();
14 | while(inn.getParent()!=null){
15 | path.add(inn.getParent());
16 | inn = inn.getParent();
17 | }
18 | if(path.contains((Node)out)){
19 | ret ++;
20 | }
21 | return ret;
22 | }
23 | }
24 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/ScoreMatrix.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | /**
4 | * @author Alexei Drummond
5 | *
6 | * @version $Id: ScoreMatrix.java 360 2006-06-22 07:42:48Z pepster $
7 | */
8 | public interface ScoreMatrix {
9 | /**
10 | *
11 | * @return human readable name
12 | */
13 | public String getName();
14 |
15 | /**
16 | * @return the score for matching char x with char y
17 | */
18 | float getScore(char x, char y);
19 |
20 | /**
21 | * @return a string containing the valid characters for this score matrix.
22 | */
23 | String getAlphabet();
24 | }
25 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/package.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 | jebl.evolution.align package
5 |
6 |
7 |
8 | Provides classes and interfaces for pairwise alignment of two sequences.
9 | All major algorithms including Smith-Waterman and Needleman-Wunsch
10 | are implemented.
11 |
12 | Some of the classes in this package are based on source code by Peter Sestoft, sestoft@dina.kvl.dk.
13 | His original source code can be at
14 | http://www.dina.kvl.dk/~sestoft/bsa.html
15 |
16 |
17 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/AminoAcidScores.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | /**
4 | * @author Alexei Drummond
5 | *
6 | * @version $Id: AminoAcidScores.java 360 2006-06-22 07:42:48Z pepster $
7 | */
8 | public class AminoAcidScores extends Scores {
9 |
10 | private String residues = "ARNDCQEGHILKMFPSTWYV";
11 |
12 | public String getName() {
13 | return toString();
14 | }
15 |
16 | public final String getAlphabet() { return residues + getExtraResidues(); }
17 |
18 |
19 | public AminoAcidScores() {
20 | }
21 |
22 | public AminoAcidScores(float m, float n) {
23 | buildScores(m, n);
24 | }
25 | }
26 |
--------------------------------------------------------------------------------
/src/jade/reconstruct/area/AncSplit.java:
--------------------------------------------------------------------------------
1 | package jade.reconstruct.area;
2 |
3 | public class AncSplit {
4 | public AncSplit(int [] ancdists, int [][] descdists, double weight, double likelihood){
5 | this.weight = weight;
6 | this.likelihood = likelihood;
7 | this.ancdist = ancdists;
8 | this.descdists = descdists;
9 | }
10 | private double weight;
11 | private double likelihood;
12 | private int [][] descdists;
13 | private int [] ancdist;
14 |
15 | public double get_weight(){return weight;}
16 | public double get_like(){return likelihood;}
17 | public int [] get_ancdist(){return ancdist;}
18 | public int [][] get_descdists(){return descdists;}
19 |
20 | }
21 |
--------------------------------------------------------------------------------
/src/jebl/evolution/sequences/Sequences.java:
--------------------------------------------------------------------------------
1 | /*
2 | * Sequences.java
3 | *
4 | * (c) 2002-2005 JEBL Development Core Team
5 | *
6 | * This package may be distributed under the
7 | * Lesser Gnu Public Licence (LGPL)
8 | */
9 | package jebl.evolution.sequences;
10 |
11 | import jebl.evolution.taxa.Taxon;
12 |
13 | import java.util.Set;
14 |
15 | /**
16 | * A set of sequence objects.
17 | *
18 | * @author Andrew Rambaut
19 | * @author Alexei Drummond
20 | *
21 | * @version $Id: Sequences.java 185 2006-01-23 23:03:18Z rambaut $
22 | */
23 | public interface Sequences {
24 |
25 | Set getSequences();
26 |
27 | Sequence getSequence(Taxon taxon);
28 | }
29 |
--------------------------------------------------------------------------------
/src/jebl/math/MatrixCalcException.java:
--------------------------------------------------------------------------------
1 | package jebl.math;
2 |
3 |
4 | public class MatrixCalcException extends Exception{
5 | public MatrixCalcException() { super(); }
6 | public MatrixCalcException(String message) { super(message); }
7 |
8 | public static class NotSquareMatrixException extends MatrixCalcException {
9 | public NotSquareMatrixException() { super(); }
10 | public NotSquareMatrixException(String message) { super(message); }
11 | }
12 | public static class PositiveDefiniteException extends MatrixCalcException {
13 | public PositiveDefiniteException() { super(); }
14 | public PositiveDefiniteException(String message) { super(message); }
15 | }
16 | }
17 |
--------------------------------------------------------------------------------
/src/org/virion/jam/html/HTMLViewer.java:
--------------------------------------------------------------------------------
1 | package org.virion.jam.html;
2 |
3 | import javax.swing.*;
4 | import java.awt.*;
5 |
6 | /**
7 | * General-purpose class to display HTML in a standalone frame.
8 | */
9 | public class HTMLViewer extends JFrame {
10 |
11 | private JEditorPane editorPane;
12 |
13 | public HTMLViewer(String title, String html) {
14 | super(title);
15 | getContentPane().setLayout(new BorderLayout());
16 | editorPane = new JEditorPane("text/html", html);
17 | editorPane.setEditable(false);
18 | getContentPane().add(new JScrollPane(editorPane), BorderLayout.CENTER);
19 | }
20 | }
21 |
22 |
23 |
24 |
25 |
26 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/Hamming.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 |
4 | /**
5 | * @author Andrew Rambaut
6 | *
7 | * @version $Id: Hamming.java 185 2006-01-23 23:03:18Z rambaut $
8 | */
9 |
10 | public class Hamming extends NucleotideScores {
11 |
12 | private final float[][] residueScores = {
13 |
14 | /* A C G T U */
15 | { 0},
16 | { -1, 0},
17 | { -1, -1, 0},
18 | { -1, -1, -1, 0},
19 | { -1, -1, -1, 0, 0}};
20 |
21 | public Hamming() { buildScores(residueScores); }
22 |
23 | public String toString() {
24 | return "Hamming (0/-1)";
25 | }
26 | }
--------------------------------------------------------------------------------
/src/org/virion/jam/controlpanels/ControlPalette.java:
--------------------------------------------------------------------------------
1 | package org.virion.jam.controlpanels;
2 |
3 | import javax.swing.*;
4 |
5 | /**
6 | * Date: 20/03/2006
7 | * Time: 10:23:21
8 | *
9 | * @author Joseph Heled
10 | * @version $Id: ControlPalette.java 482 2006-10-25 06:30:57Z twobeers $
11 | */
12 | public interface ControlPalette {
13 |
14 | JPanel getPanel();
15 |
16 | void addControlsProvider(ControlsProvider provider, boolean addAtStart);
17 |
18 | void fireControlsChanged();
19 |
20 | void addControlPanelListener(ControlPaletteListener listener);
21 |
22 | void removeControlPanelListener(ControlPaletteListener listener);
23 |
24 | void setupControls();
25 | }
26 |
--------------------------------------------------------------------------------
/src/jade/data/TransitionPenaltyTable.java:
--------------------------------------------------------------------------------
1 | // TransitionPenaltyTable.java
2 | //
3 | // (c) 1999-2001 PAL Development Core Team
4 | //
5 | // This package may be distributed under the
6 | // terms of the Lesser GNU General Public License (LGPL)
7 |
8 |
9 | package jade.data;
10 |
11 |
12 | /**
13 | * Implements a table of transition penalties for a particular datatype.
