throw new RuntimeException("Skolemised materialisation error"); // TODO check consistency
+        }
+
+        t.reset();
+        try {
+            elAnswer = elLowerStore.evaluate(extendedQueryTexts.get(0),
+                                             queryRecord.getAnswerVariables(),
+                                             queryRecord.getLowerBoundAnswers());
+            Utility.logDebug(t.duration());
+            queryRecord.updateLowerBoundAnswers(elAnswer);
+        } finally {
+            if(elAnswer != null) elAnswer.dispose();
+        }
+        queryRecord.addProcessingTime(Step.EL_LOWER_BOUND, t.duration());
+
+        if(queryRecord.isProcessed()) {
+            queryRecord.setDifficulty(Step.EL_LOWER_BOUND);
+            return true;
+        }
+
+        return false;
+    }
+
+    private OWLOntology extractRelevantOntologySubset(QueryRecord queryRecord) {
+        t.reset();
+
+        QueryTracker tracker = new QueryTracker(encoder, rlLowerStore, queryRecord);
+        OWLOntology relevantOntologySubset = tracker.extract(trackingStore, consistency.getQueryRecords(), true);
+
+        queryRecord.addProcessingTime(Step.FRAGMENT, t.duration());
+
+        return relevantOntologySubset;
+    }
+
+    private void queryUpperBound(BasicQueryEngine upperStore, QueryRecord queryRecord, String queryText, String[] answerVariables) {
+        AnswerTuples rlAnswer = null;
+        try {
+            Utility.logDebug(queryText);
+            rlAnswer = upperStore.evaluate(queryText, answerVariables);
+            Utility.logDebug(t.duration());
+            queryRecord.updateUpperBoundAnswers(rlAnswer);
+        } finally {
+            if(rlAnswer != null) rlAnswer.dispose();
+        }
+    }
+
+    private boolean querySkolemisedRelevantSubset(OWLOntology relevantSubset, QueryRecord queryRecord) {
+        DatalogProgram relevantProgram = new DatalogProgram(relevantSubset, false); // toClassify is false
+
+        MultiStageQueryEngine relevantStore =
+                new MultiStageQueryEngine("Relevant-store", true); // checkValidity is true
+//        relevantStore.importRDFData("data", relevantProgram.getAdditionalDataFile()); // tried, doesn't work
+        relevantStore.importDataFromABoxOf(relevantSubset);
+
+        int materialisationResult = relevantStore.materialiseSkolemly(relevantProgram, null);
+//        int materialisationResult = relevantStore.materialiseRestrictedly(relevantProgram, null); // DOESN'T WORK!!!
+        if(materialisationResult != 1)
+            throw new RuntimeException("Skolemised materialisation error"); // TODO check consistency
 //        relevantStore.materialiseRestrictedly(relevantProgram, null); // it has been tried
 
-                return queryUpperStore(relevantStore, queryRecord, queryRecord.getExtendedQueryText(), Step.L_SKOLEM_UPPER_BOUND);
-
-                // the following has been tried
-//        Tuple<String> extendedQueryText = queryRecord.getExtendedQueryText();
-//        if(queryRecord.hasNonAnsDistinguishedVariables()) {
-//            queryUpperBound(relevantStore, queryRecord, extendedQueryText.get(0), queryRecord.getAnswerVariables());
-//            queryUpperBound(relevantStore, queryRecord, extendedQueryText.get(1), queryRecord.getDistinguishedVariables());
-//        }
-//        else
-//            queryUpperBound(relevantStore, queryRecord, queryRecord.getQueryText(), queryRecord.getAnswerVariables());
-//
-//              return queryRecord.isProcessed();
-
-        }
-
-        @Override
-        public void evaluateUpper(QueryRecord queryRecord) {
-                // TODO add new upper store
-                AnswerTuples rlAnswer = null;
-                boolean useFull = queryRecord.isBottom() || lazyUpperStore == null;
-                try {
-                        rlAnswer =
-                                        (useFull ? trackingStore : lazyUpperStore).evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
-                        queryRecord.updateUpperBoundAnswers(rlAnswer, true);
-                } finally {
-                        if(rlAnswer != null) rlAnswer.dispose();
-                }
-        }
-
-        @Override
-        public void dispose() {
-                if (encoder != null) encoder.dispose();
-                if (rlLowerStore != null) rlLowerStore.dispose();
-                if (lazyUpperStore != null) lazyUpperStore.dispose();
-                if (elLowerStore != null) elLowerStore.dispose();
-                if (trackingStore != null) trackingStore.dispose();
-
-//              if(limitedSkolemUpperStore != null) limitedSkolemUpperStore.dispose();
-                super.dispose();
-        }
-
-        enum SatisfiabilityStatus {SATISFIABLE, UNSATISFIABLE, UNCHECKED}
+        return queryUpperStore(relevantStore, queryRecord, queryRecord.getExtendedQueryText(), Step.L_SKOLEM_UPPER_BOUND);
+
+//        return queryUpperStore(limitedSkolemUpperStore, queryRecord, queryRecord.getExtendedQueryText(), Step.L_SKOLEM_UPPER_BOUND);
+    }
+
+    enum SatisfiabilityStatus {SATISFIABLE, UNSATISFIABLE, UNCHECKED}
 
 }
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/QueryEngine.java b/src/uk/ac/ox/cs/pagoda/reasoner/QueryEngine.java
index b9abf07..3200216 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/QueryEngine.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/QueryEngine.java
@@ -1,17 +1,15 @@
 package uk.ac.ox.cs.pagoda.reasoner;
 
+import uk.ac.ox.cs.pagoda.query.AnswerTuples;
+import uk.ac.ox.cs.pagoda.util.disposable.Disposable;
+
 import java.util.Collection;
 
-import uk.ac.ox.cs.pagoda.query.AnswerTuples;
+public abstract class QueryEngine extends Disposable {
+
+        public abstract void evaluate(Collection<String> queryTexts, String answerFile);
 
-public interface QueryEngine {
+        public abstract AnswerTuples evaluate(String queryText);
 
-        public void evaluate(Collection<String> queryTexts, String answerFile);
-        
-        public AnswerTuples evaluate(String queryText);
-        
-        public AnswerTuples evaluate(String queryText, String[] answerVariables);
-        
-        public void dispose(); 
-        
+        public abstract AnswerTuples evaluate(String queryText, String[] answerVariables);
 }
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
index 118c1b2..962a78f 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
@@ -9,6 +9,8 @@ import uk.ac.ox.cs.pagoda.query.QueryRecord;
 import uk.ac.ox.cs.pagoda.util.PagodaProperties;
 import uk.ac.ox.cs.pagoda.util.Timer;
 import uk.ac.ox.cs.pagoda.util.Utility;
+import uk.ac.ox.cs.pagoda.util.disposable.Disposable;
+import uk.ac.ox.cs.pagoda.util.disposable.DisposedException;
 
 import java.io.BufferedWriter;
 import java.io.File;
@@ -18,230 +20,242 @@ import java.nio.file.Paths;
 import java.util.Collection;
 
 // TODO clean APIs
-public abstract class QueryReasoner {
-
-        public static final String ImportDataFileSeparator = ";";
-        private static final boolean DEFAULT_MULTI_STAGES = true;
-        private static final boolean DEFAULT_EQUALITIES = true;
-        public boolean fullReasoner = this instanceof MyQueryReasoner;
-        protected StringBuilder importedData = new StringBuilder();
-//      protected boolean forSemFacet = false;
-PagodaProperties properties;
-        BufferedWriter answerWriter = null;
-        private QueryManager m_queryManager = new QueryManager();
-
-        public static QueryReasoner getInstance(PagodaProperties p) {
-                OWLOntology ontology = OWLHelper.loadOntology(p.getOntologyPath());
-                QueryReasoner pagoda = getInstance(ontology, p);
-                pagoda.properties = p;
-                pagoda.loadOntology(ontology);
-                pagoda.importData(p.getDataPath());
-                if (pagoda.preprocess()) {
-                        Utility.logInfo("The ontology is consistent!");
-                        return pagoda;
-                }
-                else {
-                        System.out.println("The ontology is inconsistent!");
-                        pagoda.dispose();
-                        return null;
-                }
-        }
-
-        public static QueryReasoner getInstance(OWLOntology o) {
-                QueryReasoner pagoda = getInstance(Type.Full, o, DEFAULT_MULTI_STAGES, DEFAULT_EQUALITIES);
-                pagoda.properties = new PagodaProperties();
-                return pagoda;
-        }
-
-        private static QueryReasoner getInstance(OWLOntology o, PagodaProperties p) {
-                return getInstance(Type.Full, o, DEFAULT_MULTI_STAGES, DEFAULT_EQUALITIES);
-        }
-
-        public static QueryReasoner getInstance(Type type, OWLOntology o, boolean performMultiStages, boolean considerEqualities) {
+public abstract class QueryReasoner extends Disposable {
+
+    public static final String ImportDataFileSeparator = ";";
+    private static final boolean DEFAULT_MULTI_STAGES = true;
+    private static final boolean DEFAULT_EQUALITIES = true;
+    public boolean fullReasoner = this instanceof MyQueryReasoner;
+    protected StringBuilder importedData = new StringBuilder();
+    //  protected boolean forSemFacet = false;
+    PagodaProperties properties;
+    BufferedWriter answerWriter = null;
+    private QueryManager m_queryManager = new QueryManager();
+
+    public static QueryReasoner getInstance(PagodaProperties p) {
+        OWLOntology ontology = OWLHelper.loadOntology(p.getOntologyPath());
+        QueryReasoner pagoda = getInstance(ontology, p);
+        pagoda.properties = p;
+        pagoda.loadOntology(ontology);
+        pagoda.importData(p.getDataPath());
+        if(pagoda.preprocess()) {
+            Utility.logInfo("The ontology is consistent!");
+            return pagoda;
+        }
+        else {
+            System.out.println("The ontology is inconsistent!");
+            pagoda.dispose();
+            return null;
+        }
+    }
+
+    public static QueryReasoner getInstance(OWLOntology o) {
+        QueryReasoner pagoda = getInstance(Type.Full, o, DEFAULT_MULTI_STAGES, DEFAULT_EQUALITIES);
+        pagoda.properties = new PagodaProperties();
+        return pagoda;
+    }
+
+    private static QueryReasoner getInstance(OWLOntology o, PagodaProperties p) {
+        return getInstance(Type.Full, o, DEFAULT_MULTI_STAGES, DEFAULT_EQUALITIES);
+    }
+
+    public static QueryReasoner getInstance(Type type, OWLOntology o, boolean performMultiStages, boolean considerEqualities) {
 //              Utility.initialise();
-                QueryReasoner reasoner;
-                if (OWLHelper.isInOWL2RL(o)) reasoner = new RLQueryReasoner();
-                else if (OWLHelper.isInELHO(o)) reasoner = new ELHOQueryReasoner();
-                else
-                switch (type) {
-                        case RLU:
-                                reasoner = new RLUQueryReasoner(performMultiStages, considerEqualities);
-                                break;
-                        case ELHOU:
-                                reasoner = new ELHOUQueryReasoner(performMultiStages, considerEqualities);
-                                break;
-                        default:
-                                reasoner = new MyQueryReasoner(performMultiStages, considerEqualities);
-                        }
-                return reasoner;
-        }
-
-        public static QueryReasoner getHermiTReasoner(boolean toCheckSatisfiability) {
-                return new HermiTReasoner(toCheckSatisfiability);
-        }
-
-        public void setToClassify(boolean flag) {
-                properties.setToClassify(flag);
-        }
-
-        public void setToCallHermiT(boolean flag) {
-                properties.setToCallHermiT(flag);
-        }
-        
-        public void importData(String datafile) {
-                if (datafile != null && !datafile.equalsIgnoreCase("null"))
-                        importData(datafile.split(ImportDataFileSeparator));
-        }
-
-        public void importData(String[] datafiles) {
-                if (datafiles != null) {
-                        for (String datafile: datafiles) {
-                                File file = new File(datafile);
-                                if (file.exists()) {
-                                        if (file.isFile()) importDataFile(file);
-                                        else importDataDirectory(file);
-                                }
-                                else {
-                                        Utility.logError("warning: file " + datafile + " doesn't exists.");
-                                }
-                        }
-                }
-        }
-        
-        private void importDataDirectory(File file) {
-                for (File child: file.listFiles())
-                        if (child.isFile()) importDataFile(child);
-                        else importDataDirectory(child);
-        }
-        
-        private void importDataFile(File file) {
-                String datafile;
-                try {
-                        datafile = file.getCanonicalPath();
-                } catch (IOException e) {
-                        e.printStackTrace();
-                        return;
-                }
-                importDataFile(datafile);
-        }
-
-        protected final void importDataFile(String datafile) {
-                if (importedData.length() == 0)
-                        importedData.append(datafile);
-                else
-                        importedData.append(ImportDataFileSeparator).append(datafile);
-
-        }
-
-        public abstract void loadOntology(OWLOntology ontology);
-
-        public abstract boolean preprocess();
-
-        public abstract boolean isConsistent();
-        
-        public abstract void evaluate(QueryRecord record);
-
-        public abstract void evaluateUpper(QueryRecord record);
-        
-        public AnswerTuples evaluate(String queryText, boolean forFacetGeneration) {
-                if (forFacetGeneration) {
-                        QueryRecord record = m_queryManager.create(queryText);
-                        Utility.logInfo("---------- start evaluating upper bound for Query " + record.getQueryID() + " ----------", queryText);
-                        if(!record.isProcessed())
-                                evaluateUpper(record);
+        QueryReasoner reasoner;
+        if(OWLHelper.isInOWL2RL(o)) reasoner = new RLQueryReasoner();
+        else if(OWLHelper.isInELHO(o)) reasoner = new ELHOQueryReasoner();
+        else
+            switch(type) {
+                case RLU:
+                    reasoner = new RLUQueryReasoner(performMultiStages, considerEqualities);
+                    break;
+                case ELHOU:
+                    reasoner = new ELHOUQueryReasoner(performMultiStages, considerEqualities);
+                    break;
+                default:
+                    reasoner = new MyQueryReasoner(performMultiStages, considerEqualities);
+            }
+        return reasoner;
+    }
+
+    public static QueryReasoner getHermiTReasoner(boolean toCheckSatisfiability) {
+        return new HermiTReasoner(toCheckSatisfiability);
+    }
+
+    public void setToClassify(boolean flag) {
+        if(isDisposed()) throw new DisposedException();
+        properties.setToClassify(flag);
+    }
+
+    public void setToCallHermiT(boolean flag) {
+        if(isDisposed()) throw new DisposedException();
+        properties.setToCallHermiT(flag);
+    }
+
+    public void importData(String datafile) {
+        if(isDisposed()) throw new DisposedException();
+        if(datafile != null && !datafile.equalsIgnoreCase("null"))
+            importData(datafile.split(ImportDataFileSeparator));
+    }
+
+    public void importData(String[] datafiles) {
+        if(isDisposed()) throw new DisposedException();
+        if(datafiles != null) {
+            for(String datafile : datafiles) {
+                File file = new File(datafile);
+                if(file.exists()) {
+                    if(file.isFile()) importDataFile(file);
+                    else importDataDirectory(file);
+                }
+                else {
+                    Utility.logError("warning: file " + datafile + " doesn't exists.");
+                }
+            }
+        }
+    }
+
+    public abstract void loadOntology(OWLOntology ontology);
+
+    public abstract boolean preprocess();
+
+    public abstract boolean isConsistent();
+
+    public abstract void evaluate(QueryRecord record);
+
+    public abstract void evaluateUpper(QueryRecord record);
+
+    public AnswerTuples evaluate(String queryText, boolean forFacetGeneration) {
+        if(isDisposed()) throw new DisposedException();
+        if(forFacetGeneration) {
+            QueryRecord record = m_queryManager.create(queryText);
+            Utility.logInfo("---------- start evaluating upper bound for Query " + record.getQueryID() + " ----------", queryText);
+            if(!record.isProcessed())
+                evaluateUpper(record);
 //                      AnswerTuples tuples = record.getUpperBoundAnswers();
 //                      for (AnswerTuple tuple; tuples.isValid(); tuples.moveNext()) {
 //                              tuple = tuples.getTuple();
 //                              if (tuple.toString().contains("NC"))
 //                                      System.out.println(tuple.toString());
 //                      }
-                        return record.getUpperBoundAnswers();
-                } else
-                        return evaluate(queryText);
-        }
-        
-//      public void evaluate(Collection<QueryRecord> queryRecords) {
-//              evaluate(queryRecords);
-//      }
+            return record.getUpperBoundAnswers();
+        }
+        else
+            return evaluate(queryText);
+    }
+
+    public AnswerTuples evaluate(String queryText) {
+        if(isDisposed()) throw new DisposedException();
+        QueryRecord record = m_queryManager.create(queryText);
+        Utility.logInfo("---------- start evaluating Query " + record.getQueryID() + " ----------", queryText);
+        if(!record.isProcessed())
+            evaluate(record);
+        AnswerTuples answer = record.getAnswers();
+        record.dispose();
+        return answer;
+
+    }
+
+    public void evaluate_shell(String queryText) {
+        if(isDisposed()) throw new DisposedException();
+        QueryRecord record = m_queryManager.create(queryText);
+        Utility.logInfo("---------- start evaluating Query " + record.getQueryID() + " ----------", queryText);
+        if(!record.isProcessed())
+            evaluate(record);
+        Utility.logInfo("Answers to this query: ", record.outputSoundAnswerTuple());
+        record.dispose();
+
+    }
 
