[pagoda] Move project to Scala

This commit includes a few changes:
- The repository still uses Maven to manage dependency but it is now a
  Scala project.
- The code has been ported from OWLAPI 3.4.10 to 5.1.20
- A proof of concept program using both RSAComb and PAGOdA has been
  added.

213 files changed, 523 insertions, 334 deletions

diff --git a/external/uk/ac/ox/cs/data/OntologyStatistics.java b/external/uk/ac/ox/cs/data/OntologyStatistics.java
index de40dda..e4e7942 100644
--- a/external/uk/ac/ox/cs/data/OntologyStatistics.java
+++ b/external/uk/ac/ox/cs/data/OntologyStatistics.java
@@ -1,6 +1,7 @@
 package uk.ac.ox.cs.data;
 
 import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.parameters.Imports;
 import uk.ac.ox.cs.pagoda.owl.OWLHelper;
 
 public class OntologyStatistics {
@@ -9,7 +10,7 @@ public class OntologyStatistics {
                 args = ("/home/yzhou/ontologies/uobm/univ-bench-dl-minus.owl").split("\\ "); 
 
                 OWLOntology onto = OWLHelper.loadOntology(args[0]);
-                System.out.println(onto.getTBoxAxioms(true).size() + onto.getRBoxAxioms(true).size()); 
+                System.out.println(onto.getTBoxAxioms(Imports.INCLUDED).size() + onto.getRBoxAxioms(Imports.INCLUDED).size()); 
         }
         
 }
diff --git a/pom.xml b/pom.xml
index 466383a..63a853d 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1,16 +1,35 @@
-<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0"
-        xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-        <modelVersion>4.0.0</modelVersion>
-        <groupId>uk.ac.ox.cs.pagoda</groupId>
-        <artifactId>pagoda</artifactId>
-        <version>2.1.2</version>
+<?xml version="1.0" encoding="UTF-8"?>
+
+<project
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xmlns="http://maven.apache.org/POM/4.0.0"
+    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd"
+>
+    <modelVersion>4.0.0</modelVersion>
+
+    <name>ACQuA</name>
+    <description>Answering Conjunctive Queries using Approximation</description>
+
+    <groupId>uk.ac.ox.cs.acqua</groupId>
+    <artifactId>acqua</artifactId>
+    <version>0.1.0</version>
+
         <packaging>jar</packaging>
-        <name>PAGOdA</name>
-    <properties>
-        <skipTests>true</skipTests>
-    </properties>
+
+  <properties>
+    <maven.compiler.source>1.8</maven.compiler.source>
+    <maven.compiler.target>1.8</maven.compiler.target>
+    <!-- <encoding>UTF-8</encoding> -->
+    <scala.version>2.13.6</scala.version>
+    <scala.compat.version>2.13</scala.compat.version>
+    <spec2.version>4.2.0</spec2.version>
+    <skipTests>true</skipTests>
+  </properties>
+
     <repositories>
-        <!--other repositories if any-->
+        <!-- Old RDFox 1.0.0 dependency
+             To be eventually removed!
+          -->
         <repository>
             <id>project.local</id>
             <name>pagoda</name>
@@ -18,119 +37,18 @@
         </repository>
     </repositories>
 
-    <build>
-                <sourceDirectory>src</sourceDirectory>
-                <testSourceDirectory>test</testSourceDirectory>
-                <resources>
-                        <resource>
-                                <directory>src/resources</directory>
-                                <excludes>
-                                        <exclude>pagoda.properties</exclude>
-                                </excludes>
-                        </resource>
-
-                </resources>
-                <testResources>
-                        <testResource>
-                                <directory>test/resources</directory>
-                        </testResource>
-                </testResources>
-                <plugins>
-                        <plugin>
-                                <artifactId>maven-compiler-plugin</artifactId>
-                                <version>3.1</version>
-                                <configuration>
-                                        <source>1.8</source>
-                                        <target>1.8</target>
-                                </configuration>
-                        </plugin>
-                        <plugin>
-                                <artifactId>maven-project-info-reports-plugin</artifactId>
-                                <version>2.7</version>
-                        </plugin>
-                        <plugin>
-                                <artifactId>maven-assembly-plugin</artifactId>
-                                <configuration>
-                                        <archive>
-                                                <manifest>
-                                                        <mainClass>uk.ac.ox.cs.pagoda.Pagoda</mainClass>
-                                                </manifest>
-                                        </archive>
-                                        <descriptorRefs>
-                                                <descriptorRef>jar-with-dependencies</descriptorRef>
-                                        </descriptorRefs>
-                                </configuration>
-                                <executions>
-                                        <execution>
-                                                <id>make-assembly</id> <!-- this is used for inheritance merges -->
-                                                <phase>package</phase> <!-- bind to the packaging phase -->
-                                                <goals>
-                                                        <goal>single</goal>
-                                                </goals>
-                                        </execution>
-                                </executions>
-                        </plugin>
-                </plugins>
-        </build>
-        <reporting>
-                <plugins>
-                        <plugin>
-                                <groupId>org.apache.maven.plugins</groupId>
-                                <artifactId>maven-javadoc-plugin</artifactId>
-                                <version>2.9.1</version>
-                                <configuration>
-                                        <show>public</show>
-                                </configuration>
-                        </plugin>
-                        <plugin>
-                                <groupId>org.codehaus.mojo</groupId>
-                                <artifactId>findbugs-maven-plugin</artifactId>
-                                <version>3.0.0</version>
-                                <configuration>
-                                        <xmlOutput>true</xmlOutput>
-                                        <!-- Optional directory to put findbugs xdoc xml report -->
-                                        <xmlOutputDirectory>target/site</xmlOutputDirectory>
-                                </configuration>
-                        </plugin>
-                        <plugin>
-                                <groupId>org.apache.maven.plugins</groupId>
-                                <artifactId>maven-checkstyle-plugin</artifactId>
-                                <version>2.5</version>
-                                <configuration>
-                                        <configLocation>config/sun_checks.xml</configLocation><!-- default -->
-                                        <!-- <configLocation>config/maven_checks.xml</configLocation> -->
-                                        <!-- <configLocation>config/turbine_checks.xml</configLocation> -->
-                                        <!-- <configLocation>config/avalon_checks.xml</configLocation> -->
-                                </configuration>
-                        </plugin>
-                        <plugin>
-                                <groupId>org.apache.maven.plugins</groupId>
-                                <artifactId>maven-jxr-plugin</artifactId>
-                                <version>2.1</version>
-                        </plugin>
-                        <plugin>
-                                <groupId>org.codehaus.mojo</groupId>
-                                <artifactId>dashboard-maven-plugin</artifactId>
-                                <version>1.0.0-beta-1</version>
-                        </plugin>
-                        <!--<plugin>-->
-                                <!--<groupId>org.apache.maven.plugins</groupId>-->
-                                <!--<artifactId>maven-surefire-plugin</artifactId>-->
-                                <!--<version>2.13</version>-->
-                                <!--<configuration>-->
-                                        <!--<forkMode>always</forkMode>-->
-                                        <!--<systemPropertyVariables>-->
-                                                <!--<reporter.debug>false</reporter.debug>-->
-                                        <!--</systemPropertyVariables>-->
-                                        <!--<suiteXmlFiles>-->
-                                                <!--<suiteXmlFile>testResources/LightTests.xml</suiteXmlFile>-->
-                                        <!--</suiteXmlFiles>-->
-                                <!--</configuration>-->
-                        <!--</plugin>-->
-                </plugins>
-        </reporting>
         <dependencies>
                 <dependency>
+                        <groupId>org.scala-lang</groupId>
+                        <artifactId>scala-library</artifactId>
+            <version>${scala.version}</version>
+                </dependency>
+        <dependency>
+            <groupId>com.lihaoyi</groupId>
+            <artifactId>os-lib_2.13</artifactId>
+            <version>0.8.1</version>
+        </dependency>
+                <dependency>
                         <groupId>commons-cli</groupId>
                         <artifactId>commons-cli</artifactId>
                         <version>1.3</version>
@@ -143,7 +61,8 @@
                 <dependency>
                         <groupId>net.sourceforge.owlapi</groupId>
                         <artifactId>owlapi-distribution</artifactId>
-                        <version>3.4.10</version>
+                        <version>5.1.20</version>
+                        <!-- <version>3.4.10</version> -->
                 </dependency>
                 <dependency>
                         <groupId>org.openrdf.sesame</groupId>
@@ -207,5 +126,242 @@
                         <!--<artifactId>plexus-utils</artifactId>-->
                         <!--<version>1.1</version>-->
                 <!--</dependency>-->
+    <dependency>
+      <groupId>org.scalatest</groupId>
+      <artifactId>scalatest_${scala.compat.version}</artifactId>
+      <version>3.2.10</version>
+      <scope>test</scope>
+    </dependency>
+                <dependency>
+                        <groupId>uk.ox.ac.uk.rsacomb</groupId>
+                        <artifactId>rsacomb</artifactId>
+                        <version>1.0.0</version>
+            <scope>system</scope>
+            <systemPath>${project.basedir}/lib/RSAComb-1.0.0.jar</systemPath>
+                </dependency>
+                <dependency>
+                        <groupId>tech.oxfordsemantic.jrdfox</groupId>
+                        <artifactId>jrdfox</artifactId>
+                        <version>5.4</version>
+            <scope>system</scope>
+            <systemPath>${project.basedir}/lib/JRDFox.jar</systemPath>
+                </dependency>
+
+
+
+
         </dependencies>
+
+        <build>
+                <pluginManagement>
+                        <plugins>
+                                <plugin>
+                                        <groupId>org.apache.maven.plugins</groupId>
+                                        <artifactId>maven-compiler-plugin</artifactId>
+                                        <version>3.8.1</version>
+                                        <configuration>
+                      <source>1.8</source>
+                      <target>1.8</target>
+                    </configuration>
+                                </plugin>
+                                <plugin>
+                                        <groupId>net.alchim31.maven</groupId>
+                                        <artifactId>scala-maven-plugin</artifactId>
+                                        <version>4.5.6</version>
+                                </plugin>
+                        </plugins>
+                </pluginManagement>
+                <plugins>
+                        <plugin>
+                                <groupId>org.apache.maven.plugins</groupId>
+                                <artifactId>maven-compiler-plugin</artifactId>
+                                <configuration>
+                  <source>1.8</source>
+                  <target>1.8</target>
+                </configuration>
+                                <executions>
+                                        <execution>
+                                                <phase>compile</phase>
+                                                <goals>
+                                                        <goal>compile</goal>
+                                                </goals>
+                                        </execution>
+                                </executions>
+                        </plugin>
+                        <plugin>
+                                <groupId>net.alchim31.maven</groupId>
+                                <artifactId>scala-maven-plugin</artifactId>
+                                <executions>
+                                        <execution>
+                                                <!-- <id>scala-compile-first</id> -->
+                                                <phase>compile</phase>
+                                                <goals>
+                                                        <goal>add-source</goal>
+                                                        <goal>compile</goal>
+                                                </goals>
+                                        </execution>
+                                        <execution>
+                                                <id>scala-test-compile</id>
+                                                <phase>process-test-resources</phase>
+                                                <goals>
+                                                        <goal>testCompile</goal>
+                                                </goals>
+                                        </execution>
+                                </executions>
+                        </plugin>
+                        <plugin>
+                                <artifactId>maven-assembly-plugin</artifactId>
+                                <configuration>
+                                        <archive>
+                                                <manifest>
+                                                        <mainClass>uk.ac.ox.cs.acqua.Acqua</mainClass>
+                                                </manifest>
+                                        </archive>
+                                        <descriptorRefs>
+                                                <descriptorRef>jar-with-dependencies</descriptorRef>
+                                        </descriptorRefs>
+                                </configuration>
+                                <executions>
+                                        <execution>
+                                                <id>make-assembly</id> <!-- this is used for inheritance merges -->
+                                                <phase>package</phase> <!-- bind to the packaging phase -->
+                                                <goals>
+                                                        <goal>single</goal>
+                                                </goals>
+                                        </execution>
+                                </executions>
+                        </plugin>
+                </plugins>
+        </build>
+
+  <!--  <build>-->
+  <!--      <sourceDirectory>src/main/scala</sourceDirectory>-->
+  <!--      <testSourceDirectory>src/test/scala</testSourceDirectory>-->
+                <!--<resources>-->
+                        <!--<resource>-->
+                                <!--<directory>src/main/java/resources</directory>-->
+                                <!--<excludes>-->
+                                        <!--<exclude>pagoda.properties</exclude>-->
+                                <!--</excludes>-->
+                        <!--</resource>-->
+
+                <!--</resources>-->
+                <!--<testResources>-->
+                        <!--<testResource>-->
+  <!--              <directory>src/test/java/resources</directory>-->
+                        <!--</testResource>-->
+                <!--</testResources>-->
+                <!--<plugins>-->
+                        <!--<plugin>-->
+                                <!--<artifactId>maven-compiler-plugin</artifactId>-->
+                                <!--<version>3.1</version>-->
+                                <!--<configuration>-->
+                                        <!--<source>1.8</source>-->
+                                        <!--<target>1.8</target>-->
+                                <!--</configuration>-->
+                        <!--</plugin>-->
+
+
+                        <!--<plugin>-->
+                                <!--<artifactId>maven-project-info-reports-plugin</artifactId>-->
+                                <!--<version>2.7</version>-->
+                        <!--</plugin>-->
+
+  <!--        <plugin>-->
+  <!--          <groupId>org.apache.maven.plugins</groupId>-->
+  <!--          <artifactId>maven-surefire-plugin</artifactId>-->
+  <!--          <version>2.21.0</version>-->
+  <!--          <configuration>-->
+  <!--            <!-1- Tests will be run with scalatest-maven-plugin instead -1->-->
+  <!--            <skipTests>true</skipTests>-->
+  <!--          </configuration>-->
+  <!--        </plugin>-->
+  <!--        <plugin>-->
+  <!--          <groupId>org.scalatest</groupId>-->
+  <!--          <artifactId>scalatest-maven-plugin</artifactId>-->
+  <!--          <version>2.0.0</version>-->
+  <!--          <configuration>-->
+  <!--            <reportsDirectory>${project.build.directory}/surefire-reports</reportsDirectory>-->
+  <!--            <junitxml>.</junitxml>-->
+  <!--            <filereports>TestSuiteReport.txt</filereports>-->
+  <!--            <!-1- Comma separated list of JUnit test class names to execute -1->-->
+  <!--            <jUnitClasses>samples.AppTest</jUnitClasses>-->
+  <!--          </configuration>-->
+  <!--          <executions>-->
+  <!--            <execution>-->
+  <!--              <id>test</id>-->
+  <!--              <goals>-->
+  <!--                <goal>test</goal>-->
+  <!--              </goals>-->
+  <!--            </execution>-->
+  <!--          </executions>-->
+  <!--        </plugin>-->
+                <!--</plugins>-->
+        <!--</build>-->
+
+        <!--<reporting>-->
+                <!--<plugins>-->
+                        <!--<plugin>-->
+                                <!--<groupId>org.apache.maven.plugins</groupId>-->
+                                <!--<artifactId>maven-javadoc-plugin</artifactId>-->
+                                <!--<version>2.9.1</version>-->
+                                <!--<configuration>-->
+                                        <!--<show>public</show>-->
+                                <!--</configuration>-->
+                        <!--</plugin>-->
+                        <!--<plugin>-->
+                                <!--<groupId>org.codehaus.mojo</groupId>-->
+                                <!--<artifactId>findbugs-maven-plugin</artifactId>-->
+                                <!--<version>3.0.0</version>-->
+                                <!--<configuration>-->
+                                        <!--<xmlOutput>true</xmlOutput>-->
+                                        <!--<!-1- Optional directory to put findbugs xdoc xml report -1->-->
+                                        <!--<xmlOutputDirectory>target/site</xmlOutputDirectory>-->
+                                <!--</configuration>-->
+                        <!--</plugin>-->
+                        <!--<plugin>-->
+                                <!--<groupId>org.apache.maven.plugins</groupId>-->
+                                <!--<artifactId>maven-checkstyle-plugin</artifactId>-->
+                                <!--<version>2.5</version>-->
+                                <!--<configuration>-->
+                                        <!--<configLocation>config/sun_checks.xml</configLocation><!-1- default -1->-->
+                                        <!--<!-1- <configLocation>config/maven_checks.xml</configLocation> -1->-->
+                                        <!--<!-1- <configLocation>config/turbine_checks.xml</configLocation> -1->-->
+                                        <!--<!-1- <configLocation>config/avalon_checks.xml</configLocation> -1->-->
+                                <!--</configuration>-->
+                        <!--</plugin>-->
+                        <!--<plugin>-->
+                                <!--<groupId>org.apache.maven.plugins</groupId>-->
+                                <!--<artifactId>maven-jxr-plugin</artifactId>-->
+                                <!--<version>2.1</version>-->
+                        <!--</plugin>-->
+                        <!--<plugin>-->
+                                <!--<groupId>org.codehaus.mojo</groupId>-->
+                                <!--<artifactId>dashboard-maven-plugin</artifactId>-->
+                                <!--<version>1.0.0-beta-1</version>-->
+                        <!--</plugin>-->
+                        <!--<!-1-<plugin>-1->-->
+                                <!--<!-1-<groupId>org.apache.maven.plugins</groupId>-1->-->
+                                <!--<!-1-<artifactId>maven-surefire-plugin</artifactId>-1->-->
+                                <!--<!-1-<version>2.13</version>-1->-->
+                                <!--<!-1-<configuration>-1->-->
+                                        <!--<!-1-<forkMode>always</forkMode>-1->-->
+                                        <!--<!-1-<systemPropertyVariables>-1->-->
+                                                <!--<!-1-<reporter.debug>false</reporter.debug>-1->-->
+                                        <!--<!-1-</systemPropertyVariables>-1->-->
+                                        <!--<!-1-<suiteXmlFiles>-1->-->
+                                                <!--<!-1-<suiteXmlFile>testResources/LightTests.xml</suiteXmlFile>-1->-->
+                                        <!--<!-1-</suiteXmlFiles>-1->-->
+                                <!--<!-1-</configuration>-1->-->
+                        <!--<!-1-</plugin>-1->-->
+                <!--</plugins>-->
+        <!--</reporting>-->
+
+        <!--<dependencies>-->
+  <!--  <dependency>-->
+  <!--    <groupId>org.scala-lang</groupId>-->
+  <!--    <artifactId>scala-library</artifactId>-->
+  <!--    <version>${scala.version}</version>-->
+  <!--  </dependency>-->
+        <!--</dependencies>-->
 </project>
diff --git a/src/org/semanticweb/karma2/MyKarma.java b/src/main/java/org/semanticweb/karma2/MyKarma.java
index b2b4352..b2b4352 100644
--- a/src/org/semanticweb/karma2/MyKarma.java
+++ b/src/main/java/org/semanticweb/karma2/MyKarma.java
diff --git a/src/org/semanticweb/karma2/clausifier/OntologyProcesser.java b/src/main/java/org/semanticweb/karma2/clausifier/OntologyProcesser.java
index fee8dff..5ff339e 100644
--- a/src/org/semanticweb/karma2/clausifier/OntologyProcesser.java
+++ b/src/main/java/org/semanticweb/karma2/clausifier/OntologyProcesser.java
@@ -66,7 +66,7 @@ import org.semanticweb.owlapi.model.OWLObjectUnionOf;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLSameIndividualAxiom;
 import org.semanticweb.owlapi.profiles.OWLProfileReport;
-import org.semanticweb.owlapi.util.OWLAxiomVisitorAdapter;
+import org.semanticweb.owlapi.model.OWLAxiomVisitor;
 