14 | * Used for alignment scoring.
15 | *
16 | * @version $Id: TransitionPenaltyTable.java,v 1.2 2001/07/13 14:39:13 korbinian Exp $
17 | *
18 | * @author Alexei Drummond
19 | */
20 | public interface TransitionPenaltyTable {
21 |
22 | double penalty(int a, int b);
23 | DataType getDataType();
24 | }
25 |
--------------------------------------------------------------------------------
/src/jebl/evolution/alignments/Alignment.java:
--------------------------------------------------------------------------------
1 | /*
2 | * Alignment.java
3 | *
4 | * (c) 2005-2006 JEBL Development Team
5 | *
6 | * This package is distributed under the
7 | * Lesser Gnu Public Licence (LGPL)
8 | */
9 | package jebl.evolution.alignments;
10 |
11 | import jebl.evolution.sequences.Sequence;
12 | import jebl.evolution.sequences.Sequences;
13 |
14 | import java.util.List;
15 |
16 | /**
17 | * @author Andrew Rambaut
18 | * @author Alexei Drummond
19 | *
20 | * @version $Id: Alignment.java 314 2006-05-03 01:21:14Z alexeidrummond $
21 | */
22 | public interface Alignment extends Sequences, Patterns {
23 |
24 | List getSequenceList();
25 |
26 | int getSiteCount();
27 | }
28 |
--------------------------------------------------------------------------------
/src/jebl/evolution/graphs/Node.java:
--------------------------------------------------------------------------------
1 | /*
2 | * Node.java
3 | *
4 | * (c) 2005 JEBL Development Team
5 | *
6 | * This package is distributed under the
7 | * Lesser Gnu Public Licence (LGPL)
8 | */
9 | package jebl.evolution.graphs;
10 |
11 | import jebl.util.Attributable;
12 |
13 | /**
14 | * Represents a node in a graph or tree. In general it is
15 | * used only as a handle to traverse a graph or tree structure and
16 | * it has no methods or instance variables.
17 | *
18 | * @author Andrew Rambaut
19 | * @author Alexei Drummond
20 | *
21 | * @version $Id: Node.java 295 2006-04-14 14:59:10Z rambaut $
22 | */
23 | public interface Node extends Attributable {
24 |
25 | int getDegree();
26 | }
27 |
--------------------------------------------------------------------------------
/src/jebl/evolution/alignments/BootstrappedAlignment.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.alignments;
2 |
3 | import jebl.math.Random;
4 |
5 | /**
6 | * Date: 15/01/2006
7 | * Time: 10:13:50
8 | *
9 | * @author Joseph Heled
10 | * @version $Id: BootstrappedAlignment.java 585 2006-12-15 15:48:59Z twobeers $
11 | *
12 | */
13 | public class BootstrappedAlignment extends ResampledAlignment {
14 |
15 | public BootstrappedAlignment(Alignment srcAlignment) {
16 | final int nSites = srcAlignment.getSiteCount();
17 | int[] sites = new int[nSites];
18 |
19 | for(int n = 0; n < nSites; ++n) {
20 | sites[n] = Random.nextInt(nSites);
21 | }
22 |
23 | init(srcAlignment, sites);
24 | }
25 | }
26 |
--------------------------------------------------------------------------------
/src/org/virion/jam/toolbar/ToolbarOptions.java:
--------------------------------------------------------------------------------
1 | package org.virion.jam.toolbar;
2 |
3 | /**
4 | * @author rambaut
5 | * Date: Oct 18, 2005
6 | * Time: 10:23:01 PM
7 | */
8 | public final class ToolbarOptions {
9 |
10 | public static final int ICON_AND_TEXT = 0;
11 | public static final int ICON_ONLY = 1;
12 | public static final int TEXT_ONLY = 2;
13 |
14 | public ToolbarOptions(int display, boolean smallSize) {
15 | this.display = display;
16 | this.smallSize = smallSize;
17 | }
18 |
19 | public int getDisplay() {
20 | return display;
21 | }
22 |
23 | public boolean getSmallSize() {
24 | return smallSize;
25 | }
26 |
27 | private int display = ICON_AND_TEXT;
28 | private boolean smallSize = false;
29 | }
30 |
--------------------------------------------------------------------------------
/src/jade/math/ProbDistribution.java:
--------------------------------------------------------------------------------
1 | /*
2 | * ProbDistribution.java
3 | *
4 | * Created on August 9, 2005, 3:09 PM
5 | *
6 | * To change this template, choose Tools | Options and locate the template under
7 | * the Source Creation and Management node. Right-click the template and choose
8 | * Open. You can then make changes to the template in the Source Editor.
9 | */
10 |
11 | package jade.math;
12 |
13 | /**
14 | *
15 | * @author stephensmith
16 | */
17 | public interface ProbDistribution {
18 | /**
19 | *@return double value
20 | */
21 | public double getValue();
22 |
23 | /**
24 | *@return the integral of the probability density function from 0 to x
25 | */
26 | public double getPDF(double x);
27 | }
28 |
--------------------------------------------------------------------------------
/src/jebl/evolution/trees/HashPair.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.trees;
2 |
3 | /**
4 | * A pair suitable for use in a HashMap.