-        public AnswerTuples evaluate(String queryText) {
-                QueryRecord record = m_queryManager.create(queryText);
-                Utility.logInfo("---------- start evaluating Query " + record.getQueryID() + " ----------", queryText);
-                if(!record.isProcessed())
-                        evaluate(record);
-                AnswerTuples answer = record.getAnswers();
-                record.dispose();
-                return answer;
-
-        }
-
-        public void evaluate_shell(String queryText) {
-                QueryRecord record = m_queryManager.create(queryText);
-                Utility.logInfo("---------- start evaluating Query " + record.getQueryID() + " ----------", queryText);
-                if(!record.isProcessed())
-                        evaluate(record);
-                Utility.logInfo("Answers to this query: ", record.outputSoundAnswerTuple());
-                record.dispose();
-
-        }
-        
-        public void evaluate(Collection<QueryRecord> queryRecords) {
-                if (!isConsistent()) {
-                        Utility.logDebug("The ontology and dataset is inconsistent.");
-                        return;
-                }
-
-                if(properties.getAnswerPath() != null && answerWriter == null) {
-                        try {
-                                answerWriter = Files.newBufferedWriter(Paths.get(properties.getAnswerPath()));
-                        } catch (IOException e) {
-                                Utility.logError("The answer path is not valid!");
-                                e.printStackTrace();
-                        }
-                }
-
-                Timer t = new Timer();
-                Gson gson = QueryRecord.GsonCreator.getInstance();
-                for (QueryRecord record: queryRecords) {
+    public void evaluate(Collection<QueryRecord> queryRecords) {
+        if(isDisposed()) throw new DisposedException();
+        if(!isConsistent()) {
+            Utility.logDebug("The ontology and dataset is inconsistent.");
+            return;
+        }
+
+        if(properties.getAnswerPath() != null && answerWriter == null) {
+            try {
+                answerWriter = Files.newBufferedWriter(Paths.get(properties.getAnswerPath()));
+            } catch(IOException e) {
+                Utility.logError("The answer path is not valid!");
+                e.printStackTrace();
+            }
+        }
+
+        Timer t = new Timer();
+        Gson gson = QueryRecord.GsonCreator.getInstance();
+        for(QueryRecord record : queryRecords) {
 //                      if (Integer.parseInt(record.getQueryID()) != 218) continue;
-                        Utility.logInfo("---------- start evaluating Query " + record.getQueryID() + " ----------",
-                                        record.getQueryText());
-                        if(!record.isProcessed()) {
-                                t.reset();
-                                if(!record.isProcessed())
-                                        evaluate(record);
-                                Utility.logInfo("Total time to answer this query: " + t.duration());
-                                if(!fullReasoner && !record.isProcessed()) {
-                                        Utility.logInfo("The query has not been fully answered in " + t.duration() + " seconds.");
-                                        continue;
-                                }
-                        }
-                        record.outputAnswerStatistics();
-                        record.outputTimes();
-                }
-                /* TODO it can handle one call only
+            Utility.logInfo("---------- start evaluating Query " + record.getQueryID() + " ----------",
+                            record.getQueryText());
+            if(!record.isProcessed()) {
+                t.reset();
+                if(!record.isProcessed())
+                    evaluate(record);
+                Utility.logInfo("Total time to answer this query: " + t.duration());
+                if(!fullReasoner && !record.isProcessed()) {
+                    Utility.logInfo("The query has not been fully answered in " + t.duration() + " seconds.");
+                    continue;
+                }
+            }
+            record.outputAnswerStatistics();
+            record.outputTimes();
+        }
+        /* TODO it can handle one call only
                    if you call twice, you will end up with a json file with multiple roots */
-                if(answerWriter != null) gson.toJson(queryRecords, answerWriter);
+        if(answerWriter != null) gson.toJson(queryRecords, answerWriter);
 //              queryRecords.stream().forEach(record -> Utility.logDebug(gson.toJson(record)));
-                queryRecords.stream().forEach(record -> record.dispose());
-        }
-
-        public void dispose() {
-                if (answerWriter != null) {
-                        try {
-                                answerWriter.close();
-                        } catch (IOException e) {
-                                e.printStackTrace();
-                        }
-                }
+        queryRecords.stream().forEach(record -> record.dispose());
+    }
+
+//      public void evaluate(Collection<QueryRecord> queryRecords) {
+//              evaluate(queryRecords);
+//      }
+
+    @Override
+    public void dispose() {
+        super.dispose();
+        if(answerWriter != null) {
+            try {
+                answerWriter.close();
+            } catch(IOException e) {
+                e.printStackTrace();
+            }
+        }
 //              Utility.cleanup();
-        }
-        
-        public QueryManager getQueryManager() {
-                return m_queryManager; 
-        }
+    }
+
+    public QueryManager getQueryManager() {
+        if(isDisposed()) throw new DisposedException();
+        return m_queryManager;
+    }
+
+    private void importDataDirectory(File file) {
+        for(File child : file.listFiles())
+            if(child.isFile()) importDataFile(child);
+            else importDataDirectory(child);
+    }
+
+    private void importDataFile(File file) {
+        String datafile;
+        try {
+            datafile = file.getCanonicalPath();
+        } catch(IOException e) {
+            e.printStackTrace();
+            return;
+        }
+        importDataFile(datafile);
+    }
+
+    protected final void importDataFile(String datafile) {
+        if(importedData.length() == 0)
+            importedData.append(datafile);
+        else
+            importedData.append(ImportDataFileSeparator).append(datafile);
+
+    }
 
 
-        public enum Type {Full, RLU, ELHOU}
+    public enum Type {Full, RLU, ELHOU}
 
 }
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/RLQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/RLQueryReasoner.java
index bea5bbf..16e2627 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/RLQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/RLQueryReasoner.java
@@ -9,6 +9,7 @@ import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine;
 import uk.ac.ox.cs.pagoda.reasoner.light.RDFoxQueryEngine;
 import uk.ac.ox.cs.pagoda.rules.LowerDatalogProgram;
 import uk.ac.ox.cs.pagoda.util.Timer;
+import uk.ac.ox.cs.pagoda.util.disposable.DisposedException;
 
 class RLQueryReasoner extends QueryReasoner {
         
@@ -16,13 +17,14 @@ class RLQueryReasoner extends QueryReasoner {
 
         LowerDatalogProgram program;
         Timer t = new Timer();
-        
+
         public RLQueryReasoner() {
                 rlLowerStore = new BasicQueryEngine("rl");
         }
         
         @Override
         public void evaluate(QueryRecord queryRecord) {
+                if(isDisposed()) throw new DisposedException();
                 AnswerTuples rlAnswer = null; 
                 t.reset();
                 try {
@@ -38,12 +40,13 @@ class RLQueryReasoner extends QueryReasoner {
 
         @Override
         public void dispose() {
-                if (rlLowerStore != null) rlLowerStore.dispose();
                 super.dispose();
+                if(rlLowerStore != null) rlLowerStore.dispose();
         }
 
         @Override
         public void loadOntology(OWLOntology ontology) {
+                if(isDisposed()) throw new DisposedException();
                 program = new LowerDatalogProgram(); 
                 program.load(ontology, new UnaryBottom());
                 program.transform();
@@ -53,6 +56,7 @@ class RLQueryReasoner extends QueryReasoner {
 
         @Override
         public boolean preprocess() {
+                if(isDisposed()) throw new DisposedException();
                 rlLowerStore.importRDFData("data", importedData.toString());
                 rlLowerStore.materialise("lower program", program.toString());
 
@@ -61,6 +65,7 @@ class RLQueryReasoner extends QueryReasoner {
 
         @Override
         public boolean isConsistent() {
+                if(isDisposed()) throw new DisposedException();
                 AnswerTuples ans = null; 
                 try {
                         ans = rlLowerStore.evaluate(QueryRecord.botQueryText, new String[] {"X"});
@@ -74,6 +79,7 @@ class RLQueryReasoner extends QueryReasoner {
 
         @Override
         public void evaluateUpper(QueryRecord record) {
+                if(isDisposed()) throw new DisposedException();
                 evaluate(record); 
         }
 
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/RLUQueryReasoner.java b/src/uk/ac/ox/cs/pagoda/reasoner/RLUQueryReasoner.java
index 547140a..d0712e1 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/RLUQueryReasoner.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/RLUQueryReasoner.java
@@ -10,6 +10,7 @@ import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine;
 import uk.ac.ox.cs.pagoda.rules.DatalogProgram;
 import uk.ac.ox.cs.pagoda.util.Timer;
 import uk.ac.ox.cs.pagoda.util.Utility;
+import uk.ac.ox.cs.pagoda.util.disposable.DisposedException;
 
 class RLUQueryReasoner extends QueryReasoner {
 
@@ -19,7 +20,7 @@ class RLUQueryReasoner extends QueryReasoner {
         
         boolean multiStageTag, equalityTag;
         Timer t = new Timer();
-        
+
         public RLUQueryReasoner(boolean multiStageTag, boolean considerEqualities) {
                 this.multiStageTag = multiStageTag;
                 this.equalityTag = considerEqualities;
@@ -32,6 +33,7 @@ class RLUQueryReasoner extends QueryReasoner {
         
         @Override
         public void evaluate(QueryRecord queryRecord) {
+                if(isDisposed()) throw new DisposedException();
                 AnswerTuples ans = null;
                 t.reset(); 
                 try {
@@ -60,6 +62,7 @@ class RLUQueryReasoner extends QueryReasoner {
         
         @Override
         public void evaluateUpper(QueryRecord queryRecord) {
+                if(isDisposed()) throw new DisposedException();
                 AnswerTuples ans = null; 
                 try {
                         ans = rlUpperStore.evaluate(queryRecord.getQueryText(), queryRecord.getAnswerVariables());
@@ -72,13 +75,14 @@ class RLUQueryReasoner extends QueryReasoner {
 
         @Override
         public void dispose() {
+                super.dispose();
                 if (rlLowerStore != null) rlLowerStore.dispose();
                 if (rlUpperStore != null) rlUpperStore.dispose();
-                super.dispose();
         }
 
         @Override
         public void loadOntology(OWLOntology o) {
+                if(isDisposed()) throw new DisposedException();
                 if (!equalityTag) {
                         EqualitiesEliminator eliminator = new EqualitiesEliminator(o);
                         o = eliminator.getOutputOntology();
@@ -92,6 +96,7 @@ class RLUQueryReasoner extends QueryReasoner {
 
         @Override
         public boolean preprocess() {
+                if(isDisposed()) throw new DisposedException();
                 String datafile = importedData.toString(); 
                 rlLowerStore.importRDFData("data", datafile);
                 rlLowerStore.materialise("lower program", program.getLower().toString());
@@ -105,6 +110,7 @@ class RLUQueryReasoner extends QueryReasoner {
 
         @Override
         public boolean isConsistent() {
+                if(isDisposed()) throw new DisposedException();
                 String[] X = new String[] { "X" }; 
                 AnswerTuples ans = null; 
                 try {
@@ -125,6 +131,5 @@ class RLUQueryReasoner extends QueryReasoner {
                 Utility.logDebug("The consistency of the data has not been determined yet.");
                 return true; 
         }
-        
-        
+
 }
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java b/src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java
index 79be8aa..fe43e09 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java
@@ -1,375 +1,377 @@
 package uk.ac.ox.cs.pagoda.reasoner.light;
 
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.Set;
-
 import org.semanticweb.HermiT.model.DLClause;
-
+import uk.ac.ox.cs.JRDFox.JRDFStoreException;
+import uk.ac.ox.cs.JRDFox.store.DataStore;
+import uk.ac.ox.cs.JRDFox.store.DataStore.UpdateType;
+import uk.ac.ox.cs.JRDFox.store.Parameters;
+import uk.ac.ox.cs.JRDFox.store.TripleStatus;
+import uk.ac.ox.cs.JRDFox.store.TupleIterator;
 import uk.ac.ox.cs.pagoda.hermit.DLClauseHelper;
 import uk.ac.ox.cs.pagoda.query.AnswerTuples;
 import uk.ac.ox.cs.pagoda.query.GapByStore4ID;
 import uk.ac.ox.cs.pagoda.rules.DatalogProgram;
 import uk.ac.ox.cs.pagoda.rules.Program;
-import uk.ac.ox.cs.pagoda.util.ConjunctiveQueryHelper;
-import uk.ac.ox.cs.pagoda.util.Namespace;
+import uk.ac.ox.cs.pagoda.util.*;
 import uk.ac.ox.cs.pagoda.util.Timer;
-import uk.ac.ox.cs.pagoda.util.UFS;
-import uk.ac.ox.cs.pagoda.util.Utility;
-import uk.ac.ox.cs.JRDFox.JRDFStoreException;
-import uk.ac.ox.cs.JRDFox.store.DataStore;
-import uk.ac.ox.cs.JRDFox.store.Parameters;
-import uk.ac.ox.cs.JRDFox.store.TripleStatus;
-import uk.ac.ox.cs.JRDFox.store.TupleIterator;
-import uk.ac.ox.cs.JRDFox.store.DataStore.UpdateType;
+import uk.ac.ox.cs.pagoda.util.disposable.DisposedException;
+
+import java.util.*;
 