 import uk.ac.ox.cs.pagoda.util.Utility;
 
@@ -522,7 +522,7 @@ public class OntologyProcesser {
         }
     }
 
-         protected static class DatalogFactClausifier extends OWLAxiomVisitorAdapter {
+         protected static class DatalogFactClausifier implements OWLAxiomVisitor {
                 protected final Set<Atom> m_positiveFacts;
 
                 public DatalogFactClausifier(Set<Atom> positiveFacts) {
diff --git a/src/org/semanticweb/karma2/exception/ConstraintException.java b/src/main/java/org/semanticweb/karma2/exception/ConstraintException.java
index d02e1b1..d02e1b1 100644
--- a/src/org/semanticweb/karma2/exception/ConstraintException.java
+++ b/src/main/java/org/semanticweb/karma2/exception/ConstraintException.java
diff --git a/src/org/semanticweb/karma2/exception/IllegalInputOntologyException.java b/src/main/java/org/semanticweb/karma2/exception/IllegalInputOntologyException.java
index 18df25a..18df25a 100644
--- a/src/org/semanticweb/karma2/exception/IllegalInputOntologyException.java
+++ b/src/main/java/org/semanticweb/karma2/exception/IllegalInputOntologyException.java
diff --git a/src/org/semanticweb/karma2/exception/IllegalInputQueryException.java b/src/main/java/org/semanticweb/karma2/exception/IllegalInputQueryException.java
index bb94cb7..bb94cb7 100644
--- a/src/org/semanticweb/karma2/exception/IllegalInputQueryException.java
+++ b/src/main/java/org/semanticweb/karma2/exception/IllegalInputQueryException.java
diff --git a/src/org/semanticweb/karma2/exception/QueryExecutionException.java b/src/main/java/org/semanticweb/karma2/exception/QueryExecutionException.java
index bb393ba..bb393ba 100644
--- a/src/org/semanticweb/karma2/exception/QueryExecutionException.java
+++ b/src/main/java/org/semanticweb/karma2/exception/QueryExecutionException.java
diff --git a/src/org/semanticweb/karma2/model/ConjunctiveQuery.java b/src/main/java/org/semanticweb/karma2/model/ConjunctiveQuery.java
index 17f3169..17f3169 100644
--- a/src/org/semanticweb/karma2/model/ConjunctiveQuery.java
+++ b/src/main/java/org/semanticweb/karma2/model/ConjunctiveQuery.java
diff --git a/src/org/semanticweb/karma2/model/Equality.java b/src/main/java/org/semanticweb/karma2/model/Equality.java
index fcb270c..fcb270c 100644
--- a/src/org/semanticweb/karma2/model/Equality.java
+++ b/src/main/java/org/semanticweb/karma2/model/Equality.java
diff --git a/src/org/semanticweb/karma2/model/ExtendedConjunctiveQuery.java b/src/main/java/org/semanticweb/karma2/model/ExtendedConjunctiveQuery.java
index de2f87e..de2f87e 100644
--- a/src/org/semanticweb/karma2/model/ExtendedConjunctiveQuery.java
+++ b/src/main/java/org/semanticweb/karma2/model/ExtendedConjunctiveQuery.java
diff --git a/src/org/semanticweb/karma2/model/cqparser/ConjunctiveQuery.g b/src/main/java/org/semanticweb/karma2/model/cqparser/ConjunctiveQuery.g
index 621b0ce..621b0ce 100644
--- a/src/org/semanticweb/karma2/model/cqparser/ConjunctiveQuery.g
+++ b/src/main/java/org/semanticweb/karma2/model/cqparser/ConjunctiveQuery.g
diff --git a/src/org/semanticweb/karma2/model/cqparser/ConjunctiveQuery.tokens b/src/main/java/org/semanticweb/karma2/model/cqparser/ConjunctiveQuery.tokens
index 3b4fa39..3b4fa39 100644
--- a/src/org/semanticweb/karma2/model/cqparser/ConjunctiveQuery.tokens
+++ b/src/main/java/org/semanticweb/karma2/model/cqparser/ConjunctiveQuery.tokens
diff --git a/src/org/semanticweb/karma2/model/cqparser/ConjunctiveQueryLexer.java b/src/main/java/org/semanticweb/karma2/model/cqparser/ConjunctiveQueryLexer.java
index a97d7a4..a97d7a4 100644
--- a/src/org/semanticweb/karma2/model/cqparser/ConjunctiveQueryLexer.java
+++ b/src/main/java/org/semanticweb/karma2/model/cqparser/ConjunctiveQueryLexer.java
diff --git a/src/org/semanticweb/karma2/model/cqparser/ConjunctiveQueryParser.java b/src/main/java/org/semanticweb/karma2/model/cqparser/ConjunctiveQueryParser.java
index b934e30..b934e30 100644
--- a/src/org/semanticweb/karma2/model/cqparser/ConjunctiveQueryParser.java
+++ b/src/main/java/org/semanticweb/karma2/model/cqparser/ConjunctiveQueryParser.java
diff --git a/src/org/semanticweb/karma2/model/cqparser/ConjunctiveQueryWalker.java b/src/main/java/org/semanticweb/karma2/model/cqparser/ConjunctiveQueryWalker.java
index f10b761..f10b761 100644
--- a/src/org/semanticweb/karma2/model/cqparser/ConjunctiveQueryWalker.java
+++ b/src/main/java/org/semanticweb/karma2/model/cqparser/ConjunctiveQueryWalker.java
diff --git a/src/org/semanticweb/karma2/profile/ELHOProfile.java b/src/main/java/org/semanticweb/karma2/profile/ELHOProfile.java
index fb68b05..23761f0 100644
--- a/src/org/semanticweb/karma2/profile/ELHOProfile.java
+++ b/src/main/java/org/semanticweb/karma2/profile/ELHOProfile.java
@@ -35,10 +35,10 @@ import org.semanticweb.owlapi.profiles.OWL2ELProfile;
 import org.semanticweb.owlapi.profiles.OWLProfile;
 import org.semanticweb.owlapi.profiles.OWLProfileReport;
 import org.semanticweb.owlapi.profiles.OWLProfileViolation;
-import org.semanticweb.owlapi.profiles.UseOfDataOneOfWithMultipleLiterals;
-import org.semanticweb.owlapi.profiles.UseOfIllegalAxiom;
-import org.semanticweb.owlapi.profiles.UseOfIllegalClassExpression;
-import org.semanticweb.owlapi.profiles.UseOfObjectOneOfWithMultipleIndividuals;
+import org.semanticweb.owlapi.profiles.violations.UseOfDataOneOfWithMultipleLiterals;
+import org.semanticweb.owlapi.profiles.violations.UseOfIllegalAxiom;
+import org.semanticweb.owlapi.profiles.violations.UseOfIllegalClassExpression;
+import org.semanticweb.owlapi.profiles.violations.UseOfObjectOneOfWithMultipleIndividuals;
 import org.semanticweb.owlapi.util.OWLObjectPropertyManager;
 import org.semanticweb.owlapi.util.OWLOntologyWalker;
 import org.semanticweb.owlapi.util.OWLOntologyWalkerVisitor;
@@ -96,7 +96,7 @@ public class ELHOProfile implements OWLProfile {
         for (Iterator<OWLProfileViolation> iter = violations.iterator(); iter.hasNext(); ) {
                 OWLProfileViolation vio = iter.next(); 
                 if (vio instanceof UseOfIllegalClassExpression) {
-                        OWLClassExpression exp = ((UseOfIllegalClassExpression) vio).getOWLClassExpression(); 
+                        OWLClassExpression exp = ((UseOfIllegalClassExpression) vio).getExpression(); 
                         if (exp instanceof OWLObjectMinCardinality && ((OWLObjectMinCardinality) exp).getCardinality() == 1)
                                 iter.remove(); 
                 }
@@ -111,7 +111,7 @@ public class ELHOProfile implements OWLProfile {
                 return "ELHO";
         }
         
-         protected class ELHOProfileObjectVisitor extends OWLOntologyWalkerVisitor<Object> {
+         protected class ELHOProfileObjectVisitor extends OWLOntologyWalkerVisitor {
 
                 private final OWLOntologyManager man;
 
@@ -131,7 +131,7 @@ public class ELHOProfile implements OWLProfile {
                 @SuppressWarnings("unused")
                         private OWLObjectPropertyManager getPropertyManager() {
                     if (propertyManager == null) {
-                        propertyManager = new OWLObjectPropertyManager(man, getCurrentOntology());
+                        propertyManager = new OWLObjectPropertyManager(getCurrentOntology());
                     }
                     return propertyManager;
                 }
@@ -139,135 +139,115 @@ public class ELHOProfile implements OWLProfile {
 
                 
                 @Override
-                        public Object visit(OWLDataProperty p) {
+                        public void visit(OWLDataProperty p) {
                     profileViolations.add(new UseOfIllegalAxiom(getCurrentOntology(), getCurrentAxiom()));
-                    return null;
                 }
 
                
                 @Override
-                        public Object visit(OWLObjectOneOf desc) {
+                        public void visit(OWLObjectOneOf desc) {
                     if (desc.getIndividuals().size() != 1) {
                         profileViolations.add(new UseOfObjectOneOfWithMultipleIndividuals(getCurrentOntology(), getCurrentAxiom(), desc));
                     }
-                    return null;
                 }
                 
                 @Override
-                        public Object visit(OWLDataHasValue desc) {
+                        public void visit(OWLDataHasValue desc) {
                         profileViolations.add(new UseOfIllegalClassExpression(getCurrentOntology(), getCurrentAxiom(), desc));
-                    return null;
                 }
                 
                 @Override
-                        public Object visit(OWLDataSomeValuesFrom desc) {
+                        public void visit(OWLDataSomeValuesFrom desc) {
                         profileViolations.add(new UseOfIllegalClassExpression(getCurrentOntology(), getCurrentAxiom(), desc));
-                    return null;
                 }
                 
