3 files changed, 34 insertions, 11 deletions

diff --git a/src/uk/ac/ox/cs/pagoda/Pagoda.java b/src/uk/ac/ox/cs/pagoda/Pagoda.java
index da876b5..ace6851 100644
--- a/src/uk/ac/ox/cs/pagoda/Pagoda.java
+++ b/src/uk/ac/ox/cs/pagoda/Pagoda.java
@@ -158,13 +158,15 @@ public class Pagoda implements Runnable {
     }
 
     private String getStatisticsFilename(PagodaProperties properties, String queryFile) {
-        String statisticsFilename = "statistics_" +
-                FilenameUtils.removeExtension(FilenameUtils.getName(properties.getOntologyPath().replaceAll("_", "-")));
+        String statisticsFilename = "statistics";
+        statisticsFilename += "_" + FilenameUtils.removeExtension(FilenameUtils.getName(properties.getOntologyPath().replaceAll("_", "-")));
+        statisticsFilename += "_" + FilenameUtils.removeExtension(FilenameUtils.getName(properties.getDataPath().replaceAll("_", "-")));
         statisticsFilename += "_" + FilenameUtils.removeExtension(FilenameUtils.getName(queryFile).replaceAll("_", "-"));
         statisticsFilename += "_" + ((properties.getSkolemUpperBound() == PagodaProperties.SkolemUpperBoundOptions.DISABLED)
                 ? "" : (properties.getSkolemUpperBound() == PagodaProperties.SkolemUpperBoundOptions.BEFORE_SUMMARISATION)
                 ? "before" : "after");
-        statisticsFilename += "_" + properties.getSkolemDepth();
+        statisticsFilename += "_skd" + properties.getSkolemDepth();
+        statisticsFilename += "_maxtrpl" + properties.getMaxTriplesInSkolemStore();
         statisticsFilename += ".json";
         statisticsFilename = FilenameUtils.concat(properties.getStatisticsDir().toString(),
                                                   statisticsFilename);
diff --git a/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java b/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
index f702d5c..3f73145 100644
--- a/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
+++ b/src/uk/ac/ox/cs/pagoda/query/QueryRecord.java
@@ -31,6 +31,7 @@ public class QueryRecord extends Disposable {
     OWLOntology relevantOntology = null;
     Set<DLClause> relevantClauses = new HashSet<DLClause>();
     double[] timer;
+    int[] gapAnswersAtStep;
     int subID;
     DLClause queryClause = null;
     int queryID = -1;
@@ -80,7 +81,11 @@ public class QueryRecord extends Disposable {
 
         int length = Step.values().length;
         timer = new double[length];
-        for(int i = 0; i < length; ++i) timer[i] = 0;
+        gapAnswersAtStep = new int[length];
+        for(int i = 0; i < length; ++i) {
+            timer[i] = 0;
+            gapAnswersAtStep[i] = 0;
+        }
     }
 
     public AnswerTuples getAnswers() {
@@ -280,7 +285,8 @@ public class QueryRecord extends Disposable {
 
         double totalTime = 0.0;
         for(Step step : Step.values()) {
-            result.put(step.toString(), Double.toString(timer[step.ordinal()]));
+            result.put(step.toString() + "_time", Double.toString(timer[step.ordinal()]));
+            result.put(step.toString() + "_gap", Integer.toString(gapAnswersAtStep[step.ordinal()]));
             totalTime += timer[step.ordinal()];
         }
         result.put("totalTime", Double.toString(totalTime));
@@ -396,6 +402,10 @@ public class QueryRecord extends Disposable {
         if(isDisposed()) throw new DisposedException();
 
         timer[step.ordinal()] += time;
+        if(gapAnswerTuples != null)
+            gapAnswersAtStep[step.ordinal()] = getGapAnswersCount();
+        else
+            gapAnswersAtStep[step.ordinal()] = -1;
     }
 
     public int getArity() {
@@ -725,9 +735,9 @@ public class QueryRecord extends Disposable {
         SKOLEM_UPPER_BOUND,
         EL_LOWER_BOUND,
         FRAGMENT,
-        FRAGMENT_REFINEMENT,
+//        FRAGMENT_REFINEMENT,
         SUMMARISATION,
-        DEPENDENCY,
+//        DEPENDENCY,
         FULL_REASONING;
 
         @Override
diff --git a/src/uk/ac/ox/cs/pagoda/util/PagodaProperties.java b/src/uk/ac/ox/cs/pagoda/util/PagodaProperties.java
index 0f9ad4e..2b52a89 100644
--- a/src/uk/ac/ox/cs/pagoda/util/PagodaProperties.java
+++ b/src/uk/ac/ox/cs/pagoda/util/PagodaProperties.java
@@ -13,6 +13,7 @@ public class PagodaProperties {
 
     public enum SkolemUpperBoundOptions {DISABLED, BEFORE_SUMMARISATION, AFTER_SUMMARISATION}
 
+    public static final String DEFAULT_CONFIG_FILE = "_default_pagoda.properties";
     public static final String CONFIG_FILE = "pagoda.properties";
     public static final boolean DEFAULT_DEBUG = false;
     private static final boolean DEFAULT_USE_ALWAYS_SIMPLE_UPPER_BOUND;
@@ -26,6 +27,8 @@ public class PagodaProperties {
     private static boolean debug = DEFAULT_DEBUG;
 
     static {
+        Logger logger = Logger.getLogger("PagodaProperties");
+
         boolean defaultUseAlwaysSimpleUpperBound = false;
         SkolemUpperBoundOptions defaultSkolemUpperBound = SkolemUpperBoundOptions.DISABLED;
         int defaultSkolemDepth = 1;
@@ -33,11 +36,19 @@ public class PagodaProperties {
         Path defaultStatisticsDir = null;
         long defaultMaxTriplesInSkolemStore = 1000000;
 
-        try (InputStream in = PagodaProperties.class.getClassLoader().getResourceAsStream(CONFIG_FILE)) {
+        InputStream configStream = PagodaProperties.class.getClassLoader().getResourceAsStream(CONFIG_FILE);
+
+        if(configStream == null) {
+            logger.info("Unable to find user-defined configuration file (\"" + CONFIG_FILE + "\" in classpath)");
+            logger.info("Using default configuration");
+            configStream = PagodaProperties.class.getClassLoader().getResourceAsStream(DEFAULT_CONFIG_FILE);
+        }
+
+        try {
             Properties config = new Properties();
-            config.load(in);
-            in.close();
-            Logger logger = Logger.getLogger("PagodaProperties");
+            config.load(configStream);
+            configStream.close();
+
             if (config.containsKey("debug")) {
                 debug = Boolean.parseBoolean(config.getProperty("debug"));
                 logger.info("Debugging mode is enabled");