 public class BasicQueryEngine extends RDFoxQueryEngine {
 
-        protected DataStore store; 
-        protected Parameters parameters = new Parameters(); 
-        
-        public BasicQueryEngine(String name) {
-                super(name); 
-                store = RDFoxQueryEngine.createDataStore();
-                parameters.m_allAnswersInRoot = true; 
-                parameters.m_useBushy = true; 
-        }
-        
-        public void materialiseFoldedly(DatalogProgram dProgram, GapByStore4ID gap) {
-                if (gap != null) {
-                        materialise("lower program", dProgram.getLower().toString());
-                        String program = dProgram.getUpper().toString();
-                        try {
-                                gap.compile(program);
-                                gap.addBackTo();
-                                getDataStore().clearRulesAndMakeFactsExplicit();
-                        } catch (JRDFStoreException e) {
-                                e.printStackTrace();
-                        } finally {
-                                gap.clear(); 
-                        }
-                }
-                else 
-                        materialise("upper program", dProgram.getUpper().toString());
-        }
-        
-        public int materialiseRestrictedly(DatalogProgram dProgram, GapByStore4ID gap) {
-                if (gap != null) {
-                        materialise("lower program", dProgram.getLower().toString());
-                        String program = dProgram.getUpper().toString();
-                        try {
-                                gap.compile(program);
-                                gap.addBackTo();
-                                getDataStore().clearRulesAndMakeFactsExplicit();
-                        } catch (JRDFStoreException e) {
-                                e.printStackTrace();
-                        } finally {
-                                gap.clear(); 
-                        }
-                }
-                else 
-                        materialise("upper program", dProgram.getUpper().toString());
-                
-                return 1; 
-        }
-        
-        @Override
-        public AnswerTuples evaluate(String queryText) {
-                return evaluate(queryText, ConjunctiveQueryHelper.getAnswerVariables(queryText)[0]); 
-        }
-        
-        @Override
-        public AnswerTuples evaluate(String queryText, String[] answerVars) {
-                TupleIterator tupleIterator;
-                try {
-                        tupleIterator = store.compileQuery(queryText.replace("_:", "?"), prefixes, parameters);
-                } catch (JRDFStoreException e) {
-                        e.printStackTrace();
-                        return null; 
-                }
-                return new RDFoxAnswerTuples(answerVars, tupleIterator); 
-        }
-
-        @Override
-        public DataStore getDataStore() {
-                return store;
-        }
-
-        @Override
-        public void dispose() {
-                store.dispose();                
-        }
-
-        protected void outputClassAssertions(String filename) {
-                TupleIterator allTuples = null;
-                boolean redirect = false; 
-                try {
-                        allTuples = getDataStore().compileQuery("SELECT ?X ?Z WHERE { ?X <" + Namespace.RDF_TYPE + "> ?Z }", prefixes, parameters);
-                        redirect = Utility.redirectCurrentOut(filename);
-                        for (long multi = allTuples.open(); multi != 0; multi = allTuples.getNext()) 
-                                System.out.println(RDFoxTripleManager.getQuotedTerm(allTuples.getResource(0)) + " " + RDFoxTripleManager.getQuotedTerm(allTuples.getResource(1))); 
-                } catch (JRDFStoreException e) {
-                        e.printStackTrace();
-                } finally {
-                        if (redirect) Utility.closeCurrentOut();
-                        if (allTuples != null) allTuples.dispose();
-                }
-        }
-        
-        public void outputInstance4BinaryPredicate(String iri, String filename) {
-                Utility.redirectCurrentOut(filename);
-                outputInstance4BinaryPredicate(iri);
-                Utility.closeCurrentOut();
-        }
-        
-        public void outputInstance4BinaryPredicate(String iri) {
-                outputAnswers("select ?x ?y where { ?x <" + iri + "> ?y . }");
-        }
-        
-        public void outputInstanceNumbers(String filename) {
-                TupleIterator predicateTuples = null;
-                TupleIterator instanceTuples; 
-                Set<String> number = new HashSet<String>(); 
-                String predicate; 
-                try {
-                        predicateTuples = getDataStore().compileQuery("SELECT DISTINCT ?Y WHERE { ?X <" + Namespace.RDF_TYPE + "> ?Y }", prefixes, parameters);
-                        for (long multi = predicateTuples.open(); multi != 0; multi = predicateTuples.getNext()) {
-                                predicate = RDFoxTripleManager.getQuotedTerm(predicateTuples.getResource(0));
-                                instanceTuples = null; 
-                                try {
-                                        instanceTuples = getDataStore().compileQuery("SELECT ?X WHERE { ?X <" + Namespace.RDF_TYPE + "> " + predicate + " }", prefixes, parameters);
-                                        long totalCount = 0; 
-                                        for (long multi1 = instanceTuples.open(); multi1 != 0; multi1 = instanceTuples.getNext()) {
-                                                totalCount += instanceTuples.getMultiplicity();
-                                        }
-                                        number.add(predicate + " * " + totalCount);
-                                } finally {
-                                        if (instanceTuples != null) instanceTuples.dispose(); 
-                                }
-                        }
-                } catch (JRDFStoreException e) {
-                        e.printStackTrace();
-                } finally {                     
-                        if (predicateTuples != null) predicateTuples.dispose();
-                        predicateTuples = null; 
-                }
-                        
-                try {
-                        predicateTuples = getDataStore().compileQuery("SELECT DISTINCT ?Y WHERE { ?X ?Y ?Z }", prefixes, parameters);
-                        for (long multi = predicateTuples.open(); multi != 0; multi = predicateTuples.getNext()) {
-                                predicate = RDFoxTripleManager.getQuotedTerm(predicateTuples.getResource(0)); 
-                                instanceTuples = null; 
-                                try {
-                                        instanceTuples = getDataStore().compileQuery("SELECT ?X ?Z WHERE { ?X " + predicate + " ?Z }", prefixes, parameters);
-                                        ;
-                                        long totalCount = 0; 
-                                        for (long multi1 = instanceTuples.open(); multi1 != 0; multi1 = instanceTuples.getNext())
-                                                totalCount += instanceTuples.getMultiplicity();
-                                        number.add(predicate + " * " + totalCount); 
-                                } finally {
-                                        if (instanceTuples != null) instanceTuples.dispose(); 
-                                }
-                        }
-                        
-                } catch (JRDFStoreException e) {
-                        e.printStackTrace();
-                } finally {
-                        if (predicateTuples != null) predicateTuples.dispose();
-                        predicateTuples = null;
-                }
-                
-                Utility.redirectCurrentOut(filename);
-                String[] ordered = number.toArray(new String[0]);
-                Arrays.sort(ordered, new DLPredicateComparator());
-                for (String line: ordered) System.out.println(line); 
-                Utility.closeCurrentOut();
-                
-        }
-        
-        public TupleIterator internal_evaluateAgainstIDBs(String queryText) throws JRDFStoreException {
-                TupleIterator iter = store.compileQuery(queryText, prefixes, parameters, TripleStatus.TUPLE_STATUS_IDB.union(TripleStatus.TUPLE_STATUS_EDB), TripleStatus.TUPLE_STATUS_IDB);
+    protected DataStore store;
+    protected Parameters parameters = new Parameters();
+    Set<DLClause> materialisedRules = new HashSet<DLClause>();
+    private UFS<String> equalityGroups = null;
+
+    public BasicQueryEngine(String name) {
+        super(name);
+        store = RDFoxQueryEngine.createDataStore();
+        parameters.m_allAnswersInRoot = true;
+        parameters.m_useBushy = true;
+    }
+
+    public void materialiseFoldedly(DatalogProgram dProgram, GapByStore4ID gap) {
+        if(isDisposed()) throw new DisposedException();
+        if(gap != null) {
+            materialise("lower program", dProgram.getLower().toString());
+            String program = dProgram.getUpper().toString();
+            try {
+                gap.compile(program);
+                gap.addBackTo();
+                getDataStore().clearRulesAndMakeFactsExplicit();
+            } catch(JRDFStoreException e) {
+                e.printStackTrace();
+            } finally {
+                gap.clear();
+            }
+        }
+        else
+            materialise("upper program", dProgram.getUpper().toString());
+    }
+
+    public int materialiseRestrictedly(DatalogProgram dProgram, GapByStore4ID gap) {
+        if(isDisposed()) throw new DisposedException();
+        if(gap != null) {
+            materialise("lower program", dProgram.getLower().toString());
+            String program = dProgram.getUpper().toString();
+            try {
+                gap.compile(program);
+                gap.addBackTo();
+                getDataStore().clearRulesAndMakeFactsExplicit();
+            } catch(JRDFStoreException e) {
+                e.printStackTrace();
+            } finally {
+                gap.clear();
+            }
+        }
+        else
+            materialise("upper program", dProgram.getUpper().toString());
+
+        return 1;
+    }
+
+    @Override
+    public AnswerTuples evaluate(String queryText) {
+        if(isDisposed()) throw new DisposedException();
+        return evaluate(queryText, ConjunctiveQueryHelper.getAnswerVariables(queryText)[0]);
+    }
+
+    @Override
+    public AnswerTuples evaluate(String queryText, String[] answerVars) {
+        if(isDisposed()) throw new DisposedException();
+        TupleIterator tupleIterator;
+        try {
+            tupleIterator = store.compileQuery(queryText.replace("_:", "?"), prefixes, parameters);
+        } catch(JRDFStoreException e) {
+            e.printStackTrace();
+            return null;
+        }
+        return new RDFoxAnswerTuples(answerVars, tupleIterator);
+    }
+
+    @Override
+    public DataStore getDataStore() {
+        if(isDisposed()) throw new DisposedException();
+        return store;
+    }
+
+    @Override
+    public void dispose() {
+        super.dispose();
+        store.dispose();
+    }
+
+    public void outputInstance4BinaryPredicate(String iri, String filename) {
+        Utility.redirectCurrentOut(filename);
+        outputInstance4BinaryPredicate(iri);
+        Utility.closeCurrentOut();
+    }
+
+    public void outputInstance4BinaryPredicate(String iri) {
+        outputAnswers("select ?x ?y where { ?x <" + iri + "> ?y . }");
+    }
+
+    public void outputInstanceNumbers(String filename) {
+        TupleIterator predicateTuples = null;
+        TupleIterator instanceTuples;
+        Set<String> number = new HashSet<String>();
+        String predicate;
+        try {
+            predicateTuples =
+                    getDataStore().compileQuery("SELECT DISTINCT ?Y WHERE { ?X <" + Namespace.RDF_TYPE + "> ?Y }", prefixes, parameters);
+            for(long multi = predicateTuples.open(); multi != 0; multi = predicateTuples.getNext()) {
+                predicate = RDFoxTripleManager.getQuotedTerm(predicateTuples.getResource(0));
+                instanceTuples = null;
+                try {
+                    instanceTuples =
+                            getDataStore().compileQuery("SELECT ?X WHERE { ?X <" + Namespace.RDF_TYPE + "> " + predicate + " }", prefixes, parameters);
+                    long totalCount = 0;
+                    for(long multi1 = instanceTuples.open(); multi1 != 0; multi1 = instanceTuples.getNext()) {
+                        totalCount += instanceTuples.getMultiplicity();
+                    }
+                    number.add(predicate + " * " + totalCount);
+                } finally {
+                    if(instanceTuples != null) instanceTuples.dispose();
+                }
+            }
+        } catch(JRDFStoreException e) {
+            e.printStackTrace();
+        } finally {
+            if(predicateTuples != null) predicateTuples.dispose();
+            predicateTuples = null;
+        }
+
+        try {
+            predicateTuples =
+                    getDataStore().compileQuery("SELECT DISTINCT ?Y WHERE { ?X ?Y ?Z }", prefixes, parameters);
+            for(long multi = predicateTuples.open(); multi != 0; multi = predicateTuples.getNext()) {
+                predicate = RDFoxTripleManager.getQuotedTerm(predicateTuples.getResource(0));
+                instanceTuples = null;
+                try {
+                    instanceTuples =
+                            getDataStore().compileQuery("SELECT ?X ?Z WHERE { ?X " + predicate + " ?Z }", prefixes, parameters);
+                    long totalCount = 0;
+                    for(long multi1 = instanceTuples.open(); multi1 != 0; multi1 = instanceTuples.getNext())
+                        totalCount += instanceTuples.getMultiplicity();
+                    number.add(predicate + " * " + totalCount);
+                } finally {
+                    if(instanceTuples != null) instanceTuples.dispose();
+                }
+            }
+
+        } catch(JRDFStoreException e) {
+            e.printStackTrace();
+        } finally {
+            if(predicateTuples != null) predicateTuples.dispose();
+            predicateTuples = null;
+        }
+
+        Utility.redirectCurrentOut(filename);
+        String[] ordered = number.toArray(new String[0]);
+        Arrays.sort(ordered, new DLPredicateComparator());
+        for(String line : ordered) System.out.println(line);
+        Utility.closeCurrentOut();
+
+    }
+
+    public TupleIterator internal_evaluateAgainstIDBs(String queryText) throws JRDFStoreException {
+        TupleIterator iter =
+                store.compileQuery(queryText, prefixes, parameters, TripleStatus.TUPLE_STATUS_IDB.union(TripleStatus.TUPLE_STATUS_EDB), TripleStatus.TUPLE_STATUS_IDB);
+//              iter.open();
+        return iter;
+    }
+
+    public TupleIterator internal_evaluate(String queryText) throws JRDFStoreException {
+        TupleIterator iter = store.compileQuery(queryText, prefixes, parameters);
+//              iter.open();
+        return iter;
+    }
+
+    public void setExpandEquality(boolean flag) {
+        parameters.m_expandEquality = flag;
+    }
+
+    public TupleIterator internal_evaluateNotExpanded(String queryText) throws JRDFStoreException {
+        parameters.m_expandEquality = false;
+        TupleIterator iter = store.compileQuery(queryText, prefixes, parameters);
 //              iter.open();
-                return iter; 
-        }
-
-        public TupleIterator internal_evaluate(String queryText) throws JRDFStoreException {
-                TupleIterator iter = store.compileQuery(queryText, prefixes, parameters);
-//              iter.open(); 
-                return iter; 
-        }
-        
-        public void setExpandEquality(boolean flag) {
-                parameters.m_expandEquality = flag; 
-        }
-        
-        public TupleIterator internal_evaluateNotExpanded(String queryText) throws JRDFStoreException {
-                parameters.m_expandEquality = false; 
-                TupleIterator iter = store.compileQuery(queryText, prefixes, parameters); 
-//              iter.open(); 
-                parameters.m_expandEquality = true; 
-                return iter;
-        }
-
-        
-        public TupleIterator internal_evaluate(String queryText, boolean incrementally) throws JRDFStoreException {
-                return incrementally ? internal_evaluateAgainstIDBs(queryText) : internal_evaluate(queryText);
-        }
-
-        Set<DLClause> materialisedRules = new HashSet<DLClause>(); 
-        
-        public String getUnusedRules(Collection<DLClause> clauses, boolean toUpdate) {
-                DLClause clause;
-                for (Iterator<DLClause> iter = clauses.iterator(); iter.hasNext(); ) {
-                        if (materialisedRules.contains(clause = iter.next()))
-                                iter.remove();
-                        else if (toUpdate) materialisedRules.add(clause); 
-                }
-                
-                if (clauses.isEmpty()) return null;
-                
-                return Program.toString(clauses);
-        }
-
-        public void outputMaterialisedRules() {
-                System.out.println(DLClauseHelper.toString(materialisedRules));         
-        }
-
-        public void outputAnswers(String query) {
-                TupleIterator iter = null;
-                try {
-                        iter = internal_evaluate(query);
-                        System.out.println(query); 
-                        int arity = iter.getArity(); 
-                        for (long multi = iter.open(); multi != 0; multi = iter.getNext())  {
-                                for (int i = 0; i < arity; ++i)
-                                        System.out.print(RDFoxTripleManager.getQuotedTerm(iter.getResource(i)) + "\t");
-                                System.out.println(); 
-                        }
-                } catch (JRDFStoreException e) {
-                        e.printStackTrace();
-                } finally {
-                        if (iter != null) iter.dispose(); 
-                }
-        }
-
-        public void outputInstance4UnaryPredicate(String iri) {
-                outputAnswers("select ?x where { ?x "
-                                        + "<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <"
-                                        + iri 
-                                        + "> .}"); 
-        }
-
-        public void outputSubjects(String p, String o) {
-                outputAnswers("select x where { ?x <" + p + "> <" + o + "> . }");
-        }
-
-        public void outputObjects(String s, String p) {
-                outputAnswers("select ?x where { <" + s + "> <" + p + "> ?x . }");
-        }
-
-        public void outputIDBFacts() {
-                TupleIterator iter = null; 
-                try {
-                        iter = internal_evaluateAgainstIDBs("select distict ?x ?y ?z where { ?x ?y ?z }");
-                        for (long multi = iter.open(); multi != 0; multi = iter.getNext()) {
-                                for (int i = 0; i < 3; ++i)
-                                        System.out.print(RDFoxTripleManager.getQuotedTerm(iter.getResource(i)) + "\t"); 
-                                System.out.println(); 
-                        }
-                } catch (JRDFStoreException e) {
-                        // TODO Auto-generated catch block
-                        e.printStackTrace();
-                } finally {
-                        if (iter != null) iter.dispose();
-                }
-                
-        }
-        
-        public void outputType4Individual(String iri) {
-                outputAnswers("select ?z where { <" + iri + "> " + Namespace.RDF_TYPE_QUOTED + " ?z }");
-        }
-        
-        public int getSameAsNumber() {
-                TupleIterator iter = null; 
-                int counter = 0; 
-                try {
-                        iter = internal_evaluate("select ?x ?y where {?x " + Namespace.EQUALITY_QUOTED + " ?y . }");
-                        for (long multi = iter.open(); multi != 0; multi = iter.getNext()) 
-                                if (iter.getResourceID(0) != iter.getResourceID(1))
-                                        ++counter;
-                } catch (JRDFStoreException e) {
-                        e.printStackTrace(); 
-                } finally {
-                        if (iter != null) iter.dispose();
-                }
-                return counter; 
-        }
-        
-        private UFS<String> equalityGroups = null; 
-        
-        public UFS<String> getEqualityGroups(boolean reuse) {
-                if (reuse && equalityGroups != null) return equalityGroups; 
-
-                equalityGroups = new UFS<String>(); 
-                
-                TupleIterator answers = null; 
-                try {
-                        Timer t = new Timer(); 
-                        answers = internal_evaluate("select ?x ?z  where {?x " + Namespace.EQUALITY_QUOTED + "?z . }");
-                        for (long multi = answers.open(); multi != 0; multi = answers.getNext()) {
-                                if (answers.getResourceID(0) != answers.getResourceID(1))
-                                        equalityGroups.merge(answers.getResource(0).m_lexicalForm, answers.getResource(1).m_lexicalForm); 
-                        }
-                        Utility.logInfo("@Time to group individuals by equality: " + t.duration());
-                } catch (JRDFStoreException e) {
-                        e.printStackTrace();
-                } finally {
-                        if (answers != null) answers.dispose(); 
-                }
-
-                return equalityGroups; 
-        }
-
-        public void clearRulesAndIDBFacts(Collection<int[]> collection) {
-//              performDeletion(collection); 
-                collection.clear();
-                try {
-                        store.clearRulesAndMakeFactsExplicit();
-                } catch (JRDFStoreException e) {
-                        e.printStackTrace();
-                }
-        }
-
-        @SuppressWarnings("unused")
-        private void performDeletion(Collection<int[]> collection) {
-                Utility.logInfo("Remove all rules, idb facts and added staff...");
-                Timer timer = new Timer();  
-                TupleIterator iter = null;
-                try {
-                        UpdateType ut = UpdateType.ScheduleForDeletion; 
-                        for (int[] t: collection) 
-                                store.addTriplesByResourceIDs(t, ut);
-                        
-                        try {
-                                iter = internal_evaluateAgainstIDBs("select ?x ?y ?z where { ?x ?y ?z . }");
-                                for (long multi = iter.open(); multi != 0; multi = iter.getNext()) {
-                                        int[] triple = new int[3];
-                                        for (int i = 0; i < 3; ++i)
-                                                triple[i] = iter.getResourceID(i); 
-                                        store.addTriplesByResourceIDs(triple, ut);
-                                }
-                        } finally {
-                                if (iter != null) iter.dispose();
-                                iter = null; 
-                        }
-                        store.applyReasoning(true);
-                } catch (JRDFStoreException e) {
-                        e.printStackTrace();
-                } 
-                Utility.logInfo("Time for deletion: " + timer.duration()); 
-        }
+        parameters.m_expandEquality = true;
+        return iter;
+    }
+
+    public TupleIterator internal_evaluate(String queryText, boolean incrementally) throws JRDFStoreException {
+        return incrementally ? internal_evaluateAgainstIDBs(queryText) : internal_evaluate(queryText);
+    }
+
+    public String getUnusedRules(Collection<DLClause> clauses, boolean toUpdate) {
+        DLClause clause;
+        for(Iterator<DLClause> iter = clauses.iterator(); iter.hasNext(); ) {
+            if(materialisedRules.contains(clause = iter.next()))
+                iter.remove();
+            else if(toUpdate) materialisedRules.add(clause);
+        }
+
+        if(clauses.isEmpty()) return null;
+
+        return Program.toString(clauses);
+    }
+
+    public void outputMaterialisedRules() {
+        System.out.println(DLClauseHelper.toString(materialisedRules));
+    }
+
+    public void outputAnswers(String query) {
+        TupleIterator iter = null;
+        try {
+            iter = internal_evaluate(query);
+            System.out.println(query);
+            int arity = iter.getArity();
+            for(long multi = iter.open(); multi != 0; multi = iter.getNext()) {
+                for(int i = 0; i < arity; ++i)
+                    System.out.print(RDFoxTripleManager.getQuotedTerm(iter.getResource(i)) + "\t");
+                System.out.println();
+            }
+        } catch(JRDFStoreException e) {
+            e.printStackTrace();
+        } finally {
+            if(iter != null) iter.dispose();
+        }
+    }
+
+    public void outputInstance4UnaryPredicate(String iri) {
+        outputAnswers("select ?x where { ?x "
+                              + "<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <"
+                              + iri
+                              + "> .}");
+    }
+
+    public void outputSubjects(String p, String o) {
+        outputAnswers("select x where { ?x <" + p + "> <" + o + "> . }");
+    }
+
+    public void outputObjects(String s, String p) {
+        outputAnswers("select ?x where { <" + s + "> <" + p + "> ?x . }");
+    }
+
+    public void outputIDBFacts() {
+        TupleIterator iter = null;
+        try {
+            iter = internal_evaluateAgainstIDBs("select distict ?x ?y ?z where { ?x ?y ?z }");
+            for(long multi = iter.open(); multi != 0; multi = iter.getNext()) {
+                for(int i = 0; i < 3; ++i)
+                    System.out.print(RDFoxTripleManager.getQuotedTerm(iter.getResource(i)) + "\t");
+                System.out.println();
+            }
+        } catch(JRDFStoreException e) {
+            // TODO Auto-generated catch block
+            e.printStackTrace();
+        } finally {
+            if(iter != null) iter.dispose();
+        }
+
+    }
+
+    public void outputType4Individual(String iri) {
+        outputAnswers("select ?z where { <" + iri + "> " + Namespace.RDF_TYPE_QUOTED + " ?z }");
+    }
+
+    public int getSameAsNumber() {
+        TupleIterator iter = null;
+        int counter = 0;
+        try {
+            iter = internal_evaluate("select ?x ?y where {?x " + Namespace.EQUALITY_QUOTED + " ?y . }");
+            for(long multi = iter.open(); multi != 0; multi = iter.getNext())
+                if(iter.getResourceID(0) != iter.getResourceID(1))
+                    ++counter;
+        } catch(JRDFStoreException e) {
+            e.printStackTrace();
+        } finally {
+            if(iter != null) iter.dispose();
+        }
+        return counter;
+    }
+
+    public UFS<String> getEqualityGroups(boolean reuse) {
+        if(reuse && equalityGroups != null) return equalityGroups;
+
+        equalityGroups = new UFS<String>();
+
+        TupleIterator answers = null;
+        try {
+            Timer t = new Timer();
+            answers = internal_evaluate("select ?x ?z  where {?x " + Namespace.EQUALITY_QUOTED + "?z . }");
+            for(long multi = answers.open(); multi != 0; multi = answers.getNext()) {
+                if(answers.getResourceID(0) != answers.getResourceID(1))
+                    equalityGroups.merge(answers.getResource(0).m_lexicalForm, answers.getResource(1).m_lexicalForm);
+            }
+            Utility.logInfo("@Time to group individuals by equality: " + t.duration());
+        } catch(JRDFStoreException e) {
+            e.printStackTrace();
+        } finally {
+            if(answers != null) answers.dispose();
+        }
+
+        return equalityGroups;
+    }
+
+    public void clearRulesAndIDBFacts(Collection<int[]> collection) {
+//              performDeletion(collection);
+        collection.clear();
+        try {
+            store.clearRulesAndMakeFactsExplicit();
+        } catch(JRDFStoreException e) {
+            e.printStackTrace();
+        }
+    }
+
+    protected void outputClassAssertions(String filename) {
+        TupleIterator allTuples = null;
+        boolean redirect = false;
+        try {
+            allTuples =
+                    getDataStore().compileQuery("SELECT ?X ?Z WHERE { ?X <" + Namespace.RDF_TYPE + "> ?Z }", prefixes, parameters);
+            redirect = Utility.redirectCurrentOut(filename);
+            for(long multi = allTuples.open(); multi != 0; multi = allTuples.getNext())
+                System.out.println(RDFoxTripleManager.getQuotedTerm(allTuples.getResource(0)) + " " + RDFoxTripleManager
+                        .getQuotedTerm(allTuples.getResource(1)));
+        } catch(JRDFStoreException e) {
+            e.printStackTrace();
+        } finally {
+            if(redirect) Utility.closeCurrentOut();
+            if(allTuples != null) allTuples.dispose();
+        }
+    }
+
+    @SuppressWarnings("unused")
+    private void performDeletion(Collection<int[]> collection) {
+        Utility.logInfo("Remove all rules, idb facts and added staff...");
+        Timer timer = new Timer();
+        TupleIterator iter = null;
+        try {
+            UpdateType ut = UpdateType.ScheduleForDeletion;
+            for(int[] t : collection)
+                store.addTriplesByResourceIDs(t, ut);
+
+            try {
+                iter = internal_evaluateAgainstIDBs("select ?x ?y ?z where { ?x ?y ?z . }");
+                for(long multi = iter.open(); multi != 0; multi = iter.getNext()) {
+                    int[] triple = new int[3];
+                    for(int i = 0; i < 3; ++i)
+                        triple[i] = iter.getResourceID(i);
+                    store.addTriplesByResourceIDs(triple, ut);
+                }
+            } finally {
+                if(iter != null) iter.dispose();
+                iter = null;
+            }
+            store.applyReasoning(true);
+        } catch(JRDFStoreException e) {
+            e.printStackTrace();
+        }
+        Utility.logInfo("Time for deletion: " + timer.duration());
+    }
 
