Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NumberSequence.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NumberSequence.java (revision 1579) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/algorithms/NumberSequence.java (revision 1580) @@ -1,9 +1,8 @@ package de.ugoe.cs.autoquest.tasktrees.alignment.algorithms; -import java.io.Serializable; -import java.util.ArrayList; + import java.util.Random; -public class NumberSequence implements Serializable { +public class NumberSequence { private int[] sequence; private int signature; 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 1579) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/DifferenceSubstitutionMatrix.java (revision 1580) @@ -4,9 +4,4 @@ package de.ugoe.cs.autoquest.tasktrees.alignment.matrix; -import java.util.Collection; -import java.util.List; - -import de.ugoe.cs.autoquest.eventcore.Event; -import de.ugoe.cs.autoquest.tasktrees.treeifc.IUserSession; /** 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 1579) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/NearbySubstitutionMatrix.java (revision 1580) @@ -3,10 +3,4 @@ */ package de.ugoe.cs.autoquest.tasktrees.alignment.matrix; - -import java.util.Collection; -import java.util.List; - -import de.ugoe.cs.autoquest.eventcore.Event; -import de.ugoe.cs.autoquest.tasktrees.treeifc.IUserSession; /** Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/UPGMAMatrix.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/UPGMAMatrix.java (revision 1579) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/matrix/UPGMAMatrix.java (revision 1580) @@ -1,5 +1,4 @@ package de.ugoe.cs.autoquest.tasktrees.alignment.matrix; -import de.ugoe.cs.autoquest.tasktrees.alignment.pal.misc.Identifier; Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/FengDoolittleNode.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/FengDoolittleNode.java (revision 1579) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/FengDoolittleNode.java (revision 1580) @@ -374,5 +374,5 @@ newNode.addChild(child2); newNode.setIdentifier(new Identifier(child1.getIdentifier().getName() + " " + child2.getIdentifier().getName())); - System.out.println("Merging " + child1.getIdentifier() + " with " + child2.getIdentifier()); + //System.out.println("Merging " + child1.getIdentifier() + " with " + child2.getIdentifier()); if(newNode instanceof FengDoolittleNode) { @@ -410,5 +410,5 @@ } else { - + System.out.println("This should never happen, it's a binary tree."); } Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/Node.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/Node.java (revision 1579) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/Node.java (revision 1580) @@ -134,5 +134,4 @@ ArrayList getSequences(); - void joinChildren( int n1, int n2); Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/NodeUtils.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/NodeUtils.java (revision 1579) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/NodeUtils.java (revision 1580) @@ -9,7 +9,5 @@ package de.ugoe.cs.autoquest.tasktrees.alignment.pal.tree; -import java.io.*; - -import de.ugoe.cs.autoquest.tasktrees.alignment.pal.io.FormattedOutput; + import de.ugoe.cs.autoquest.tasktrees.alignment.pal.misc.Identifier; @@ -377,74 +375,7 @@ } - /** - * prints node in New Hamshire format. - */ - static void printNH(PrintWriter out, Node node, - boolean printLengths, boolean printInternalLabels) { - - printNH(out, node, printLengths, printInternalLabels, 0, true); - } - - - static int printNH(PrintWriter out, Node node, - boolean printLengths, boolean printInternalLabels, int column, boolean breakLines) { - - if (breakLines) column = breakLine(out, column); - - if (!node.isLeaf()) - { - out.print("("); - column++; - - for (int i = 0; i < node.getChildCount(); i++) - { - if (i != 0) - { - out.print(","); - column++; - } - - column = printNH(out, node.getChild(i), printLengths, printInternalLabels, column, breakLines); - } - - out.print(")"); - column++; - } - - if (!node.isRoot()) - { - if (node.isLeaf() || printInternalLabels) - { - if (breakLines) column = breakLine(out, column); - - String id = node.getIdentifier().toString(); - out.print(id); - column += id.length(); - } - - if (printLengths) - { - out.print(":"); - column++; - - if (breakLines) column = breakLine(out, column); - - column += FormattedOutput.getInstance().displayDecimal(out, node.getBranchLength(), 7); - } - } - - return column; - } - - private static int breakLine(PrintWriter out, int column) - { - if (column > 70) - { - out.println(); - column = 0; - } - - return column; - } + + + /** * Returns the first nodes in this tree that has the Index: /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/SimpleTree.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/SimpleTree.java (revision 1579) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/tree/SimpleTree.java (revision 1580) @@ -8,8 +8,4 @@ package de.ugoe.cs.autoquest.tasktrees.alignment.pal.tree; - -import java.io.PrintWriter; -import java.io.StringWriter; - import de.ugoe.cs.autoquest.tasktrees.alignment.pal.misc.Identifier; @@ -198,14 +194,4 @@ - public String toString() { - StringWriter sw = new StringWriter(); - NodeUtils.printNH(new PrintWriter(sw), getRoot(), false, true, 0, true); - sw.write(";"); - return sw.toString(); - } - - - - Index: anches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/util/ComparableDouble.java =================================================================== --- /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/alignment/pal/util/ComparableDouble.java (revision 1579) +++ (revision ) @@ -1,49 +1,0 @@ -// ComparableDouble.java -// -// (c) 1999-2001 PAL Development Core Team -// -// This package may be distributed under the -// terms of the Lesser GNU General Public License (LGPL) - -package de.ugoe.cs.autoquest.tasktrees.alignment.pal.util; - -/** - * This class is unfortunate but necessary to conform to JDK 1.1 - * - * @version $Id: ComparableDouble.java,v 1.3 2001/07/13 14:39:13 korbinian Exp $ - * - * @author Alexei Drummond - */ -public class ComparableDouble implements Comparable { - - private double value; - - public ComparableDouble(double d) { - value = d; - } - - public int compareTo(Object o) { - - ComparableDouble cd = (ComparableDouble)o; - - if (value < cd.value) { - return -1; - } else if (value > cd.value) { - return 1; - } else return 0; - } - - public boolean equals(Object o) { - - ComparableDouble cd = (ComparableDouble)o; - return cd.value == value; - } - - public double doubleValue() { - return value; - } - - public String toString() { - return value + ""; - } -} 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 1579) +++ /branches/ralph/src/main/java/de/ugoe/cs/autoquest/tasktrees/temporalrelation/SequenceForTaskDetectionRuleAlignment.java (revision 1580) @@ -46,5 +46,4 @@ import de.ugoe.cs.autoquest.tasktrees.treeifc.IUserSession; import de.ugoe.cs.autoquest.usageprofiles.SymbolMap; -import de.ugoe.cs.autoquest.usageprofiles.Trie; import de.ugoe.cs.autoquest.usageprofiles.TrieProcessor; import de.ugoe.cs.util.StopWatch;