5 | *
6 | * @author Joseph Heled
7 | *
8 | * @version $Id: HashPair.java 544 2006-11-28 00:06:19Z twobeers $
9 | */
10 |
11 | class HashPair {
12 | HashPair(T a, T b) {
13 | first = a;
14 | second = b;
15 | }
16 |
17 | public int hashCode() {
18 | return first.hashCode() + second.hashCode();
19 | }
20 |
21 | public boolean equals(Object x) {
22 | if( x instanceof HashPair ) {
23 | return ((HashPair) x).first.equals(first) && ((HashPair )x).second.equals(second);
24 | }
25 | return false;
26 | }
27 |
28 | public final T first;
29 | public final T second;
30 | }
--------------------------------------------------------------------------------
/src/jebl/evolution/align/MultipleAligner.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align;
2 |
3 | import jebl.evolution.alignments.Alignment;
4 | import jebl.evolution.sequences.Sequence;
5 | import jebl.evolution.trees.RootedTree;
6 | import jebl.util.ProgressListener;
7 |
8 | import java.util.List;
9 |
10 | /**
11 | * @author Joseph Heled
12 | * @version $Id: MultipleAligner.java 482 2006-10-25 06:30:57Z twobeers $
13 | * Date: 6/05/2006 Time: 08:08:22
14 | */
15 | public interface MultipleAligner {
16 | Alignment doAlign(List seqs, RootedTree guideTree, ProgressListener progress);
17 |
18 | Alignment doAlign(Alignment a1, Alignment a2, ProgressListener progress);
19 |
20 | Alignment doAlign(Alignment alignment, Sequence sequence, ProgressListener progress);
21 | }
22 |
--------------------------------------------------------------------------------
/src/jebl/evolution/io/ImmediateSequenceImporter.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.io;
2 |
3 | import jebl.evolution.sequences.Sequence;
4 | import jebl.util.ProgressListener;
5 |
6 | import java.io.IOException;
7 |
8 | /**
9 | *
10 | * A sequence importer sending the sequences back one by one, which makes it
11 | * possible to import larger documents if handled wisely on the other side.
12 | *
13 | * @author Joseph Heled
14 | * @version $Id: ImmediateSequenceImporter.java 465 2006-10-04 04:24:20Z twobeers $
15 | *
16 | */
17 | public interface ImmediateSequenceImporter {
18 | public interface Callback {
19 | void add(Sequence seq);
20 | }
21 |
22 | void importSequences(Callback callback, ProgressListener progressListener) throws IOException, ImportException;
23 | }
24 |
--------------------------------------------------------------------------------
/src/jebl/evolution/io/SequenceImporter.java:
--------------------------------------------------------------------------------
1 | /*
2 | * SequenceImporter.java
3 | *
4 | * (c) 2002-2005 BEAST Development Core Team
5 | *
6 | * This package may be distributed under the
7 | * Lesser Gnu Public Licence (LGPL)
8 | */
9 |
10 | package jebl.evolution.io;
11 |
12 | import jebl.evolution.sequences.Sequence;
13 |
14 | import java.io.IOException;
15 | import java.util.List;
16 |
17 | /**
18 | * Interface for importers that do sequences
19 | *
20 | * @author Andrew Rambaut
21 | * @author Alexei Drummond
22 | *
23 | * @version $Id: SequenceImporter.java 442 2006-09-05 21:59:20Z matt_kearse $
24 | */
25 | public interface SequenceImporter {
26 |
27 | /**
28 | * importSequences.
29 | */
30 | List importSequences() throws IOException, ImportException;
31 | }
32 |
--------------------------------------------------------------------------------
/src/jade/reconstruct/area/BayesChain.java:
--------------------------------------------------------------------------------
1 | package jade.reconstruct.area;
2 |
3 | import java.util.*;
4 |
5 | public class BayesChain {
6 | public BayesChain(double disp_sliding_window,double ext_sliding_window){
7 | this.disp_sliding_window = disp_sliding_window;
8 | this.ext_sliding_window = ext_sliding_window;
9 | }
10 | public double score;
11 | public double vag;
12 | public double ext;
13 | public double ext_sliding_window;
14 | public double disp_sliding_window;
15 | public double next_ext(double cur){
16 | return Math.abs(cur -(ext_sliding_window/2)+(ext_sliding_window*ran.nextDouble()));
17 | }
18 | public double next_disp(double cur){
19 | return Math.abs(cur -(disp_sliding_window/2)+(disp_sliding_window*ran.nextDouble()));
20 | }
21 | private Random ran = new Random();
22 | }
23 |
--------------------------------------------------------------------------------
/src/jebl/evolution/io/TreeExporter.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.io;
2 |
3 | import jebl.evolution.alignments.Alignment;
4 | import jebl.evolution.trees.Tree;
5 |
6 | import java.io.IOException;
7 | import java.util.Collection;
8 |
9 | /**
10 | * @author Andrew Rambaut
11 | * @author Alexei Drummond
12 | *
13 | * @version $Id: TreeExporter.java 429 2006-08-26 18:17:39Z rambaut $
14 | */
15 | public interface TreeExporter {
16 |
17 | /**
18 | * Export a single tree
19 | * @param tree
20 | * @throws IOException
21 | */
22 | void exportTree(Tree tree) throws IOException;
23 |
24 | /**
25 | * Export a collection of trees
26 | * @param trees
27 | * @throws IOException
28 | */
29 | void exportTrees(Collection trees) throws IOException;
30 | }
31 |
--------------------------------------------------------------------------------
/src/jade/reconstruct/area/P.java:
--------------------------------------------------------------------------------
1 | /*
2 | * P.java
3 | *
4 | * Created on April 11, 2005, 9:30 PM
5 | */
6 |
7 | package jade.reconstruct.area;
8 |
9 |
10 | /**
11 | *
12 | * @author stephensmith
13 | */
14 | public class P {
15 |
16 | /** Creates a new instance of P */
17 | public P(Q qin) {
18 | q=qin;
19 | me = new MatrixExponential(q.getQ().length);
20 | me.updateByRelativeRates(q.getQ());
21 | }
22 |
23 | public double getRateChangeProbability(int row, int column){
24 | return me.getTransitionProbability(row,column);
25 | }
26 |
27 | public void setBL(double b){
28 | me.setDistance(b);
29 | }
30 |
31 | //private double [][]arr;
32 | //private double bl;
33 | private Q q;
34 | private MatrixExponential me;
35 | }
36 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/PairwiseAligner.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align;
2 |
3 | import jebl.evolution.sequences.Sequence;
4 | import jebl.evolution.alignments.Alignment;
5 | import jebl.util.ProgressListener;
6 |
7 | /**
8 | * @author Joseph Heled
9 | * @version $Id: PairwiseAligner.java 315 2006-05-03 02:13:54Z alexeidrummond $
10 | *
11 | */
12 | public interface PairwiseAligner {
13 |
14 | public class Result {
15 | final public Alignment alignment;
16 | final public double score;
17 |
18 | Result(Alignment alignment, double score) {
19 | this.alignment = alignment;
20 | this.score = score;
21 | }
22 | }
23 |
24 | Result doAlignment(Sequence seq1, Sequence seq2, ProgressListener progress);
25 |
26 | double getScore(Sequence seq1, Sequence seq2);
27 | }
28 |
--------------------------------------------------------------------------------
/src/jebl/evolution/sequences/TranslatedSequence.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.sequences;
2 |
3 | /**
4 | * @author rambaut
5 | * Date: Jul 27, 2005
6 | * Time: 12:48:31 AM
7 | */
8 | public class TranslatedSequence extends FilteredSequence {
9 |
10 | public TranslatedSequence(Sequence source, GeneticCode geneticCode) {
11 | super(source);
12 |
13 | this.geneticCode = geneticCode;
14 | }
15 |
16 | protected State[] filterSequence(Sequence source) {
17 | return jebl.evolution.sequences.Utils.translate(source.getStates(), geneticCode);
18 | }
19 |
20 | /**
21 | * @return the type of symbols that this sequence is made up of.