 
 }
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/light/KarmaQueryEngine.java b/src/uk/ac/ox/cs/pagoda/reasoner/light/KarmaQueryEngine.java
index f068164..98f0c35 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/light/KarmaQueryEngine.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/light/KarmaQueryEngine.java
@@ -12,6 +12,7 @@ import uk.ac.ox.cs.pagoda.query.AnswerTuples;
 import uk.ac.ox.cs.pagoda.query.AnswerTuplesImp;
 import uk.ac.ox.cs.pagoda.util.ConjunctiveQueryHelper;
 import uk.ac.ox.cs.pagoda.util.Utility;
+import uk.ac.ox.cs.pagoda.util.disposable.DisposedException;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -19,82 +20,90 @@ import java.nio.file.Paths;
 import java.util.Set;
 
 public class KarmaQueryEngine extends RDFoxQueryEngine {
-        
-        private MyKarma reasoner = null;
-        
-        String karmaDataFile = null, karmaRuleFile = null; 
-        
-        public KarmaQueryEngine(String name) {
-                super(name);
-                
+
+    String karmaDataFile = null, karmaRuleFile = null;
+    private MyKarma reasoner = null;
+
+    public KarmaQueryEngine(String name) {
+        super(name);
+
 //              int Base = 1 << 6; 
 //              int index = (new Random().nextInt() % Base + Base) % Base;
 //              karmaDataFile = "karma_data" + index + ".ttl"; 
 //              karmaRuleFile = "karma_rule" + index + ".dlog";
-                karmaDataFile = Paths.get(Utility.getGlobalTempDirAbsolutePath(), "karma_data.ttl").toString();
-                karmaRuleFile =  Paths.get(Utility.getGlobalTempDirAbsolutePath(), "karma_rule.dlog").toString();
-                
-                reasoner = new MyKarma(); 
-        }
-        
-        public MyKarma getReasoner() {
-                return reasoner; 
-        }
-        
-        public void processOntology(OWLOntology elhoOntology) {
-                try {
-                        OntologyProcesser.transformOntology(elhoOntology, new File(karmaDataFile), new File(karmaRuleFile));
-                } catch (IllegalInputOntologyException e) {
-                        e.printStackTrace();
-                }
-        }
-
-        @Override
-        public void dispose() {
-                reasoner.dispose(); 
-        }
-        
-        @Override
-        public AnswerTuples evaluate(String queryText) {
-                return evaluate(queryText, ConjunctiveQueryHelper.getAnswerVariables(queryText)[0], null); 
-        }
-        
-        @Override
-        public AnswerTuples evaluate(String queryText, String[] answerVars) {
-                return evaluate(queryText, answerVars, null); 
-        }
-        
-        public AnswerTuples evaluate(String queryText, AnswerTuples soundAnswerTuples) {
-                return evaluate(queryText, ConjunctiveQueryHelper.getAnswerVariables(queryText)[0], soundAnswerTuples); 
-        }
-        
-        public AnswerTuples evaluate(String queryText, String[] answerVars, AnswerTuples soundAnswerTuples) {
-                KarmaQuery karmaQuery = new KarmaQuery(queryText.replace("_:", "?"));
-                reasoner.setConcurrence(false);
-                ConjunctiveQuery cq = karmaQuery.getConjunctiveQuery(); 
-                if (cq == null) return null; 
-                Set<AnswerTuple> answers = reasoner.answerCQ(cq, soundAnswerTuples, !queryText.contains("_:"));
-                return new AnswerTuplesImp(answerVars, answers); 
-        }
-
-        @Override
-        public DataStore getDataStore() {
-                return reasoner.getStore();
-        }
-        
-        public void initialiseKarma() {
-                try {
-                        reasoner.initializeData(new File(karmaDataFile));
-                        reasoner.materialise(new File(karmaRuleFile));
-                        
-                        File tmp; 
-                        if (karmaDataFile != null && ((tmp = new File(karmaDataFile)).exists())) tmp.delete(); 
-                        if (karmaRuleFile != null && ((tmp = new File(karmaRuleFile)).exists())) tmp.delete(); 
-                } catch (FileNotFoundException e) {
-                        e.printStackTrace();
-                } catch (JRDFStoreException e) {
-                        e.printStackTrace();
-                }
-        }
+        karmaDataFile = Paths.get(Utility.getGlobalTempDirAbsolutePath(), "karma_data.ttl").toString();
+        karmaRuleFile = Paths.get(Utility.getGlobalTempDirAbsolutePath(), "karma_rule.dlog").toString();
+
+        reasoner = new MyKarma();
+    }
+
+    public MyKarma getReasoner() {
+        if(isDisposed()) throw new DisposedException();
+        return reasoner;
+    }
+
+    public void processOntology(OWLOntology elhoOntology) {
+        if(isDisposed()) throw new DisposedException();
+        try {
+            OntologyProcesser.transformOntology(elhoOntology, new File(karmaDataFile), new File(karmaRuleFile));
+        } catch(IllegalInputOntologyException e) {
+            e.printStackTrace();
+        }
+    }
+
+    @Override
+    public void dispose() {
+        super.dispose();
+        reasoner.dispose();
+    }
+
+    @Override
+    public AnswerTuples evaluate(String queryText) {
+        if(isDisposed()) throw new DisposedException();
+        return evaluate(queryText, ConjunctiveQueryHelper.getAnswerVariables(queryText)[0], null);
+    }
+
+    @Override
+    public AnswerTuples evaluate(String queryText, String[] answerVars) {
+        if(isDisposed()) throw new DisposedException();
+        return evaluate(queryText, answerVars, null);
+    }
+
+    public AnswerTuples evaluate(String queryText, AnswerTuples soundAnswerTuples) {
+        if(isDisposed()) throw new DisposedException();
+        return evaluate(queryText, ConjunctiveQueryHelper.getAnswerVariables(queryText)[0], soundAnswerTuples);
+    }
+
+    public AnswerTuples evaluate(String queryText, String[] answerVars, AnswerTuples soundAnswerTuples) {
+        if(isDisposed()) throw new DisposedException();
+        KarmaQuery karmaQuery = new KarmaQuery(queryText.replace("_:", "?"));
+        reasoner.setConcurrence(false);
+        ConjunctiveQuery cq = karmaQuery.getConjunctiveQuery();
+        if(cq == null) return null;
+        Set<AnswerTuple> answers = reasoner.answerCQ(cq, soundAnswerTuples, !queryText.contains("_:"));
+        return new AnswerTuplesImp(answerVars, answers);
+    }
+
+    @Override
+    public DataStore getDataStore() {
+        if(isDisposed()) throw new DisposedException();
+        return reasoner.getStore();
+    }
+
+    public void initialiseKarma() {
+        if(isDisposed()) throw new DisposedException();
+        try {
+            reasoner.initializeData(new File(karmaDataFile));
+            reasoner.materialise(new File(karmaRuleFile));
+
+            File tmp;
+            if(karmaDataFile != null && ((tmp = new File(karmaDataFile)).exists())) tmp.delete();
+            if(karmaRuleFile != null && ((tmp = new File(karmaRuleFile)).exists())) tmp.delete();
+        } catch(FileNotFoundException e) {
+            e.printStackTrace();
+        } catch(JRDFStoreException e) {
+            e.printStackTrace();
+        }
+    }
 
 }
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxAnswerTuples.java b/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxAnswerTuples.java
index dd71809..1e8181f 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxAnswerTuples.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxAnswerTuples.java
@@ -3,15 +3,14 @@ package uk.ac.ox.cs.pagoda.reasoner.light;
 import org.semanticweb.HermiT.model.Constant;
 import org.semanticweb.HermiT.model.Individual;
 import org.semanticweb.HermiT.model.Term;
-
-import uk.ac.ox.cs.pagoda.query.AnswerTuple;
-import uk.ac.ox.cs.pagoda.query.AnswerTuples;
-import uk.ac.ox.cs.pagoda.util.Utility;
 import uk.ac.ox.cs.JRDFox.JRDFStoreException;
 import uk.ac.ox.cs.JRDFox.model.GroundTerm;
 import uk.ac.ox.cs.JRDFox.store.TupleIterator;
+import uk.ac.ox.cs.pagoda.query.AnswerTuple;
+import uk.ac.ox.cs.pagoda.query.AnswerTuples;
+import uk.ac.ox.cs.pagoda.util.Utility;
 
-public class RDFoxAnswerTuples implements AnswerTuples {
+public class RDFoxAnswerTuples extends AnswerTuples {
 
         long multi; 
         TupleIterator m_iter; 
@@ -22,7 +21,18 @@ public class RDFoxAnswerTuples implements AnswerTuples {
                 m_iter = iter; 
                 reset(); 
         }
-        
+
+        public static Term getHermitTerm(GroundTerm t) {
+                if(t instanceof uk.ac.ox.cs.JRDFox.model.Individual) {
+                        uk.ac.ox.cs.JRDFox.model.Individual individual = (uk.ac.ox.cs.JRDFox.model.Individual) t;
+                        return Individual.create(individual.getIRI());
+                }
+                else {
+                        uk.ac.ox.cs.JRDFox.model.Literal literal = ((uk.ac.ox.cs.JRDFox.model.Literal) t);
+                        return Constant.create(literal.getLexicalForm(), literal.getDatatype().getIRI());
+                }
+        }
+
         @Override
         public boolean isValid() {
                 return multi != 0;
@@ -34,7 +44,7 @@ public class RDFoxAnswerTuples implements AnswerTuples {
                         return m_iter.getArity();
                 } catch (JRDFStoreException e) {
                         e.printStackTrace();
-                        return -1; 
+                        return -1;
                 }
         }
 
@@ -44,15 +54,12 @@ public class RDFoxAnswerTuples implements AnswerTuples {
                         multi = m_iter.getNext();
                 } catch (JRDFStoreException e) {
                         e.printStackTrace();
-                }  
+                }
         }
 
         @Override
         public void dispose() {
-                m_iter.dispose();
-        }
-        
-        protected void finalize() {
+                super.dispose();
                 m_iter.dispose();
         }
         
@@ -85,16 +92,9 @@ public class RDFoxAnswerTuples implements AnswerTuples {
         public String[] getAnswerVariables() {
                 return m_answerVars;
         }
-        
-        public static Term getHermitTerm(GroundTerm t) {
-                if (t instanceof uk.ac.ox.cs.JRDFox.model.Individual) {
-                        uk.ac.ox.cs.JRDFox.model.Individual individual = (uk.ac.ox.cs.JRDFox.model.Individual) t; 
-                        return Individual.create(individual.getIRI());
-                }
-                else {
-                        uk.ac.ox.cs.JRDFox.model.Literal literal = ((uk.ac.ox.cs.JRDFox.model.Literal) t); 
-                        return Constant.create(literal.getLexicalForm(), literal.getDatatype().getIRI());
-                }
+
+        protected void finalize() {
+                m_iter.dispose();
         }
         
 }
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxQueryEngine.java b/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxQueryEngine.java
index 61500f5..f835ba9 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxQueryEngine.java
+++ b/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxQueryEngine.java
@@ -13,119 +13,126 @@ import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner;
 import uk.ac.ox.cs.pagoda.tracking.AnswerTuplesWriter;
 import uk.ac.ox.cs.pagoda.util.Timer;
 import uk.ac.ox.cs.pagoda.util.Utility;
+import uk.ac.ox.cs.pagoda.util.disposable.DisposedException;
 
 import java.io.File;
 import java.util.Collection;
 
-public abstract class RDFoxQueryEngine implements QueryEngine {
-        
-        public static final int matNoOfThreads = Runtime.getRuntime().availableProcessors() * 2;
-        protected String name;
-        protected Prefixes prefixes = MyPrefixes.PAGOdAPrefixes.getRDFoxPrefixes();
+public abstract class RDFoxQueryEngine extends QueryEngine {
 
-        public RDFoxQueryEngine(String name) {
-                this.name = name;
-        }
+    public static final int matNoOfThreads = Runtime.getRuntime().availableProcessors() * 2;
+    protected String name;
+    protected Prefixes prefixes = MyPrefixes.PAGOdAPrefixes.getRDFoxPrefixes();
 