                 @Override
-                        public Object visit(OWLDataIntersectionOf desc) {
+                        public void visit(OWLDataIntersectionOf desc) {
                         profileViolations.add(new UseOfIllegalAxiom(getCurrentOntology(), getCurrentAxiom()));
-                    return null;
                 }
                 
                 @Override
-                        public Object visit(OWLSubDataPropertyOfAxiom desc) {
+                        public void visit(OWLSubDataPropertyOfAxiom desc) {
                         profileViolations.add(new UseOfIllegalAxiom(getCurrentOntology(), getCurrentAxiom()));
-                    return null;
                 }
                 
                 @Override
-                        public Object visit(OWLEquivalentDataPropertiesAxiom desc) {
+                        public void visit(OWLEquivalentDataPropertiesAxiom desc) {
                         profileViolations.add(new UseOfIllegalAxiom(getCurrentOntology(), getCurrentAxiom()));
-                    return null;
                 }
                 
                 @Override
-                        public Object visit(OWLTransitiveObjectPropertyAxiom desc) {
+                        public void visit(OWLTransitiveObjectPropertyAxiom desc) {
                         profileViolations.add(new UseOfIllegalAxiom(getCurrentOntology(), getCurrentAxiom()));
-                    return null;
                 }
                 
                 @Override
-                        public Object visit(OWLReflexiveObjectPropertyAxiom desc) {
+                        public void visit(OWLReflexiveObjectPropertyAxiom desc) {
                         profileViolations.add(new UseOfIllegalAxiom(getCurrentOntology(), getCurrentAxiom()));
-                    return null;
                 }
                 
                 @Override
-                        public Object visit(OWLDataPropertyDomainAxiom desc) {
+                        public void visit(OWLDataPropertyDomainAxiom desc) {
                         profileViolations.add(new UseOfIllegalAxiom(getCurrentOntology(), getCurrentAxiom()));
-                    return null;
                 }
                 
                 @Override
-                        public Object visit(OWLDataPropertyRangeAxiom desc) {
+                        public void visit(OWLDataPropertyRangeAxiom desc) {
                         profileViolations.add(new UseOfIllegalAxiom(getCurrentOntology(), getCurrentAxiom()));
-                    return null;
                 }
                 
                 
                 
                 @Override
-                        public Object visit(OWLDataPropertyAssertionAxiom desc) {
+                        public void visit(OWLDataPropertyAssertionAxiom desc) {
                         profileViolations.add(new UseOfIllegalAxiom(getCurrentOntology(), getCurrentAxiom()));
-                    return null;
                 }
                 
                 @Override
-                        public Object visit(OWLNegativeDataPropertyAssertionAxiom desc) {
+                        public void visit(OWLNegativeDataPropertyAssertionAxiom desc) {
                         profileViolations.add(new UseOfIllegalAxiom(getCurrentOntology(), getCurrentAxiom()));
-                    return null;
                 }
                 
                 @Override
-                        public Object visit(OWLNegativeObjectPropertyAssertionAxiom desc) {
+                        public void visit(OWLNegativeObjectPropertyAssertionAxiom desc) {
                         profileViolations.add(new UseOfIllegalAxiom(getCurrentOntology(), getCurrentAxiom()));
-                    return null;
                 }
                 
                 @Override
-                        public Object visit(OWLFunctionalDataPropertyAxiom desc) {
+                        public void visit(OWLFunctionalDataPropertyAxiom desc) {
                         profileViolations.add(new UseOfIllegalAxiom(getCurrentOntology(), getCurrentAxiom()));
-                    return null;
                 }
                 
                 @Override
-                        public Object visit(OWLHasKeyAxiom desc) {
+                        public void visit(OWLHasKeyAxiom desc) {
                         profileViolations.add(new UseOfIllegalAxiom(getCurrentOntology(), getCurrentAxiom()));
-                    return null;
                 }
                
                 
                 
                 
                 @Override
-                        public Object visit(OWLObjectHasSelf node) {
+                        public void visit(OWLObjectHasSelf node) {
                        profileViolations.add(new UseOfIllegalClassExpression(getCurrentOntology(), getCurrentAxiom(), node));
-                    return null;
                 }
 
                 
                 @Override
-                        public Object visit(OWLDataOneOf node) {
+                        public void visit(OWLDataOneOf node) {
                        profileViolations.add(new UseOfDataOneOfWithMultipleLiterals(getCurrentOntology(), getCurrentAxiom(), node));
-                    return null;
                 }
 
                 
 
                 @Override
-                        public Object visit(OWLSubPropertyChainOfAxiom axiom) {
+                        public void visit(OWLSubPropertyChainOfAxiom axiom) {
                         profileViolations.add(new UseOfIllegalAxiom(getCurrentOntology(), getCurrentAxiom()));
 
-                    return null;
                 }
 
                 @Override
-                        public Object visit(OWLOntology ontology) {
+                        public void visit(OWLOntology ontology) {
                     propertyManager = null;
-                    return null;
                 }
             }
 
diff --git a/src/org/semanticweb/karma2/profile/MyOWLOntologyWalker.java b/src/main/java/org/semanticweb/karma2/profile/MyOWLOntologyWalker.java
index 508632f..1ce8076 100644
--- a/src/org/semanticweb/karma2/profile/MyOWLOntologyWalker.java
+++ b/src/main/java/org/semanticweb/karma2/profile/MyOWLOntologyWalker.java
@@ -125,7 +125,8 @@ public class MyOWLOntologyWalker extends OWLOntologyWalker {
     /**
      * @param v visitor to use over the objects
      */
-    public void walkStructure(OWLObjectVisitorEx<?> v) {
+    //public void walkStructure(OWLObjectVisitorEx<?> v) {
+    public void walkStructure(OWLObjectVisitor v) {
         this.visitor = v;
         StructureWalker walker = new StructureWalker();
         for (OWLOntology o : ontologies) {
diff --git a/src/org/semanticweb/simpleETL/RDFHandlerWriter.java b/src/main/java/org/semanticweb/simpleETL/RDFHandlerWriter.java
index e5e2e2a..e5e2e2a 100644
--- a/src/org/semanticweb/simpleETL/RDFHandlerWriter.java
+++ b/src/main/java/org/semanticweb/simpleETL/RDFHandlerWriter.java
diff --git a/src/org/semanticweb/simpleETL/SimpleETL.java b/src/main/java/org/semanticweb/simpleETL/SimpleETL.java
index cc91e1f..cc91e1f 100644
--- a/src/org/semanticweb/simpleETL/SimpleETL.java
+++ b/src/main/java/org/semanticweb/simpleETL/SimpleETL.java
diff --git a/src/resources/_default_pagoda.properties b/src/main/java/resources/_default_pagoda.properties
index 7bd5dd3..7bd5dd3 100644
--- a/src/resources/_default_pagoda.properties
+++ b/src/main/java/resources/_default_pagoda.properties
diff --git a/src/resources/log4j.properties b/src/main/java/resources/log4j.properties
index 52688d5..52688d5 100644
--- a/src/resources/log4j.properties
+++ b/src/main/java/resources/log4j.properties
diff --git a/src/resources/pagoda.properties b/src/main/java/resources/pagoda.properties
index 646744c..646744c 100644
--- a/src/resources/pagoda.properties
+++ b/src/main/java/resources/pagoda.properties
diff --git a/src/uk/ac/ox/cs/pagoda/MyPrefixes.java b/src/main/java/uk/ac/ox/cs/pagoda/MyPrefixes.java
index 98a4e97..98a4e97 100644
--- a/src/uk/ac/ox/cs/pagoda/MyPrefixes.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/MyPrefixes.java
diff --git a/src/uk/ac/ox/cs/pagoda/Pagoda.java b/src/main/java/uk/ac/ox/cs/pagoda/Pagoda.java
index 6a1946e..6a1946e 100644
--- a/src/uk/ac/ox/cs/pagoda/Pagoda.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/Pagoda.java
diff --git a/src/uk/ac/ox/cs/pagoda/approx/Clause.java b/src/main/java/uk/ac/ox/cs/pagoda/approx/Clause.java
index 29bc74e..3783e8c 100644
--- a/src/uk/ac/ox/cs/pagoda/approx/Clause.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/approx/Clause.java
@@ -232,11 +232,10 @@ public class Clause {
                                                         .add(getClassExpression((AtomicConcept) predicate));

                         } else if (predicate instanceof AtomicRole) {

                                 if (!dataProperties.contains(((AtomicRole) predicate).getIRI())) {

-                                        objExp = factory.getOWLObjectProperty(IRI

-                                                        .create(((AtomicRole) predicate).getIRI()));

+                                        objExp = factory.getOWLObjectProperty(IRI.create(((AtomicRole) predicate).getIRI()));

                                         Term V = atom.getArgument(1);

                                         if (V == X) {

-                                                objExp = factory.getOWLObjectInverseOf(objExp);

+                                                objExp = factory.getOWLObjectInverseOf(objExp.asOWLObjectProperty());

                                                 V = atom.getArgument(0);

                                         }

         

@@ -576,7 +575,7 @@ public class Clause {
                                 objExp = factory.getOWLObjectProperty(IRI.create(((AtomicRole) predicate).getIRI()));

                                 if (eVariables.contains(first)) {

                                         second = first;

-                                        objExp = factory.getOWLObjectInverseOf(objExp);

+                                        objExp = factory.getOWLObjectInverseOf(objExp.asOWLObjectProperty());

                                 }

 

                                 for (Term t: equEdges.get(second)) {

diff --git a/src/uk/ac/ox/cs/pagoda/approx/Clausifier.java b/src/main/java/uk/ac/ox/cs/pagoda/approx/Clausifier.java
index ee23def..ee23def 100644
--- a/src/uk/ac/ox/cs/pagoda/approx/Clausifier.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/approx/Clausifier.java
diff --git a/src/uk/ac/ox/cs/pagoda/approx/KnowledgeBase.java b/src/main/java/uk/ac/ox/cs/pagoda/approx/KnowledgeBase.java
index 4b3c057..4b3c057 100644
--- a/src/uk/ac/ox/cs/pagoda/approx/KnowledgeBase.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/approx/KnowledgeBase.java
diff --git a/src/uk/ac/ox/cs/pagoda/approx/RLOntology.java b/src/main/java/uk/ac/ox/cs/pagoda/approx/RLOntology.java
index dba6a56..dba6a56 100644
--- a/src/uk/ac/ox/cs/pagoda/approx/RLOntology.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/approx/RLOntology.java
diff --git a/src/uk/ac/ox/cs/pagoda/approx/RLPlusOntology.java b/src/main/java/uk/ac/ox/cs/pagoda/approx/RLPlusOntology.java
index 638a151..53a8a9e 100644
--- a/src/uk/ac/ox/cs/pagoda/approx/RLPlusOntology.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/approx/RLPlusOntology.java
@@ -70,7 +70,7 @@ public class RLPlusOntology implements KnowledgeBase {
                         IRI.create("http://www.example.org/", matcher.group("id") + "." + DEFAULT_ONTOLOGY_FILE_EXTENSION);
             }
             else
-                ontologyIri = inputOntology.getOntologyID().getOntologyIRI();
+                ontologyIri = inputOntology.getOntologyID().getOntologyIRI().get();
 