22 | */
23 | public SequenceType getSequenceType() {
24 | return SequenceType.AMINO_ACID;
25 | }
26 |
27 | private final GeneticCode geneticCode;
28 |
29 | }
30 |
--------------------------------------------------------------------------------
/src/org/virion/jam/panels/StatusBar.java:
--------------------------------------------------------------------------------
1 | package org.virion.jam.panels;
2 |
3 | import javax.swing.*;
4 | import java.awt.*;
5 |
6 | /**
7 | * @author rambaut
8 | * Date: Oct 12, 2004
9 | * Time: 12:18:09 AM
10 | */
11 | public class StatusBar extends StatusPanel {
12 | public StatusBar(String initialText) {
13 | super(initialText);
14 |
15 | setBorder(BorderFactory.createCompoundBorder(
16 | BorderFactory.createMatteBorder(0, 0, 1, 0, Color.gray),
17 | BorderFactory.createEmptyBorder(2, 12, 2, 12)));
18 | // panel.setBackground(new Color(0.0F, 0.0F, 0.0F, 0.05F));
19 |
20 | }
21 |
22 | public void paintComponent(Graphics g) {
23 | super.paintComponent(g);
24 | g.setColor(new Color(0.0F, 0.0F, 0.0F, 0.05F));
25 | g.fillRect(0, 0, getWidth(), getHeight());
26 | }
27 |
28 | }
29 |
--------------------------------------------------------------------------------
/src/jebl/evolution/sequences/CodonState.java:
--------------------------------------------------------------------------------
1 | /*
2 | * CodonState.java
3 | *
4 | * (c) 2002-2005 JEBL Development Core Team
5 | *
6 | * This package may be distributed under the
7 | * Lesser Gnu Public Licence (LGPL)
8 | */
9 | package jebl.evolution.sequences;
10 |
11 | /**
12 | * @author Andrew Rambaut
13 | * @author Alexei Drummond
14 | *
15 | * @version $Id: CodonState.java 225 2006-02-16 14:50:36Z rambaut $
16 | */
17 | public final class CodonState extends State {
18 |
19 | CodonState(String name, String stateCode, int index) {
20 | super(name, stateCode, index);
21 | }
22 |
23 | CodonState(String name, String stateCode, int index, CodonState[] ambiguities) {
24 | super(name, stateCode, index, ambiguities);
25 | }
26 |
27 | public boolean isGap() {
28 | return this == Codons.GAP_STATE;
29 | }
30 | }
31 |
--------------------------------------------------------------------------------
/src/jebl/evolution/aligners/Aligner.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.aligners;
2 |
3 | import jebl.evolution.alignments.Alignment;
4 | import jebl.evolution.sequences.Sequence;
5 | import jebl.util.ProgressListener;
6 |
7 | import java.util.Collection;
8 |
9 | /**
10 | *
11 | * As of 2006-12-06, this interface is not used anywhere in JEBL, and it doesn't have
12 | * any implementing classes. It is only a proposed future alternative to the existing
13 | * abstract class Align
14 | *
15 | * @author Andrew Rambaut
16 | * @author Alexei Drummond
17 | * @version $Id: Aligner.java 559 2006-12-06 22:20:38Z twobeers $
18 | */
19 | public interface Aligner {
20 |
21 | Alignment alignSequences(Collection sequences);
22 |
23 | void addProgressListener(ProgressListener listener);
24 |
25 | void removeProgressListener(ProgressListener listener);
26 | }
27 |
--------------------------------------------------------------------------------
/src/jebl/gui/trees/treeviewer/painters/AbstractPainter.java:
--------------------------------------------------------------------------------
1 | package jebl.gui.trees.treeviewer.painters;
2 |
3 | import java.util.ArrayList;
4 | import java.util.List;
5 |
6 | /**
7 | * @author Andrew Rambaut
8 | * @version $Id: AbstractPainter.java 181 2006-01-23 17:31:10Z rambaut $
9 | */
10 | public abstract class AbstractPainter implements Painter {
11 | public void addPainterListener(PainterListener listener) {
12 | listeners.add(listener);
13 | }
14 |
15 | public void removePainterListener(PainterListener listener) {
16 | listeners.remove(listener);
17 | }
18 |
19 | public void firePainterChanged() {
20 | for (PainterListener listener : listeners) {
21 | listener.painterChanged();
22 | }
23 | }
24 | private final List listeners = new ArrayList();
25 | }
26 |
--------------------------------------------------------------------------------
/src/org/virion/jam/panels/SearchPanelListener.java:
--------------------------------------------------------------------------------
1 | package org.virion.jam.panels;
2 |
3 | /**
4 | * An interface for listeners to the SearchPanel class.
5 | * @author Andrew Rambaut
6 | * Date: Jul 26, 2004
7 | * Time: 5:37:15 PM
8 | */
9 | public interface SearchPanelListener {
10 |
11 | /**
12 | * Called when the user requests a search by pressing return having
13 | * typed a search string into the text field. If the continuousUpdate
14 | * flag is true then this method is called when the user types into
15 | * the text field.
16 | * @param searchString the user's search string
17 | */
18 | void searchStarted(String searchString);
19 |
20 | /**
21 | * Called when the user presses the cancel search button or presses
22 | * escape while the search is in focus.