-        public static DataStore createDataStore() {
-                DataStore instance = null;
-                try {
+    public RDFoxQueryEngine(String name) {
+        this.name = name;
+    }
+
+    public static DataStore createDataStore() {
+        DataStore instance = null;
+        try {
 //                      instance = new DataStore("par-head-n");
-                        instance = new DataStore(StoreType.NarrowParallelHead);
-                        instance.setNumberOfThreads(matNoOfThreads);
-                        instance.initialize();
-                } catch(JRDFStoreException e) {
-                        e.printStackTrace();
-                }
-                return instance;
-        }
-        
-        public String getName() {
-                return name;
-        }
-        
-        public abstract DataStore getDataStore();
-
-        public abstract void dispose();
-
-        public void importRDFData(String fileName, String importedFile) {
-                if(importedFile == null || importedFile.isEmpty()) return;
-                Timer t = new Timer();
-                DataStore store = getDataStore();
-                try {
-                        long oldTripleCount = store.getTriplesCount(), tripleCount;
-                        for (String file: importedFile.split(QueryReasoner.ImportDataFileSeparator)) {
-                                store.importTurtleFile(new File(file), prefixes);
-                        }
-                        tripleCount = store.getTriplesCount();
-                        Utility.logDebug(name + " store after importing " + fileName + ": " + tripleCount + " (" + (tripleCount - oldTripleCount) + " new)");
-                        store.clearRulesAndMakeFactsExplicit();
-                } catch (JRDFStoreException e) {
-                        e.printStackTrace();
-                }
-                Utility.logDebug(name + " store finished importing " + fileName + " in " + t.duration() + " seconds.");
-        }
-
-        public void importDataFromABoxOf(OWLOntology ontology) {
-                DataStore store = getDataStore();
-                try {
-                        long prevTriplesCount = store.getTriplesCount();
-                        store.importOntology(ontology.getOWLOntologyManager().createOntology(ontology.getABoxAxioms(true)));
-                        long loadedTriples = store.getTriplesCount() - prevTriplesCount;
-                        Utility.logInfo(name + ": loaded " + loadedTriples + " triples from " + ontology.getABoxAxioms(true)
-                                                                                                                                                                                        .size() + " ABox axioms");
-                } catch(JRDFStoreException | OWLOntologyCreationException e) {
-                        e.printStackTrace();
-                        System.exit(1);
-                }
-
-        }
-
-        public void materialise(String programName, String programText) {
-                if(programText == null) return;
-                Timer t = new Timer();
-                DataStore store = getDataStore();
-                try {
-                        long oldTripleCount = store.getTriplesCount(), tripleCount;
+            instance = new DataStore(StoreType.NarrowParallelHead);
+            instance.setNumberOfThreads(matNoOfThreads);
+            instance.initialize();
+        } catch(JRDFStoreException e) {
+            e.printStackTrace();
+        }
+        return instance;
+    }
+
+    public String getName() {
+        if(isDisposed()) throw new DisposedException();
+        return name;
+    }
+
+    public abstract DataStore getDataStore();
+
+    public void importRDFData(String fileName, String importedFile) {
+        if(isDisposed()) throw new DisposedException();
+        if(importedFile == null || importedFile.isEmpty()) return;
+        Timer t = new Timer();
+        DataStore store = getDataStore();
+        try {
+            long oldTripleCount = store.getTriplesCount(), tripleCount;
+            for(String file : importedFile.split(QueryReasoner.ImportDataFileSeparator)) {
+                store.importTurtleFile(new File(file), prefixes);
+            }
+            tripleCount = store.getTriplesCount();
+            Utility.logDebug(name + " store after importing " + fileName + ": " + tripleCount + " (" + (tripleCount - oldTripleCount) + " new)");
+            store.clearRulesAndMakeFactsExplicit();
+        } catch(JRDFStoreException e) {
+            e.printStackTrace();
+        }
+        Utility.logDebug(name + " store finished importing " + fileName + " in " + t.duration() + " seconds.");
+    }
+
+    public void importDataFromABoxOf(OWLOntology ontology) {
+        if(isDisposed()) throw new DisposedException();
+        DataStore store = getDataStore();
+        try {
+            long prevTriplesCount = store.getTriplesCount();
+            store.importOntology(ontology.getOWLOntologyManager().createOntology(ontology.getABoxAxioms(true)));
+            long loadedTriples = store.getTriplesCount() - prevTriplesCount;
+            Utility.logInfo(name + ": loaded " + loadedTriples + " triples from " + ontology.getABoxAxioms(true)
+                                                                                            .size() + " ABox axioms");
+        } catch(JRDFStoreException | OWLOntologyCreationException e) {
+            e.printStackTrace();
+            System.exit(1);
+        }
+
+    }
+
+    public void materialise(String programName, String programText) {
+        if(isDisposed()) throw new DisposedException();
+        if(programText == null) return;
+        Timer t = new Timer();
+        DataStore store = getDataStore();
+        try {
+            long oldTripleCount = store.getTriplesCount(), tripleCount;
 //                      store.addRules(new String[] {programText});
-                        store.importRules(programText);
-                        store.applyReasoning();
-                        tripleCount = store.getTriplesCount();
-                        Utility.logDebug(name + " store after materialising " + programName + ": " + tripleCount + " (" + (tripleCount - oldTripleCount) + " new)");
-                        store.clearRulesAndMakeFactsExplicit();
-                } catch (JRDFStoreException e) {
-                        e.printStackTrace();
-                }
-                Utility.logDebug(name + " store finished the materialisation of " + programName + " in " + t.duration() + " seconds.");
-        }
-
-        @Override
-        public void evaluate(Collection<String> queryTexts, String answerFile) {
-                if (queryTexts == null)
-                        return ;
-
-                int queryID = 0;
-                AnswerTuplesWriter answerWriter = new AnswerTuplesWriter(answerFile);
-                AnswerTuples answerTuples;
-                Timer t = new Timer();
-                try {
-                        for (String query: queryTexts) {
-                                t.reset();
-                                answerTuples = null;
-                                try {
-                                        answerTuples = evaluate(query);
-                                        Utility.logDebug("time to answer Query " + ++queryID + ": " + t.duration());
-                                        answerWriter.write(answerTuples.getAnswerVariables(), answerTuples);
-                                } finally {
-                                        if (answerTuples != null) answerTuples.dispose();
-                                }
-                        }
-                } finally {
-                        answerWriter.close();
-                }
-
-                Utility.logDebug("done computing query answers by RDFox.");
-
-        }
+            store.importRules(programText);
+            store.applyReasoning();
+            tripleCount = store.getTriplesCount();
+            Utility.logDebug(name + " store after materialising " + programName + ": " + tripleCount + " (" + (tripleCount - oldTripleCount) + " new)");
+            store.clearRulesAndMakeFactsExplicit();
+        } catch(JRDFStoreException e) {
+            e.printStackTrace();
+        }
+        Utility.logDebug(name + " store finished the materialisation of " + programName + " in " + t.duration() + " seconds.");
+    }
+
+    @Override
+    public void evaluate(Collection<String> queryTexts, String answerFile) {
+        if(isDisposed()) throw new DisposedException();
+        if(queryTexts == null)
+            return;
+
+        int queryID = 0;
+        AnswerTuplesWriter answerWriter = new AnswerTuplesWriter(answerFile);
+        AnswerTuples answerTuples;
+        Timer t = new Timer();
+        try {
+            for(String query : queryTexts) {
+                t.reset();
+                answerTuples = null;
+                try {
+                    answerTuples = evaluate(query);
+                    Utility.logDebug("time to answer Query " + ++queryID + ": " + t.duration());
+                    answerWriter.write(answerTuples.getAnswerVariables(), answerTuples);
+                } finally {
+                    if(answerTuples != null) answerTuples.dispose();
+                }
+            }
+        } finally {
+            answerWriter.close();
+        }
+
+        Utility.logDebug("done computing query answers by RDFox.");
+    }
 
+    @Override
+    public void dispose() {
+        super.dispose();
+    }
 }
diff --git a/src/uk/ac/ox/cs/pagoda/rules/DatalogProgram.java b/src/uk/ac/ox/cs/pagoda/rules/DatalogProgram.java
index 1f7148c..29e74c2 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/DatalogProgram.java
+++ b/src/uk/ac/ox/cs/pagoda/rules/DatalogProgram.java
@@ -1,64 +1,74 @@
 package uk.ac.ox.cs.pagoda.rules;
 
 import org.semanticweb.owlapi.model.OWLOntology;
+import uk.ac.ox.cs.pagoda.constraints.BottomStrategy;
+import uk.ac.ox.cs.pagoda.constraints.PredicateDependency;
+import uk.ac.ox.cs.pagoda.constraints.UpperUnaryBottom;
+import uk.ac.ox.cs.pagoda.util.disposable.Disposable;
+import uk.ac.ox.cs.pagoda.util.disposable.DisposedException;
 
-import uk.ac.ox.cs.pagoda.constraints.*;
+public class DatalogProgram extends Disposable {
 
-public class DatalogProgram {
+    UpperDatalogProgram upperProgram = new UpperDatalogProgram();
+    LowerDatalogProgram lowerProgram;
+    GeneralProgram program = new GeneralProgram();
 
-        UpperDatalogProgram upperProgram = new UpperDatalogProgram(); 
-        LowerDatalogProgram lowerProgram; 
-        GeneralProgram program = new GeneralProgram();
-        
-        BottomStrategy upperBottom; 
-        
-        public DatalogProgram(OWLOntology o) {
-                lowerProgram = new LowerDatalogProgram();
-                init(o, false); 
-        }
-        
-        public DatalogProgram(OWLOntology o, boolean toClassify) {
-                lowerProgram = new LowerDatalogProgram(toClassify);
-                init(o, toClassify); 
-        }
+    BottomStrategy upperBottom;
 
-        private void init(OWLOntology o, boolean forSemFacet) {
-                upperProgram.load(o, upperBottom = new UpperUnaryBottom());
-//              upperProgram.load(o, upperBottom = new UnaryBottom());
-                lowerProgram.clone(upperProgram);
-                program.clone(upperProgram);
-//              program.botStrategy = new UnaryBottom(); 
-                
-                upperProgram.transform();
-                lowerProgram.transform();
-                program.transform();
-                
-                program.buildDependencyGraph();
-                PredicateDependency graph = upperProgram.buildDependencyGraph(); 
-                lowerProgram.dependencyGraph = graph; 
-        }
+    public DatalogProgram(OWLOntology o) {
+        lowerProgram = new LowerDatalogProgram();
+        init(o, false);
+    }
+
+    public DatalogProgram(OWLOntology o, boolean toClassify) {
+        lowerProgram = new LowerDatalogProgram(toClassify);
+        init(o, toClassify);
+    }
+
+    public LowerDatalogProgram getLower() {
+        if(isDisposed()) throw new DisposedException();
+        return lowerProgram;
+    }
+
+    public UpperDatalogProgram getUpper() {
+        if(isDisposed()) throw new DisposedException();
+        return upperProgram;
+    }
+
+    public GeneralProgram getGeneral() {
+        if(isDisposed()) throw new DisposedException();
+        return program;
+    }
 
-        public LowerDatalogProgram getLower() {
-                return lowerProgram; 
-        }
-        
-        public UpperDatalogProgram getUpper() {
-                return upperProgram; 
-        }
-        
-        public GeneralProgram getGeneral() {
-                return program; 
-        }
-        
-        public String getAdditionalDataFile() {
-                return upperProgram.getAdditionalDataFile();
-        }
+    public String getAdditionalDataFile() {
+        if(isDisposed()) throw new DisposedException();
+        return upperProgram.getAdditionalDataFile();
+    }
+
+    public BottomStrategy getUpperBottomStrategy() {
+        if(isDisposed()) throw new DisposedException();
+        return upperBottom;
+    }
+
+    @Override
+    public void dispose() {
+        super.dispose();
+        if(upperProgram != null) upperProgram.deleteABoxTurtleFile();
+    }
+
+    private void init(OWLOntology o, boolean forSemFacet) {
+        upperProgram.load(o, upperBottom = new UpperUnaryBottom());
+//              upperProgram.load(o, upperBottom = new UnaryBottom());
+        lowerProgram.clone(upperProgram);
+        program.clone(upperProgram);
+//              program.botStrategy = new UnaryBottom();
 
-        public BottomStrategy getUpperBottomStrategy() {
-                return upperBottom;
-        }
+        upperProgram.transform();
+        lowerProgram.transform();
+        program.transform();
 
-        public void deleteABoxTurtleFile() {
-                if (upperProgram  != null) upperProgram.deleteABoxTurtleFile();  
-        }
+        program.buildDependencyGraph();
+        PredicateDependency graph = upperProgram.buildDependencyGraph();
+        lowerProgram.dependencyGraph = graph;
+    }
 }
diff --git a/src/uk/ac/ox/cs/pagoda/rules/Program.java b/src/uk/ac/ox/cs/pagoda/rules/Program.java
index 2e5302b..4e147bb 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/Program.java
+++ b/src/uk/ac/ox/cs/pagoda/rules/Program.java
@@ -1,5 +1,6 @@
 package uk.ac.ox.cs.pagoda.rules;
 
+import org.apache.commons.io.FilenameUtils;
 import org.semanticweb.HermiT.Configuration;
 import org.semanticweb.HermiT.model.*;
 import org.semanticweb.HermiT.structural.OWLClausification;
@@ -24,78 +25,180 @@ public abstract class Program implements KnowledgeBase {
         protected OWLOntology ontology; 
         protected DLOntology dlOntology;
         protected BottomStrategy botStrategy; 
-
-        private String additionalDataFile = null; 
-        
         protected Collection<DLClause> clauses = new HashSet<DLClause>();
 //      protected Set<DLClause> used = new HashSet<DLClause>();
-        protected PredicateDependency dependencyGraph; 
-        
-        /**
-         * clone all information of another program after load()
-         * 
-         * @param program
-         */
-        void clone(Program program) {
-                this.ontologyDirectory = program.ontologyDirectory; 
-                this.ontology = program.ontology; 
-                this.dlOntology = program.dlOntology;
-                this.botStrategy = program.botStrategy; 
-                this.additionalDataFile = program.additionalDataFile; 
-                this.transitiveAxioms = program.transitiveAxioms;  
-                this.transitiveClauses = program.transitiveClauses; 
-                this.subPropChainAxioms = program.subPropChainAxioms; 
-                this.subPropChainClauses = program.subPropChainClauses; 
+protected PredicateDependency dependencyGraph;
+        protected LinkedList<OWLTransitiveObjectPropertyAxiom> transitiveAxioms;
+        protected LinkedList<DLClause> transitiveClauses;
+        protected LinkedList<OWLSubPropertyChainOfAxiom> subPropChainAxioms;
+        protected LinkedList<DLClause> subPropChainClauses;
+        private String additionalDataFile = null;
+
+        public static String toString(Collection<DLClause> clauses) {
+                StringBuilder sb = new StringBuilder(DLClauseHelper.toString(clauses));
+                sb.insert(0, MyPrefixes.PAGOdAPrefixes.prefixesText());
+                return sb.toString();
         }
-        
+
         public void load(OWLOntology o, BottomStrategy botStrategy) {
-                this.botStrategy = botStrategy; 
-                RLPlusOntology owlOntology = new RLPlusOntology(); 
+                this.botStrategy = botStrategy;
+                RLPlusOntology owlOntology = new RLPlusOntology();
                 owlOntology.load(o, new NullaryBottom());
                 owlOntology.simplify();
 
-                ontology = owlOntology.getTBox(); 
-                String ontologyPath = OWLHelper.getOntologyPath(ontology); 
-                ontologyDirectory = ontologyPath.substring(0, ontologyPath.lastIndexOf(Utility.JAVA_FILE_SEPARATOR));
-                clausify(); 
-                
+                ontology = owlOntology.getTBox();
+//              String ontologyPath = OWLHelper.getOntologyPath(ontology);
+//              ontologyDirectory = ontologyPath.substring(0, ontologyPath.lastIndexOf(Utility.JAVA_FILE_SEPARATOR));
+                String ontologyPath = ontology.getOWLOntologyManager().getOntologyDocumentIRI(ontology).toURI().getPath();
+                ontologyDirectory = FilenameUtils.getFullPath(ontologyPath);
+                clausify();
+
                 String aboxOWLFile = owlOntology.getABoxPath();
                 OWLOntology abox = OWLHelper.loadOntology(aboxOWLFile);
-                OWLOntologyManager manager = abox.getOWLOntologyManager(); 
-                OWLAxiom axiom; 
+                OWLOntologyManager manager = abox.getOWLOntologyManager();
+                OWLAxiom axiom;
                 for (Atom atom: dlOntology.getPositiveFacts()) {
                         if ((axiom = OWLHelper.getABoxAssertion(manager.getOWLDataFactory(), atom)) != null)
-                                manager.addAxiom(abox, axiom); 
+                                manager.addAxiom(abox, axiom);
                 }
-                
+
                 try {
-                        FileOutputStream out = new FileOutputStream(aboxOWLFile); 
+                        FileOutputStream out = new FileOutputStream(aboxOWLFile);
                         manager.saveOntology(abox, out);
                         out.close();
-                } catch (OWLOntologyStorageException e) {
-                        // TODO Auto-generated catch block
-                        e.printStackTrace();
-                } catch (FileNotFoundException e) {
-                        // TODO Auto-generated catch block
-                        e.printStackTrace();
-                } catch (IOException e) {
-                        // TODO Auto-generated catch block
+                } catch(IOException | OWLOntologyStorageException e) {
                         e.printStackTrace();
+                        System.exit(1);
                 }
-                
+
                 if (!abox.isEmpty()) {
                         SimpleETL rewriter = new SimpleETL(owlOntology.getOntologyIRI(), aboxOWLFile);
                         try {
                                 rewriter.rewrite();
                         } catch (Exception e) {
                                 e.printStackTrace();
-                        } 
-                        additionalDataFile = rewriter.getExportedFile(); 
+                        }
+                        additionalDataFile = rewriter.getExportedFile();
                         new File(aboxOWLFile).delete();
                 }
-                
+
+        }
+        
+        public String getAdditionalDataFile() {
+                return additionalDataFile;
+        }
+
+        @Override
+        public void transform() {
+                for(DLClause dlClause : dlOntology.getDLClauses()) {
+                        DLClause simplifiedDLClause = DLClauseHelper.removeNominalConcept(dlClause);
+                        simplifiedDLClause = removeAuxiliaryBodyAtoms(simplifiedDLClause);
+                        simplifiedDLClause = DLClauseHelper.replaceWithDataValue(simplifiedDLClause);
+                        convert(simplifiedDLClause);
+                }
+
+                addingTransitiveAxioms();
+                addingSubPropertyChainAxioms();
+
+                Collection<DLClause> botRelated = new LinkedList<DLClause>();
+                Variable X = Variable.create("X");
+                botRelated.add(DLClause.create(new Atom[0], new Atom[]{Atom.create(Inequality.INSTANCE, X, X)}));
+                clauses.addAll(botStrategy.process(botRelated));
+
+                if(this instanceof GeneralProgram)
+                        Utility.logInfo("The number of rules: " + (clauses.size() - 1));
         }
         