             String ontologyIriPrefix = ontologyIri.getNamespace();
             ontologyIRI = ontologyIri.toString();
diff --git a/src/uk/ac/ox/cs/pagoda/constraints/BottomStrategy.java b/src/main/java/uk/ac/ox/cs/pagoda/constraints/BottomStrategy.java
index 4d25593..4d25593 100644
--- a/src/uk/ac/ox/cs/pagoda/constraints/BottomStrategy.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/constraints/BottomStrategy.java
diff --git a/src/uk/ac/ox/cs/pagoda/constraints/DependencyGraph.java b/src/main/java/uk/ac/ox/cs/pagoda/constraints/DependencyGraph.java
index d1615c7..d1615c7 100644
--- a/src/uk/ac/ox/cs/pagoda/constraints/DependencyGraph.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/constraints/DependencyGraph.java
diff --git a/src/uk/ac/ox/cs/pagoda/constraints/NullaryBottom.java b/src/main/java/uk/ac/ox/cs/pagoda/constraints/NullaryBottom.java
index 16a9d45..16a9d45 100644
--- a/src/uk/ac/ox/cs/pagoda/constraints/NullaryBottom.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/constraints/NullaryBottom.java
diff --git a/src/uk/ac/ox/cs/pagoda/constraints/OWLEntityDependency.java b/src/main/java/uk/ac/ox/cs/pagoda/constraints/OWLEntityDependency.java
index 60fea28..60fea28 100644
--- a/src/uk/ac/ox/cs/pagoda/constraints/OWLEntityDependency.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/constraints/OWLEntityDependency.java
diff --git a/src/uk/ac/ox/cs/pagoda/constraints/PredicateDependency.java b/src/main/java/uk/ac/ox/cs/pagoda/constraints/PredicateDependency.java
index 70f841f..70f841f 100644
--- a/src/uk/ac/ox/cs/pagoda/constraints/PredicateDependency.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/constraints/PredicateDependency.java
diff --git a/src/uk/ac/ox/cs/pagoda/constraints/ToBeRemovedBottom.java b/src/main/java/uk/ac/ox/cs/pagoda/constraints/ToBeRemovedBottom.java
index 415119a..415119a 100644
--- a/src/uk/ac/ox/cs/pagoda/constraints/ToBeRemovedBottom.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/constraints/ToBeRemovedBottom.java
diff --git a/src/uk/ac/ox/cs/pagoda/constraints/UnaryBottom.java b/src/main/java/uk/ac/ox/cs/pagoda/constraints/UnaryBottom.java
index 5339c50..5339c50 100644
--- a/src/uk/ac/ox/cs/pagoda/constraints/UnaryBottom.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/constraints/UnaryBottom.java
diff --git a/src/uk/ac/ox/cs/pagoda/constraints/UpperUnaryBottom.java b/src/main/java/uk/ac/ox/cs/pagoda/constraints/UpperUnaryBottom.java
index 2b57a52..2b57a52 100644
--- a/src/uk/ac/ox/cs/pagoda/constraints/UpperUnaryBottom.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/constraints/UpperUnaryBottom.java
diff --git a/src/uk/ac/ox/cs/pagoda/endomorph/Clique.java b/src/main/java/uk/ac/ox/cs/pagoda/endomorph/Clique.java
index 9b0d88e..9b0d88e 100644
--- a/src/uk/ac/ox/cs/pagoda/endomorph/Clique.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/endomorph/Clique.java
diff --git a/src/uk/ac/ox/cs/pagoda/endomorph/DependencyGraph.java b/src/main/java/uk/ac/ox/cs/pagoda/endomorph/DependencyGraph.java
index 0f215ad..0f215ad 100644
--- a/src/uk/ac/ox/cs/pagoda/endomorph/DependencyGraph.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/endomorph/DependencyGraph.java
diff --git a/src/uk/ac/ox/cs/pagoda/endomorph/Endomorph.java b/src/main/java/uk/ac/ox/cs/pagoda/endomorph/Endomorph.java
index 9ca73a1..9ca73a1 100644
--- a/src/uk/ac/ox/cs/pagoda/endomorph/Endomorph.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/endomorph/Endomorph.java
diff --git a/src/uk/ac/ox/cs/pagoda/endomorph/EndomorphChecker.java b/src/main/java/uk/ac/ox/cs/pagoda/endomorph/EndomorphChecker.java
index 46ddbb3..46ddbb3 100644
--- a/src/uk/ac/ox/cs/pagoda/endomorph/EndomorphChecker.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/endomorph/EndomorphChecker.java
diff --git a/src/uk/ac/ox/cs/pagoda/endomorph/EndomorphChecker1.java b/src/main/java/uk/ac/ox/cs/pagoda/endomorph/EndomorphChecker1.java
index c2117b6..c2117b6 100644
--- a/src/uk/ac/ox/cs/pagoda/endomorph/EndomorphChecker1.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/endomorph/EndomorphChecker1.java
diff --git a/src/uk/ac/ox/cs/pagoda/endomorph/EndomorphChecker2.java b/src/main/java/uk/ac/ox/cs/pagoda/endomorph/EndomorphChecker2.java
index aac5f3c..aac5f3c 100644
--- a/src/uk/ac/ox/cs/pagoda/endomorph/EndomorphChecker2.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/endomorph/EndomorphChecker2.java
diff --git a/src/uk/ac/ox/cs/pagoda/endomorph/plan/CheckPlan.java b/src/main/java/uk/ac/ox/cs/pagoda/endomorph/plan/CheckPlan.java
index ab3735f..ab3735f 100644
--- a/src/uk/ac/ox/cs/pagoda/endomorph/plan/CheckPlan.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/endomorph/plan/CheckPlan.java
diff --git a/src/uk/ac/ox/cs/pagoda/endomorph/plan/OpenEndMultiThreadPlan.java b/src/main/java/uk/ac/ox/cs/pagoda/endomorph/plan/OpenEndMultiThreadPlan.java
index 4e2fc5f..4e2fc5f 100644
--- a/src/uk/ac/ox/cs/pagoda/endomorph/plan/OpenEndMultiThreadPlan.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/endomorph/plan/OpenEndMultiThreadPlan.java
diff --git a/src/uk/ac/ox/cs/pagoda/endomorph/plan/OpenEndPlan.java b/src/main/java/uk/ac/ox/cs/pagoda/endomorph/plan/OpenEndPlan.java
index 076427e..076427e 100644
--- a/src/uk/ac/ox/cs/pagoda/endomorph/plan/OpenEndPlan.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/endomorph/plan/OpenEndPlan.java
diff --git a/src/uk/ac/ox/cs/pagoda/endomorph/plan/PlainPlan.java b/src/main/java/uk/ac/ox/cs/pagoda/endomorph/plan/PlainPlan.java
index 5e1a700..5e1a700 100644
--- a/src/uk/ac/ox/cs/pagoda/endomorph/plan/PlainPlan.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/endomorph/plan/PlainPlan.java
diff --git a/src/uk/ac/ox/cs/pagoda/hermit/DLClauseHelper.java b/src/main/java/uk/ac/ox/cs/pagoda/hermit/DLClauseHelper.java
index c3f7a2a..c3f7a2a 100644
--- a/src/uk/ac/ox/cs/pagoda/hermit/DLClauseHelper.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/hermit/DLClauseHelper.java
diff --git a/src/uk/ac/ox/cs/pagoda/hermit/RuleHelper.java b/src/main/java/uk/ac/ox/cs/pagoda/hermit/RuleHelper.java
index 43c5849..43c5849 100644
--- a/src/uk/ac/ox/cs/pagoda/hermit/RuleHelper.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/hermit/RuleHelper.java
diff --git a/src/uk/ac/ox/cs/pagoda/hermit/TermGraph.java b/src/main/java/uk/ac/ox/cs/pagoda/hermit/TermGraph.java
index 0041cca..0041cca 100644
--- a/src/uk/ac/ox/cs/pagoda/hermit/TermGraph.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/hermit/TermGraph.java
diff --git a/src/uk/ac/ox/cs/pagoda/model/AnswerTerm.java b/src/main/java/uk/ac/ox/cs/pagoda/model/AnswerTerm.java
index 777a35c..777a35c 100644
--- a/src/uk/ac/ox/cs/pagoda/model/AnswerTerm.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/model/AnswerTerm.java
diff --git a/src/uk/ac/ox/cs/pagoda/model/IRI.java b/src/main/java/uk/ac/ox/cs/pagoda/model/IRI.java
index 7dc5242..7dc5242 100644
--- a/src/uk/ac/ox/cs/pagoda/model/IRI.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/model/IRI.java
diff --git a/src/uk/ac/ox/cs/pagoda/model/Literal.java b/src/main/java/uk/ac/ox/cs/pagoda/model/Literal.java
index 0a4dff2..0a4dff2 100644
--- a/src/uk/ac/ox/cs/pagoda/model/Literal.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/model/Literal.java
diff --git a/src/uk/ac/ox/cs/pagoda/model/Trie.java b/src/main/java/uk/ac/ox/cs/pagoda/model/Trie.java
index eb9e71b..eb9e71b 100644
--- a/src/uk/ac/ox/cs/pagoda/model/Trie.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/model/Trie.java
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/AnswerTupleID.java b/src/main/java/uk/ac/ox/cs/pagoda/multistage/AnswerTupleID.java
index 2b288c4..2b288c4 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/AnswerTupleID.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/multistage/AnswerTupleID.java
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/EqualityManager.java b/src/main/java/uk/ac/ox/cs/pagoda/multistage/EqualityManager.java
index 403fdb0..403fdb0 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/EqualityManager.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/multistage/EqualityManager.java
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/FoldedApplication.java b/src/main/java/uk/ac/ox/cs/pagoda/multistage/FoldedApplication.java
index c75083b..c75083b 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/FoldedApplication.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/multistage/FoldedApplication.java
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/IncrementalMultiStageQueryEngine.java b/src/main/java/uk/ac/ox/cs/pagoda/multistage/IncrementalMultiStageQueryEngine.java
index 30ba9da..30ba9da 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/IncrementalMultiStageQueryEngine.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/multistage/IncrementalMultiStageQueryEngine.java
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/LimitedSkolemisationApplication.java b/src/main/java/uk/ac/ox/cs/pagoda/multistage/LimitedSkolemisationApplication.java
index efcf9ba..efcf9ba 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/LimitedSkolemisationApplication.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/multistage/LimitedSkolemisationApplication.java
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java b/src/main/java/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java
index 209e1d7..209e1d7 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/multistage/MultiStageQueryEngine.java
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/MultiStageUpperProgram.java b/src/main/java/uk/ac/ox/cs/pagoda/multistage/MultiStageUpperProgram.java
index e64c5e6..e64c5e6 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/MultiStageUpperProgram.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/multistage/MultiStageUpperProgram.java
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/Normalisation.java b/src/main/java/uk/ac/ox/cs/pagoda/multistage/Normalisation.java
index c5482e7..c5482e7 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/Normalisation.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/multistage/Normalisation.java
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/RestrictedApplication.java b/src/main/java/uk/ac/ox/cs/pagoda/multistage/RestrictedApplication.java
index b16e645..b16e645 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/RestrictedApplication.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/multistage/RestrictedApplication.java
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/StageQueryEngine.java b/src/main/java/uk/ac/ox/cs/pagoda/multistage/StageQueryEngine.java
index 65184ee..65184ee 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/StageQueryEngine.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/multistage/StageQueryEngine.java
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/Violation.java b/src/main/java/uk/ac/ox/cs/pagoda/multistage/Violation.java
index 2f98784..2f98784 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/Violation.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/multistage/Violation.java
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/ViolationTuple.java b/src/main/java/uk/ac/ox/cs/pagoda/multistage/ViolationTuple.java
index 129f5dd..129f5dd 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/ViolationTuple.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/multistage/ViolationTuple.java
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConcept.java b/src/main/java/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConcept.java
index f88a4d7..f88a4d7 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConcept.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConcept.java
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConceptNaive.java b/src/main/java/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConceptNaive.java
index 2fc2683..2fc2683 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConceptNaive.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConceptNaive.java
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConceptQuerySpecific.java b/src/main/java/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConceptQuerySpecific.java
index 675bfc3..675bfc3 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConceptQuerySpecific.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/multistage/treatement/Pick4NegativeConceptQuerySpecific.java
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/treatement/SimpleComparator.java b/src/main/java/uk/ac/ox/cs/pagoda/multistage/treatement/SimpleComparator.java
index a92a917..a92a917 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/treatement/SimpleComparator.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/multistage/treatement/SimpleComparator.java
diff --git a/src/uk/ac/ox/cs/pagoda/multistage/treatement/Treatment.java b/src/main/java/uk/ac/ox/cs/pagoda/multistage/treatement/Treatment.java
index de76d27..de76d27 100644
--- a/src/uk/ac/ox/cs/pagoda/multistage/treatement/Treatment.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/multistage/treatement/Treatment.java
diff --git a/src/uk/ac/ox/cs/pagoda/owl/EqualitiesEliminator.java b/src/main/java/uk/ac/ox/cs/pagoda/owl/EqualitiesEliminator.java
index 50865d4..50865d4 100644
--- a/src/uk/ac/ox/cs/pagoda/owl/EqualitiesEliminator.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/owl/EqualitiesEliminator.java
diff --git a/src/uk/ac/ox/cs/pagoda/owl/MyHornAxiomVisitorEx.java b/src/main/java/uk/ac/ox/cs/pagoda/owl/MyHornAxiomVisitorEx.java
index be22ded..be22ded 100644
--- a/src/uk/ac/ox/cs/pagoda/owl/MyHornAxiomVisitorEx.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/owl/MyHornAxiomVisitorEx.java
diff --git a/src/uk/ac/ox/cs/pagoda/owl/OWLHelper.java b/src/main/java/uk/ac/ox/cs/pagoda/owl/OWLHelper.java
index fd20f88..e7be96b 100644
--- a/src/uk/ac/ox/cs/pagoda/owl/OWLHelper.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/owl/OWLHelper.java
@@ -49,9 +49,9 @@ import org.semanticweb.owlapi.model.UnknownOWLOntologyException;
 import org.semanticweb.owlapi.profiles.OWL2RLProfile;
 import org.semanticweb.owlapi.profiles.OWLProfileReport;
 import org.semanticweb.owlapi.profiles.OWLProfileViolation;
-import org.semanticweb.owlapi.profiles.UseOfUndeclaredClass;
-import org.semanticweb.owlapi.profiles.UseOfUndeclaredDataProperty;
-import org.semanticweb.owlapi.profiles.UseOfUndeclaredObjectProperty;
+import org.semanticweb.owlapi.profiles.violations.UseOfUndeclaredClass;
+import org.semanticweb.owlapi.profiles.violations.UseOfUndeclaredDataProperty;
+import org.semanticweb.owlapi.profiles.violations.UseOfUndeclaredObjectProperty;
 import org.semanticweb.owlapi.util.OWLOntologyMerger;
 
 import uk.ac.ox.cs.pagoda.approx.Clause;
diff --git a/src/uk/ac/ox/cs/pagoda/owl/QueryRoller.java b/src/main/java/uk/ac/ox/cs/pagoda/owl/QueryRoller.java
index f486bbf..f486bbf 100644
--- a/src/uk/ac/ox/cs/pagoda/owl/QueryRoller.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/owl/QueryRoller.java
diff --git a/src/uk/ac/ox/cs/pagoda/query/AnswerTuple.java b/src/main/java/uk/ac/ox/cs/pagoda/query/AnswerTuple.java
index 1e5fbd4..1e5fbd4 100644
--- a/src/uk/ac/ox/cs/pagoda/query/AnswerTuple.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/query/AnswerTuple.java
diff --git a/src/uk/ac/ox/cs/pagoda/query/AnswerTuples.java b/src/main/java/uk/ac/ox/cs/pagoda/query/AnswerTuples.java
index 81efed0..81efed0 100644
--- a/src/uk/ac/ox/cs/pagoda/query/AnswerTuples.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/query/AnswerTuples.java
diff --git a/src/uk/ac/ox/cs/pagoda/query/AnswerTuplesImp.java b/src/main/java/uk/ac/ox/cs/pagoda/query/AnswerTuplesImp.java
index fd3fb1f..fd3fb1f 100644
--- a/src/uk/ac/ox/cs/pagoda/query/AnswerTuplesImp.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/query/AnswerTuplesImp.java
diff --git a/src/uk/ac/ox/cs/pagoda/query/DeserializedQueryRecord.java b/src/main/java/uk/ac/ox/cs/pagoda/query/DeserializedQueryRecord.java
index 3d25eaf..3d25eaf 100644
--- a/src/uk/ac/ox/cs/pagoda/query/DeserializedQueryRecord.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/query/DeserializedQueryRecord.java
diff --git a/src/uk/ac/ox/cs/pagoda/query/GapByStore4ID.java b/src/main/java/uk/ac/ox/cs/pagoda/query/GapByStore4ID.java
index 84929ad..84929ad 100644
--- a/src/uk/ac/ox/cs/pagoda/query/GapByStore4ID.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/query/GapByStore4ID.java
diff --git a/src/uk/ac/ox/cs/pagoda/query/GapByStore4ID2.java b/src/main/java/uk/ac/ox/cs/pagoda/query/GapByStore4ID2.java
index f8e1709..f8e1709 100644
--- a/src/uk/ac/ox/cs/pagoda/query/GapByStore4ID2.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/query/GapByStore4ID2.java
diff --git a/src/uk/ac/ox/cs/pagoda/query/GapByTriple.java b/src/main/java/uk/ac/ox/cs/pagoda/query/GapByTriple.java
index eaa629b..eaa629b 100644
--- a/src/uk/ac/ox/cs/pagoda/query/GapByTriple.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/query/GapByTriple.java
diff --git a/src/uk/ac/ox/cs/pagoda/query/GapTupleIterator.java b/src/main/java/uk/ac/ox/cs/pagoda/query/GapTupleIterator.java
index bf11168..bf11168 100644
--- a/src/uk/ac/ox/cs/pagoda/query/GapTupleIterator.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/query/GapTupleIterator.java
diff --git a/src/uk/ac/ox/cs/pagoda/query/QueryManager.java b/src/main/java/uk/ac/ox/cs/pagoda/query/QueryManager.java
index 419cb97..419cb97 100644
--- a/src/uk/ac/ox/cs/pagoda/query/QueryManager.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/query/QueryManager.java
diff --git a/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java b/src/main/java/uk/ac/ox/cs/pagoda/query/QueryRecord.java
index 3f73145..5fa1b23 100644
--- a/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/query/QueryRecord.java
@@ -5,6 +5,7 @@ import com.google.gson.reflect.TypeToken;
 import org.apache.commons.lang.WordUtils;
 import org.semanticweb.HermiT.model.*;
 import org.semanticweb.owlapi.model.*;
+import org.semanticweb.owlapi.model.parameters.Imports;
 import uk.ac.ox.cs.pagoda.hermit.DLClauseHelper;
 import uk.ac.ox.cs.pagoda.reasoner.light.RDFoxAnswerTuples;
 import uk.ac.ox.cs.pagoda.rules.GeneralProgram;
@@ -448,7 +449,7 @@ public class QueryRecord extends Disposable {
             BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(filename)));
             OWLIndividual a, b;
             StringBuilder builder = new StringBuilder();
-            for(OWLAxiom axiom : relevantOntology.getABoxAxioms(true)) {
+            for(OWLAxiom axiom : relevantOntology.getABoxAxioms(Imports.INCLUDED)) {
                 if(axiom instanceof OWLClassAssertionAxiom) {
                     OWLClassAssertionAxiom classAssertion = (OWLClassAssertionAxiom) axiom;
                     OWLClass c = (OWLClass) classAssertion.getClassExpression();
diff --git a/src/uk/ac/ox/cs/pagoda/query/rollup/QueryGraph.java b/src/main/java/uk/ac/ox/cs/pagoda/query/rollup/QueryGraph.java
index 9b4ce01..9b4ce01 100644
--- a/src/uk/ac/ox/cs/pagoda/query/rollup/QueryGraph.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/query/rollup/QueryGraph.java
diff --git a/src/uk/ac/ox/cs/pagoda/query/rollup/VariableConstant.java b/src/main/java/uk/ac/ox/cs/pagoda/query/rollup/VariableConstant.java
index b8035c5..b8035c5 100644
--- a/src/uk/ac/ox/cs/pagoda/query/rollup/VariableConstant.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/query/rollup/VariableConstant.java
diff --git a/src/uk/ac/ox/cs/pagoda/query/rollup/VariableIndividual.java b/src/main/java/uk/ac/ox/cs/pagoda/query/rollup/VariableIndividual.java
index 1c924b2..de302b5 100644
--- a/src/uk/ac/ox/cs/pagoda/query/rollup/VariableIndividual.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/query/rollup/VariableIndividual.java
@@ -68,101 +68,101 @@ class VariableIndividual implements OWLNamedIndividual {
                 return null;
         }
 
