Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/Constants.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/Constants.java (revision 1578) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/Constants.java (revision 1578) @@ -0,0 +1,8 @@ +package de.ugoe.cs.autoquest.tasktrees.alignment.algorithms; + +public class Constants { + + public static final int GAP_SYMBOL = -1; + public static final int UNMATCHED_SYMBOL = -2; + +} Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWaterman.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWaterman.java (revision 1577) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWaterman.java (revision 1578) @@ -97,5 +97,5 @@ // return (input1[i - 1] == input2[j - 1]) ? MATCH_SCORE : // MISMATCH_SCORE; - return submat.getDistance(input1[i - 1], input2[j - 1]); + return submat.getScore(input1[i - 1], input2[j - 1]); } Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java (revision 1577) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java (revision 1578) @@ -2,10 +2,9 @@ import java.util.ArrayList; -import java.util.Iterator; -import java.util.LinkedList; import java.util.List; import java.util.logging.Level; import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix; +import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.Constants; import de.ugoe.cs.util.console.Console; @@ -79,5 +78,5 @@ */ private double similarity(int i, int j) { - return submat.getDistance(input1[i - 1], input2[j - 1]); + return submat.getScore(input1[i - 1], input2[j - 1]); } @@ -129,5 +128,4 @@ } - tempMax -= scoreThreshold; @@ -145,5 +143,5 @@ { matrix[i][0].setXvalue(input1[i-1]); - matrix[i][0].setYvalue(-2); + matrix[i][0].setYvalue(Constants.UNMATCHED_SYMBOL); } else { @@ -161,5 +159,5 @@ // find the directions that give the maximum scores. - // Multiple directions are ignored TODO + // TODO: Multiple directions are ignored, we choose the first maximum score //True if we had a match if (diagScore == matrix[i][j].getScore()) { @@ -171,10 +169,10 @@ if (leftScore == matrix[i][j].getScore()) { matrix[i][j].setXvalue(input1[i-1]); - matrix[i][j].setYvalue(-1); + matrix[i][j].setYvalue(Constants.GAP_SYMBOL); matrix[i][j].setPrevious(matrix[i-1][j]); } //true if we took an event from sequence y and not from x if (upScore == matrix[i][j].getScore()) { - matrix[i][j].setXvalue(-1); + matrix[i][j].setXvalue(Constants.GAP_SYMBOL); matrix[i][j].setYvalue(input2[j-1]); matrix[i][j].setPrevious(matrix[i][j-1]); @@ -184,5 +182,5 @@ matrix[i][j].setPrevious(matrix[i][0]); matrix[i][j].setXvalue(input1[i-1]); - matrix[i][j].setYvalue(-2); + matrix[i][j].setYvalue(Constants.UNMATCHED_SYMBOL); } } @@ -271,8 +269,8 @@ String append2=""; - if(tmp.getXvalue() == -1) { + if(tmp.getXvalue() == Constants.GAP_SYMBOL) { append1 = " ___"; } - else if(tmp.getXvalue() == -2) { + else if(tmp.getXvalue() == Constants.UNMATCHED_SYMBOL) { append1 = " ..."; } @@ -281,8 +279,8 @@ } - if(tmp.getYvalue() == -1) { + if(tmp.getYvalue() == Constants.GAP_SYMBOL) { append2 = " ___"; } - else if(tmp.getYvalue() == -2) { + else if(tmp.getYvalue() == Constants.UNMATCHED_SYMBOL) { append2 = " ..."; } Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/DifferenceSubstitutionMatrix.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/DifferenceSubstitutionMatrix.java (revision 1577) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/DifferenceSubstitutionMatrix.java (revision 1578) @@ -29,5 +29,5 @@ * @see de.ugoe.cs.autoquest.plugin.alignment.SubstitutionMatrix#getDistance(int, int) */ - public double getDistance(int pos1, int pos2) { + public double getScore(int pos1, int pos2) { return maxValue - (input1[pos1] - input2[pos2]); } Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/NearbySubstitutionMatrix.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/NearbySubstitutionMatrix.java (revision 1577) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/NearbySubstitutionMatrix.java (revision 1578) @@ -29,5 +29,5 @@ * @see de.ugoe.cs.autoquest.plugin.alignment.SubstitutionMatrix#getDistance(int, int) */ - public double getDistance(int pos1, int pos2) { + public double getScore(int pos1, int pos2) { int difference = Math.abs(input1[pos1]-input2[pos2]); if(difference < range) { Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/ObjectDistanceSubstitionMatrix.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/ObjectDistanceSubstitionMatrix.java (revision 1577) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/ObjectDistanceSubstitionMatrix.java (revision 1578) @@ -5,7 +5,7 @@ import java.util.Iterator; - import de.ugoe.cs.autoquest.eventcore.guimodel.IGUIElement; import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentHelpers; +import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.Constants; import de.ugoe.cs.autoquest.tasktrees.treeifc.IEventTaskInstance; import de.ugoe.cs.autoquest.tasktrees.treeifc.ITask; @@ -40,8 +40,7 @@ @Override public void generate() { + int index = 0; - //TODO We need to determine this parameter before generating the matrix.. - //float meandistance = 18; - //TODO We need to determine this parameter before generating the matrix.. + float maxDistance =34; for (Iterator it = uniqueTasks.getSymbols().iterator(); it @@ -52,5 +51,4 @@ eti1 = (IEventTaskInstance) obj1; } - //System.out.println(eti1.getTask().toString()); for (Iterator jt = uniqueTasks.getSymbols() @@ -97,11 +95,12 @@ matrix.set(tempindex1, tempindex2,distance); - + } } - //System.out.println("ObjectDistanceMatrix: MaxDistance: " + maxDistance); + //System.out.println(meandistance/(uniqueTasks.size()*uniqueTasks.size())); //System.out.println(idmapping.toString()); //System.out.println(matrix.toString()); + //System.out.println("ObjectDistanceMatrix: MaxDistance: " + maxDistance); //System.out.println(idmapping.keySet().toString()); //System.out.println(idmapping.values().toString()); @@ -113,8 +112,12 @@ } - @Override - public double getDistance(int taskId1, int taskId2) { - //System.out.println("Taskid1: " + taskId1 + " Taskid2: " + taskId2 + " Idmapping1: " + idmapping.get(taskId1) + " Idmapping2: " + idmapping.get(taskId2)); - return matrix.get(idmapping.get(taskId1),idmapping.get(taskId2)); + public double getScore(int taskId1, int taskId2) { + if(taskId1 == Constants.GAP_SYMBOL || taskId1 == Constants.UNMATCHED_SYMBOL || taskId2 == Constants.GAP_SYMBOL || taskId2 == Constants.UNMATCHED_SYMBOL ) { + return 0.0; + } + else { + return matrix.get(idmapping.get(taskId1),idmapping.get(taskId2)); + } + } Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/SubstitutionMatrix.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/SubstitutionMatrix.java (revision 1577) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/SubstitutionMatrix.java (revision 1578) @@ -6,5 +6,5 @@ - public double getDistance(int pos1, int pos2); + public double getScore(int pos1, int pos2); public double getGapPenalty(); Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java (revision 1577) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java (revision 1578) @@ -63,9 +63,5 @@ *