+        @Override
+        public void save() {
+                try {
+                        BufferedWriter ruleWriter = new BufferedWriter(new OutputStreamWriter(
+                                        new FileOutputStream(getOutputPath())));
+                        ruleWriter.write(toString());
+                        ruleWriter.close();
+                } catch(IOException e) {
+                        e.printStackTrace();
+                }
+                Utility.logDebug("The rules are saved in " + getOutputPath() + ".");
+        }
+
+        @Override
+        public String toString() {
+                return toString(clauses);
+        }
+
+        public final void convert(DLClause clause) {
+                Collection<DLClause> tempClauses = convert2Clauses(clause);
+                clauses.addAll(tempClauses);
+        }
+
+        public abstract Collection<DLClause> convert2Clauses(DLClause clause);
+
+        public abstract String getOutputPath();
+
+        public OWLOntology getOntology() {
+                return ontology;
+        }
+
+        public Collection<DLClause> getClauses() {
+                return clauses;
+        }
+
+        public Collection<DLClause> getClauses(DLClause queryClause) {
+//              if (true) return new HashSet<DLClause>(clauses);
+                Set<DLPredicate> predicates = new HashSet<DLPredicate>();
+                predicates.addAll(dependencyGraph.collectPredicate(queryClause.getBodyAtoms()));
+
+                Set<DLPredicate> dependence = new HashSet<DLPredicate>();
+                for(DLPredicate predicate : predicates)
+                        dependence.addAll(dependencyGraph.getAncesters(predicate));
+
+                Collection<DLClause> relevantClauses = new LinkedList<DLClause>();
+                for(DLClause clause : clauses) {
+                        if(relevant(clause, dependence))
+                                relevantClauses.add(clause);
+
+                }
+                return relevantClauses;
+        }
+
+        public PredicateDependency buildDependencyGraph() {
+                if(dependencyGraph == null)
+                        return dependencyGraph = new PredicateDependency(clauses);
+                else
+                        return dependencyGraph;
+        }
+
+        public void getDependencyGraph(PredicateDependency g) {
+                dependencyGraph = g;
+        }
+
+        public final String getDirectory() {
+                return Utility.getGlobalTempDirAbsolutePath();
+        }
+
+        public void deleteABoxTurtleFile() {
+                if(additionalDataFile != null)
+                        new File(additionalDataFile).delete();
+        }
+
+        /**
+         * clone all information of another program after load()
+         *
+         * @param program
+         */
+        void clone(Program program) {
+                this.ontologyDirectory = program.ontologyDirectory;
+                this.ontology = program.ontology;
+                this.dlOntology = program.dlOntology;
+                this.botStrategy = program.botStrategy;
+                this.additionalDataFile = program.additionalDataFile;
+                this.transitiveAxioms = program.transitiveAxioms;
+                this.transitiveClauses = program.transitiveClauses;
+                this.subPropChainAxioms = program.subPropChainAxioms;
+                this.subPropChainClauses = program.subPropChainClauses;
+        }
+
         private void clausify() {
                 Configuration conf = new Configuration();
                 OWLClausification clausifier = new OWLClausification(conf);
@@ -103,121 +206,94 @@ public abstract class Program implements KnowledgeBase {
                 OWLOntologyManager manager = ontology.getOWLOntologyManager();
                 try {
                         filteredOntology = manager.createOntology();
-                } catch (OWLOntologyCreationException e) {
+                } catch(OWLOntologyCreationException e) {
                         e.printStackTrace();
                 }
-                
+
                 transitiveAxioms = new LinkedList<OWLTransitiveObjectPropertyAxiom>();
                 subPropChainAxioms = new LinkedList<OWLSubPropertyChainOfAxiom>();
-                
-                OWLDatatype date = ontology.getOWLOntologyManager().getOWLDataFactory().getOWLDatatype(IRI.create("http://www.w3.org/2001/XMLSchema#date")); 
-                int noOfDataPropertyRangeAxioms = 0, noOfAxioms = 0; 
-                for (OWLOntology onto: ontology.getImportsClosure())
-                        for (OWLAxiom axiom: onto.getAxioms()) {
-                                if (axiom instanceof OWLTransitiveObjectPropertyAxiom) 
+
+                OWLDatatype date = ontology.getOWLOntologyManager()
+                                                                   .getOWLDataFactory()
+                                                                   .getOWLDatatype(IRI.create("http://www.w3.org/2001/XMLSchema#date"));
+                int noOfDataPropertyRangeAxioms = 0, noOfAxioms = 0;
+                for(OWLOntology onto : ontology.getImportsClosure())
+                        for(OWLAxiom axiom : onto.getAxioms()) {
+                                if(axiom instanceof OWLTransitiveObjectPropertyAxiom)
                                         transitiveAxioms.add((OWLTransitiveObjectPropertyAxiom) axiom);
-                                else if (axiom instanceof OWLSubPropertyChainOfAxiom) 
+                                else if(axiom instanceof OWLSubPropertyChainOfAxiom)
                                         subPropChainAxioms.add((OWLSubPropertyChainOfAxiom) axiom);
-                                // TODO to filter out datatype axioms
-                                else if (axiom instanceof OWLDataPropertyRangeAxiom) {
-                                        ++noOfDataPropertyRangeAxioms; 
+                                        // TODO to filter out datatype axioms
+                                else if(axiom instanceof OWLDataPropertyRangeAxiom) {
+                                        ++noOfDataPropertyRangeAxioms;
                                         Utility.logInfo("The axiom: " + axiom + " is being ignored.");
                                 }
                                 else {
-                                        if (axiom.getDatatypesInSignature().contains(date)) {
+                                        if(axiom.getDatatypesInSignature().contains(date)) {
                                                 Utility.logInfo("The axiom: " + axiom + " is being ignored.");
                                         }
                                         else manager.addAxiom(filteredOntology, axiom);
                                 }
-                                
-                                if (axiom instanceof OWLAnnotationAssertionAxiom ||
+
+                                if(axiom instanceof OWLAnnotationAssertionAxiom ||
                                                 axiom instanceof OWLSubAnnotationPropertyOfAxiom ||
                                                 axiom instanceof OWLDeclarationAxiom ||
                                                 axiom instanceof OWLDataPropertyRangeAxiom) {
                                 }
                                 else {
-//                                      System.out.println(axiom); 
+//                                      System.out.println(axiom);
                                         ++noOfAxioms;
                                 }
-                                        
+
                         }
                 Utility.logInfo("The number of data property range axioms that are ignored: " + noOfDataPropertyRangeAxioms + "(" + noOfAxioms + ")");
-                
-                dlOntology = (DLOntology)clausifier.preprocessAndClausify(filteredOntology, null)[1];
+
+                dlOntology = (DLOntology) clausifier.preprocessAndClausify(filteredOntology, null)[1];
                 clausifier = null;
         }
-        
-        public String getAdditionalDataFile() {
-                return additionalDataFile; 
-        }
-
-        protected LinkedList<OWLTransitiveObjectPropertyAxiom> transitiveAxioms;
-        protected LinkedList<DLClause> transitiveClauses;
-        
-        protected LinkedList<OWLSubPropertyChainOfAxiom> subPropChainAxioms; 
-        protected LinkedList<DLClause> subPropChainClauses;
-        
-        @Override
-        public void transform() {
-                for (DLClause dlClause: dlOntology.getDLClauses()) {
-                        DLClause simplifiedDLClause = DLClauseHelper.removeNominalConcept(dlClause);
-                        simplifiedDLClause = removeAuxiliaryBodyAtoms(simplifiedDLClause);
-                        simplifiedDLClause  = DLClauseHelper.replaceWithDataValue(simplifiedDLClause);
-                        convert(simplifiedDLClause);
-                }
 
-                addingTransitiveAxioms();
-                addingSubPropertyChainAxioms();
-                
-                Collection<DLClause> botRelated = new LinkedList<DLClause>(); 
-                Variable X = Variable.create("X"); 
-                botRelated.add(DLClause.create(new Atom[0], new Atom[] {Atom.create(Inequality.INSTANCE, X, X)}));
-                clauses.addAll(botStrategy.process(botRelated)); 
-                
-                if (this instanceof GeneralProgram)
-                        Utility.logInfo("The number of rules: " + (clauses.size() - 1));
-        }
-        
         private DLClause removeAuxiliaryBodyAtoms(DLClause dlClause) {
                 Collection<Atom> newBodyAtoms = new LinkedList<Atom>();
-                DLPredicate p; 
-                for (Atom bodyAtom: dlClause.getBodyAtoms()) {
-                        p = bodyAtom.getDLPredicate(); 
-                        if (p instanceof AtomicConcept || 
+                DLPredicate p;
+                for(Atom bodyAtom : dlClause.getBodyAtoms()) {
+                        p = bodyAtom.getDLPredicate();
+                        if(p instanceof AtomicConcept ||
                                         p instanceof AtomicRole || p instanceof InverseRole ||
                                         p instanceof Equality || p instanceof AnnotatedEquality || p instanceof Inequality)
-                                newBodyAtoms.add(bodyAtom); 
+                                newBodyAtoms.add(bodyAtom);
                 }
                 LinkedList<Atom> newHeadAtoms = new LinkedList<Atom>();
-                Map<Variable, Term> assign = new HashMap<Variable, Term>(); 
-                for (Atom headAtom: dlClause.getHeadAtoms()) {
-                        p = headAtom.getDLPredicate(); 
-                        if (p instanceof AtomicNegationDataRange) {
-                                AtomicDataRange positive = ((AtomicNegationDataRange) p).getNegatedDataRange(); 
-                                if (!(positive instanceof ConstantEnumeration)) 
+                Map<Variable, Term> assign = new HashMap<Variable, Term>();
+                for(Atom headAtom : dlClause.getHeadAtoms()) {
+                        p = headAtom.getDLPredicate();
+                        if(p instanceof AtomicNegationDataRange) {
+                                AtomicDataRange positive = ((AtomicNegationDataRange) p).getNegatedDataRange();
+                                if(!(positive instanceof ConstantEnumeration))
                                         newBodyAtoms.add(Atom.create(positive, headAtom.getArgument(0)));
-                                else if (((ConstantEnumeration) positive).getNumberOfConstants() == 1) {
-                                        assign.put((Variable) headAtom.getArgument(0), ((ConstantEnumeration) positive).getConstant(0)); 
-//                                      newBodyAtoms.add(Atom.create(Equality.INSTANCE, headAtom.getArgument(0), ((ConstantEnumeration) positive).getConstant(0))); 
+                                else if(((ConstantEnumeration) positive).getNumberOfConstants() == 1) {
+                                        assign.put((Variable) headAtom.getArgument(0), ((ConstantEnumeration) positive).getConstant(0));
+//                                      newBodyAtoms.add(Atom.create(Equality.INSTANCE, headAtom.getArgument(0), ((ConstantEnumeration) positive).getConstant(0)));
                                 }
-                                else newHeadAtoms.add(headAtom); 
+                                else newHeadAtoms.add(headAtom);
                         }
-                        else 
-                                newHeadAtoms.add(headAtom); 
+                        else
+                                newHeadAtoms.add(headAtom);
                 }
-                
-                if (assign.isEmpty() && newHeadAtoms.isEmpty() && newBodyAtoms.size() == dlClause.getBodyLength())
-                        return dlClause; 
-
-                Atom[] headArray = newHeadAtoms.size() == dlClause.getHeadLength() ? dlClause.getHeadAtoms() : newHeadAtoms.toArray(new Atom[0]);
-                Atom[] bodyArray = newBodyAtoms.size() == dlClause.getBodyLength() ? dlClause.getBodyAtoms() : newBodyAtoms.toArray(new Atom[0]);
-                if (!assign.isEmpty()) {
-                        for (int i = 0; i < headArray.length; ++i)
-                                headArray[i] = DLClauseHelper.getInstance(headArray[i], assign); 
-                        for (int i = 0; i < bodyArray.length; ++i)
-                                bodyArray[i] = DLClauseHelper.getInstance(bodyArray[i], assign); 
+
+                if(assign.isEmpty() && newHeadAtoms.isEmpty() && newBodyAtoms.size() == dlClause.getBodyLength())
+                        return dlClause;
+
+                Atom[] headArray =
+                                newHeadAtoms.size() == dlClause.getHeadLength() ? dlClause.getHeadAtoms() : newHeadAtoms.toArray(new Atom[0]);
+                Atom[] bodyArray =
+                                newBodyAtoms.size() == dlClause.getBodyLength() ? dlClause.getBodyAtoms() : newBodyAtoms.toArray(new Atom[0]);
+                if(!assign.isEmpty()) {
+                        for(int i = 0; i < headArray.length; ++i)
+                                headArray[i] = DLClauseHelper.getInstance(headArray[i], assign);
+                        for(int i = 0; i < bodyArray.length; ++i)
+                                bodyArray[i] = DLClauseHelper.getInstance(bodyArray[i], assign);
                 }
-                return DLClause.create(headArray, bodyArray); 
+                return DLClause.create(headArray, bodyArray);
         }
 
         private void addingTransitiveAxioms() {
@@ -225,136 +301,58 @@ public abstract class Program implements KnowledgeBase {
                 Atom headAtom;
                 Variable X = Variable.create("X"), Y = Variable.create("Y"), Z = Variable.create("Z");
                 transitiveClauses = new LinkedList<DLClause>();
-                for (OWLTransitiveObjectPropertyAxiom axiom: transitiveAxioms) {
-                        OWLObjectPropertyExpression objExp = axiom.getProperty(); 
+                for(OWLTransitiveObjectPropertyAxiom axiom : transitiveAxioms) {
+                        OWLObjectPropertyExpression objExp = axiom.getProperty();
                         headAtom = getAtom(objExp, X, Z);
                         Atom[] bodyAtoms = new Atom[2];
-                        bodyAtoms[0] = getAtom(objExp, X, Y); 
-                        bodyAtoms[1] = getAtom(objExp, Y, Z); 
-                        transitiveClause = DLClause.create(new Atom[] {headAtom}, bodyAtoms); 
+                        bodyAtoms[0] = getAtom(objExp, X, Y);
+                        bodyAtoms[1] = getAtom(objExp, Y, Z);
+                        transitiveClause = DLClause.create(new Atom[]{headAtom}, bodyAtoms);
                         clauses.add(transitiveClause);
                         transitiveClauses.add(transitiveClause);
                 }
         }
-        
+
         private Atom getAtom(OWLObjectPropertyExpression exp, Variable x, Variable y) {
-                if (exp instanceof OWLObjectProperty)
+                if(exp instanceof OWLObjectProperty)
                         return Atom.create(AtomicRole.create(((OWLObjectProperty) exp).toStringID()), x, y);
-                OWLObjectInverseOf inverseOf; 
-                if (exp instanceof OWLObjectInverseOf && (inverseOf = (OWLObjectInverseOf) exp).getInverse() instanceof OWLObjectProperty)
+                OWLObjectInverseOf inverseOf;
+                if(exp instanceof OWLObjectInverseOf && (inverseOf =
+                                (OWLObjectInverseOf) exp).getInverse() instanceof OWLObjectProperty)
                         return Atom.create(AtomicRole.create(((OWLObjectProperty) inverseOf).toStringID()), x, y);
                 return null;
         }
 
         private void addingSubPropertyChainAxioms() {
-                DLClause dlClause; 
+                DLClause dlClause;
                 subPropChainClauses = new LinkedList<DLClause>();
                 Atom headAtom;
-                Iterator<OWLObjectPropertyExpression> iterExp; 
-                OWLObjectPropertyExpression objExp; 
-                for (OWLSubPropertyChainOfAxiom axiom: subPropChainAxioms) {
+                Iterator<OWLObjectPropertyExpression> iterExp;
+                OWLObjectPropertyExpression objExp;
+                for(OWLSubPropertyChainOfAxiom axiom : subPropChainAxioms) {
                         objExp = axiom.getSuperProperty();
                         List<OWLObjectPropertyExpression> objs = axiom.getPropertyChain();
                         headAtom = getAtom(objExp, Variable.create("X"), Variable.create("X" + objs.size()));
                         iterExp = objs.iterator();
-                        int index = 1; 
-                        Atom[] bodyAtoms = new Atom[objs.size()]; 
-                        bodyAtoms[0] = getAtom(iterExp.next(), Variable.create("X"), Variable.create("X1")); 
-                        while (index < objs.size()) {
-                                bodyAtoms[index] = getAtom(iterExp.next(), Variable.create("X" + index), Variable.create("X" + (index + 1)));
-                                ++index; 
+                        int index = 1;
+                        Atom[] bodyAtoms = new Atom[objs.size()];
+                        bodyAtoms[0] = getAtom(iterExp.next(), Variable.create("X"), Variable.create("X1"));
+                        while(index < objs.size()) {
+                                bodyAtoms[index] =
+                                                getAtom(iterExp.next(), Variable.create("X" + index), Variable.create("X" + (index + 1)));
+                                ++index;
                         }
-                        dlClause = DLClause.create(new Atom[] {headAtom}, bodyAtoms); 
-                        clauses.add(dlClause); 
-                        subPropChainClauses.add(dlClause); 
+                        dlClause = DLClause.create(new Atom[]{headAtom}, bodyAtoms);
+                        clauses.add(dlClause);
+                        subPropChainClauses.add(dlClause);
                 }
         }
 
-        @Override
-        public void save() {
-                try {
-                        BufferedWriter ruleWriter = new BufferedWriter(new OutputStreamWriter(
-                                        new FileOutputStream(getOutputPath())));
-                        ruleWriter.write(toString());
-                        ruleWriter.close();
-                } catch (IOException e) {
-                        e.printStackTrace();
-                }
-                Utility.logDebug("The rules are saved in " + getOutputPath() + "."); 
-        }
-        
-        @Override
-        public String toString() {
-                return toString(clauses); 
-        }
-        
-        public static String toString(Collection<DLClause> clauses) {
-                StringBuilder sb = new StringBuilder(DLClauseHelper.toString(clauses)); 
-                sb.insert(0, MyPrefixes.PAGOdAPrefixes.prefixesText()); 
-                return sb.toString(); 
-        }
-        
-        public final void convert(DLClause clause) {
-                Collection<DLClause> tempClauses = convert2Clauses(clause);
-                clauses.addAll(tempClauses);
-        }
-        
-        public abstract Collection<DLClause> convert2Clauses(DLClause clause);
-
-        public abstract String getOutputPath();
-        
-        
-        public OWLOntology getOntology() {
-                return ontology;
-        }
-        
-        public Collection<DLClause> getClauses() {
-                return clauses;
-        }
-        
-        public Collection<DLClause> getClauses(DLClause queryClause) {
-//              if (true) return new HashSet<DLClause>(clauses); 
-                Set<DLPredicate> predicates = new HashSet<DLPredicate>();
-                predicates.addAll(dependencyGraph.collectPredicate(queryClause.getBodyAtoms())); 
-                
-                Set<DLPredicate> dependence = new HashSet<DLPredicate>(); 
-                for (DLPredicate predicate: predicates)
-                        dependence.addAll(dependencyGraph.getAncesters(predicate));
-                
-                Collection<DLClause> relevantClauses = new LinkedList<DLClause>(); 
-                for (DLClause clause: clauses) {
-                        if (relevant(clause, dependence))
-                                relevantClauses.add(clause);
-                        
-                }
-                return relevantClauses; 
-        }
-
         private boolean relevant(DLClause clause, Set<DLPredicate> set) {
-                for (DLPredicate p: dependencyGraph.collectPredicate(clause.getHeadAtoms()))
-                        if (set.contains(p))
+                for(DLPredicate p : dependencyGraph.collectPredicate(clause.getHeadAtoms()))
+                        if(set.contains(p))
                                 return true;
-                return false; 
-        }
-
-        public PredicateDependency buildDependencyGraph() {
-                if (dependencyGraph == null)
-                        return dependencyGraph = new PredicateDependency(clauses);  
-                else 
-                        return dependencyGraph; 
-        }
-        
-        public void getDependencyGraph(PredicateDependency g) {
-                dependencyGraph = g; 
-        }
-        
-        public final String getDirectory() {
-                return Utility.getGlobalTempDirAbsolutePath();
-        }
-        
-        public void deleteABoxTurtleFile() {
-                if (additionalDataFile != null)
-                        new File(additionalDataFile).delete();
+                return false;
         }
 
