Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/.classpath =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/.classpath (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/.classpath (revision 2054) @@ -0,0 +1,27 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/.project =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/.project (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/.project (revision 2054) @@ -0,0 +1,23 @@ + + + autoquest-plugin-alignment + + + + + + org.eclipse.jdt.core.javabuilder + + + + + org.eclipse.m2e.core.maven2Builder + + + + + + org.eclipse.m2e.core.maven2Nature + org.eclipse.jdt.core.javanature + + Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/.settings/org.eclipse.jdt.core.prefs =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/.settings/org.eclipse.jdt.core.prefs (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/.settings/org.eclipse.jdt.core.prefs (revision 2054) @@ -0,0 +1,12 @@ +eclipse.preferences.version=1 +org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled +org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7 +org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve +org.eclipse.jdt.core.compiler.compliance=1.7 +org.eclipse.jdt.core.compiler.debug.lineNumber=generate +org.eclipse.jdt.core.compiler.debug.localVariable=generate +org.eclipse.jdt.core.compiler.debug.sourceFile=generate +org.eclipse.jdt.core.compiler.problem.assertIdentifier=error +org.eclipse.jdt.core.compiler.problem.enumIdentifier=error +org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning +org.eclipse.jdt.core.compiler.source=1.7 Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/pom.xml =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/pom.xml (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/pom.xml (revision 2054) @@ -0,0 +1,85 @@ + + + de.ugoe.cs.autoquest + autoquest + 0.0.1-SNAPSHOT + + 4.0.0 + autoquest-plugin-alignment + autoquest-plugin-alignment + + + The Apache Software License, Version 2.0 + http://www.apache.org/licenses/LICENSE-2.0.txt + + + + ${autoquest-scm-trunk-dir}/${project.artifactId} + scm:svn:${autoquest-scm-trunk-dir}/${project.artifactId} + + + + org.apache.maven.plugins + maven-resources-plugin + 2.4.3 + + + + de.ugoe.cs + java-utils + 0.0.1-SNAPSHOT + + + de.ugoe.cs.autoquest + autoquest-plugin-core + ${project.parent.version} + + + de.ugoe.cs.autoquest + autoquest-core-events + ${project.parent.version} + + + de.ugoe.cs.autoquest + autoquest-core-usageprofiles + + + de.ugoe.cs.autoquest + autoquest-misc + ${project.parent.version} + + + de.ugoe.cs.autoquest + autoquest-core-tasktrees + ${project.parent.version} + + + + + + org.apache.maven.plugins + maven-jar-plugin + + + + true + + + + + + + + + + de.ugoe.cs.autoquest + autoquest-core-usageprofiles + ${project.parent.version} + + + + Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/ALIGNMENTPlugin.java =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/ALIGNMENTPlugin.java (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/ALIGNMENTPlugin.java (revision 2054) @@ -0,0 +1,60 @@ +// Copyright 2012 Georg-August-Universität Göttingen, Germany +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package de.ugoe.cs.autoquest.plugin.alignment; + +import java.util.Arrays; +import java.util.Collections; +import java.util.List; + +import de.ugoe.cs.autoquest.plugin.AutoQUESTPlugin; + +/** + *

+ * Identifier class for the AutoQUEST Alignment plugin + *

+ * + * @author Ralph Krimmel + * @version 1.0 + */ +public class ALIGNMENTPlugin implements AutoQUESTPlugin { + + /** + *

