Changeset 1760 for branches/autoquest-core-tasktrees-alignment

Timestamp:

09/23/14 13:55:37 (10 years ago)

Author:

rkrimmel

Message:

Memory improvement and bugs

Location:

branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees

Files:

• alignment/algorithms/Match.java (modified) (10 diffs)
• alignment/algorithms/SmithWatermanRepeated.java (modified) (1 diff)
• temporalrelation/RuleUtils.java (modified) (1 diff)
• temporalrelation/SequenceForTaskDetectionRuleAlignment.java (modified) (5 diffs)

branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/Match.java

@@ -4 +4 @@
 package de.ugoe.cs.autoquest.tasktrees.alignment.algorithms;
 
-import java.io.Serializable;
-import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.LinkedList;
@@ -13 +11 @@
  * The Class Match.
  */
-public class Match implements Cloneable,Comparable<Match>,Serializable {
-        
-        /** The Constant serialVersionUID. */
-        private static final long serialVersionUID = -3206992723755714741L;
+public class Match {
 
         /** The matchseqs. */
-        private final ArrayList<NumberSequence> matchseqs;
+        private final NumberSequence[] matchseqs;
 
         /** The occurences. */
@@ -28 +23 @@
          */
         public Match() {
-                matchseqs = new ArrayList<NumberSequence>(2);
+                matchseqs = new NumberSequence[2];
                 occurrences = new LinkedList<MatchOccurrence>();
-                matchseqs.add(null);
-                matchseqs.add(null);
-        }               // TODO Auto-generated method stub
+                
+        }               
 
         /**
-         * Adds the occurence.
+         * Adds the occurrence.
          *
-         * @param occurence the occurence
+         * @param occurence the occurrence
          */
         public void addOccurence(MatchOccurrence occurence) {
@@ -74 +68 @@
          */
         public NumberSequence getFirstSequence() {
-                return matchseqs.get(0);
+                return matchseqs[0];
         }
 
@@ -92 +86 @@
          */
         public NumberSequence getSecondSequence() {
-                return matchseqs.get(1);
+                return matchseqs[1];
         }
 
@@ -110 +104 @@
          */
         public void setFirstSequence(NumberSequence seq) {
-                matchseqs.set(0, seq);
+                matchseqs[0] = seq;
         }
 
@@ -128 +122 @@
          */
         public void setSecondSequence(NumberSequence seq) {
-                matchseqs.set(1, seq);
+                matchseqs[1] = seq;
         }
 
@@ -169 +163 @@
          * @throws CloneNotSupportedException the clone not supported exception
          */
+        /*
         public Match cloneWithoutOccurrences()   {
                 Match result = new Match();
@@ -174 +169 @@
                 result.setSecondSequence(this.getSecondSequence());
                 return result;
-        }
+        }*/
         
-        
-        
+
         /**
          * Size.
@@ -185 +179 @@
         public int size() {
                 // Both sequences should be equally long
-                return matchseqs.get(0).size();
+                return matchseqs[0].size();
         }
-
-        /* (non-Javadoc)
-         * @see java.lang.Comparable#compareTo(java.lang.Object)
-         */
-        @Override
-        public int compareTo(Match arg0) {
-                
-                return 0;
-        }
-
 }

branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java

@@ -126 +126 @@
 
                                 for (int j = 2; j <= length2; j++) {
-                                        if (matrix[i - 1][j].getScore() > tempMax) {
+                                        if (matrix[i - 1][j].getScore()-scoreThreshold > tempMax) {
                                                 tempMax = matrix[i - 1][j].getScore();
                                                 maxRowIndex = j;

branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/RuleUtils.java

@@ -17 +17 @@
 import de.ugoe.cs.autoquest.tasktrees.treeifc.IIteration;
 import de.ugoe.cs.autoquest.tasktrees.treeifc.IMarkingTemporalRelationship;
-import de.ugoe.cs.autoquest.tasktrees.treeifc.IStructuringTemporalRelationship;
 import de.ugoe.cs.autoquest.tasktrees.treeifc.IOptional;
 import de.ugoe.cs.autoquest.tasktrees.treeifc.IOptionalInstance;

branches/autoquest-core-tasktrees-alignment/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java

@@ -16 +16 @@
 
 import java.io.Serializable;
+import java.util.ArrayDeque;
 import java.util.ArrayList;
 import java.util.Collections;
@@ -167 +168 @@
             appData.getStopWatch().stop("task replacement");
             appData.getStopWatch().stop("whole loop");
-            // appData.getStopWatch().dumpStatistics(System.out);
+            appData.getStopWatch().dumpStatistics(System.out);
             appData.getStopWatch().reset();
 
-            // } while (appData.detectedAndReplacedTasks()||iteration < maxIterations);
-        }
-        while (iteration < maxIterations);
+        } while (appData.detectedAndReplacedTasks());
+        //} while (iteration < maxIterations);
         Console.println("created " + appData.getResult().getNewlyCreatedTasks().size() +
             " new tasks and " + appData.getResult().getNewlyCreatedTaskInstances().size() +
@@ -666 +666 @@
             }
         }
+        appData.matchseqs =null;
     }
 
@@ -1123 +1124 @@
         private final ObjectDistanceSubstitionMatrix submat;
 
-        private LinkedList<PlannedReplacement>[] plannedReplacements;
+        private ArrayDeque<PlannedReplacement>[] plannedReplacements;
 
         /** The list of all found matches */
@@ -1173 +1174 @@
 
         private void initializeQueues(int size) {
-            plannedReplacements = new LinkedList[size];
+            plannedReplacements = new ArrayDeque[size];
             for (int i = 0; i < size; i++) {
-                plannedReplacements[i] = new LinkedList<PlannedReplacement>();
-            }
-        }
-
-        public Queue<PlannedReplacement>[] getPlannedReplacements() {
+                plannedReplacements[i] = new ArrayDeque<PlannedReplacement>(30);
+            }
+        }
+
+        public ArrayDeque<PlannedReplacement>[] getPlannedReplacements() {
             return plannedReplacements;
         }