 }
diff --git a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoder.java b/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoder.java
index f3cc937..d8ebc55 100644
--- a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoder.java
+++ b/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoder.java
@@ -1,387 +1,387 @@
 package uk.ac.ox.cs.pagoda.tracking;
 
-import java.io.BufferedWriter;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.OutputStreamWriter;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.LinkedList;
-import java.util.Map;
-import java.util.Set;
-
-import org.semanticweb.HermiT.model.AnnotatedEquality;
-import org.semanticweb.HermiT.model.Atom;
-import org.semanticweb.HermiT.model.AtomicConcept;
-import org.semanticweb.HermiT.model.AtomicRole;
-import org.semanticweb.HermiT.model.Constant;
-import org.semanticweb.HermiT.model.DLClause;
-import org.semanticweb.HermiT.model.DLPredicate;
-import org.semanticweb.HermiT.model.DatatypeRestriction;
-import org.semanticweb.HermiT.model.Equality;
-import org.semanticweb.HermiT.model.Individual;
-import org.semanticweb.HermiT.model.Inequality;
-import org.semanticweb.HermiT.model.Variable;
+import org.semanticweb.HermiT.model.*;
 import org.semanticweb.owlapi.model.OWLOntology;
-
 import uk.ac.ox.cs.JRDFox.model.Datatype;
 import uk.ac.ox.cs.JRDFox.model.GroundTerm;
 import uk.ac.ox.cs.JRDFox.model.Literal;
 import uk.ac.ox.cs.pagoda.MyPrefixes;
 import uk.ac.ox.cs.pagoda.hermit.DLClauseHelper;
-import uk.ac.ox.cs.pagoda.query.*; 
+import uk.ac.ox.cs.pagoda.query.AnswerTuple;
+import uk.ac.ox.cs.pagoda.query.AnswerTuples;
+import uk.ac.ox.cs.pagoda.query.GapTupleIterator;
+import uk.ac.ox.cs.pagoda.query.QueryRecord;
 import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine;
 import uk.ac.ox.cs.pagoda.reasoner.light.RDFoxTripleManager;
 import uk.ac.ox.cs.pagoda.rules.UpperDatalogProgram;
 import uk.ac.ox.cs.pagoda.util.Namespace;
 import uk.ac.ox.cs.pagoda.util.Utility;
+import uk.ac.ox.cs.pagoda.util.disposable.Disposable;
+import uk.ac.ox.cs.pagoda.util.disposable.DisposedException;
+
+import java.io.BufferedWriter;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.util.*;
+
+public abstract class TrackingRuleEncoder extends Disposable {
+    public static final String trackingPredicateRelation = Namespace.PAGODA_AUX + "isTrackingPredicateFor";
+    public static final String QueryPredicate = Namespace.PAGODA_AUX + "Query";
+    protected BasicQueryEngine store;
+    protected QueryRecord currentQuery;
+    protected Set<String> unaryPredicates = new HashSet<String>();
+    protected Set<String> binaryPredicates = new HashSet<String>();
+    UpperDatalogProgram program;
+    Collection<DLClause> trackingClauses = new HashSet<DLClause>();
+    Collection<DLClause> queryClauses = new LinkedList<DLClause>();
+    Map<Integer, DLClause> index2clause = new HashMap<Integer, DLClause>();
+    Map<DLClause, Integer> clause2index = new HashMap<DLClause, Integer>();
+    String equalityRelatedRuleText = null;
+    boolean ruleEncoded = false;
+    DLPredicate selected;
+    private boolean queryEncoded = false;
+    private LinkedList<int[]> addedData = new LinkedList<int[]>();
+    private String trackingSuffix;
+
+    public TrackingRuleEncoder(UpperDatalogProgram program, BasicQueryEngine store) {
+        this.program = program;
+        this.store = store;
+    }
+
+    public static String getRawTerm(GroundTerm r) {
+        if(r instanceof uk.ac.ox.cs.JRDFox.model.Individual)
+            return ((uk.ac.ox.cs.JRDFox.model.Individual) r).getIRI();
+        else {
+            Literal l = (Literal) r;
+            if(l.getDatatype().equals(Datatype.XSD_STRING) && l.getDatatype().equals(Datatype.RDF_PLAIN_LITERAL))
+                return "\"" + l.getLexicalForm() + "\"";
+            else
+                return "\"" + l.getLexicalForm() + "\"^^<" + l.getDatatype().getIRI() + ">";
+        }
+    }
+
+    protected static String getTrackingSuffix(String queryID) {
+        return "_AUXt" + queryID;
+    }
+
+    public boolean encodingRules() {
+        if(isDisposed()) throw new DisposedException();
+        if(ruleEncoded) return false;
+        ruleEncoded = true;
 