+ * The command packages of this plug-in. + *

+ */ + private final static String[] commandPackages = new String[] { "de.ugoe.cs.autoquest.plugin.alignment.commands" }; + + /* + * (non-Javadoc) + * + * @see de.ugoe.cs.autoquest.plugin.AutoQUESTPlugin#getTitle() + */ + @Override + public String getTitle() { + return "Alignment-Plugin"; + } + + /* + * (non-Javadoc) + * + * @see de.ugoe.cs.autoquest.plugin.AutoQUESTPlugin#getCommandPackages() + */ + @Override + public List getCommandPackages() { + return Collections.unmodifiableList(Arrays.asList(commandPackages)); + } + +} Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/Alignment.java =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/Alignment.java (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/Alignment.java (revision 2054) @@ -0,0 +1,8 @@ +package de.ugoe.cs.autoquest.plugin.alignment; + +import java.util.List; + +public interface Alignment { + public List getMatches(); + +} Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/FengDoolittle.java =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/FengDoolittle.java (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/FengDoolittle.java (revision 2054) @@ -0,0 +1,5 @@ +package de.ugoe.cs.autoquest.plugin.alignment; + +public class FengDoolittle { + +} Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/Match.java =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/Match.java (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/Match.java (revision 2054) @@ -0,0 +1,9 @@ +package de.ugoe.cs.autoquest.plugin.alignment; + +public class Match { + + + private float score; + private int start; + private int end; +} Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/ProgressiveMultiAlignment.java =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/ProgressiveMultiAlignment.java (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/ProgressiveMultiAlignment.java (revision 2054) @@ -0,0 +1,5 @@ +package de.ugoe.cs.autoquest.plugin.alignment; + +public class ProgressiveMultiAlignment { + +} Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/SmithWaterman.java =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/SmithWaterman.java (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/SmithWaterman.java (revision 2054) @@ -0,0 +1,331 @@ +package de.ugoe.cs.autoquest.plugin.alignment; + +import java.util.ArrayList; +import java.util.List; + +import de.ugoe.cs.autoquest.plugin.alignment.substitution.SubstitutionMatrix; + +public class SmithWaterman implements Alignment { + + /** + * The first input + */ + private int[] input1; + + /** + * The second input String + */ + private int[] input2; + + /** + * The lengths of the input + */ + private int length1, length2; + + /** + * The score matrix. The true scores should be divided by the normalization + * factor. + */ + private double[][] score; + + /** + * Score threshold + */ + private int scoreThreshold;; + + /** + * The similarity function constants. + */ + // static final int MATCH_SCORE = 10; + // static final int MISMATCH_SCORE = -8; + // static final int INDEL_SCORE = -9; + + /** + * Constants of directions. Multiple directions are stored by bits. The zero + * direction is the starting point. + */ + static final int DR_LEFT = 1; // 0001 + static final int DR_UP = 2; // 0010 + static final int DR_DIAG = 4; // 0100 + static final int DR_ZERO = 8; // 1000 + + /** + * The directions pointing to the cells that give the maximum score at the + * current cell. The first index is the column index. The second index is + * the row index. + */ + private int[][] prevCells; + + /** + * Substitution matrix to calculate scores + */ + private SubstitutionMatrix submat; + + public SmithWaterman(int[] input1, int[] input2, SubstitutionMatrix submat) { + 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.info()); + scoreThreshold = 20; + score = new double[length1 + 1][length2 + 1]; + prevCells = new int[length1 + 1][length2 + 1]; + + buildMatrix(); + } + + /** + * Compute the similarity score of substitution The position of the first + * character is 1. A position of 0 represents a gap. + * + * @param i + * Position of the character in str1 + * @param j + * Position of the character in str2 + * @return Cost of substitution of the character in str1 by the one in str2 + */ + private double similarity(int i, int j) { + if (i == 0 || j == 0) { + // it's a gap (indel) + return submat.getGapPenalty(); + } + // System.out.println("Diag letters: " + input1[i-1] + " " + + // input2[j-1]); + // return (input1[i - 1] == input2[j - 1]) ? MATCH_SCORE : + // MISMATCH_SCORE; + return submat.getDistance(i - 1, j - 1); + } + + /** + * Build the score matrix using dynamic programming. Note: The indel scores + * must be negative. Otherwise, the part handling the first row and column + * has to be modified. + */ + private void buildMatrix() { + if (submat.getGapPenalty() >= 0) { + throw new Error("Indel score must be negative"); + } + + int i; // length of prefix substring of str1 + int j; // length of prefix substring of str2 + + // base case + score[0][0] = 0; + prevCells[0][0] = DR_ZERO; // starting point + + // the first row + for (i = 1; i <= length1; i++) { + score[i][0] = 0; + prevCells[i][0] = DR_ZERO; + } + + // the first column + for (j = 1; j <= length2; j++) { + score[0][j] = 0; + prevCells[0][j] = DR_ZERO; + } + + // the rest of the matrix + for (i = 1; i <= length1; i++) { + for (j = 1; j <= length2; j++) { + double diagScore = score[i - 1][j - 1] + similarity(i, j); + double upScore = score[i][j - 1] + similarity(0, j); + double leftScore = score[i - 1][j] + similarity(i, 0); + + score[i][j] = Math.max(diagScore, + Math.max(upScore, Math.max(leftScore, 0))); + prevCells[i][j] = 0; + + // find the directions