23 | */
24 | void searchStopped();
25 |
26 | }
27 |
--------------------------------------------------------------------------------
/src/jade/math/IncompleteGammaFunctionSeries.java:
--------------------------------------------------------------------------------
1 | /*
2 | * IncompleteGammaFunctionSeries.java
3 | *
4 | * Created on August 19, 2005, 11:21 AM
5 | *
6 | * author: Stephen A. Smith
7 | */
8 |
9 | package jade.math;
10 |
11 | /**
12 | *
13 | * @author stephensmith
14 | */
15 | public class IncompleteGammaFunctionSeries extends InfiniteSeries{
16 |
17 | /** Creates a new instance of IncompleteGammaFunctionSeries */
18 | public IncompleteGammaFunctionSeries(double x) {
19 | alpha = x;
20 | }
21 |
22 | protected void computeTermAt(int n){
23 | sum += 1;
24 | lastTerm *= x/sum;
25 | return;
26 | }
27 |
28 | protected double initialValue(){
29 | lastTerm = 1/alpha;
30 | sum = alpha;
31 | return lastTerm;
32 | }
33 |
34 | private double alpha;
35 | private double sum;
36 | }
37 |
--------------------------------------------------------------------------------
/src/jade/simulate/ExtinctionFunction.java:
--------------------------------------------------------------------------------
1 | package jade.simulate;
2 |
3 | public class ExtinctionFunction {
4 | public ExtinctionFunction(double intime, double endtime, double value){
5 | start = intime;
6 | end = endtime;
7 | this.value = value;
8 | }
9 | public double getStartTime(){return start;}
10 | public double getEndTime(){return end;}
11 | public double getFunction(){
12 | return value;
13 | }
14 | public void setTimes(double intime, double endtime){
15 | start = intime;
16 | end = endtime;
17 | }
18 | public String toString(){
19 | String x = "";
20 | x = "from "+start+" to "+end+" connection is 0 else extinction is "+value;
21 | return x;
22 | }
23 | //start time
24 | private double start;
25 | //end time
26 | private double end;
27 | //value
28 | private double value;
29 | }
30 |
--------------------------------------------------------------------------------
/src/jade/math/IncompleteGammaFunctionFraction.java:
--------------------------------------------------------------------------------
1 | /*
2 | * IncompleteGammaFunctionFraction.java
3 | *
4 | * Created on August 19, 2005, 12:27 PM
5 | *
6 | * author: Stephen A. Smith
7 | */
8 |
9 | package jade.math;
10 |
11 | /**
12 | *
13 | * @author stephensmith
14 | */
15 | public class IncompleteGammaFunctionFraction extends ContinuedFraction{
16 |
17 | /** Creates a new instance of IncompleteGammaFunctionFraction */
18 | public IncompleteGammaFunctionFraction(double a) {
19 | alpha = a;
20 | }
21 |
22 | protected void computeFactorsAt(int n){
23 | sum+=2;
24 | factors[0] = (alpha-n)*n;
25 | factors[1] = sum;
26 | return;
27 | }
28 |
29 | protected double initialValue(){
30 | sum = x-alpha+1;
31 | return sum;
32 | }
33 |
34 | private double alpha;
35 | private double sum;
36 | }
37 |
--------------------------------------------------------------------------------
/src/org/virion/jam/demo/DemoMenuBarFactory.java:
--------------------------------------------------------------------------------
1 | package org.virion.jam.demo;
2 |
3 | import org.virion.jam.framework.*;
4 | import org.virion.jam.mac.*;
5 | import org.virion.jam.demo.menus.DemoMenuFactory;
6 |
7 |
8 | public class DemoMenuBarFactory extends DefaultMenuBarFactory {
9 |
10 | public DemoMenuBarFactory() {
11 | if (org.virion.jam.mac.Utils.isMacOSX()) {
12 | registerMenuFactory(new MacFileMenuFactory(true));
13 | registerMenuFactory(new DefaultEditMenuFactory());
14 | registerMenuFactory(new DemoMenuFactory());
15 | registerMenuFactory(new MacWindowMenuFactory());
16 | registerMenuFactory(new MacHelpMenuFactory());
17 | } else {
18 | registerMenuFactory(new DefaultFileMenuFactory(true));
19 | registerMenuFactory(new DefaultEditMenuFactory());
20 | registerMenuFactory(new DemoMenuFactory());
21 | registerMenuFactory(new DefaultHelpMenuFactory());
22 | }
23 | }
24 |
25 | }
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/src/jebl/evolution/substmodel/AminoAcidModel.java:
--------------------------------------------------------------------------------
1 | // AminoAcidModel.java
2 | //
3 | // (c) 1999-2001 PAL Development Core Team
4 | //
5 | // This package may be distributed under the
6 | // terms of the Lesser GNU General Public License (LGPL)
7 |
8 | package jebl.evolution.substmodel;
9 |
10 | import jebl.evolution.sequences.SequenceType;
11 |
12 |
13 | /**
14 | * base class of rate matrices for amino acids
15 | *
16 | * @version $Id: AminoAcidModel.java 185 2006-01-23 23:03:18Z rambaut $
17 | *
18 | * @author Korbinian Strimmer
19 | */
20 | public abstract class AminoAcidModel extends AbstractRateMatrix
21 | {
22 |
23 | //
24 | // Protected stuff
25 | //
26 |
27 | // Constructor
28 | protected AminoAcidModel(double[] f)
29 | {
30 | // Dimension = 20
31 | super(20);
32 |
33 | setSequenceType(SequenceType.AMINO_ACID);
34 | setFrequencies(f);
35 | }
36 | }
37 |
--------------------------------------------------------------------------------
/src/jebl/evolution/alignments/JackknifedAlignment.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.alignments;
2 |
3 | import jebl.math.Random;
4 |
5 | /**
6 | * Date: 17/01/2006
7 | * Time: 08:18:32
8 | *
9 | * @author Joseph Heled
10 | * @version $Id: JackknifedAlignment.java 482 2006-10-25 06:30:57Z twobeers $
11 | *
12 | */
13 | public class JackknifedAlignment extends ResampledAlignment {
14 | public JackknifedAlignment(Alignment srcAlignment, double percent) {
15 | final int nSites = srcAlignment.getSiteCount();
16 | final int nNewSites = (int)Math.ceil(nSites * percent);
17 | int[] sites = new int[nSites];
18 |
19 | for(int n = 0; n < nSites; ++n) {
20 | sites[n] = n;
21 | }
22 |
23 | Random.shuffle(sites);
24 |
25 | int[] newSites = new int[nNewSites];
26 | System.arraycopy(sites, 0, newSites, 0, nNewSites);
27 | init(srcAlignment, newSites);
28 | }
29 | }
30 |
--------------------------------------------------------------------------------
/src/org/virion/jam/framework/MultiDocMenuBarFactory.java:
--------------------------------------------------------------------------------
1 | /*
2 | * Copyright (c) 2005 Biomatters LTD. All Rights Reserved.