-        @Override
-        public Set<OWLClassExpression> getTypes(OWLOntology ontology) {
-                // TODO Auto-generated method stub
-                return null;
-        }
-
-        @Override
-        public Set<OWLClassExpression> getTypes(Set<OWLOntology> ontologies) {
-                // TODO Auto-generated method stub
-                return null;
-        }
-
-        @Override
-        public Map<OWLObjectPropertyExpression, Set<OWLIndividual>> getObjectPropertyValues(
-                        OWLOntology ontology) {
-                // TODO Auto-generated method stub
-                return null;
-        }
-
-        @Override
-        public Set<OWLIndividual> getObjectPropertyValues(
-                        OWLObjectPropertyExpression property, OWLOntology ontology) {
-                // TODO Auto-generated method stub
-                return null;
-        }
-
-        @Override
-        public boolean hasObjectPropertyValue(OWLObjectPropertyExpression property,
-                        OWLIndividual individual, OWLOntology ontology) {
-                // TODO Auto-generated method stub
-                return false;
-        }
-
-        @Override
-        public boolean hasDataPropertyValue(OWLDataPropertyExpression property,
-                        OWLLiteral value, OWLOntology ontology) {
-                // TODO Auto-generated method stub
-                return false;
-        }
-
-        @Override
-        public boolean hasNegativeObjectPropertyValue(
-                        OWLObjectPropertyExpression property, OWLIndividual individual,
-                        OWLOntology ontology) {
-                // TODO Auto-generated method stub
-                return false;
-        }
-
-        @Override
-        public Map<OWLObjectPropertyExpression, Set<OWLIndividual>> getNegativeObjectPropertyValues(
-                        OWLOntology ontology) {
-                // TODO Auto-generated method stub
-                return null;
-        }
-
-        @Override
-        public Map<OWLDataPropertyExpression, Set<OWLLiteral>> getDataPropertyValues(
-                        OWLOntology ontology) {
-                // TODO Auto-generated method stub
-                return null;
-        }
-
-        @Override
-        public Set<OWLLiteral> getDataPropertyValues(
-                        OWLDataPropertyExpression property, OWLOntology ontology) {
-                // TODO Auto-generated method stub
-                return null;
-        }
-
-        @Override
-        public Map<OWLDataPropertyExpression, Set<OWLLiteral>> getNegativeDataPropertyValues(
-                        OWLOntology ontology) {
-                // TODO Auto-generated method stub
-                return null;
-        }
-
-        @Override
-        public boolean hasNegativeDataPropertyValue(
-                        OWLDataPropertyExpression property, OWLLiteral literal,
-                        OWLOntology ontology) {
-                // TODO Auto-generated method stub
-                return false;
-        }
-
-        @Override
-        public Set<OWLIndividual> getSameIndividuals(OWLOntology ontology) {
-                // TODO Auto-generated method stub
-                return null;
-        }
-
-        @Override
-        public Set<OWLIndividual> getDifferentIndividuals(OWLOntology ontology) {
-                // TODO Auto-generated method stub
-                return null;
-        }
+        // @Override
+        // public Set<OWLClassExpression> getTypes(OWLOntology ontology) {
+        //      // TODO Auto-generated method stub
+        //      return null;
+        // }
+
+        // @Override
+        // public Set<OWLClassExpression> getTypes(Set<OWLOntology> ontologies) {
+        //      // TODO Auto-generated method stub
+        //      return null;
+        // }
+
+        // @Override
+        // public Map<OWLObjectPropertyExpression, Set<OWLIndividual>> getObjectPropertyValues(
+        //              OWLOntology ontology) {
+        //      // TODO Auto-generated method stub
+        //      return null;
+        // }
+
+        // @Override
+        // public Set<OWLIndividual> getObjectPropertyValues(
+        //              OWLObjectPropertyExpression property, OWLOntology ontology) {
+        //      // TODO Auto-generated method stub
+        //      return null;
+        // }
+
+        // @Override
+        // public boolean hasObjectPropertyValue(OWLObjectPropertyExpression property,
+        //              OWLIndividual individual, OWLOntology ontology) {
+        //      // TODO Auto-generated method stub
+        //      return false;
+        // }
+
+        // @Override
+        // public boolean hasDataPropertyValue(OWLDataPropertyExpression property,
+        //              OWLLiteral value, OWLOntology ontology) {
+        //      // TODO Auto-generated method stub
+        //      return false;
+        // }
+
+        // @Override
+        // public boolean hasNegativeObjectPropertyValue(
+        //              OWLObjectPropertyExpression property, OWLIndividual individual,
+        //              OWLOntology ontology) {
+        //      // TODO Auto-generated method stub
+        //      return false;
+        // }
+
+        // @Override
+        // public Map<OWLObjectPropertyExpression, Set<OWLIndividual>> getNegativeObjectPropertyValues(
+        //              OWLOntology ontology) {
+        //      // TODO Auto-generated method stub
+        //      return null;
+        // }
+
+        // @Override
+        // public Map<OWLDataPropertyExpression, Set<OWLLiteral>> getDataPropertyValues(
+        //              OWLOntology ontology) {
+        //      // TODO Auto-generated method stub
+        //      return null;
+        // }
+
+        // @Override
+        // public Set<OWLLiteral> getDataPropertyValues(
+        //              OWLDataPropertyExpression property, OWLOntology ontology) {
+        //      // TODO Auto-generated method stub
+        //      return null;
+        // }
+
+        // @Override
+        // public Map<OWLDataPropertyExpression, Set<OWLLiteral>> getNegativeDataPropertyValues(
+        //              OWLOntology ontology) {
+        //      // TODO Auto-generated method stub
+        //      return null;
+        // }
+
+        // @Override
+        // public boolean hasNegativeDataPropertyValue(
+        //              OWLDataPropertyExpression property, OWLLiteral literal,
+        //              OWLOntology ontology) {
+        //      // TODO Auto-generated method stub
+        //      return false;
+        // }
+
+        // @Override
+        // public Set<OWLIndividual> getSameIndividuals(OWLOntology ontology) {
+        //      // TODO Auto-generated method stub
+        //      return null;
+        // }
+
+        // @Override
+        // public Set<OWLIndividual> getDifferentIndividuals(OWLOntology ontology) {
+        //      // TODO Auto-generated method stub
+        //      return null;
+        // }
 
         @Override
         public String toStringID() {
@@ -266,11 +266,11 @@ class VariableIndividual implements OWLNamedIndividual {
                 return null;
         }
 
-        @Override
-        public <E extends OWLEntity> E getOWLEntity(EntityType<E> entityType) {
-                // TODO Auto-generated method stub
-                return null;
-        }
+        // @Override
+        // public <E extends OWLEntity> E getOWLEntity(EntityType<E> entityType) {
+        //      // TODO Auto-generated method stub
+        //      return null;
+        // }
 
         @Override
         public boolean isType(EntityType<?> entityType) {
@@ -278,25 +278,25 @@ class VariableIndividual implements OWLNamedIndividual {
                 return false;
         }
 
-        @Override
-        public Set<OWLAnnotation> getAnnotations(OWLOntology ontology) {
-                // TODO Auto-generated method stub
-                return null;
-        }
+        // @Override
+        // public Set<OWLAnnotation> getAnnotations(OWLOntology ontology) {
+        //      // TODO Auto-generated method stub
+        //      return null;
+        // }
 
-        @Override
-        public Set<OWLAnnotation> getAnnotations(OWLOntology ontology,
-                        OWLAnnotationProperty annotationProperty) {
-                // TODO Auto-generated method stub
-                return null;
-        }
+        // @Override
+        // public Set<OWLAnnotation> getAnnotations(OWLOntology ontology,
+        //              OWLAnnotationProperty annotationProperty) {
+        //      // TODO Auto-generated method stub
+        //      return null;
+        // }
 
-        @Override
-        public Set<OWLAnnotationAssertionAxiom> getAnnotationAssertionAxioms(
-                        OWLOntology ontology) {
-                // TODO Auto-generated method stub
-                return null;
-        }
+        // @Override
+        // public Set<OWLAnnotationAssertionAxiom> getAnnotationAssertionAxioms(
+        //              OWLOntology ontology) {
+        //      // TODO Auto-generated method stub
+        //      return null;
+        // }
 
         @Override
         public boolean isBuiltIn() {
@@ -370,18 +370,18 @@ class VariableIndividual implements OWLNamedIndividual {
                 return null;
         }
 
-        @Override
-        public Set<OWLAxiom> getReferencingAxioms(OWLOntology ontology) {
-                // TODO Auto-generated method stub
-                return null;
-        }
+        // @Override
+        // public Set<OWLAxiom> getReferencingAxioms(OWLOntology ontology) {
+        //      // TODO Auto-generated method stub
+        //      return null;
+        // }
 
-        @Override
-        public Set<OWLAxiom> getReferencingAxioms(OWLOntology ontology,
-                        boolean includeImports) {
-                // TODO Auto-generated method stub
-                return null;
-        }
+        // @Override
+        // public Set<OWLAxiom> getReferencingAxioms(OWLOntology ontology,
+        //              boolean includeImports) {
+        //      // TODO Auto-generated method stub
+        //      return null;
+        // }
 
         @Override
         public void accept(OWLEntityVisitor visitor) {
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
index 3fd2fbd..3fd2fbd 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/ConsistencyManager.java
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java
index cc2c4c0..29754ce 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/ELHOQueryReasoner.java
@@ -12,7 +12,7 @@ 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 {
+public class ELHOQueryReasoner extends QueryReasoner {
 
     LowerDatalogProgram program;
 
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
index 15dfa03..15dfa03 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/ELHOUQueryReasoner.java
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java
index ac62488..ac62488 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/HermiTReasoner.java
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/IterativeRefinement.java b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/IterativeRefinement.java
index 7847e7c..7847e7c 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/IterativeRefinement.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/IterativeRefinement.java
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
index 8cc9209..f2e29f2 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/MyQueryReasoner.java
@@ -2,6 +2,7 @@ package uk.ac.ox.cs.pagoda.reasoner;
 
 import org.semanticweb.karma2.profile.ELHOProfile;
 import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.parameters.Imports;
 import uk.ac.ox.cs.JRDFox.JRDFStoreException;
 import uk.ac.ox.cs.pagoda.multistage.MultiStageQueryEngine;
 import uk.ac.ox.cs.pagoda.owl.EqualitiesEliminator;
@@ -29,7 +30,7 @@ import uk.ac.ox.cs.pagoda.util.tuples.Tuple;
 import java.util.Collection;
 import java.util.LinkedList;
 
-class MyQueryReasoner extends QueryReasoner {
+public class MyQueryReasoner extends QueryReasoner {
 
     OWLOntology ontology;
     OWLOntology elho_ontology;
@@ -367,7 +368,7 @@ class MyQueryReasoner extends QueryReasoner {
 
         queryRecord.addProcessingTime(Step.FRAGMENT, t.duration());
 
-        int numOfABoxAxioms = relevantOntologySubset.getABoxAxioms(true).size();
+        int numOfABoxAxioms = relevantOntologySubset.getABoxAxioms(Imports.INCLUDED).size();
         int numOfTBoxAxioms = relevantOntologySubset.getAxiomCount() - numOfABoxAxioms;
         Utility.logInfo("Relevant ontology-subset has been extracted: |ABox|="
                                 + numOfABoxAxioms + ", |TBox|=" + numOfTBoxAxioms);
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/QueryEngine.java b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/QueryEngine.java
index 3200216..3200216 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/QueryEngine.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/QueryEngine.java
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
index e8daa3b..e8daa3b 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/QueryReasoner.java
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/RLQueryReasoner.java b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/RLQueryReasoner.java
index 3934498..32f5541 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/RLQueryReasoner.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/RLQueryReasoner.java
@@ -11,7 +11,7 @@ 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 {
+public class RLQueryReasoner extends QueryReasoner {
         
         RDFoxQueryEngine rlLowerStore = null;
 