that give the maximum scores. + // the bitwise OR operator is used to record multiple + // directions. + if (diagScore == score[i][j]) { + prevCells[i][j] |= DR_DIAG; + } + if (leftScore == score[i][j]) { + prevCells[i][j] |= DR_LEFT; + } + if (upScore == score[i][j]) { + prevCells[i][j] |= DR_UP; + } + if (0 == score[i][j]) { + prevCells[i][j] |= DR_ZERO; + } + } + } + } + + /** + * Get the maximum value in the score matrix. + */ + private double getMaxScore() { + double maxScore = 0; + + // skip the first row and column + for (int i = 1; i <= length1; i++) { + for (int j = 1; j <= length2; j++) { + if (score[i][j] > maxScore) { + maxScore = score[i][j]; + } + } + } + + return maxScore; + } + + /** + * Get the alignment score between the two input strings. + */ + public double getAlignmentScore() { + return getMaxScore(); + } + + /** + * TODO: Iterative Version!!! Output the local alignments ending in the (i, + * j) cell. aligned1 and aligned2 are suffixes of final aligned strings + * found in backtracking before calling this function. Note: the strings are + * replicated at each recursive call. Use buffers or stacks to improve + * efficiency. + */ + private void printAlignments(int i, int j, String aligned1, String aligned2) { + // we've reached the starting point, so print the alignments + + if ((prevCells[i][j] & DR_ZERO) > 0) { + System.out.println(aligned1); + System.out.println(aligned2); + System.out.println(); + + // Note: we could check other directions for longer alignments + // with the same score. we don't do it here. + return; + } + + // find out which directions to backtrack + if ((prevCells[i][j] & DR_LEFT) > 0) { + printAlignments(i - 1, j, input1[i - 1] + aligned1, "_ " + aligned2); + } + if ((prevCells[i][j] & DR_UP) > 0) { + printAlignments(i, j - 1, "_ " + aligned1, input2[j - 1] + aligned2); + } + if ((prevCells[i][j] & DR_DIAG) > 0) { + printAlignments(i - 1, j - 1, input1[i - 1] + " " + aligned1, + input2[j - 1] + " " + aligned2); + } + } + + /** + * given the bottom right corner point trace back the top left conrner. at + * entry: i, j hold bottom right (end of Aligment coords) at return: hold + * top left (start of Alignment coords) + */ + private int[] traceback(int i, int j) { + + // find out which directions to backtrack + while (true) { + if ((prevCells[i][j] & DR_LEFT) > 0) { + if (score[i - 1][j] > 0) + i--; + else + break; + } + if ((prevCells[i][j] & DR_UP) > 0) { + // return traceback(i, j-1); + if (score[i][j - 1] > 0) + j--; + else + break; + } + if ((prevCells[i][j] & DR_DIAG) > 0) { + // return traceback(i-1, j-1); + if (score[i - 1][j - 1] > 0) { + i--; + j--; + } else + break; + } + } + int[] m = { i, j }; + return m; + } + + /** + * Output the local alignments with the maximum score. + */ + public void printAlignments() { + // find the cell with the maximum score + double maxScore = getMaxScore(); + + /* + * for (int i = 0; i < matches.length; i++) { + * System.out.println("Match #" + i + ":" + matches.get(i)); } + */ + + // skip the first row and column + for (int i = 1; i <= length1; i++) { + for (int j = 1; j <= length2; j++) { + if (score[i][j] == maxScore) { + printAlignments(i, j, "", ""); + } + } + } + // Note: empty alignments are not printed. + } + + /** + * print the dynmaic programming matrix + */ + public void printDPMatrix() { + System.out.print(" "); + for (int j = 1; j <= length2; j++) + System.out.print(" " + input2[j - 1]); + System.out.println(); + for (int i = 0; i <= length1; i++) { + if (i > 0) + System.out.print(input1[i - 1] + " "); + else + System.out.print(" "); + for (int j = 0; j <= length2; j++) { + System.out.print(score[i][j] + " "); + } + System.out.println(); + } + } + + /** + * Return a set of Matches identified in Dynamic programming matrix. A match + * is a pair of subsequences whose score is higher than the preset + * scoreThreshold + **/ + public List getMatches() { + ArrayList matchList = new ArrayList(); + int fA = 0, fB = 0; + // skip the first row and column, find the next maxScore after + // prevmaxScore + for (int i = 1; i <= length1; i++) { + for (int j = 1; j <= length2; j++) { + if (score[i][j] > scoreThreshold + && score[i][j] > score[i - 1][j - 1] + && score[i][j] > score[i - 1][j] + && score[i][j] > score[i][j - 1]) { + if (i == length1 || j == length2 + || score[i][j] > score[i + 1][j + 1]) { + // should be lesser than prev maxScore + fA = i; + fB = j; + int[] f = traceback(fA, fB); // sets the x, y to + // startAlignment + // coordinates + System.out.println(f[0] + " " + i + " " + f[1] + " " + + j + " " + score[i][j]); + // TODO Add matches to matchList + } + } + } + } + return matchList; + } + +} Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDbinaryAlignment.java =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDbinaryAlignment.java (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDbinaryAlignment.java (revision 2054) @@ -0,0 +1,101 @@ +// Copyright 2012 Georg-August-Universität Göttingen, Germany +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package de.ugoe.cs.autoquest.plugin.alignment.commands; + +import java.util.Collection; +import java.util.LinkedList; +import java.util.List; + +import de.ugoe.cs.autoquest.eventcore.Event; +import de.ugoe.cs.autoquest.plugin.alignment.SmithWaterman; +import de.ugoe.cs.autoquest.plugin.alignment.seqgen.SequenceGenerator; +import de.ugoe.cs.autoquest.plugin.alignment.seqgen.SimpleSequenceGenerator; +import de.ugoe.cs.autoquest.plugin.alignment.substitution.NearbySubstitutionMatrix; +import de.ugoe.cs.autoquest.plugin.alignment.substitution.ObjectDistanceSubstitionMatrix; +import de.ugoe.cs.util.console.Command; +import de.ugoe.cs.util.console.Console; +import de.ugoe.cs.util.console.GlobalDataContainer; + +/** + *