3 | */
4 |
5 | package org.virion.jam.framework;
6 |
7 | import org.virion.jam.mac.MacFileMenuFactory;
8 | import org.virion.jam.mac.MacHelpMenuFactory;
9 | import org.virion.jam.mac.MacWindowMenuFactory;
10 |
11 |
12 | public class MultiDocMenuBarFactory extends DefaultMenuBarFactory {
13 |
14 |
15 | public MultiDocMenuBarFactory() {
16 | if (org.virion.jam.mac.Utils.isMacOSX()) {
17 | registerMenuFactory(new MacFileMenuFactory(true));
18 | registerMenuFactory(new DefaultEditMenuFactory());
19 | registerMenuFactory(new MacHelpMenuFactory());
20 | registerMenuFactory(new MacWindowMenuFactory());
21 | } else {
22 | registerMenuFactory(new DefaultFileMenuFactory(true));
23 | registerMenuFactory(new DefaultEditMenuFactory());
24 | registerMenuFactory(new DefaultHelpMenuFactory());
25 | }
26 | }
27 | }
--------------------------------------------------------------------------------
/src/org/virion/jam/framework/SingleDocMenuBarFactory.java:
--------------------------------------------------------------------------------
1 | /*
2 | * Copyright (c) 2005 Biomatters LTD. All Rights Reserved.
3 | */
4 |
5 | package org.virion.jam.framework;
6 |
7 | import org.virion.jam.mac.MacFileMenuFactory;
8 | import org.virion.jam.mac.MacHelpMenuFactory;
9 | import org.virion.jam.mac.MacWindowMenuFactory;
10 |
11 |
12 | public class SingleDocMenuBarFactory extends DefaultMenuBarFactory {
13 |
14 | public SingleDocMenuBarFactory() {
15 | if (org.virion.jam.mac.Utils.isMacOSX()) {
16 | registerMenuFactory(new MacFileMenuFactory(false));
17 | registerMenuFactory(new DefaultEditMenuFactory());
18 | registerMenuFactory(new MacWindowMenuFactory());
19 | registerMenuFactory(new MacHelpMenuFactory());
20 | } else {
21 | registerMenuFactory(new DefaultFileMenuFactory(false));
22 | registerMenuFactory(new DefaultEditMenuFactory());
23 | registerMenuFactory(new DefaultHelpMenuFactory());
24 | }
25 | }
26 |
27 | }
--------------------------------------------------------------------------------
/src/jebl/util/AttributableHelper.java:
--------------------------------------------------------------------------------
1 | package jebl.util;
2 |
3 | import java.util.Collections;
4 | import java.util.HashMap;
5 | import java.util.Map;
6 | import java.util.Set;
7 |
8 | /**
9 | * @author rambaut
10 | * Date: Nov 27, 2005
11 | * Time: 1:31:50 PM
12 | */
13 | public class AttributableHelper implements Attributable {
14 |
15 | public void setAttribute(String name, Object value) {
16 | attributeMap.put(name, value);
17 | }
18 |
19 | public Object getAttribute(String name) {
20 | return attributeMap.get(name);
21 | }
22 |
23 | public void removeAttribute(String name) {
24 | attributeMap.remove(name);
25 | }
26 |
27 | public Set getAttributeNames() {
28 | return attributeMap.keySet();
29 | }
30 |
31 | public Map getAttributeMap() {
32 | return Collections.unmodifiableMap(attributeMap);
33 | }
34 |
35 | Map attributeMap = new HashMap();
36 | }
37 |
38 |
--------------------------------------------------------------------------------
/src/jade/runners/ConcatMain.java:
--------------------------------------------------------------------------------
1 | package jade.runners;
2 |
3 | import java.util.*;
4 |
5 | import jade.data.*;
6 |
7 | public class ConcatMain {
8 | public ConcatMain(String [] args){
9 | if(args.length<1){
10 | printInfo();
11 | System.exit(0);
12 | }
13 | else{
14 | ArrayList files = new ArrayList();
15 | for(int i=0;i
9 | * created on 04.12.2006 15:15:54
10 | */
11 | public enum IllegalCharacterPolicy {
12 | abort("Abort"),
13 | strip("Strip offending characters"),
14 | askUser("Ask");
15 |
16 | public final String description;
17 | IllegalCharacterPolicy(String description) {
18 | this.description = description;
19 | }
20 |
21 | public static IllegalCharacterPolicy instanceOf(String description) {
22 | for (IllegalCharacterPolicy p : values()) {
23 | if (p.description.equals(description)) {
24 | return p;
25 | }
26 | }
27 | return null;
28 | }
29 |
30 | public String toString() {
31 | return description;
32 | }
33 | }
34 |
--------------------------------------------------------------------------------
/src/org/virion/jam/framework/MenuFactory.java:
--------------------------------------------------------------------------------
1 | /**
2 | * MenuBarFactory.java
3 | */
4 |
5 | package org.virion.jam.framework;
6 |
7 | import javax.swing.*;
8 |
9 | public interface MenuFactory {
10 |
11 | public final static int LEFT = 0;
12 | public final static int CENTER = 1;
13 | public final static int RIGHT = 2;
14 |
15 | /**
16 | * Give the name of this menu. If multiple MenuFactories are
17 | * registered with the same name, then these will be appended
18 | * into a single actual menu.
19 | */
20 | String getMenuName();
21 |
22 | /**
23 | * This method should populate the menu with menu items. Reference
24 | * can be made to the frame in order to get Actions.
25 | * @param menu
26 | * @param frame
27 | */
28 | void populateMenu(JMenu menu, AbstractFrame frame);
29 |
30 | /**
31 | * Returns the preferred alignment of the menu in the menu bar. This
32 | * should be one of MenuFactory.LEFT, MenuFactory.CENTER or MenuFactory.RIGHT.
33 | * @return the alignment
34 | */
35 | int getPreferredAlignment();
36 | }
--------------------------------------------------------------------------------
/src/org/virion/jam/util/SimpleLongTask.java:
--------------------------------------------------------------------------------
1 | package org.virion.jam.util;
2 |
3 | public abstract class SimpleLongTask extends LongTask {
4 |
5 | boolean background = false;
6 | private SwingWorker worker = null;
7 | public int current = 0;
8 | public int length = 1;
9 | public boolean pleaseStop = false;
10 | public String message = "";
11 | public String description = "";
12 |
13 | /**
14 | * Called to find out how much work needs
15 | * to be done.
16 | */
17 | public int getLengthOfTask() {
18 | return length;
19 | }
20 |
21 | /**
22 | * Called to find out how much has been done.
