Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/AlignmentAlgorithm.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/AlignmentAlgorithm.java (revision 1611) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/AlignmentAlgorithm.java (revision 1612) @@ -3,6 +3,10 @@ import java.util.ArrayList; +import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix; + public interface AlignmentAlgorithm { + public abstract void align(int[] input1, int[] input2, SubstitutionMatrix submat,float threshold); + /** * Get the alignment score between the two input strings. Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/AlignmentAlgorithmFactory.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/AlignmentAlgorithmFactory.java (revision 1611) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/AlignmentAlgorithmFactory.java (revision 1612) @@ -1,3 +1,6 @@ package de.ugoe.cs.autoquest.tasktrees.alignment.algorithms; + +import java.lang.reflect.Constructor; +import java.lang.reflect.InvocationTargetException; import de.ugoe.cs.autoquest.tasktrees.alignment.matrix.SubstitutionMatrix; @@ -5,10 +8,28 @@ public class AlignmentAlgorithmFactory { + public static void setDefaultAlgorithm(String algorithmname) { + //TODO: check for valid algorihm class names here + algorithmclass = algorithmname; + } - public static AlignmentAlgorithm create(int[] input1, int[] input2, SubstitutionMatrix submat,float threshold) { - + private static String algorithmclass = "de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.SmithWatermanRepeated"; + + + + public static AlignmentAlgorithm create() { + Class newclass; + Object object = null; + try { + newclass = Class.forName(algorithmclass); + object = newclass.newInstance(); + + } catch (ClassNotFoundException | SecurityException | InstantiationException | IllegalAccessException | IllegalArgumentException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } //return new SmithWaterman(input1,input2,submat,threshold); //return new NeedlemanWunsch(input1,input2,submat,threshold); - return new SmithWatermanRepeated(input1,input2,submat,threshold); + //return new SmithWatermanRepeated(input1,input2,submat,threshold); + return (AlignmentAlgorithm) object; } } Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NeedlemanWunsch.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NeedlemanWunsch.java (revision 1611) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NeedlemanWunsch.java (revision 1612) @@ -39,28 +39,4 @@ private SubstitutionMatrix submat; - public NeedlemanWunsch(int[] input1, int[] input2, SubstitutionMatrix submat, - float threshold) { - this.input1 = input1; - this.input2 = input2; - length1 = input1.length; - length2 = input2.length; - this.submat = submat; - - // System.out.println("Starting SmithWaterman algorithm with a " - // + submat.getClass() + " Substitution Matrix: " + - // submat.getClass().getCanonicalName()); - - matrix = new MatrixEntry[length1 + 1][length2 + 1]; - alignment = new ArrayList(); - - for (int i = 0; i < length1+1; i++) { - for (int j = 0; j < length2+1; j++) { - matrix[i][j] = new MatrixEntry(); - } - } - - buildMatrix(); - traceback(); - } /** @@ -289,4 +265,31 @@ } + @Override + public void align(int[] input1, int[] input2, SubstitutionMatrix submat, + float threshold) { + this.input1 = input1; + this.input2 = input2; + length1 = input1.length; + length2 = input2.length; + this.submat = submat; + + // System.out.println("Starting SmithWaterman algorithm with a " + // + submat.getClass() + " Substitution Matrix: " + + // submat.getClass().getCanonicalName()); + + matrix = new MatrixEntry[length1 + 1][length2 + 1]; + alignment = new ArrayList(); + + for (int i = 0; i < length1+1; i++) { + for (int j = 0; j < length2+1; j++) { + matrix[i][j] = new MatrixEntry(); + } + } + + buildMatrix(); + traceback(); + + } + 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 1611) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWaterman.java (revision 1612) @@ -38,28 +38,4 @@ private SubstitutionMatrix submat; - public SmithWaterman(int[] input1, int[] input2, SubstitutionMatrix submat, - float threshold) { - this.input1 = input1; - this.input2 = input2; - length1 = input1.length; - length2 = input2.length; - this.submat = submat; - - // System.out.println("Starting SmithWaterman algorithm with a " - // + submat.getClass() + " Substitution Matrix: " + - // submat.getClass().getCanonicalName()); - - matrix = new MatrixEntry[length1 + 1][length2 + 1]; - alignment = new ArrayList(); - - for (int i = 0; i < length1+1; i++) { - for (int j = 0; j < length2+1; j++) { - matrix[i][j] = new MatrixEntry(); - } - } - - buildMatrix(); - traceback(); - } /** @@ -294,3 +270,30 @@ } + @Override + public void align(int[] input1, int[] input2, SubstitutionMatrix submat, + float threshold) { + this.input1 = input1; + this.input2 = input2; + length1 = input1.length; + length2 = input2.length; + this.submat = submat; + + // System.out.println("Starting SmithWaterman algorithm with a " + // + submat.getClass() + " Substitution Matrix: " + + // submat.getClass().getCanonicalName()); + + matrix = new MatrixEntry[length1 + 1][length2 + 1]; + alignment = new ArrayList(); + + for (int i = 0; i < length1+1; i++) { + for (int j = 0; j < length2+1; j++) { + matrix[i][j] = new MatrixEntry(); + } + } + + buildMatrix(); + traceback(); + + } + } 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 1611) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/SmithWatermanRepeated.java (revision 1612) @@ -43,27 +43,6 @@ private SubstitutionMatrix submat; - public SmithWatermanRepeated(int[] input1, int[] input2, SubstitutionMatrix submat,float threshold) { - this.input1 = input1; - this.input2 = input2; - length1 = input1.length; - length2 = input2.length; - this.submat = submat; - - //System.out.println("Starting SmithWaterman algorithm with a " - // + submat.getClass() + " Substitution Matrix: " + submat.getClass().getCanonicalName()); - this.scoreThreshold = threshold; - - matrix = new MatrixEntry[length1+2][length2+1]; - alignment = new ArrayList(); - - for (int i = 0; i <= length1+1; i++) { - for(int j = 0; j< length2; j++) { - matrix[i][j] = new MatrixEntry(); - } - } - - - buildMatrix(); - traceback(); + public SmithWatermanRepeated() { + } @@ -374,3 +353,30 @@ } + @Override + public void align(int[] input1, int[] input2, SubstitutionMatrix submat, + float threshold) { + this.input1 = input1; + this.input2 = input2; + length1 = input1.length; + length2 = input2.length; + this.submat = submat; + + //System.out.println("Starting SmithWaterman algorithm with a " + // + submat.getClass() + " Substitution Matrix: " + submat.getClass().getCanonicalName()); + this.scoreThreshold = threshold; + + matrix = new MatrixEntry[length1+2][length2+1]; + alignment = new ArrayList(); + + for (int i = 0; i <= length1+1; i++) { + for(int j = 0; j< length2; j++) { + matrix[i][j] = new MatrixEntry(); + } + } + + + buildMatrix(); + traceback(); + } + } Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/PairwiseAlignmentGenerator.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/PairwiseAlignmentGenerator.java (revision 1611) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/PairwiseAlignmentGenerator.java (revision 1612) @@ -21,20 +21,23 @@ if (i != j) { int smithWatermanThreshold = 10; - - alignments.set(i, j,AlignmentAlgorithmFactory.create( - ns1.getSequence(), ns2.getSequence(), submat, - smithWatermanThreshold)); + AlignmentAlgorithm aa = AlignmentAlgorithmFactory.create(); + aa.align(ns1.getSequence(), ns2.getSequence(), submat, + smithWatermanThreshold); + alignments.set(i,j,aa); + - AlignmentAlgorithm sameSequence1 = AlignmentAlgorithmFactory.create( + AlignmentAlgorithm sameSequence1 = AlignmentAlgorithmFactory.create(); + sameSequence1.align( ns1.getSequence(), ns1.getSequence(), submat, smithWatermanThreshold); - AlignmentAlgorithm sameSequence2 = AlignmentAlgorithmFactory.create( - ns2.getSequence(), ns2.getSequence(), submat, + AlignmentAlgorithm sameSequence2 = AlignmentAlgorithmFactory.create(); + sameSequence2.align(ns2.getSequence(), ns2.getSequence(), submat, smithWatermanThreshold); - AlignmentAlgorithm randomSequence = AlignmentAlgorithmFactory.create( - ns1.shuffle().getSequence(),ns2.shuffle().getSequence(),submat,smithWatermanThreshold); + AlignmentAlgorithm randomSequence = AlignmentAlgorithmFactory.create(); + randomSequence.align(ns1.shuffle().getSequence(),ns2.shuffle().getSequence(),submat,smithWatermanThreshold); // Score of the aligmnment double score = alignments.get(i,j).getAlignmentScore(); + /* if(score > 0) { System.out.println("Alignment: " + i + " " + j); @@ -52,4 +55,5 @@ System.out.println(); } + */ // Scores of the sequence being aligned to itself (maximum score) double sSelf1 = sameSequence1.getAlignmentScore(); Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/UPGMAAligningTree.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/UPGMAAligningTree.java (revision 1611) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/UPGMAAligningTree.java (revision 1612) @@ -18,4 +18,5 @@ import java.util.logging.Level; +import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithm; import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.AlignmentAlgorithmFactory; import de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NumberSequence; @@ -221,5 +222,7 @@ //Align 2 sequences if(seqCount1 == 1 && seqCount2 == 1) { - alignment = (alignments.get(node1.getNumber(), node2.getNumber())).getAlignment(); + AlignmentAlgorithm aa = AlignmentAlgorithmFactory.create(); + aa.align(node1.getSequence(0).getSequence(), node2.getSequence(0).getSequence(), submat, 5); + alignment = aa.getAlignment(); } @@ -231,6 +234,9 @@ double maxScore = 0.0; int maxIndex = 0; - for(int i=0;i *

- + * * * @author Patrick Harms @@ -158,12 +157,27 @@ submat.generate(); + ArrayList matchseqs = new ArrayList(); + PairwiseAlignmentStorage alignments = PairwiseAlignmentGenerator.generate(numberseqs,submat); - PairwiseAlignmentStorage alignments = PairwiseAlignmentGenerator.generate(numberseqs,submat); - - + for (int i=0; i< numberseqs.size();i++) { + for(int j=0; j< numberseqs.size();j++) { + if(i != j) { + ArrayList> tmp = alignments.get(i, j).getMatches(); + for(Iterator> it = tmp.iterator();it.hasNext();) { + matchseqs.addAll(it.next()); + } + } + } + } + AlignmentAlgorithmFactory.setDefaultAlgorithm("de.ugoe.cs.autoquest.tasktrees.alignment.algorithms.NeedlemanWunsch"); + PairwiseAlignmentStorage matchAlignments = PairwiseAlignmentGenerator.generate(numberseqs, submat); + UPGMAAligningTree guidetree = new UPGMAAligningTree(matchseqs,matchAlignments,submat); System.out.println(alignments.getDistanceMatrix()); //UPGMAAligningTree guidetree = new UPGMAAligningTree(numberseqs, alignments,submat); - + for(Iterator it = guidetree.getRoot().getSequences().iterator();it.hasNext();) { + NumberSequence tmp = (NumberSequence) it.next(); + tmp.printSequence(); + }