+ * Command to generate a binary alignment of two sequences + *

+ * + * @author Ralph Krimmel + * @version 1.0 + */ +public class CMDbinaryAlignment implements Command { + + /* + * (non-Javadoc) + * + * @see de.ugoe.cs.util.console.Command#run(java.util.List) + */ + @SuppressWarnings("unchecked") + public void run(List parameters) { + String sequencesName = "numberSequences"; + String substitutionName = "substitutionMatrix"; + String algorithm = "smithwaterman"; + try { + sequencesName = (String) parameters.get(0); + substitutionName = (String) parameters.get(1); + if (parameters.size() > 2) { + algorithm = (String) parameters.get(2); + } + } catch (Exception e) { + throw new IllegalArgumentException(); + } + + SimpleSequenceGenerator gen; + Object obj = GlobalDataContainer.getInstance().getData(sequencesName); + if (obj != null) { + if (obj instanceof SimpleSequenceGenerator) { + gen = (SimpleSequenceGenerator) obj; + Console.println("Number of sequences: " + gen.sequenceCount()); + + int[] seq1 = gen.get(0).getSequence(); + int[] seq2 = gen.get(0).getSequence(); + + ObjectDistanceSubstitionMatrix submat = new + ObjectDistanceSubstitionMatrix(); + submat.generate(sequences); + // SmithWaterman sw = new SmithWaterman(seq1, seq2, + // new NearbySubstitutionMatrix(seq1, seq2, 10)); + // sw.printDPMatrix(); + // System.out.println(); + // sw.printAlignments(); + // sw.getMatches(); + System.out.println("foo"); + + } else { + Console.printerr("No number sequences generated. Please run the generateNumberSequences before."); + + } + + } + + } + + /* + * (non-Javadoc) + * + * @see de.ugoe.cs.util.console.Command#help() + */ + @Override + public String help() { + return "binaryAlignment {}"; + } + +} Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDdeleteShortSequences.java =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDdeleteShortSequences.java (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDdeleteShortSequences.java (revision 2054) @@ -0,0 +1,97 @@ +// Copyright 2012 Georg-August-Universität Göttingen, Germany +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package de.ugoe.cs.autoquest.plugin.alignment.commands; + +import java.util.Collection; +import java.util.Iterator; +import java.util.LinkedList; +import java.util.List; +import java.util.logging.Level; + +import de.ugoe.cs.autoquest.eventcore.Event; +import de.ugoe.cs.autoquest.plugin.alignment.SmithWaterman; +import de.ugoe.cs.autoquest.plugin.alignment.seqgen.SimpleSequenceGenerator; +import de.ugoe.cs.autoquest.plugin.alignment.substitution.NearbySubstitutionMatrix; +import de.ugoe.cs.autoquest.plugin.alignment.substitution.ObjectDistanceSubstitionMatrix; +import de.ugoe.cs.util.console.Command; +import de.ugoe.cs.util.console.Console; +import de.ugoe.cs.util.console.GlobalDataContainer; + +/** + *

+ * Command to generate a binary alignment of two sequences + *

+ * + * @author Ralph Krimmel + * @version 1.0 + */ +public class CMDdeleteShortSequences implements Command { + + /* + * (non-Javadoc) + * + * @see de.ugoe.cs.util.console.Command#run(java.util.List) + */ + @SuppressWarnings("unchecked") + public void run(List parameters) { + String sequencesName = "sequences"; + int delcount = 0; + int limit = 10; + try { + sequencesName = (String) parameters.get(0); + if (parameters.size() > 1) { + try { + limit = Integer.parseInt((String) parameters.get(1)); + } + catch (NumberFormatException e) + { + Console.traceln(Level.WARNING,"Parameter not an integer. Using the default value."); + } + } + } catch (Exception e) { + throw new IllegalArgumentException(); + } + + Collection> sequences = new LinkedList>(); + Object obj = GlobalDataContainer.getInstance().getData(sequencesName); + if (obj.getClass().equals(sequences.getClass())) { + sequences = (Collection>) obj; + } + + if (sequences != null) { + Console.println("Number of sequences: " + sequences.size()); + Iterator> iter = sequences.iterator(); + while(iter.hasNext()) { + if (iter.next().size() < limit) { + iter.remove(); + delcount++; + } + } + + Console.traceln(Level.INFO, "Deleted "+ delcount + " short sequences from " + sequencesName); + } + } + + /* + * (non-Javadoc) + * + * @see de.ugoe.cs.util.console.Command#help() + */ + @Override + public String help() { + return "deleteShortSequences "; + } + +} Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDgenerateNumberSequences.java =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDgenerateNumberSequences.java (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDgenerateNumberSequences.java (revision 2054) @@ -0,0 +1,88 @@ +// Copyright 2012 Georg-August-Universität Göttingen, Germany +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package de.ugoe.cs.autoquest.plugin.alignment.commands; + + +import java.util.Collection; +import java.util.LinkedList; +import java.util.List; + +import de.ugoe.cs.autoquest.eventcore.Event; +import de.ugoe.cs.autoquest.plugin.alignment.SmithWaterman; +import de.ugoe.cs.autoquest.plugin.alignment.seqgen.SimpleSequenceGenerator; +import de.ugoe.cs.autoquest.plugin.alignment.substitution.NearbySubstitutionMatrix; +import de.ugoe.cs.autoquest.plugin.alignment.substitution.ObjectDistanceSubstitionMatrix; +import de.ugoe.cs.util.console.Command; +import de.ugoe.cs.util.console.Console; +import de.ugoe.cs.util.console.GlobalDataContainer; + +/** + *