23 | */
24 | public int getCurrent() {
25 | return current;
26 | }
27 |
28 | /**
29 | * Called to stop task.
30 | */
31 | public void stop() {
32 | pleaseStop = true;
33 | }
34 |
35 | public String getMessage() {
36 | return message;
37 | }
38 |
39 | public String getDescription() {
40 | return description;
41 | }
42 | }
43 |
--------------------------------------------------------------------------------
/src/jebl/math/UnivariateFunction.java:
--------------------------------------------------------------------------------
1 | // UnivariateFunction.java
2 | //
3 | // (c) 2006- JEBL development team
4 | //
5 | // based on LGPL code from the Phylogenetic Analysis Library (PAL),
6 | // http://www.cebl.auckland.ac.nz/pal-project/
7 | // which is (c) 1999-2001 PAL Development Core Team
8 | //
9 | // This package may be distributed under the
10 | // terms of the Lesser GNU General Public License (LGPL)
11 |
12 |
13 | package jebl.math;
14 |
15 |
16 | /**
17 | * interface for a function of one variable
18 | *
19 | * @author Korbinian Strimmer
20 | */
21 | public interface UnivariateFunction
22 | {
23 | /**
24 | * compute function value
25 | *
26 | * @param argument function argument
27 | *
28 | * @return function value
29 | */
30 | double evaluate(double argument);
31 |
32 | /**
33 | * get lower bound of argument
34 | *
35 | * @return lower bound
36 | */
37 | double getLowerBound();
38 |
39 | /**
40 | * get upper bound of argument
41 | *
42 | * @return upper bound
43 | */
44 | double getUpperBound();
45 | }
46 |
--------------------------------------------------------------------------------
/src/jebl/gui/trees/treeviewer_dev/painters/AbstractPainter.java:
--------------------------------------------------------------------------------
1 | package jebl.gui.trees.treeviewer_dev.painters;
2 |
3 | import java.util.ArrayList;
4 | import java.util.List;
5 |
6 | /**
7 | * @author Andrew Rambaut
8 | * @version $Id: AbstractPainter.java 373 2006-07-01 15:18:27Z rambaut $
9 | */
10 | public abstract class AbstractPainter implements Painter {
11 | public void addPainterListener(PainterListener listener) {
12 | listeners.add(listener);
13 | }
14 |
15 | public void removePainterListener(PainterListener listener) {
16 | listeners.remove(listener);
17 | }
18 |
19 | public void firePainterChanged() {
20 | for (PainterListener listener : listeners) {
21 | listener.painterChanged();
22 | }
23 | }
24 |
25 | public void firePainterSettingsChanged() {
26 | for (PainterListener listener : listeners) {
27 | listener.painterSettingsChanged();
28 | }
29 | }
30 |
31 | private final List listeners = new ArrayList();
32 | }
33 |
--------------------------------------------------------------------------------
/src/org/virion/jam/html/SimpleLinkListener.java:
--------------------------------------------------------------------------------
1 | package org.virion.jam.html;
2 |
3 |
4 | import javax.swing.event.*;
5 |
6 | import org.virion.jam.util.BrowserLauncher;
7 |
8 | /**
9 | * iSeek prototype. Codename seekquence.
10 | *
11 | * This class listens to Hyperlink Events, and opens the url in a browser window.
12 | *
13 | * Open a browser from a Java application on Windows, Unix, or Macintosh.
14 | * see http://ostermiller.org/utils/Browser.html for more information
15 | *
16 | * @author Nasser
17 | * @version $Id: SimpleLinkListener.java 183 2006-01-23 21:29:48Z rambaut $
18 | * Date: 26/01/2005
19 | * Time: 11:54:50
20 | */
21 | public class SimpleLinkListener implements HyperlinkListener {
22 |
23 | public void hyperlinkUpdate(HyperlinkEvent he) {
24 |
25 | if (he.getEventType() == HyperlinkEvent.EventType.ACTIVATED) {
26 | try{
27 | BrowserLauncher.openURL(he.getDescription());
28 | }catch(Exception ioe){
29 | ioe.printStackTrace();
30 | }
31 | }
32 | }
33 | }
34 |
--------------------------------------------------------------------------------
/src/jade/math/InfiniteSeries.java:
--------------------------------------------------------------------------------
1 | /*
2 | * InfiniteSeries.java
3 | *
4 | * Created on August 19, 2005, 11:24 AM
5 | *
6 | * author: Stephen A. Smith
7 | */
8 |
9 | package jade.math;
10 |
11 | /**
12 | *
13 | * @author stephensmith
14 | */
15 | public abstract class InfiniteSeries extends IterativeProcess{
16 |
17 | /** Creates a new instance of InfiniteSeries */
18 | public InfiniteSeries() {
19 | }
20 |
21 | protected abstract void computeTermAt(int n);
22 | public double evaluateIteration(){
23 | computeTermAt(getIterations());
24 | result+=lastTerm;
25 | return relativePrecision(Math.abs(lastTerm), Math.abs(result));
26 | }
27 | public double getResult(){
28 | return result;
29 | }
30 | public void initializeIterations(){
31 | result = initialValue();
32 | }
33 | protected abstract double initialValue();
34 | public void setArgument(double r){
35 | x = r;
36 | return;
37 | }
38 |
39 | private double result;
40 | protected double x;
41 | protected double lastTerm;
42 | }
43 |
--------------------------------------------------------------------------------
/src/jebl/evolution/alignments/Patterns.java:
--------------------------------------------------------------------------------
1 | /*
2 | * Patterns.java
3 | *
4 | * (c) 2005 JEBL Development Team
5 | *
6 | * This package is distributed under the
7 | * Lesser Gnu Public Licence (LGPL)
8 | */
9 | package jebl.evolution.alignments;
10 |
11 | import jebl.evolution.sequences.SequenceType;
12 | import jebl.evolution.taxa.Taxon;
13 |
14 | import java.util.List;
15 |
16 | /**
17 | * An interface representing a set of site patterns.
18 | *
19 | * @author Andrew Rambaut
20 | * @author Alexei Drummond
21 | *
22 | * @version $Id: Patterns.java 185 2006-01-23 23:03:18Z rambaut $
23 | */
24 | public interface Patterns {
25 |
26 | int getPatternCount();
27 |
28 | int getPatternLength();
29 |
30 | /**
31 | * Get a list of all the patterns
32 | * @return the list
33 | */
34 | List getPatterns();
35 |
36 | /**
37 | * @return the list of taxa that the state values correspond to.
38 | */
39 | List getTaxa();
40 |
41 | /**
42 | * @return the data type of the states in these site patterns.