*

- * For determining the longest sequence occurring most often, the implementation - * uses a {@link Trie}. The depth of the tree is initially 3. If the algorithm - * has a longest sequence occurring most often whose length is equal to the - * depth of the trie, it recalculates the trie with an increased depth. - *

+ * * @author Patrick Harms @@ -183,13 +179,13 @@ ns2.getSequence(), ns2.getSequence(), submat, smithWatermanThreshold); - SmithWatermanRepeated randomSequence = new SmithWatermanRepeated( ns1.shuffle().getSequence(),ns2.shuffle().getSequence(),submat,smithWatermanThreshold); + // Score of the aligmnment double score = twoSequences.getAlignmentScore(); - // Scores of the sequence being aligned to itself + // Scores of the sequence being aligned to itself (maximum score) double sSelf1 = sameSequence1.getAlignmentScore(); double sSelf2 = sameSequence2.getAlignmentScore(); - + // Score of sequences shuffled before aligned double sRand = randomSequence.getAlignmentScore(); @@ -210,10 +206,10 @@ } } + //System.out.println(sequenceDistances.toString()); UPGMATree guidetree = new UPGMATree(numberseqs, sequenceDistances); + /* do { - System.out.println(); - //FengDoolittle fd = new FengDoolittle(); // appData.getStopWatch().start("whole loop");