+ * Command to generate a binary alignment of two sequences + *

+ * + * @author Ralph Krimmel + * @version 1.0 + */ +public class CMDgenerateNumberSequences implements Command { + + /* + * (non-Javadoc) + * + * @see de.ugoe.cs.util.console.Command#run(java.util.List) + */ + @SuppressWarnings("unchecked") + public void run(List parameters) { + String sequencesName = "sequences"; + try { + sequencesName = (String) parameters.get(0); + } catch (Exception e) { + throw new IllegalArgumentException(); + } + + Collection> sequences = new LinkedList>(); + Object obj = GlobalDataContainer.getInstance().getData(sequencesName); + if(obj != null) { + + if(obj.getClass().equals(sequences.getClass())) { + sequences = (Collection>) obj; + } + + + Console.println("Number of sequences: " + sequences.size()); + + SimpleSequenceGenerator gen = new SimpleSequenceGenerator(); + gen.generate(sequences); + gen.print(); + GlobalDataContainer.getInstance().addData("numberSequences", gen); + + + + + } + } + + + /* + * (non-Javadoc) + * + * @see de.ugoe.cs.util.console.Command#help() + */ + @Override + public String help() { + return "generateNumberSequences {}"; + } + +} Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDgenerateSubstitutionMatrix.java =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDgenerateSubstitutionMatrix.java (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDgenerateSubstitutionMatrix.java (revision 2054) @@ -0,0 +1,89 @@ +// Copyright 2012 Georg-August-Universität Göttingen, Germany +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package de.ugoe.cs.autoquest.plugin.alignment.commands; + + +import java.util.Collection; +import java.util.LinkedList; +import java.util.List; + +import de.ugoe.cs.autoquest.eventcore.Event; +import de.ugoe.cs.autoquest.plugin.alignment.SmithWaterman; +import de.ugoe.cs.autoquest.plugin.alignment.seqgen.SimpleSequenceGenerator; +import de.ugoe.cs.autoquest.plugin.alignment.substitution.NearbySubstitutionMatrix; +import de.ugoe.cs.autoquest.plugin.alignment.substitution.ObjectDistanceSubstitionMatrix; +import de.ugoe.cs.util.console.Command; +import de.ugoe.cs.util.console.Console; +import de.ugoe.cs.util.console.GlobalDataContainer; + +/** + *

+ * Command to generate a binary alignment of two sequences + *

+ * + * @author Ralph Krimmel + * @version 1.0 + */ +public class CMDgenerateSubstitutionMatrix implements Command { + + /* + * (non-Javadoc) + * + * @see de.ugoe.cs.util.console.Command#run(java.util.List) + */ + @SuppressWarnings("unchecked") + public void run(List parameters) { + String sequencesName = "numberSequences"; + try { + sequencesName = (String) parameters.get(0); + } catch (Exception e) { + throw new IllegalArgumentException(); + } + + Collection> sequences = new LinkedList>(); + Object obj = GlobalDataContainer.getInstance().getData(sequencesName); + if(obj != null) { + + if(obj.getClass().equals(sequences.getClass())) { + sequences = (Collection>) obj; + } + + + Console.println("Number of sequences: " + sequences.size()); + + SimpleSequenceGenerator gen = new SimpleSequenceGenerator(); + gen.generate(sequences); + gen.print(); + GlobalDataContainer.getInstance().addData("numberSequences", gen); + + + + + } + } + + + /* + * (non-Javadoc) + * + * @see de.ugoe.cs.util.console.Command#help() + */ + @Override + public String help() { + return "generateSubstitutionMatrix {}"; + } + + +} Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDsequenceStats.java =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDsequenceStats.java (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDsequenceStats.java (revision 2054) @@ -0,0 +1,108 @@ +// Copyright 2012 Georg-August-Universität Göttingen, Germany +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. + +package de.ugoe.cs.autoquest.plugin.alignment.commands; + +import java.util.ArrayList; +import java.util.Collection; +import java.util.Collections; +import java.util.Comparator; +import java.util.Iterator; +import java.util.LinkedList; +import java.util.List; +import java.util.logging.Level; + +import de.ugoe.cs.autoquest.eventcore.Event; +import de.ugoe.cs.autoquest.plugin.alignment.SmithWaterman; +import de.ugoe.cs.autoquest.plugin.alignment.seqgen.SimpleSequenceGenerator; +import de.ugoe.cs.autoquest.plugin.alignment.substitution.NearbySubstitutionMatrix; +import de.ugoe.cs.autoquest.plugin.alignment.substitution.ObjectDistanceSubstitionMatrix; +import de.ugoe.cs.util.console.Command; +import de.ugoe.cs.util.console.Console; +import de.ugoe.cs.util.console.GlobalDataContainer; + +/** + *