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/RLUQueryReasoner.java b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/RLUQueryReasoner.java
index 368fbb2..368fbb2 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/RLUQueryReasoner.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/RLUQueryReasoner.java
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/full/Checker.java b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/full/Checker.java
index 07adc6d..07adc6d 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/full/Checker.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/full/Checker.java
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java
index 0362fc2..3f3c22d 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/full/HermitChecker.java
@@ -5,6 +5,7 @@ import org.semanticweb.HermiT.model.DLClause;
 import org.semanticweb.HermiT.model.Term;
 import org.semanticweb.HermiT.model.Variable;
 import org.semanticweb.owlapi.model.*;
+import org.semanticweb.owlapi.model.parameters.Imports;
 import uk.ac.ox.cs.pagoda.endomorph.Clique;
 import uk.ac.ox.cs.pagoda.endomorph.DependencyGraph;
 import uk.ac.ox.cs.pagoda.hermit.DLClauseHelper;
@@ -219,7 +220,7 @@ public class HermitChecker extends Checker {
         }
         else botAnswerTuple = null;
 
-        for(OWLAxiom axiom : ontology.getABoxAxioms(true))
+        for(OWLAxiom axiom : ontology.getABoxAxioms(Imports.INCLUDED))
             if(axiom instanceof OWLClassAssertionAxiom) {
                 OWLClassAssertionAxiom ca = (OWLClassAssertionAxiom) axiom;
                 sub = ca.getIndividual();
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java
index 034827e..034827e 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/light/BasicQueryEngine.java
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/light/DLPredicateComparator.java b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/light/DLPredicateComparator.java
index 05e399e..05e399e 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/light/DLPredicateComparator.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/light/DLPredicateComparator.java
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/light/KarmaQuery.java b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/light/KarmaQuery.java
index 03d2b67..03d2b67 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/light/KarmaQuery.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/light/KarmaQuery.java
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/light/KarmaQueryEngine.java b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/light/KarmaQueryEngine.java
index 98f0c35..98f0c35 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/light/KarmaQueryEngine.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/light/KarmaQueryEngine.java
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxAnswerTuples.java b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxAnswerTuples.java
index f823232..f823232 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxAnswerTuples.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxAnswerTuples.java
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxQueryEngine.java b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxQueryEngine.java
index 8b22919..f19f253 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxQueryEngine.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxQueryEngine.java
@@ -2,6 +2,7 @@ package uk.ac.ox.cs.pagoda.reasoner.light;
 
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+import org.semanticweb.owlapi.model.parameters.Imports;
 import uk.ac.ox.cs.JRDFox.JRDFStoreException;
 import uk.ac.ox.cs.JRDFox.Prefixes;
 import uk.ac.ox.cs.JRDFox.store.DataStore;
@@ -72,9 +73,9 @@ public abstract class RDFoxQueryEngine extends QueryEngine {
         DataStore store = getDataStore();
         try {
             long prevTriplesCount = store.getTriplesCount();
-            store.importOntology(ontology.getOWLOntologyManager().createOntology(ontology.getABoxAxioms(true)));
+            store.importOntology(ontology.getOWLOntologyManager().createOntology(ontology.getABoxAxioms(Imports.INCLUDED)));
             long loadedTriples = store.getTriplesCount() - prevTriplesCount;
-            Utility.logDebug(name + ": loaded " + loadedTriples + " triples from " + ontology.getABoxAxioms(true)
+            Utility.logDebug(name + ": loaded " + loadedTriples + " triples from " + ontology.getABoxAxioms(Imports.INCLUDED)
                                                                                             .size() + " ABox axioms");
         } catch(JRDFStoreException | OWLOntologyCreationException e) {
             e.printStackTrace();
diff --git a/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxTripleManager.java b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxTripleManager.java
index 62885be..62885be 100644
--- a/src/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxTripleManager.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/reasoner/light/RDFoxTripleManager.java
diff --git a/src/uk/ac/ox/cs/pagoda/rules/ApproxProgram.java b/src/main/java/uk/ac/ox/cs/pagoda/rules/ApproxProgram.java
index acbf354..acbf354 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/ApproxProgram.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/rules/ApproxProgram.java
diff --git a/src/uk/ac/ox/cs/pagoda/rules/DatalogProgram.java b/src/main/java/uk/ac/ox/cs/pagoda/rules/DatalogProgram.java
index e2a171d..e2a171d 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/DatalogProgram.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/rules/DatalogProgram.java
diff --git a/src/uk/ac/ox/cs/pagoda/rules/DisjunctiveProgram.java b/src/main/java/uk/ac/ox/cs/pagoda/rules/DisjunctiveProgram.java
index d50c2d4..d50c2d4 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/DisjunctiveProgram.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/rules/DisjunctiveProgram.java
diff --git a/src/uk/ac/ox/cs/pagoda/rules/EqualityAxiomatiser.java b/src/main/java/uk/ac/ox/cs/pagoda/rules/EqualityAxiomatiser.java
index 81b8a01..81b8a01 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/EqualityAxiomatiser.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/rules/EqualityAxiomatiser.java
diff --git a/src/uk/ac/ox/cs/pagoda/rules/ExistConstantApproximator.java b/src/main/java/uk/ac/ox/cs/pagoda/rules/ExistConstantApproximator.java
index a7afa2e..a7afa2e 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/ExistConstantApproximator.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/rules/ExistConstantApproximator.java
diff --git a/src/uk/ac/ox/cs/pagoda/rules/ExistentialProgram.java b/src/main/java/uk/ac/ox/cs/pagoda/rules/ExistentialProgram.java
index e825917..e825917 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/ExistentialProgram.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/rules/ExistentialProgram.java
diff --git a/src/uk/ac/ox/cs/pagoda/rules/ExistentialToDisjunctive.java b/src/main/java/uk/ac/ox/cs/pagoda/rules/ExistentialToDisjunctive.java
index 2098f73..2098f73 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/ExistentialToDisjunctive.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/rules/ExistentialToDisjunctive.java
diff --git a/src/uk/ac/ox/cs/pagoda/rules/GeneralProgram.java b/src/main/java/uk/ac/ox/cs/pagoda/rules/GeneralProgram.java
index e390a29..e390a29 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/GeneralProgram.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/rules/GeneralProgram.java
diff --git a/src/uk/ac/ox/cs/pagoda/rules/IncrementalProgram.java b/src/main/java/uk/ac/ox/cs/pagoda/rules/IncrementalProgram.java
index 339738a..339738a 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/IncrementalProgram.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/rules/IncrementalProgram.java
diff --git a/src/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java b/src/main/java/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java
index a2676e8..a2676e8 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/rules/LowerDatalogProgram.java
diff --git a/src/uk/ac/ox/cs/pagoda/rules/Program.java b/src/main/java/uk/ac/ox/cs/pagoda/rules/Program.java
index de06f52..de06f52 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/Program.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/rules/Program.java
diff --git a/src/uk/ac/ox/cs/pagoda/rules/UpperDatalogProgram.java b/src/main/java/uk/ac/ox/cs/pagoda/rules/UpperDatalogProgram.java
index 611e183..611e183 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/UpperDatalogProgram.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/rules/UpperDatalogProgram.java
diff --git a/src/uk/ac/ox/cs/pagoda/rules/UpperProgram.java b/src/main/java/uk/ac/ox/cs/pagoda/rules/UpperProgram.java
index 52d60b7..52d60b7 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/UpperProgram.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/rules/UpperProgram.java
diff --git a/src/uk/ac/ox/cs/pagoda/rules/approximators/Approximator.java b/src/main/java/uk/ac/ox/cs/pagoda/rules/approximators/Approximator.java
index f910c64..f910c64 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/approximators/Approximator.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/rules/approximators/Approximator.java
diff --git a/src/uk/ac/ox/cs/pagoda/rules/approximators/LimitedSkolemisationApproximator.java b/src/main/java/uk/ac/ox/cs/pagoda/rules/approximators/LimitedSkolemisationApproximator.java
index a140225..a140225 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/approximators/LimitedSkolemisationApproximator.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/rules/approximators/LimitedSkolemisationApproximator.java
diff --git a/src/uk/ac/ox/cs/pagoda/rules/approximators/OverApproxBoth.java b/src/main/java/uk/ac/ox/cs/pagoda/rules/approximators/OverApproxBoth.java
index ae2a2cf..ae2a2cf 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/approximators/OverApproxBoth.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/rules/approximators/OverApproxBoth.java
diff --git a/src/uk/ac/ox/cs/pagoda/rules/approximators/OverApproxDisj.java b/src/main/java/uk/ac/ox/cs/pagoda/rules/approximators/OverApproxDisj.java
index 05d9442..05d9442 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/approximators/OverApproxDisj.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/rules/approximators/OverApproxDisj.java
diff --git a/src/uk/ac/ox/cs/pagoda/rules/approximators/OverApproxExist.java b/src/main/java/uk/ac/ox/cs/pagoda/rules/approximators/OverApproxExist.java
index 028568c..028568c 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/approximators/OverApproxExist.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/rules/approximators/OverApproxExist.java
diff --git a/src/uk/ac/ox/cs/pagoda/rules/approximators/SkolemTermsManager.java b/src/main/java/uk/ac/ox/cs/pagoda/rules/approximators/SkolemTermsManager.java
index ed93d0e..ed93d0e 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/approximators/SkolemTermsManager.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/rules/approximators/SkolemTermsManager.java
diff --git a/src/uk/ac/ox/cs/pagoda/rules/approximators/TupleDependentApproximator.java b/src/main/java/uk/ac/ox/cs/pagoda/rules/approximators/TupleDependentApproximator.java
index c99a1ad..c99a1ad 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/approximators/TupleDependentApproximator.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/rules/approximators/TupleDependentApproximator.java
diff --git a/src/uk/ac/ox/cs/pagoda/rules/clauses/Clause.java b/src/main/java/uk/ac/ox/cs/pagoda/rules/clauses/Clause.java
index 2adb66b..2adb66b 100644
--- a/src/uk/ac/ox/cs/pagoda/rules/clauses/Clause.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/rules/clauses/Clause.java
diff --git a/src/uk/ac/ox/cs/pagoda/summary/Edge.java b/src/main/java/uk/ac/ox/cs/pagoda/summary/Edge.java
index 79d3041..79d3041 100644
--- a/src/uk/ac/ox/cs/pagoda/summary/Edge.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/summary/Edge.java
diff --git a/src/uk/ac/ox/cs/pagoda/summary/EstimatedFeatureComparator.java b/src/main/java/uk/ac/ox/cs/pagoda/summary/EstimatedFeatureComparator.java
index 59fdf7f..59fdf7f 100644
--- a/src/uk/ac/ox/cs/pagoda/summary/EstimatedFeatureComparator.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/summary/EstimatedFeatureComparator.java
diff --git a/src/uk/ac/ox/cs/pagoda/summary/Graph.java b/src/main/java/uk/ac/ox/cs/pagoda/summary/Graph.java
index cfa94a4..ecd0f03 100644
--- a/src/uk/ac/ox/cs/pagoda/summary/Graph.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/summary/Graph.java
@@ -18,6 +18,7 @@ import org.semanticweb.owlapi.model.OWLClassAssertionAxiom;
 import org.semanticweb.owlapi.model.OWLObjectProperty;
 import org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom;
 import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.parameters.Imports;
 
 import uk.ac.ox.cs.JRDFox.model.GroundTerm;
 import uk.ac.ox.cs.JRDFox.model.Literal;
@@ -33,7 +34,7 @@ public class Graph {
                 Map<Node, Collection<Edge>> outGoingEdges = new HashMap<Node, Collection<Edge>>(); 
                 Map<Node, Collection<Edge>> inComingEdges = new HashMap<Node, Collection<Edge>>();
                 
-                for (OWLAxiom axiom: ontology.getABoxAxioms(true))
+                for (OWLAxiom axiom: ontology.getABoxAxioms(Imports.INCLUDED))
                         if (axiom instanceof OWLClassAssertionAxiom) 
                                 addClassAssertion((OWLClassAssertionAxiom) axiom); 
                         else if (axiom instanceof OWLObjectPropertyAssertionAxiom)
diff --git a/src/uk/ac/ox/cs/pagoda/summary/HermitSummaryFilter.java b/src/main/java/uk/ac/ox/cs/pagoda/summary/HermitSummaryFilter.java
index 6fcf887..1154546 100644
--- a/src/uk/ac/ox/cs/pagoda/summary/HermitSummaryFilter.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/summary/HermitSummaryFilter.java
@@ -1,6 +1,7 @@
 package uk.ac.ox.cs.pagoda.summary;
 
 import org.semanticweb.owlapi.model.*;
+import org.semanticweb.owlapi.model.parameters.Imports;
 import uk.ac.ox.cs.JRDFox.model.Individual;
 import uk.ac.ox.cs.pagoda.endomorph.Endomorph;
 import uk.ac.ox.cs.pagoda.owl.OWLHelper;
@@ -76,7 +77,7 @@ public class HermitSummaryFilter extends Checker {
 
                 System.out.println("Axioms in " + onto.getOntologyID().getOntologyIRI() + " related to " + str);
 
-                for(OWLAxiom axiom : onto.getABoxAxioms(true))
+                for(OWLAxiom axiom : onto.getABoxAxioms(Imports.INCLUDED))
                         if(axiom.toString().contains(str))
                                 System.out.println(axiom);
 
@@ -87,11 +88,11 @@ public class HermitSummaryFilter extends Checker {
 
                 System.out.println("Axioms in " + onto.getOntologyID().getOntologyIRI() + " related to " + str);
 
-                for(OWLAxiom axiom : onto.getTBoxAxioms(true))
+                for(OWLAxiom axiom : onto.getTBoxAxioms(Imports.INCLUDED))
                         if(axiom.toString().contains(str))
                                 System.out.println(axiom);
 
-                for(OWLAxiom axiom : onto.getRBoxAxioms(true))
+                for(OWLAxiom axiom : onto.getRBoxAxioms(Imports.INCLUDED))
                         if(axiom.toString().contains(str))
                                 System.out.println(axiom);
 
diff --git a/src/uk/ac/ox/cs/pagoda/summary/Node.java b/src/main/java/uk/ac/ox/cs/pagoda/summary/Node.java
index 6fca4bb..6fca4bb 100644
--- a/src/uk/ac/ox/cs/pagoda/summary/Node.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/summary/Node.java
diff --git a/src/uk/ac/ox/cs/pagoda/summary/NodeTuple.java b/src/main/java/uk/ac/ox/cs/pagoda/summary/NodeTuple.java
index bf8d55a..bf8d55a 100644
--- a/src/uk/ac/ox/cs/pagoda/summary/NodeTuple.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/summary/NodeTuple.java
diff --git a/src/uk/ac/ox/cs/pagoda/summary/Summary.java b/src/main/java/uk/ac/ox/cs/pagoda/summary/Summary.java
index 264ff76..c4f54b0 100644
--- a/src/uk/ac/ox/cs/pagoda/summary/Summary.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/summary/Summary.java
@@ -23,6 +23,7 @@ import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
 import org.semanticweb.owlapi.model.OWLOntologyManager;
 import org.semanticweb.owlapi.model.OWLOntologyStorageException;
+import org.semanticweb.owlapi.model.parameters.Imports;
 
 import uk.ac.ox.cs.JRDFox.model.GroundTerm;
 import uk.ac.ox.cs.JRDFox.model.Literal;
@@ -79,11 +80,11 @@ public class Summary {
                 OWLOntologyManager manager = ontology.getOWLOntologyManager(); 
                 groupIndividualsByConcepts();
 