-public abstract class TrackingRuleEncoder {
-        UpperDatalogProgram program;
-        Collection<DLClause> trackingClauses = new HashSet<DLClause>();
-        Collection<DLClause> queryClauses = new LinkedList<DLClause>();
-        
-        Map<Integer, DLClause> index2clause = new HashMap<Integer, DLClause>();
-        Map<DLClause, Integer> clause2index = new HashMap<DLClause, Integer>();
-        
-        String equalityRelatedRuleText = null; 
-        protected BasicQueryEngine store;  
-        
-        public TrackingRuleEncoder(UpperDatalogProgram program, BasicQueryEngine store) {
-                this.program = program;
-                this.store = store; 
-        }
-        
-        protected abstract String getEqualityRelatedRuleText();
-
-        boolean ruleEncoded = false; 
-        
-        public boolean encodingRules() {
-                if (ruleEncoded) return false;
-                ruleEncoded = true; 
-                
 //              for (DLClause clause: program.getClauses(currentQuery.getClause())) {
-                for (DLClause clause: program.getClauses()) {
-                        encodingRule(clause);
-                }
-                return true; 
-        }
-        
-        protected String getIRI(String name) {
-                return program.getOntology().getOntologyID().getOntologyIRI().toString() + "#" + name;
-        }
-
-        protected abstract void encodingRule(DLClause clause);
-        
-        protected Individual getIndividual4GeneralRule(DLClause clause) {
-                clause = program.getCorrespondingClause(clause);
+        for(DLClause clause : program.getClauses()) {
+            encodingRule(clause);
+        }
+        return true;
+    }
+
+    public Collection<int[]> getAddedData() {
+        if(isDisposed()) throw new DisposedException();
+        return addedData;
+    }
+
+    public String getTrackingPredicate(String predicateIRI) {
+        if(isDisposed()) throw new DisposedException();
+        if(predicateIRI.startsWith("<"))
+            return predicateIRI.replace(">", getTrackingSuffix(currentQuery.getQueryID()) + ">");
+        else
+            return predicateIRI + getTrackingSuffix(currentQuery.getQueryID());
+    }
+
+    public void setCurrentQuery(QueryRecord record) {
+        if(isDisposed()) throw new DisposedException();
+        deprecateTrackingAndQueryRules();
+        currentQuery = record;
+        selected = AtomicConcept.create(getSelectedPredicate());
+        trackingSuffix = "_AUXt" + currentQuery.getQueryID();
+    }
+
+    @Override
+    public void dispose() {
+        super.dispose();
+        deprecateTrackingAndQueryRules();
+    }
+
+    public String getTrackingProgram() {
+        if(isDisposed()) throw new DisposedException();
+        StringBuilder sb = getTrackingProgramBody();
+        sb.insert(0, MyPrefixes.PAGOdAPrefixes.prefixesText());
+        return sb.toString();
+    }
+
+    public void saveTrackingRules(String fileName) {
+        if(isDisposed()) throw new DisposedException();
+        BufferedWriter writer = null;
+        try {
+            writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(fileName)));
+            writer.write(getTrackingProgram());
+            writer.close();
+        } catch(IOException e) {
+            e.printStackTrace();
+            return;
+        }
+        Utility.logDebug("The tracking rules are saved in " + fileName + ".");
+    }
+
+    public String getSelectedPredicate() {
+        if(isDisposed()) throw new DisposedException();
+        return getIRI("_selected" + currentQuery.getQueryID());
+    }
+
+    public DLClause getSelectedClause(String iri) {
+        if(isDisposed()) throw new DisposedException();
+        int index = iri.lastIndexOf("_r") + 2;
+        int ruleIndex = Integer.parseInt(iri.substring(index));
+        return index2clause.get(ruleIndex);
+    }
+
+    /**
+     * SELECT ?X
+     * WHERE {
+     * ?X <http://www.w3.org/1999/02/22-rdf-syntax-ns#:type> :_selected?
+     * }
+     */
+    public String getSelectedSPARQLQuery() {
+        if(isDisposed()) throw new DisposedException();
+        StringBuilder builder = new StringBuilder();
+        builder.append("SELECT ?X\nWHERE {\n?X <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ");
+        builder.append(selected.toString()).append("\n}");
+        return builder.toString();
+    }
+
+    public OWLOntology getOntology() {
+        if(isDisposed()) throw new DisposedException();
+        return program.getOntology();
+    }
+
+    public UpperDatalogProgram getProgram() {
+        if(isDisposed()) throw new DisposedException();
+        return program;
+    }
+
+    public String getOriginalPredicate(String p) {
+        if(isDisposed()) throw new DisposedException();
+        if(p.startsWith("<")) {
+            if(!p.endsWith(trackingSuffix + ">")) return null;
+        }
+        else if(!p.endsWith(trackingSuffix)) return null;
+
+        return p.replace(trackingSuffix, "");
+    }
+
+    public boolean isAuxPredicate(String p) {
+        if(isDisposed()) throw new DisposedException();
+        return false;
+    }
+
+    protected abstract String getEqualityRelatedRuleText();
+
+    protected String getIRI(String name) {
+        return program.getOntology().getOntologyID().getOntologyIRI().toString() + "#" + name;
+    }
+
+    protected abstract void encodingRule(DLClause clause);
+
+    protected Individual getIndividual4GeneralRule(DLClause clause) {
+        clause = program.getCorrespondingClause(clause);
 //              if (clause == null)
-//                      return Individual.create(getIRI("_r0")); 
-                        
-                int index; 
-                if (clause2index.containsKey(clause)) 
-                        index = clause2index.get(clause); 
-                else {
-                        index = clause2index.size() + 1; 
-                        index2clause.put(index, clause);
-                        clause2index.put(clause, index); 
-                }
-
-                return Individual.create(getIRI("_r" + index));
-        }
-
-        private boolean queryEncoded = false; 
-        private LinkedList<int[]> addedData = new LinkedList<int[]>();
-        
-        public Collection<int[]> getAddedData() {
-                return addedData; 
-        }
-        
-        private void encodingQuery(QueryRecord[] botQuerRecords) {
-                if (queryEncoded) return ; 
-                queryEncoded = true;
-                
-                if (currentQuery.getArity() > 0 && currentQuery.getArity() < 3) {
-                        encodingAtomicQuery(botQuerRecords);
-
-                } else {
-                        DLClause queryClause = currentQuery.getClause(); 
-                        Atom[] bodyAtoms = queryClause.getBodyAtoms(); 
-                        for (Atom bodyAtom: bodyAtoms) 
-                                addQueryRule(bodyAtom, bodyAtoms); 
-                }
-        }
-        
-        private void addQueryRule(Atom atom, Atom[] atoms) {
-                DLClause newClause; 
-                Atom headAtom; 
-                
-                headAtom = Atom.create(
-                                getTrackingDLPredicate(atom.getDLPredicate()), 
-                                DLClauseHelper.getArguments(atom));
-                newClause = DLClause.create(new Atom[] {headAtom}, atoms); 
-                queryClauses.add(newClause);
-        }
-
-        public static final String trackingPredicateRelation = Namespace.PAGODA_AUX + "isTrackingPredicateFor"; 
-        
-        public static final String QueryPredicate = Namespace.PAGODA_AUX + "Query"; 
-        
-        protected String getCurrentQueryPredicate() {
-                return QueryPredicate + currentQuery.getQueryID(); 
-        }
-
-        protected void encodingAtomicQuery(QueryRecord[] botQuerRecords) {
-                encodingAtomicQuery(botQuerRecords, false);
-        }
-        
-        protected void encodingAtomicQuery(QueryRecord[] botQuerRecords, boolean includingBottom) {
-                DLClause queryClause = currentQuery.getClause(); 
-                AnswerTuples answerTuples = currentQuery.getGapAnswers(); 
-                String[] answerVariables = currentQuery.getAnswerVariables(); 
-                
-                String currentQueryPredicate = getCurrentQueryPredicate();
-                Atom newAtom; 
-                if (answerVariables.length == 1) {
-                        AtomicConcept queryConcept = AtomicConcept.create(currentQueryPredicate);
-                        newAtom = Atom.create(queryConcept, Variable.create(answerVariables[0]));
-                }
-                else {
-                        AtomicRole queryRole = AtomicRole.create(currentQueryPredicate); 
-                        newAtom = Atom.create(queryRole, Variable.create(answerVariables[0]), Variable.create(answerVariables[1]));  
-                }
-                
-                Atom[] bodyAtoms = queryClause.getBodyAtoms();
-                Atom[] newBodyAtoms = new Atom[queryClause.getBodyLength() + 1]; 
-                for (int i = 0; i < bodyAtoms.length; ++i)
-                        newBodyAtoms[i + 1] = bodyAtoms[i]; 
-                newBodyAtoms[0] = newAtom;
-                
-                for (Atom bodyAtom: bodyAtoms) 
-                        addQueryRule(bodyAtom, newBodyAtoms);
-
-                RDFoxTripleManager tripleManager = new RDFoxTripleManager(store.getDataStore(), true);
+//                      return Individual.create(getIRI("_r0"));
+
+        int index;
+        if(clause2index.containsKey(clause))
+            index = clause2index.get(clause);
+        else {
+            index = clause2index.size() + 1;
+            index2clause.put(index, clause);
+            clause2index.put(clause, index);
+        }
+
+        return Individual.create(getIRI("_r" + index));
+    }
+
+    private void encodingQuery(QueryRecord[] botQuerRecords) {
+        if(queryEncoded) return;
+        queryEncoded = true;
+
+        if(currentQuery.getArity() > 0 && currentQuery.getArity() < 3) {
+            encodingAtomicQuery(botQuerRecords);
+
+        }
+        else {
+            DLClause queryClause = currentQuery.getClause();
+            Atom[] bodyAtoms = queryClause.getBodyAtoms();
+            for(Atom bodyAtom : bodyAtoms)
+                addQueryRule(bodyAtom, bodyAtoms);
+        }
+    }
+
+    private void addQueryRule(Atom atom, Atom[] atoms) {
+        DLClause newClause;
+        Atom headAtom;
+
+        headAtom = Atom.create(
+                getTrackingDLPredicate(atom.getDLPredicate()),
+                DLClauseHelper.getArguments(atom));
+        newClause = DLClause.create(new Atom[]{headAtom}, atoms);
+        queryClauses.add(newClause);
+    }
+
+    protected String getCurrentQueryPredicate() {
+        return QueryPredicate + currentQuery.getQueryID();
+    }
+
+    protected void encodingAtomicQuery(QueryRecord[] botQuerRecords) {
+        encodingAtomicQuery(botQuerRecords, false);
+    }
+
+    protected void encodingAtomicQuery(QueryRecord[] botQuerRecords, boolean includingBottom) {
+        DLClause queryClause = currentQuery.getClause();
+        AnswerTuples answerTuples = currentQuery.getGapAnswers();
+        String[] answerVariables = currentQuery.getAnswerVariables();
+
+        String currentQueryPredicate = getCurrentQueryPredicate();
+        Atom newAtom;
+        if(answerVariables.length == 1) {
+            AtomicConcept queryConcept = AtomicConcept.create(currentQueryPredicate);
+            newAtom = Atom.create(queryConcept, Variable.create(answerVariables[0]));
+        }
+        else {
+            AtomicRole queryRole = AtomicRole.create(currentQueryPredicate);
+            newAtom = Atom.create(queryRole, Variable.create(answerVariables[0]), Variable.create(answerVariables[1]));
+        }
+
+        Atom[] bodyAtoms = queryClause.getBodyAtoms();
+        Atom[] newBodyAtoms = new Atom[queryClause.getBodyLength() + 1];
+        for(int i = 0; i < bodyAtoms.length; ++i)
+            newBodyAtoms[i + 1] = bodyAtoms[i];
+        newBodyAtoms[0] = newAtom;
+
+        for(Atom bodyAtom : bodyAtoms)
+            addQueryRule(bodyAtom, newBodyAtoms);
+
+        RDFoxTripleManager tripleManager = new RDFoxTripleManager(store.getDataStore(), true);
 //              MyPrefixes prefixes = MyPrefixes.PAGOdAPrefixes;
-                int[] triple; 
-                int predicate = tripleManager.getResourceID(AtomicConcept.create(currentQueryPredicate));   
-                int rdftype = tripleManager.getResourceID(AtomicRole.create(Namespace.RDF_TYPE));
-                if (answerVariables.length == 1) {              
-                        for (AnswerTuple answer; answerTuples.isValid(); answerTuples.moveNext()) {
-                                answer = answerTuples.getTuple();
-                                triple = new int[] { tripleManager.getResourceID(getRawTerm(answer.getGroundTerm(0))), rdftype, predicate }; 
-                                addedData.add(triple);
-                                tripleManager.addTripleByID(triple);
-//                              System.out.println("To be removed ... \n" + tripleManager.getRawTerm(tripleManager.getResourceID(prefixes.expandIRI(answer.getRawTerm(0)))) + " " + tripleManager.getRawTerm(rdftype) + " " + tripleManager.getRawTerm(predicate)); 
-                        }
-                }
-                else {
-                        for (AnswerTuple answer; answerTuples.isValid(); answerTuples.moveNext()) {
-                                answer = answerTuples.getTuple();
-                                triple = new int[] { tripleManager.getResourceID(getRawTerm(answer.getGroundTerm(0))), predicate, tripleManager.getResourceID(getRawTerm(answer.getGroundTerm(1))) }; 
-                                addedData.add(triple);
-                                tripleManager.addTripleByID(triple);
-                        }
-                }
-                answerTuples.dispose();
-
-                if (includingBottom && botQuerRecords != null) {
-                        int index = 0; 
-                        GroundTerm t; 
-                        String raw; 
-                        for (QueryRecord  botQueryRecord: botQuerRecords) {
-                                answerTuples = botQueryRecord.getGapAnswers();
-                                int subID = 0;//botQueryRecord.getSubID(); 
-                                String p = subID == 0 ? AtomicConcept.NOTHING.getIRI() : Namespace.OWL_NS + "Nothing_final" + (++index); 
-                                predicate = tripleManager.getResourceID(AtomicConcept.create(p = getTrackingPredicate(p)));
-                                for (AnswerTuple answer; answerTuples.isValid(); answerTuples.moveNext()) {
-                                        answer = answerTuples.getTuple(); 
+        int[] triple;
+        int predicate = tripleManager.getResourceID(AtomicConcept.create(currentQueryPredicate));
+        int rdftype = tripleManager.getResourceID(AtomicRole.create(Namespace.RDF_TYPE));
+        if(answerVariables.length == 1) {
+            for(AnswerTuple answer; answerTuples.isValid(); answerTuples.moveNext()) {
+                answer = answerTuples.getTuple();
+                triple =
+                        new int[]{tripleManager.getResourceID(getRawTerm(answer.getGroundTerm(0))), rdftype, predicate};
+                addedData.add(triple);
+                tripleManager.addTripleByID(triple);
+//                              System.out.println("To be removed ... \n" + tripleManager.getRawTerm(tripleManager.getResourceID(prefixes.expandIRI(answer.getRawTerm(0)))) + " " + tripleManager.getRawTerm(rdftype) + " " + tripleManager.getRawTerm(predicate));
+            }
+        }
+        else {
+            for(AnswerTuple answer; answerTuples.isValid(); answerTuples.moveNext()) {
+                answer = answerTuples.getTuple();
+                triple =
+                        new int[]{tripleManager.getResourceID(getRawTerm(answer.getGroundTerm(0))), predicate, tripleManager
+                                .getResourceID(getRawTerm(answer.getGroundTerm(1)))};
+                addedData.add(triple);
+                tripleManager.addTripleByID(triple);
+            }
+        }
+//        answerTuples.dispose();
+
+        if(includingBottom && botQuerRecords != null) {
+            int index = 0;
+            GroundTerm t;
+            String raw;
+            for(QueryRecord botQueryRecord : botQuerRecords) {
+                answerTuples = botQueryRecord.getGapAnswers();
+                int subID = 0;//botQueryRecord.getSubID();
+                String p = subID == 0 ? AtomicConcept.NOTHING.getIRI() : Namespace.OWL_NS + "Nothing_final" + (++index);
+                predicate = tripleManager.getResourceID(AtomicConcept.create(p = getTrackingPredicate(p)));
+                for(AnswerTuple answer; answerTuples.isValid(); answerTuples.moveNext()) {
+                    answer = answerTuples.getTuple();
 //                                      System.out.println("To be removed ... " + answer.getRawTerm(0));
-                                        raw = ((t = answer.getGroundTerm(0)) instanceof uk.ac.ox.cs.JRDFox.model.Individual) ? ((uk.ac.ox.cs.JRDFox.model.Individual) t).getIRI() : t.toString(); 
-                                        triple = new int[] { tripleManager.getResourceID(raw), rdftype, predicate }; 
-                                        addedData.add(triple);
-                                        tripleManager.addTripleByID(triple);
-                                }
-                                answerTuples.dispose();
-                        }
-                }
-                
-                Utility.logInfo(addedData.size() + " triples are added into the store.");
-        }
-        
-        public static String getRawTerm(GroundTerm r) {
-                if (r instanceof uk.ac.ox.cs.JRDFox.model.Individual)
-                        return ((uk.ac.ox.cs.JRDFox.model.Individual) r).getIRI(); 
-                else {
-                        Literal l = (Literal) r; 
-                        if (l.getDatatype().equals(Datatype.XSD_STRING) && l.getDatatype().equals(Datatype.RDF_PLAIN_LITERAL))
-                                return "\"" + l.getLexicalForm() + "\""; 
-                        else
-                                return "\"" + l.getLexicalForm() + "\"^^<" + l.getDatatype().getIRI() + ">"; 
-                }
-        }
-
-        protected DLPredicate getGapDLPredicate(DLPredicate dlPredicate) {
-                return getDLPredicate(dlPredicate, GapTupleIterator.gapPredicateSuffix); 
-        }
-
-        DLPredicate getDLPredicate(DLPredicate p, String suffix) {
-                if (p instanceof AtomicConcept) 
-                        return AtomicConcept.create(((AtomicConcept) p).getIRI() + suffix);
-                else if (p instanceof DatatypeRestriction) {
-                        DatatypeRestriction restriction = (DatatypeRestriction) p; 
-                        String newURI = restriction.getDatatypeURI() + suffix; 
-                        return getDatatypeRestriction(restriction, newURI);
-                }
-                else if (p instanceof AtomicRole)
-                        return AtomicRole.create(((AtomicRole) p).getIRI() + suffix);
-                else if (p instanceof AnnotatedEquality || p instanceof Equality) 
-                        return AtomicRole.create(Namespace.EQUALITY + suffix);
-                else if (p instanceof Inequality) 
-                        return AtomicRole.create(Namespace.INEQUALITY + suffix);
-                else if (p instanceof DatatypeRestriction)
-                        return AtomicConcept.create(((DatatypeRestriction) p).getDatatypeURI() + suffix);
-                else {
-                        Utility.logDebug("strange DL predicate appeared ... " + p, 
-                                        "the program paused here in TrackingRuleEncoderDisj.java"); 
-                        return null;
-                }
-        }
-
-        protected DLPredicate getTrackingDLPredicate(DLPredicate dlPredicate) {
-                return getDLPredicate(dlPredicate, getTrackingSuffix(currentQuery.getQueryID())); 
-        }
-        
-        protected static String getTrackingSuffix(String queryID) {
-                return "_AUXt" + queryID; 
-        }
-        
-        public String getTrackingPredicate(String predicateIRI) {
-                if (predicateIRI.startsWith("<"))
-                        return predicateIRI.replace(">", getTrackingSuffix(currentQuery.getQueryID()) + ">");
-                else 
-                        return predicateIRI + getTrackingSuffix(currentQuery.getQueryID());
-        }
-
-        protected DLPredicate getDatatypeRestriction(DatatypeRestriction restriction, String newName) {
-                int length = restriction.getNumberOfFacetRestrictions(); 
-                String[] facets = new String[length]; 
-                Constant[] values = new Constant[length]; 
-                for (int i = 0; i < length; ++i) {
-                        facets[i] = restriction.getFacetURI(i);
-                        values[i] = restriction.getFacetValue(i); 
-                }
-                return DatatypeRestriction.create(newName, facets, values); 
-        }
-
-        protected QueryRecord currentQuery;
-        DLPredicate selected; 
-        
-        public void setCurrentQuery(QueryRecord record) {
-                deprecateTrackingAndQueryRules();
-                currentQuery = record;
-                selected = AtomicConcept.create(getSelectedPredicate());
-                trackingSuffix = "_AUXt" + currentQuery.getQueryID(); 
-        }
-        
-        public void dispose() {
-                deprecateTrackingAndQueryRules();
-        }
-        
-        private String getTrackingRuleText() {
-                return DLClauseHelper.toString(trackingClauses);
-        }
-        
-        private String getQueryRuleText() {
-                return DLClauseHelper.toString(queryClauses);
-        }
-        
-        public String getTrackingProgram() {
-                StringBuilder sb = getTrackingProgramBody();
-                sb.insert(0, MyPrefixes.PAGOdAPrefixes.prefixesText()); 
-                return sb.toString(); 
-        }
-        
-        protected StringBuilder getTrackingProgramBody() {
-                encodingRules();
-                encodingQuery(new QueryRecord[0]);
-
-                StringBuilder sb = new StringBuilder(); 
-                sb.append(getTrackingRuleText());
-                sb.append(getEqualityRelatedRuleText());
-                sb.append(getQueryRuleText());
-                return sb; 
-        }
-
-        public void saveTrackingRules(String fileName) {
-                BufferedWriter writer = null;
-                try {
-                        writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(fileName)));
-                        writer.write(getTrackingProgram());
-                        writer.close();
-                } catch (IOException e) {
-                        e.printStackTrace();
-                        return ;
-                }
-                Utility.logDebug("The tracking rules are saved in " + fileName + "."); 
-        }
-
-        private void deprecateTrackingAndQueryRules() {
-                trackingClauses.clear(); 
-                queryClauses.clear();
-                addedData.clear();
-                ruleEncoded = false; 
-                queryEncoded = false; 
-        }
-
-        public String getSelectedPredicate() {
-                return getIRI("_selected" + currentQuery.getQueryID()); 
-        }
-
-        public DLClause getSelectedClause(String iri) {
-                int index = iri.lastIndexOf("_r") + 2;
-                int ruleIndex = Integer.parseInt(iri.substring(index));
-                return index2clause.get(ruleIndex);
-        }
-        
-        /**
-         * SELECT ?X
-         * WHERE {
-         *      ?X <http://www.w3.org/1999/02/22-rdf-syntax-ns#:type> :_selected?
-         * }
-         */
-        public String getSelectedSPARQLQuery() {
-                StringBuilder builder = new StringBuilder(); 
-                builder.append("SELECT ?X\nWHERE {\n?X <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> "); 
-                builder.append(selected.toString()).append("\n}");  
-                return builder.toString(); 
-        }
-
-        public OWLOntology getOntology() {
-                return program.getOntology(); 
-        }
-
-        public UpperDatalogProgram getProgram() {
-                return program;
-        }
-        
-        private String trackingSuffix; 
-        
-        public String getOriginalPredicate(String p) {
-                if (p.startsWith("<")) {
-                        if (!p.endsWith(trackingSuffix + ">")) return null;
-                }
-                else 
-                        if (!p.endsWith(trackingSuffix)) return null;
-                
-                return p.replace(trackingSuffix, ""); 
-        }
-
-        public boolean isAuxPredicate(String p) {
-                return false; 
-        }
-        
-        protected Set<String> unaryPredicates = new HashSet<String>(); 
-        protected Set<String> binaryPredicates = new HashSet<String>();
-        
+                    raw = ((t =
+                            answer.getGroundTerm(0)) instanceof uk.ac.ox.cs.JRDFox.model.Individual) ? ((uk.ac.ox.cs.JRDFox.model.Individual) t)
+                            .getIRI() : t.toString();
+                    triple = new int[]{tripleManager.getResourceID(raw), rdftype, predicate};
+                    addedData.add(triple);
+                    tripleManager.addTripleByID(triple);
+                }
+//                answerTuples.dispose();
+            }
+        }
+
+        Utility.logInfo(addedData.size() + " triples are added into the store.");
+    }
+
+    protected DLPredicate getGapDLPredicate(DLPredicate dlPredicate) {
+        return getDLPredicate(dlPredicate, GapTupleIterator.gapPredicateSuffix);
+    }
+
+    DLPredicate getDLPredicate(DLPredicate p, String suffix) {
+        if(isDisposed()) throw new DisposedException();
+        if(p instanceof AtomicConcept)
+            return AtomicConcept.create(((AtomicConcept) p).getIRI() + suffix);
+        else if(p instanceof DatatypeRestriction) {
+            DatatypeRestriction restriction = (DatatypeRestriction) p;
+            String newURI = restriction.getDatatypeURI() + suffix;
+            return getDatatypeRestriction(restriction, newURI);
+        }
+        else if(p instanceof AtomicRole)
+            return AtomicRole.create(((AtomicRole) p).getIRI() + suffix);
+        else if(p instanceof AnnotatedEquality || p instanceof Equality)
+            return AtomicRole.create(Namespace.EQUALITY + suffix);
+        else if(p instanceof Inequality)
+            return AtomicRole.create(Namespace.INEQUALITY + suffix);
+        else if(p instanceof DatatypeRestriction)
+            return AtomicConcept.create(((DatatypeRestriction) p).getDatatypeURI() + suffix);
+        else {
+            Utility.logDebug("strange DL predicate appeared ... " + p,
+                             "the program paused here in TrackingRuleEncoderDisj.java");
+            return null;
+        }
+    }
+
+    protected DLPredicate getTrackingDLPredicate(DLPredicate dlPredicate) {
+        return getDLPredicate(dlPredicate, getTrackingSuffix(currentQuery.getQueryID()));
+    }
+
+    protected DLPredicate getDatatypeRestriction(DatatypeRestriction restriction, String newName) {
+        int length = restriction.getNumberOfFacetRestrictions();
+        String[] facets = new String[length];
+        Constant[] values = new Constant[length];
+        for(int i = 0; i < length; ++i) {
+            facets[i] = restriction.getFacetURI(i);
+            values[i] = restriction.getFacetValue(i);
+        }
+        return DatatypeRestriction.create(newName, facets, values);
+    }
+
+    private String getTrackingRuleText() {
+        return DLClauseHelper.toString(trackingClauses);
+    }
+
+    private String getQueryRuleText() {
+        return DLClauseHelper.toString(queryClauses);
+    }
+
+    protected StringBuilder getTrackingProgramBody() {
+        encodingRules();
+        encodingQuery(new QueryRecord[0]);
+
+        StringBuilder sb = new StringBuilder();
+        sb.append(getTrackingRuleText());
+        sb.append(getEqualityRelatedRuleText());
+        sb.append(getQueryRuleText());
+        return sb;
+    }
+
+    private void deprecateTrackingAndQueryRules() {
+        trackingClauses.clear();
+        queryClauses.clear();
+        addedData.clear();
+        ruleEncoded = false;
+        queryEncoded = false;
+    }
+
 }
diff --git a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java b/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java
index c3694ad..4ece796 100644
--- a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java
+++ b/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java
@@ -17,7 +17,7 @@ import java.util.LinkedList;
 import java.util.Set;
 
 public class TrackingRuleEncoderWithGap extends TrackingRuleEncoder {
-        
+
         public TrackingRuleEncoderWithGap(UpperDatalogProgram program, BasicQueryEngine store) {
                 super(program, store);
         }
@@ -113,6 +113,4 @@ public class TrackingRuleEncoderWithGap extends TrackingRuleEncoder {
                 }
                 
         }
-
-
 }
diff --git a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithoutGap.java b/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithoutGap.java
index be9e45c..f898114 100644
--- a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithoutGap.java
+++ b/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithoutGap.java
@@ -1,24 +1,19 @@
 package uk.ac.ox.cs.pagoda.tracking;
 
-import java.util.Collection;
-import java.util.LinkedList;
-
-import org.semanticweb.HermiT.model.Atom;
-import org.semanticweb.HermiT.model.AtomicConcept;
-import org.semanticweb.HermiT.model.AtomicRole;
-import org.semanticweb.HermiT.model.DLClause;
-import org.semanticweb.HermiT.model.Variable;
+import org.semanticweb.HermiT.model.*;
 import org.semanticweb.owlapi.model.OWLClass;
 import org.semanticweb.owlapi.model.OWLObjectProperty;
 import org.semanticweb.owlapi.model.OWLOntology;
-
 import uk.ac.ox.cs.pagoda.hermit.DLClauseHelper;
 import uk.ac.ox.cs.pagoda.reasoner.light.BasicQueryEngine;
 import uk.ac.ox.cs.pagoda.rules.UpperDatalogProgram;
 import uk.ac.ox.cs.pagoda.util.Namespace;
 
+import java.util.Collection;
+import java.util.LinkedList;
+
 public class TrackingRuleEncoderWithoutGap extends TrackingRuleEncoder {
-        
+
         public TrackingRuleEncoderWithoutGap(UpperDatalogProgram program, BasicQueryEngine store) {
                 super(program, store); 
         }
@@ -105,5 +100,4 @@ public class TrackingRuleEncoderWithoutGap extends TrackingRuleEncoder {
                 }
                 
         }
-
 }
diff --git a/src/uk/ac/ox/cs/pagoda/util/disposable/Disposable.java b/src/uk/ac/ox/cs/pagoda/util/disposable/Disposable.java
new file mode 100644
index 0000000..b208cc3
--- /dev/null
+++ b/src/uk/ac/ox/cs/pagoda/util/disposable/Disposable.java
@@ -0,0 +1,39 @@
+package uk.ac.ox.cs.pagoda.util.disposable;
+
+
+/**
+ * Every public method of a subclass of this class,
+ * as first instruction, should check if the object has already been disposed
+ * and, if so, should throw a <tt>DisposedException</tt>.
+ */
+public abstract class Disposable {
+
+    private boolean disposed = false;
+
+    /**
+     * This method must be called after the use of the object.
+     * <p>
+     * Every overriding method must call <tt>super.dispose()</tt> as first instruction.
+     */
+    public void dispose() {
+        if(isDisposed()) throw new AlreadyDisposedException();
+        disposed = true;
+    }
+
+    public final boolean isDisposed() {
+        return disposed;
+    }
+
+    private class AlreadyDisposedException extends RuntimeException {
+
+        public AlreadyDisposedException() {
+            super();
+        }
+
+        public AlreadyDisposedException(String msg) {
+            super(msg);
+        }
+    }
+
+
+}
diff --git a/src/uk/ac/ox/cs/pagoda/util/disposable/DisposedException.java b/src/uk/ac/ox/cs/pagoda/util/disposable/DisposedException.java
new file mode 100644
index 0000000..eb8c039
--- /dev/null
+++ b/src/uk/ac/ox/cs/pagoda/util/disposable/DisposedException.java
@@ -0,0 +1,12 @@
+package uk.ac.ox.cs.pagoda.util.disposable;
+
+public class DisposedException extends RuntimeException {
+
+    public DisposedException() {
+        super();
+    }
+
+    public DisposedException(String msg) {
+        super(msg);
+    }
+}
diff --git a/test/resources/LightTests.xml b/test/resources/LightTests.xml
index a30c436..ccafa25 100644
--- a/test/resources/LightTests.xml
+++ b/test/resources/LightTests.xml
@@ -10,8 +10,8 @@
         </groups>
 
         <classes>
-            <class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaUOBM"/>
-            <!--<class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaLUBM"/>-->
+            <!--<class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaUOBM"/>-->
+            <class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaLUBM"/>
             <!--<class name="uk.ac.ox.cs.pagoda.global_tests.TestPagodaFLY"/>-->
         </classes>
     </test>