+ * Command to generate a binary alignment of two sequences + *

+ * + * @author Ralph Krimmel + * @version 1.0 + */ +public class CMDsequenceStats implements Command { + + /* + * (non-Javadoc) + * + * @see de.ugoe.cs.util.console.Command#run(java.util.List) + */ + @SuppressWarnings("unchecked") + public void run(List parameters) { + String sequencesName = "sequences"; + double standarddev = 0.0; + double mean = 0; + double median = 0; + double sum = 0; + + try { + sequencesName = (String) parameters.get(0); + } catch (Exception e) { + throw new IllegalArgumentException(); + } + + Collection> sequences = new LinkedList>(); + Object obj = GlobalDataContainer.getInstance().getData(sequencesName); + if (obj != null) { + + if (obj.getClass().equals(sequences.getClass())) { + sequences = (Collection>) obj; + } + + + Console.println("Number of sequences: " + sequences.size()); + //Calculate the mean size + for(Iterator> iter = sequences.iterator();iter.hasNext();) { + sum += iter.next().size(); + + } + mean = sum/sequences.size(); + + + //Calculate the median + List> list = new ArrayList>(sequences); + Collections.sort(list,new SizeComparator()); + + Console.println("Mean size: " +mean); + Console.println("Median size: " + list.get(Math.round(list.size()/2)).size()); + + } + } + + class SizeComparator implements Comparator> { + @Override + public int compare(List a, List b) { + return a.size() < b.size() ? -1 : a.size() == b.size() ? 0 : 1; + } + } + /* + * (non-Javadoc) + * + * @see de.ugoe.cs.util.console.Command#help() + */ + @Override + public String help() { + return "sequenceStats "; + } + +} Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/NumberSequence.java =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/NumberSequence.java (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/NumberSequence.java (revision 2054) @@ -0,0 +1,28 @@ +package de.ugoe.cs.autoquest.plugin.alignment.seqgen; + +import java.io.Serializable; +import java.util.ArrayList; + +public class NumberSequence implements Serializable { + private int[] sequence; + private int signature; + + public NumberSequence(int size) { + + sequence = new int[size]; + } + + public int[] getSequence() { + return sequence; + } + public void setSequence(int[] sequence) { + this.sequence = sequence; + } + public int getSignature() { + return signature; + } + public void setSignature(int signature) { + this.signature = signature; + } + +} Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/RandomSequenceGenerator.java =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/RandomSequenceGenerator.java (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/RandomSequenceGenerator.java (revision 2054) @@ -0,0 +1,45 @@ +package de.ugoe.cs.autoquest.plugin.alignment.seqgen; +import de.ugoe.cs.autoquest.eventcore.Event; + +import java.util.Collection; +import java.util.List; + +public class RandomSequenceGenerator implements SequenceGenerator{ + + private int min; + private int max; + private int count; + + + public RandomSequenceGenerator(int min, int max, int count) { + this.min = min; + this.max = max; + this.count = count; + } + + public int[] generate(List eventList) { + int[] result = new int[count]; + for (int i=0; i> eventList) { + // TODO Auto-generated method stub + + } + + @Override + public NumberSequence get(int index) { + // TODO Auto-generated method stub + return null; + } + + @Override + public int sequenceCount() { + return count; + } + +} Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/SequenceGenerator.java =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/SequenceGenerator.java (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/SequenceGenerator.java (revision 2054) @@ -0,0 +1,17 @@ +package de.ugoe.cs.autoquest.plugin.alignment.seqgen; + +import java.util.Collection; +import java.util.List; + +import de.ugoe.cs.autoquest.eventcore.Event; + +public interface SequenceGenerator { + + public void generate(Collection> eventList); + public NumberSequence get(int index); + public int sequenceCount(); + + + + +} Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/SimpleSequenceGenerator.java =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/SimpleSequenceGenerator.java (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/SimpleSequenceGenerator.java (revision 2054) @@ -0,0 +1,98 @@ +package de.ugoe.cs.autoquest.plugin.alignment.seqgen; + + +import java.io.Serializable; +import java.util.ArrayList; +import java.util.Collection; +import java.util.List; + +import de.ugoe.cs.autoquest.eventcore.Event; +import de.ugoe.cs.autoquest.tasktrees.manager.TaskTreeManager; +import de.ugoe.cs.autoquest.tasktrees.taskequality.TaskEquality; +import de.ugoe.cs.autoquest.tasktrees.temporalrelation.TaskHandlingStrategy; +import de.ugoe.cs.autoquest.tasktrees.temporalrelation.TaskInstanceComparator; +import de.ugoe.cs.autoquest.tasktrees.treeifc.ITask; +import de.ugoe.cs.autoquest.tasktrees.treeifc.ITaskBuilder; +import de.ugoe.cs.autoquest.tasktrees.treeifc.ITaskInstance; +import de.ugoe.cs.autoquest.tasktrees.treeifc.IUserSession; +import de.ugoe.cs.autoquest.tasktrees.treeimpl.TaskBuilder; +import de.ugoe.cs.autoquest.usageprofiles.SymbolMap; +import de.ugoe.cs.util.console.Console; + + +public class SimpleSequenceGenerator implements SequenceGenerator, Serializable { + + private ArrayList numberseqs; + + + public SimpleSequenceGenerator() { + this.numberseqs = new ArrayList(); + + } + + public void print() { + for (NumberSequence sequence : numberseqs) { + System.out.println(sequence.toString()); + } + + } + + public void generate(Collection> sequences) { + + + if (sequences != null) { + TaskTreeManager ttm = new TaskTreeManager(); + + ttm.createTaskModel(sequences); + + TaskHandlingStrategy preparationTaskHandlingStrategy = new TaskHandlingStrategy(TaskEquality.SEMANTICALLY_EQUAL); + SymbolMap uniqueTasks = preparationTaskHandlingStrategy + .createSymbolMap(); + TaskInstanceComparator comparator = preparationTaskHandlingStrategy + .getTaskComparator(); + ITask task; + ITaskBuilder taskBuilder = new TaskBuilder(); + + List sessions = ttm.getTaskModel().getUserSessions(); + + for (IUserSession session : sessions) { + //Creating a new sequence that just consists of integers + NumberSequence templist = new NumberSequence(session.size()) ; + for (int i = 0; i < session.size(); i++) { + ITaskInstance taskInstance = session.get(i); + task = uniqueTasks.getValue(taskInstance); + + if (task == null) { + uniqueTasks.addSymbol(taskInstance, + taskInstance.getTask()); + + templist.getSequence()[i]=taskInstance.getTask().getId(); + + } else { + taskBuilder.setTask(taskInstance, task); + templist.getSequence()[i]=task.getId(); + + } + + } + + comparator.clearBuffers(); + numberseqs.add(templist); + } + + } + + } + + + public NumberSequence get(int index) { + return numberseqs.get(index); + } + + + public int sequenceCount() { + return numberseqs.size(); + } + +} + Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/DifferenceSubstitutionMatrix.java =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/DifferenceSubstitutionMatrix.java (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/DifferenceSubstitutionMatrix.java (revision 2054) @@ -0,0 +1,65 @@ +/** + * + */ +package de.ugoe.cs.autoquest.plugin.alignment.substitution; + +import java.util.Collection; +import java.util.List; + +import de.ugoe.cs.autoquest.eventcore.Event; + +/** + * @author Ralph Krimmel + * + */ +public class DifferenceSubstitutionMatrix implements SubstitutionMatrix { + + private int[] input1; + private int[] input2; + private int maxValue; + + public DifferenceSubstitutionMatrix(int[] input1,int[] input2) { + this.input1 = input1; + this.input2 = input2; + this.maxValue = getMaxValue(); + } + + /* (non-Javadoc) + * @see de.ugoe.cs.autoquest.plugin.alignment.SubstitutionMatrix#getDistance(int, int) + */ + public double getDistance(int pos1, int pos2) { + return maxValue - (input1[pos1] - input2[pos2]); + } + + private int getMaxValue() { + int max = input1[0]; + for (int i=0; i < input1.length; i++) { + if(input1[i] > max) { + max = input1[i]; + } + } + for (int j=0; j < input2.length; j++) { + if(input2[j] > max) { + max = input2[j]; + } + } + return max; + } + + @Override + public double getGapPenalty() { + return -maxValue; + } + + @Override + public String info() { + return "Max Value: " + maxValue; + } + + @Override + public void generate(Collection> eventList) { + // TODO Auto-generated method stub + + } + +} Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/NearbySubstitutionMatrix.java =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/NearbySubstitutionMatrix.java (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/NearbySubstitutionMatrix.java (revision 2054) @@ -0,0 +1,57 @@ +/** + * + */ +package de.ugoe.cs.autoquest.plugin.alignment.substitution; + +import java.util.Collection; +import java.util.List; + +import de.ugoe.cs.autoquest.eventcore.Event; + +/** + * @author Ralph Krimmel + * + */ +public class NearbySubstitutionMatrix implements SubstitutionMatrix { + + private int[] input1; + private int[] input2; + private int range; + + public NearbySubstitutionMatrix(int[] input1,int[] input2, int range) { + this.input1 = input1; + this.input2 = input2; + this.range = range; + } + + /* (non-Javadoc) + * @see de.ugoe.cs.autoquest.plugin.alignment.SubstitutionMatrix#getDistance(int, int) + */ + public double getDistance(int pos1, int pos2) { + int difference = Math.abs(input1[pos1]-input2[pos2]); + if(difference < range) { + return range-difference; + } + else { + return -range; + } + } + + + @Override + public double getGapPenalty() { + return -range-1; + } + + @Override + public String info() { + return "Range: " + range; + } + + @Override + public void generate(Collection> eventList) { + // TODO Auto-generated method stub + + } + +} Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/ObjectDistanceSubstitionMatrix.java =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/ObjectDistanceSubstitionMatrix.java (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/ObjectDistanceSubstitionMatrix.java (revision 2054) @@ -0,0 +1,68 @@ +package de.ugoe.cs.autoquest.plugin.alignment.substitution; + +import java.util.ArrayList; +import java.util.Collection; +import java.util.Iterator; + +import de.ugoe.cs.autoquest.eventcore.guimodel.GUIModel; +import de.ugoe.cs.autoquest.eventcore.guimodel.IGUIElement; + +import java.util.List; + +import misc.AlignmentHelpers; +import de.ugoe.cs.autoquest.eventcore.Event; +import de.ugoe.cs.util.console.GlobalDataContainer; + +public class ObjectDistanceSubstitionMatrix implements SubstitutionMatrix { + + private ArrayList matrix; + private int currentSequence; + + + public ObjectDistanceSubstitionMatrix() { + currentSequence = 0; + matrix = new ArrayList(); + } + + @Override + public String info() { + // TODO Auto-generated method stub + return null; + } + + @Override + public double getDistance(int pos1, int pos2) { + // TODO Auto-generated method stub + + return matrix.get(currentSequence)[pos1][pos2]; + } + + public double getDistance(int sequence, int pos1, int pos2) { + return matrix.get(sequence)[pos1][pos2]; + + + } + + @Override + public double getGapPenalty() { + // TODO Auto-generated method stub + return 0; + } + + @Override + public void generate(Collection> eventList) { + + for(Iterator> seqs = eventList.iterator(); seqs.hasNext();) { + matrix.add(new int[eventList.size()][eventList.size()]); + List tmpList = seqs.next(); + + for (int i=0; i < tmpList.size(); i++) { + for (int j=0; j < tmpList.size(); j++) { + IGUIElement first = (IGUIElement) tmpList.get(i).getTarget(); + IGUIElement second =(IGUIElement) tmpList.get(j).getTarget(); + matrix.get(currentSequence)[i][j] = AlignmentHelpers.distanceBetween(first, second); + } + } + } + } +} Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/SubstitutionMatrix.java =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/SubstitutionMatrix.java (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/substitution/SubstitutionMatrix.java (revision 2054) @@ -0,0 +1,18 @@ +package de.ugoe.cs.autoquest.plugin.alignment.substitution; + +import java.util.Collection; +import java.util.List; + +import de.ugoe.cs.autoquest.eventcore.Event; + +public interface SubstitutionMatrix { + + public String info(); + + public double getDistance(int pos1, int pos2); + + public double getGapPenalty(); + + public void generate(Collection> eventList); + +} Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/misc/AlignmentHelpers.java =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/misc/AlignmentHelpers.java (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/java/misc/AlignmentHelpers.java (revision 2054) @@ -0,0 +1,108 @@ +package misc; + +import java.util.ArrayList; +import java.util.List; + +import de.ugoe.cs.autoquest.eventcore.guimodel.GUIModel; +import de.ugoe.cs.autoquest.eventcore.guimodel.IGUIElement; + + +public class AlignmentHelpers extends GUIModel { + + + + /** + * + */ + private static final long serialVersionUID = -2593092958275693133L; + + /** + *