-                manager.addAxioms(abstractOntology, ontology.getRBoxAxioms(true)); 
-                manager.addAxioms(abstractOntology, ontology.getTBoxAxioms(true));
+                manager.addAxioms(abstractOntology, ontology.getRBoxAxioms(Imports.INCLUDED)); 
+                manager.addAxioms(abstractOntology, ontology.getTBoxAxioms(Imports.INCLUDED));
 
                 OWLAxiom newAxiom; 
-                for (OWLAxiom axiom: ontology.getABoxAxioms(true)) {
+                for (OWLAxiom axiom: ontology.getABoxAxioms(Imports.INCLUDED)) {
                         newAxiom = summeriseAxiom(axiom); 
                         manager.addAxiom(abstractOntology, newAxiom);
                 }
diff --git a/src/uk/ac/ox/cs/pagoda/tracking/AnswerTuplesWriter.java b/src/main/java/uk/ac/ox/cs/pagoda/tracking/AnswerTuplesWriter.java
index a83a4e9..a83a4e9 100644
--- a/src/uk/ac/ox/cs/pagoda/tracking/AnswerTuplesWriter.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/tracking/AnswerTuplesWriter.java
diff --git a/src/uk/ac/ox/cs/pagoda/tracking/BottomFragmentManager.java b/src/main/java/uk/ac/ox/cs/pagoda/tracking/BottomFragmentManager.java
index 09915e2..6521e72 100644
--- a/src/uk/ac/ox/cs/pagoda/tracking/BottomFragmentManager.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/tracking/BottomFragmentManager.java
@@ -14,6 +14,7 @@ import org.semanticweb.owlapi.model.OWLDataProperty;
 import org.semanticweb.owlapi.model.OWLDataPropertyAssertionAxiom;
 import org.semanticweb.owlapi.model.OWLObjectProperty;
 import org.semanticweb.owlapi.model.OWLObjectPropertyAssertionAxiom;
+import org.semanticweb.owlapi.model.parameters.Imports;
 
 import uk.ac.ox.cs.pagoda.constraints.PredicateDependency;
 import uk.ac.ox.cs.pagoda.query.QueryRecord;
@@ -73,7 +74,7 @@ public class BottomFragmentManager {
                 int tboxCounter = axioms.size(); 
                 Utility.logDebug("There are " + tboxCounter + " TBox axioms in the bottom fragment related to this query."); 
                 String name; 
-                for (OWLAxiom axiom: m_record.getRelevantOntology().getABoxAxioms(true)) {
+                for (OWLAxiom axiom: m_record.getRelevantOntology().getABoxAxioms(Imports.INCLUDED)) {
                         if (axiom instanceof OWLClassAssertionAxiom) {
                                 OWLClass cls = (OWLClass) ((OWLClassAssertionAxiom) axiom).getClassExpression();
                                 name = cls.getIRI().toString();
diff --git a/src/uk/ac/ox/cs/pagoda/tracking/QueryTracker.java b/src/main/java/uk/ac/ox/cs/pagoda/tracking/QueryTracker.java
index 27d3a53..27d3a53 100644
--- a/src/uk/ac/ox/cs/pagoda/tracking/QueryTracker.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/tracking/QueryTracker.java
diff --git a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoder.java b/src/main/java/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoder.java
index d05731a..d05731a 100644
--- a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoder.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoder.java
diff --git a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderDisj.java b/src/main/java/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderDisj.java
index b169053..b169053 100644
--- a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderDisj.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderDisj.java
diff --git a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderDisj1.java b/src/main/java/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderDisj1.java
index d6b5e8b..d6b5e8b 100644
--- a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderDisj1.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderDisj1.java
diff --git a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderDisj2.java b/src/main/java/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderDisj2.java
index 8d79090..8d79090 100644
--- a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderDisj2.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderDisj2.java
diff --git a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderDisjVar1.java b/src/main/java/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderDisjVar1.java
index d96c747..d96c747 100644
--- a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderDisjVar1.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderDisjVar1.java
diff --git a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderDisjVar2.java b/src/main/java/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderDisjVar2.java
index 7311a86..7311a86 100644
--- a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderDisjVar2.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderDisjVar2.java
diff --git a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java b/src/main/java/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java
index 4ece796..4ece796 100644
--- a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithGap.java
diff --git a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithoutGap.java b/src/main/java/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithoutGap.java
index f898114..f898114 100644
--- a/src/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithoutGap.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/tracking/TrackingRuleEncoderWithoutGap.java
diff --git a/src/uk/ac/ox/cs/pagoda/util/ConjunctiveQueryHelper.java b/src/main/java/uk/ac/ox/cs/pagoda/util/ConjunctiveQueryHelper.java
index 937c2c4..937c2c4 100644
--- a/src/uk/ac/ox/cs/pagoda/util/ConjunctiveQueryHelper.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/util/ConjunctiveQueryHelper.java
diff --git a/src/uk/ac/ox/cs/pagoda/util/ExponentialInterpolation.java b/src/main/java/uk/ac/ox/cs/pagoda/util/ExponentialInterpolation.java
index 1d12169..1d12169 100644
--- a/src/uk/ac/ox/cs/pagoda/util/ExponentialInterpolation.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/util/ExponentialInterpolation.java
diff --git a/src/uk/ac/ox/cs/pagoda/util/Namespace.java b/src/main/java/uk/ac/ox/cs/pagoda/util/Namespace.java
index 07c8ebd..07c8ebd 100644
--- a/src/uk/ac/ox/cs/pagoda/util/Namespace.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/util/Namespace.java
diff --git a/src/uk/ac/ox/cs/pagoda/util/PagodaProperties.java b/src/main/java/uk/ac/ox/cs/pagoda/util/PagodaProperties.java
index 2b52a89..2b52a89 100644
--- a/src/uk/ac/ox/cs/pagoda/util/PagodaProperties.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/util/PagodaProperties.java
diff --git a/src/uk/ac/ox/cs/pagoda/util/Separator.java b/src/main/java/uk/ac/ox/cs/pagoda/util/Separator.java
index 1e6ad9c..1e6ad9c 100644
--- a/src/uk/ac/ox/cs/pagoda/util/Separator.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/util/Separator.java
diff --git a/src/uk/ac/ox/cs/pagoda/util/SimpleProgressBar.java b/src/main/java/uk/ac/ox/cs/pagoda/util/SimpleProgressBar.java
index 3c4aad7..3c4aad7 100644
--- a/src/uk/ac/ox/cs/pagoda/util/SimpleProgressBar.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/util/SimpleProgressBar.java
diff --git a/src/uk/ac/ox/cs/pagoda/util/SparqlHelper.java b/src/main/java/uk/ac/ox/cs/pagoda/util/SparqlHelper.java
index 1e53b9c..1e53b9c 100644
--- a/src/uk/ac/ox/cs/pagoda/util/SparqlHelper.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/util/SparqlHelper.java
diff --git a/src/uk/ac/ox/cs/pagoda/util/Timer.java b/src/main/java/uk/ac/ox/cs/pagoda/util/Timer.java
index d1814a4..d1814a4 100644
--- a/src/uk/ac/ox/cs/pagoda/util/Timer.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/util/Timer.java
diff --git a/src/uk/ac/ox/cs/pagoda/util/TurtleHelper.java b/src/main/java/uk/ac/ox/cs/pagoda/util/TurtleHelper.java
index 6887b9f..6887b9f 100644
--- a/src/uk/ac/ox/cs/pagoda/util/TurtleHelper.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/util/TurtleHelper.java
diff --git a/src/uk/ac/ox/cs/pagoda/util/UFS.java b/src/main/java/uk/ac/ox/cs/pagoda/util/UFS.java
index 0869fb7..0869fb7 100644
--- a/src/uk/ac/ox/cs/pagoda/util/UFS.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/util/UFS.java
diff --git a/src/uk/ac/ox/cs/pagoda/util/Utility.java b/src/main/java/uk/ac/ox/cs/pagoda/util/Utility.java
index cef4abd..cef4abd 100644
--- a/src/uk/ac/ox/cs/pagoda/util/Utility.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/util/Utility.java
diff --git a/src/uk/ac/ox/cs/pagoda/util/data_structures/Graph.java b/src/main/java/uk/ac/ox/cs/pagoda/util/data_structures/Graph.java
index 4f454df..4f454df 100644
--- a/src/uk/ac/ox/cs/pagoda/util/data_structures/Graph.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/util/data_structures/Graph.java
diff --git a/src/uk/ac/ox/cs/pagoda/util/disposable/Disposable.java b/src/main/java/uk/ac/ox/cs/pagoda/util/disposable/Disposable.java
index 4015b66..4015b66 100644
--- a/src/uk/ac/ox/cs/pagoda/util/disposable/Disposable.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/util/disposable/Disposable.java
diff --git a/src/uk/ac/ox/cs/pagoda/util/disposable/DisposedException.java b/src/main/java/uk/ac/ox/cs/pagoda/util/disposable/DisposedException.java
index eb8c039..eb8c039 100644
--- a/src/uk/ac/ox/cs/pagoda/util/disposable/DisposedException.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/util/disposable/DisposedException.java
diff --git a/src/uk/ac/ox/cs/pagoda/util/tuples/Tuple.java b/src/main/java/uk/ac/ox/cs/pagoda/util/tuples/Tuple.java
index 0a5983c..0a5983c 100644
--- a/src/uk/ac/ox/cs/pagoda/util/tuples/Tuple.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/util/tuples/Tuple.java
diff --git a/src/uk/ac/ox/cs/pagoda/util/tuples/TupleBuilder.java b/src/main/java/uk/ac/ox/cs/pagoda/util/tuples/TupleBuilder.java
index 172e249..172e249 100644
--- a/src/uk/ac/ox/cs/pagoda/util/tuples/TupleBuilder.java
+++ b/src/main/java/uk/ac/ox/cs/pagoda/util/tuples/TupleBuilder.java
diff --git a/src/main/scala/uk/ac/ox/cs/acqua/Main.scala b/src/main/scala/uk/ac/ox/cs/acqua/Main.scala
new file mode 100644
index 0000000..749a492
--- /dev/null
+++ b/src/main/scala/uk/ac/ox/cs/acqua/Main.scala
@@ -0,0 +1,41 @@
+package uk.ac.ox.cs.acqua
+
+import uk.ac.ox.cs.rsacomb.ontology.Ontology
+
+import uk.ac.ox.cs.pagoda.owl.OWLHelper
+import uk.ac.ox.cs.pagoda.reasoner.{ELHOQueryReasoner,QueryReasoner,RLQueryReasoner}
+// import uk.ac.ox.cs.pagoda.Pagoda
+// import uk.ac.ox.cs.pagoda.util.PagodaProperties;
+
+object Acqua extends App {
+
+  val ontopath = os.Path("tests/lubm/univ-bench.owl", base = os.pwd)
+  val ontology = Ontology(ontopath, List.empty)
+
+  val performMultiStages = true
+  val considerEqualities = true
+
+  val reasoner: QueryReasoner = if (OWLHelper.isInOWL2RL(ontology.origin)) {
+    new RLQueryReasoner();
+  } else if (OWLHelper.isInELHO(ontology.origin)) {
+    new ELHOQueryReasoner();
+  } else if (ontology.isRSA) {
+    // Use combined approach for RSA
+    ???
+  } else {
+    new MyQueryReasoner(performMultiStages, considerEqualities);
+  }
+        // 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;
+
+}
diff --git a/test/resources/AllTests.xml b/src/test/java/resources/AllTests.xml
index bc3e5cc..bc3e5cc 100644
--- a/test/resources/AllTests.xml
+++ b/src/test/java/resources/AllTests.xml
diff --git a/test/resources/BugTests.xml b/src/test/java/resources/BugTests.xml
index 92ac26d..92ac26d 100644
--- a/test/resources/BugTests.xml
+++ b/src/test/java/resources/BugTests.xml
diff --git a/test/resources/ComparisonTests.xml b/src/test/java/resources/ComparisonTests.xml
index 0095724..0095724 100644
--- a/test/resources/ComparisonTests.xml
+++ b/src/test/java/resources/ComparisonTests.xml
diff --git a/test/resources/Correctness.xml b/src/test/java/resources/Correctness.xml
index 18a69fa..18a69fa 100644
--- a/test/resources/Correctness.xml
+++ b/src/test/java/resources/Correctness.xml
diff --git a/test/resources/ExistentialEvaluation.xml b/src/test/java/resources/ExistentialEvaluation.xml
index 225f6cd..225f6cd 100644
--- a/test/resources/ExistentialEvaluation.xml
+++ b/src/test/java/resources/ExistentialEvaluation.xml
diff --git a/test/resources/FullEvaluation.xml b/src/test/java/resources/FullEvaluation.xml
index c4a3ebe..c4a3ebe 100644
--- a/test/resources/FullEvaluation.xml
+++ b/src/test/java/resources/FullEvaluation.xml
diff --git a/test/resources/HeavyTests.xml b/src/test/java/resources/HeavyTests.xml
index c0b0044..c0b0044 100644
--- a/test/resources/HeavyTests.xml
+++ b/src/test/java/resources/HeavyTests.xml
diff --git a/test/resources/MainTests.xml b/src/test/java/resources/MainTests.xml
index fdecc72..fdecc72 100644
--- a/test/resources/MainTests.xml
+++ b/src/test/java/resources/MainTests.xml
diff --git a/test/resources/MiscellaneousTests.xml b/src/test/java/resources/MiscellaneousTests.xml
index 21b64f7..21b64f7 100644
--- a/test/resources/MiscellaneousTests.xml
+++ b/src/test/java/resources/MiscellaneousTests.xml
diff --git a/test/resources/SygeniaTests.xml b/src/test/java/resources/SygeniaTests.xml
index 4daecf5..4daecf5 100644
--- a/test/resources/SygeniaTests.xml
+++ b/src/test/java/resources/SygeniaTests.xml
diff --git a/test/resources/answers/pagoda-fly-rolledup.json b/src/test/java/resources/answers/pagoda-fly-rolledup.json
index 21518ca..21518ca 100644
--- a/test/resources/answers/pagoda-fly-rolledup.json
+++ b/src/test/java/resources/answers/pagoda-fly-rolledup.json
diff --git a/test/resources/answers/pagoda-fly-with-GJ-FC-individuals.json b/src/test/java/resources/answers/pagoda-fly-with-GJ-FC-individuals.json
index e37d3f5..e37d3f5 100644
--- a/test/resources/answers/pagoda-fly-with-GJ-FC-individuals.json
+++ b/src/test/java/resources/answers/pagoda-fly-with-GJ-FC-individuals.json
diff --git a/test/resources/answers/pagoda-lubm1.json b/src/test/java/resources/answers/pagoda-lubm1.json
index ad57660..ad57660 100644
--- a/test/resources/answers/pagoda-lubm1.json
+++ b/src/test/java/resources/answers/pagoda-lubm1.json
diff --git a/test/resources/answers/pagoda-uobm1.json b/src/test/java/resources/answers/pagoda-uobm1.json
index 79a1ce4..79a1ce4 100644
--- a/test/resources/answers/pagoda-uobm1.json
+++ b/src/test/java/resources/answers/pagoda-uobm1.json
diff --git a/test/resources/answers/pagoda-uobm2.json b/src/test/java/resources/answers/pagoda-uobm2.json
index ba09463..ba09463 100644
--- a/test/resources/answers/pagoda-uobm2.json
+++ b/src/test/java/resources/answers/pagoda-uobm2.json
diff --git a/test/resources/answers/pagoda-uobm3.json b/src/test/java/resources/answers/pagoda-uobm3.json
index 5e82eb1..5e82eb1 100644
--- a/test/resources/answers/pagoda-uobm3.json
+++ b/src/test/java/resources/answers/pagoda-uobm3.json
diff --git a/test/resources/answers/pagoda-uobm4.json b/src/test/java/resources/answers/pagoda-uobm4.json
index 878f0e9..878f0e9 100644
--- a/test/resources/answers/pagoda-uobm4.json
+++ b/src/test/java/resources/answers/pagoda-uobm4.json
diff --git a/test/resources/test.properties b/src/test/java/resources/test.properties
index 08caeba..08caeba 100644
--- a/test/resources/test.properties
+++ b/src/test/java/resources/test.properties
diff --git a/test/uk/ac/ox/cs/hermit/HermitQueryReasoner.java b/src/test/java/uk/ac/ox/cs/hermit/HermitQueryReasoner.java
index 008fcb2..957790f 100644
--- a/test/uk/ac/ox/cs/hermit/HermitQueryReasoner.java
+++ b/src/test/java/uk/ac/ox/cs/hermit/HermitQueryReasoner.java
@@ -4,6 +4,7 @@ import org.semanticweb.HermiT.Reasoner;
 import org.semanticweb.HermiT.model.Atom;
 import org.semanticweb.HermiT.model.AtomicRole;
 import org.semanticweb.owlapi.model.*;
+import org.semanticweb.owlapi.model.parameters.Imports;
 import org.semanticweb.owlapi.reasoner.Node;
 import uk.ac.ox.cs.pagoda.owl.OWLHelper;
 import uk.ac.ox.cs.pagoda.owl.QueryRoller;
@@ -69,7 +70,7 @@ public class HermitQueryReasoner {
                         e.printStackTrace();
                 }
                 System.out.println("Ontology loaded in " + t.duration()); 
-                System.out.println("ABox axioms:" + onto.getABoxAxioms(true).size()); 
+                System.out.println("ABox axioms:" + onto.getABoxAxioms(Imports.INCLUDED).size()); 
 //              for (OWLOntology o: onto.getImportsClosure())
 //                      for (OWLAxiom axiom: o.getAxioms())
 //                              System.out.println(axiom); 
diff --git a/test/uk/ac/ox/cs/hermit/HermitTester.java b/src/test/java/uk/ac/ox/cs/hermit/HermitTester.java
index dc70284..dc70284 100644
--- a/test/uk/ac/ox/cs/hermit/HermitTester.java
+++ b/src/test/java/uk/ac/ox/cs/hermit/HermitTester.java
diff --git a/test/uk/ac/ox/cs/hermit/JAIR_HermiT.java b/src/test/java/uk/ac/ox/cs/hermit/JAIR_HermiT.java
index 72e7af8..72e7af8 100644
--- a/test/uk/ac/ox/cs/hermit/JAIR_HermiT.java
+++ b/src/test/java/uk/ac/ox/cs/hermit/JAIR_HermiT.java
diff --git a/test/uk/ac/ox/cs/jrdfox/Tester.java b/src/test/java/uk/ac/ox/cs/jrdfox/Tester.java
index 94f5401..94f5401 100644
--- a/test/uk/ac/ox/cs/jrdfox/Tester.java
+++ b/src/test/java/uk/ac/ox/cs/jrdfox/Tester.java
diff --git a/test/uk/ac/ox/cs/pagoda/approx/ApproxTester.java b/src/test/java/uk/ac/ox/cs/pagoda/approx/ApproxTester.java
index 63fe7b7..63fe7b7 100644
--- a/test/uk/ac/ox/cs/pagoda/approx/ApproxTester.java
+++ b/src/test/java/uk/ac/ox/cs/pagoda/approx/ApproxTester.java
diff --git a/test/uk/ac/ox/cs/pagoda/approx/ClauseTester.java b/src/test/java/uk/ac/ox/cs/pagoda/approx/ClauseTester.java
index cff1d1c..cff1d1c 100644
--- a/test/uk/ac/ox/cs/pagoda/approx/ClauseTester.java
+++ b/src/test/java/uk/ac/ox/cs/pagoda/approx/ClauseTester.java
diff --git a/test/uk/ac/ox/cs/pagoda/endomorph/DependencyGraphTest.java b/src/test/java/uk/ac/ox/cs/pagoda/endomorph/DependencyGraphTest.java
index a4579a3..a4579a3 100644
--- a/test/uk/ac/ox/cs/pagoda/endomorph/DependencyGraphTest.java
+++ b/src/test/java/uk/ac/ox/cs/pagoda/endomorph/DependencyGraphTest.java
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/BugTests.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/BugTests.java
index 3f14ec7..3f14ec7 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/BugTests.java
+++ b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/BugTests.java
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/CostEvaluation.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/CostEvaluation.java
index 01e8203..01e8203 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/CostEvaluation.java
+++ b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/CostEvaluation.java
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_PAGOdA.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/JAIR_PAGOdA.java
index 18f6cf9..18f6cf9 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_PAGOdA.java
+++ b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/JAIR_PAGOdA.java
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_Scalability.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/JAIR_Scalability.java
index 01f3568..01f3568 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/JAIR_Scalability.java
+++ b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/JAIR_Scalability.java
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/LightEvaluation.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/LightEvaluation.java
index 3551b9b..3551b9b 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/LightEvaluation.java
+++ b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/LightEvaluation.java
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/MadeUpCases.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/MadeUpCases.java
index 3d154cb..3d154cb 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/MadeUpCases.java
+++ b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/MadeUpCases.java
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/SkolemisationTests.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/SkolemisationTests.java
index 2fc682b..2fc682b 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/SkolemisationTests.java
+++ b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/SkolemisationTests.java
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestGapMappedToLower.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestGapMappedToLower.java
index 4b1ec6d..4b1ec6d 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestGapMappedToLower.java
+++ b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestGapMappedToLower.java
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaDBPedia.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaDBPedia.java
index 3642147..3642147 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaDBPedia.java
+++ b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaDBPedia.java
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java
index 3eb956f..3eb956f 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java
+++ b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaFLY.java
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaLUBM.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaLUBM.java
index 019fafa..019fafa 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaLUBM.java
+++ b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaLUBM.java
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaNPD.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaNPD.java
index 939ee6e..939ee6e 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaNPD.java
+++ b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaNPD.java
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java
index 8a8a596..8a8a596 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java
+++ b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaUOBM.java b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaUOBM.java
index 4dae223..4dae223 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaUOBM.java
+++ b/src/test/java/uk/ac/ox/cs/pagoda/global_tests/TestPagodaUOBM.java
diff --git a/test/uk/ac/ox/cs/pagoda/hermit/TestRuleHelper.java b/src/test/java/uk/ac/ox/cs/pagoda/hermit/TestRuleHelper.java
index 3a2cad8..3a2cad8 100644
--- a/test/uk/ac/ox/cs/pagoda/hermit/TestRuleHelper.java
+++ b/src/test/java/uk/ac/ox/cs/pagoda/hermit/TestRuleHelper.java
diff --git a/test/uk/ac/ox/cs/pagoda/junit/ClauseTester.java b/src/test/java/uk/ac/ox/cs/pagoda/junit/ClauseTester.java
index ad4b2de..ad4b2de 100644
--- a/test/uk/ac/ox/cs/pagoda/junit/ClauseTester.java
+++ b/src/test/java/uk/ac/ox/cs/pagoda/junit/ClauseTester.java
diff --git a/test/uk/ac/ox/cs/pagoda/query/CheckAnswers.java b/src/test/java/uk/ac/ox/cs/pagoda/query/CheckAnswers.java
index 71730c3..71730c3 100644
--- a/test/uk/ac/ox/cs/pagoda/query/CheckAnswers.java
+++ b/src/test/java/uk/ac/ox/cs/pagoda/query/CheckAnswers.java
diff --git a/test/uk/ac/ox/cs/pagoda/rules/approximators/TestSkolemTermsManager.java b/src/test/java/uk/ac/ox/cs/pagoda/rules/approximators/TestSkolemTermsManager.java
index 6bd8f05..6bd8f05 100644
--- a/test/uk/ac/ox/cs/pagoda/rules/approximators/TestSkolemTermsManager.java
+++ b/src/test/java/uk/ac/ox/cs/pagoda/rules/approximators/TestSkolemTermsManager.java
diff --git a/test/uk/ac/ox/cs/pagoda/summary/SummaryTester.java b/src/test/java/uk/ac/ox/cs/pagoda/summary/SummaryTester.java
index 18b6090..60c8ed4 100644
--- a/test/uk/ac/ox/cs/pagoda/summary/SummaryTester.java
+++ b/src/test/java/uk/ac/ox/cs/pagoda/summary/SummaryTester.java
@@ -14,6 +14,7 @@ import org.semanticweb.owlapi.model.OWLDataFactory;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
 import org.semanticweb.owlapi.model.OWLOntologyStorageException;
+import org.semanticweb.owlapi.model.parameters.Imports;
 