+ * return a common denominator for the provided list of GUI elements, i.e. a + * GUI element, that is part of the parent GUI hiearchy of all GUI elements + * in the list. If there is no common denominator, the method returns null. + *

+ */ + private static IGUIElement getCommonDenominator(List guiElements) { + IGUIElement commonDenominator = null; + + if (guiElements.size() > 0) { + List commonDenominatorPath = new ArrayList(); + + // create a reference list using the first GUI element + IGUIElement guiElement = guiElements.get(0); + while (guiElement != null) { + // We can use every type + // if (guiElementMatchesConsideredTypes(guiElement)) { + commonDenominatorPath.add(0, guiElement); + // } + guiElement = guiElement.getParent(); + } + + if (commonDenominatorPath.size() == 0) { + return null; + } + + // for each other GUI element, check the reference list for the + // first element in the + // path, that is not common to the current one, and delete it as + // well as it subsequent + // siblings + List currentPath = new ArrayList(); + for (int i = 1; i < guiElements.size(); i++) { + currentPath.clear(); + guiElement = guiElements.get(i); + while (guiElement != null) { + // if (guiElementMatchesConsideredTypes(guiElement)) { + currentPath.add(0, guiElement); + // } + guiElement = guiElement.getParent(); + } + + // determine the index of the first unequal path element + int index = 0; + while ((index < commonDenominatorPath.size()) + && (index < currentPath.size()) + && commonDenominatorPath.get(index).equals( + currentPath.get(index))) { + index++; + } + + // remove all elements from the common denonimator path, that do + // not match + while (index < commonDenominatorPath.size()) { + commonDenominatorPath.remove(index); + } + } + + if (commonDenominatorPath.size() > 0) { + commonDenominator = commonDenominatorPath + .get(commonDenominatorPath.size() - 1); + } + } + return commonDenominator; + } + + public static int distanceBetween(IGUIElement first, IGUIElement second) { + + int hopcount1 = 0; + int hopcount2 = 0; + List tmp = new ArrayList(); + tmp.add(first); + tmp.add(second); + IGUIElement commonDenominator = getCommonDenominator(tmp); + + while(!(first.equals(commonDenominator))) { + first = first.getParent(); + hopcount1++; + } + + while(!(second.equals(commonDenominator))) { + second = second.getParent(); + hopcount2++; + } + + return hopcount1 + hopcount2; + } + +} Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/resources/manuals/efgTestCasesToSequences =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/resources/manuals/efgTestCasesToSequences (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/resources/manuals/efgTestCasesToSequences (revision 2054) @@ -0,0 +1,10 @@ +Loads GUITAR test cases from a directory and treats each test case as a sequence. The result is a collection of sequences. + +$USAGE$ + name of the directory + name of the sequences + optional; if specified, this GUI file is used to retrieve widgetIds in addtion to the eventIds + +Example(s): +efgTestCasesToSequences testcaseDir sequences +efgTestCasesToSequences testcaseDir sequences guifile.gui Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/resources/manuals/efgToDFA =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/resources/manuals/efgToDFA (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/resources/manuals/efgToDFA (revision 2054) @@ -0,0 +1,8 @@ +Loads a GUITAR EFG file and creates a DFA based on the contents. + +$USAGE$ + name of the efg file + name of the DFA + +Example(s): +efgToDFA efgfile.efg dfa Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/resources/manuals/efgToMM =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/resources/manuals/efgToMM (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/src/main/resources/manuals/efgToMM (revision 2054) @@ -0,0 +1,8 @@ +Loads a GUITAR EFG file and creates a first-order Markov model based on the contents. All transitions in the Markov model are equally probable. + +$USAGE$ + name of the efg file + name of the Markov model + +Example(s): +efgToMM efgfile.efg markovModel Index: /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/target/maven-archiver/pom.properties =================================================================== --- /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/target/maven-archiver/pom.properties (revision 2054) +++ /trunk/deprecated/master-thesis-rkrimmel/autoquest-plugin-alignment/target/maven-archiver/pom.properties (revision 2054) @@ -0,0 +1,5 @@ +#Generated by Maven +#Wed Nov 06 00:13:59 CET 2013 +version=0.0.1-SNAPSHOT +groupId=de.ugoe.cs.autoquest +artifactId=autoquest-plugin-alignment