 import uk.ac.ox.cs.pagoda.hermit.DLClauseHelper;
 import uk.ac.ox.cs.pagoda.owl.OWLHelper;
@@ -129,11 +130,11 @@ public class SummaryTester {
         }
 
         private static void outputStatistics(OWLOntology onto) {
-                System.out.println("TBox: " + onto.getTBoxAxioms(true).size() +
-                                "\tRBox: " + onto.getRBoxAxioms(true).size() + 
-                                "\tABox: " + onto.getABoxAxioms(true).size());
-                System.out.println("Class Assertions: " + onto.getAxiomCount(AxiomType.CLASS_ASSERTION, true) + 
-                                "\tObject Property Assertions: " + onto.getAxiomCount(AxiomType.OBJECT_PROPERTY_ASSERTION, true)); 
+                System.out.println("TBox: " + onto.getTBoxAxioms(Imports.INCLUDED).size() +
+                                "\tRBox: " + onto.getRBoxAxioms(Imports.INCLUDED).size() + 
+                                "\tABox: " + onto.getABoxAxioms(Imports.INCLUDED).size());
+                System.out.println("Class Assertions: " + onto.getAxiomCount(AxiomType.CLASS_ASSERTION, Imports.INCLUDED) + 
+                                "\tObject Property Assertions: " + onto.getAxiomCount(AxiomType.OBJECT_PROPERTY_ASSERTION, Imports.INCLUDED)); 
         }
 
 }
diff --git a/test/uk/ac/ox/cs/pagoda/tester/OWLTester.java b/src/test/java/uk/ac/ox/cs/pagoda/tester/OWLTester.java
index 5bc1a9b..25162c8 100644
--- a/test/uk/ac/ox/cs/pagoda/tester/OWLTester.java
+++ b/src/test/java/uk/ac/ox/cs/pagoda/tester/OWLTester.java
@@ -3,6 +3,7 @@ package uk.ac.ox.cs.pagoda.tester;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
 import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.semanticweb.owlapi.model.parameters.Imports;
 
 import uk.ac.ox.cs.pagoda.owl.OWLHelper;
 
@@ -16,13 +17,13 @@ public class OWLTester {
 //              System.out.println("data: " + data.getAxiomCount() + " " + data.getABoxAxioms(true).size()); 
                 for (OWLOntology t: manager.getOntologies()) {
                         System.out.println(t.getOntologyID());
-                        System.out.println(t.getAxiomCount() + " " + onto.getABoxAxioms(true).size()); 
+                        System.out.println(t.getAxiomCount() + " " + onto.getABoxAxioms(Imports.INCLUDED).size()); 
                 }
                 System.out.println("In closure: " + onto.getImportsClosure().size()); 
                 for (OWLOntology t: onto.getImportsClosure())
                         System.out.println(t.getOntologyID());
                 
-                System.out.println(onto.getAxiomCount() + " " + onto.getABoxAxioms(true).size()); 
+                System.out.println(onto.getAxiomCount() + " " + onto.getABoxAxioms(Imports.INCLUDED).size()); 
         }
 
 }
diff --git a/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java b/src/test/java/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
index d741d3b..d741d3b 100644
--- a/test/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
+++ b/src/test/java/uk/ac/ox/cs/pagoda/tester/PagodaTester.java
diff --git a/test/uk/ac/ox/cs/pagoda/tester/Statistics.java b/src/test/java/uk/ac/ox/cs/pagoda/tester/Statistics.java
index 13d7f90..13d7f90 100644
--- a/test/uk/ac/ox/cs/pagoda/tester/Statistics.java
+++ b/src/test/java/uk/ac/ox/cs/pagoda/tester/Statistics.java
diff --git a/test/uk/ac/ox/cs/pagoda/util/SimpleProgressBarTester.java b/src/test/java/uk/ac/ox/cs/pagoda/util/SimpleProgressBarTester.java
index 3de30e4..3de30e4 100644
--- a/test/uk/ac/ox/cs/pagoda/util/SimpleProgressBarTester.java
+++ b/src/test/java/uk/ac/ox/cs/pagoda/util/SimpleProgressBarTester.java
diff --git a/test/uk/ac/ox/cs/pagoda/util/TestUtil.java b/src/test/java/uk/ac/ox/cs/pagoda/util/TestUtil.java
index c7f024a..c7f024a 100644
--- a/test/uk/ac/ox/cs/pagoda/util/TestUtil.java
+++ b/src/test/java/uk/ac/ox/cs/pagoda/util/TestUtil.java