43 | */
44 | SequenceType getSequenceType();
45 |
46 | }
47 |
--------------------------------------------------------------------------------
/src/org/virion/jam/mac/MacWindowMenuFactory.java:
--------------------------------------------------------------------------------
1 | package org.virion.jam.mac;
2 |
3 | import org.virion.jam.framework.MenuFactory;
4 | import org.virion.jam.framework.AbstractFrame;
5 | import org.virion.jam.framework.Application;
6 | import org.virion.jam.framework.MenuBarFactory;
7 |
8 | import javax.swing.*;
9 | import java.awt.event.KeyEvent;
10 |
11 | /**
12 | * @author rambaut
13 | * Date: Dec 26, 2004
14 | * Time: 11:03:39 AM
15 | */
16 | public class MacWindowMenuFactory implements MenuFactory {
17 | public String getMenuName() {
18 | return "Window";
19 | }
20 |
21 | public void populateMenu(JMenu menu, AbstractFrame frame) {
22 |
23 | Application application = Application.getApplication();
24 |
25 | JMenuItem item;
26 |
27 | item = new JMenuItem(frame.getZoomWindowAction());
28 | menu.add(item);
29 |
30 | item = new JMenuItem(frame.getMinimizeWindowAction());
31 | item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_M, MenuBarFactory.MENU_MASK));
32 | menu.add(item);
33 |
34 | }
35 |
36 | public int getPreferredAlignment() {
37 | return RIGHT;
38 | }
39 | }
40 |
--------------------------------------------------------------------------------
/src/jebl/evolution/treemetrics/BilleraMetric.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.treemetrics;
2 |
3 | import jebl.evolution.taxa.Taxon;
4 | import jebl.evolution.trees.RootedTree;
5 | import jebl.evolution.trees.TreeBiPartitionInfo;
6 |
7 | import java.util.ArrayList;
8 | import java.util.List;
9 |
10 | /**
11 | * Billera tree distance - sum of change in branch lengths required to transform one tree to the second
12 | *
13 | * Note that this interface is not optimal for a large set where all pairs are required.
14 | * Creating TreeBiPartitionInfo's as a pre step is better unless memory is an issue.
15 | *
16 | * @author Joseph Heled
17 | * @version $Id$
18 | */
19 | public class BilleraMetric implements RootedTreeMetric {
20 | public double getMetric(RootedTree tree1, RootedTree tree2) {
21 | List taxa = new ArrayList(tree1.getTaxa());
22 | TreeBiPartitionInfo p1 = new TreeBiPartitionInfo(tree1, taxa);
23 | TreeBiPartitionInfo p2 = new TreeBiPartitionInfo(tree2, taxa);
24 | return TreeBiPartitionInfo.distance(p1, p2, TreeBiPartitionInfo.DistanceNorm.NORM1);
25 | }
26 | }
27 |
--------------------------------------------------------------------------------
/src/jade/math/NormalDistribution.java:
--------------------------------------------------------------------------------
1 | /*
2 | * NormalDistribution.java
3 | *
4 | * Created on August 9, 2005, 3:24 PM
5 | *
6 | * author: Stephen A. Smith
7 | */
8 |
9 | package jade.math;
10 |
11 | import java.util.*;
12 | /**
13 | *
14 | * @author stephensmith
15 | */
16 | public class NormalDistribution implements ProbDistribution{
17 |
18 | /** Creates a new instance of NormalDistribution */
19 | public NormalDistribution() {
20 | }
21 |
22 | public NormalDistribution(double mean, double stdev){
23 | this.mean = mean;
24 | this.stdev = stdev;
25 | }
26 |
27 | public void setStDev(double stdev){ this.stdev = stdev; }
28 |
29 | public void setMean(double mean){ this.mean = mean; }
30 |
31 | public double getValue(){
32 | return (r.nextGaussian()*stdev)+mean;
33 | }
34 |
35 | public double getPDF(double x){
36 | //add error function
37 | return (x-mean)/stdev;
38 | }
39 |
40 | //private methods
41 | private double stdev;
42 | private double mean;
43 | private Random r = new Random();
44 | }
45 |
--------------------------------------------------------------------------------
/src/org/virion/jam/panels/RuleModel.java:
--------------------------------------------------------------------------------
1 | /**
2 | * RuleModel.java
3 | */
4 |
5 | package org.virion.jam.panels;
6 |
7 |
8 | /**
9 | * RuleModel.
10 | *
11 | * @author Andrew Rambaut
12 | * @version $Id: RuleModel.java 182 2006-01-23 21:24:01Z rambaut $
13 | */
14 |
15 |
16 | public interface RuleModel {
17 |
18 | /**
19 | * Returns an array of strings to be presented as a combo box which
20 | * are available fields to define rules on.
21 | *
22 | * @return the field names
23 | */
24 | Object[] getFields();
25 |
26 | /**
27 | * Returns an array of strings to be presented as a combo box which
28 | * are possible rule conditions for the specified field.
29 | *
30 | * @return the condition names
31 | */
32 | Object[] getConditions(Object field);
33 |
34 | /**
35 | * Returns an array of strings to be presented as a combo box which
36 | * are possible values for the field. Should return null if a text
37 | * box is required.
38 | *
39 | * @return the values
40 | */
41 | Object[] getValues(Object field, Object condition);
42 |
43 | }
--------------------------------------------------------------------------------
/src/org/virion/jam/console/ConsoleMenuBarFactory.java:
--------------------------------------------------------------------------------
1 | /**
2 | * ConsoleMenuBarFactory.java
3 | */
4 |
5 | package org.virion.jam.console;
6 |
7 | import org.virion.jam.framework.*;
8 | import org.virion.jam.mac.MacFileMenuFactory;
9 | import org.virion.jam.mac.MacHelpMenuFactory;
10 | import org.virion.jam.mac.MacWindowMenuFactory;
11 |
12 | public class ConsoleMenuBarFactory extends DefaultMenuBarFactory {
13 |
14 | public ConsoleMenuBarFactory() {
15 | // org.virion stuff shouldn't be called from here - it's a separate project!
16 |
17 | // no its not. This class is part of JAM.
18 | if (org.virion.jam.mac.Utils.isMacOSX()) {
19 | //if (System.getProperty("mrj.version") != null) {
20 | registerMenuFactory(new MacFileMenuFactory(false));
21 | registerMenuFactory(new DefaultEditMenuFactory());
22 | registerMenuFactory(new MacWindowMenuFactory());
23 | registerMenuFactory(new MacHelpMenuFactory());
24 | } else {
25 | registerMenuFactory(new DefaultFileMenuFactory(false));
26 | registerMenuFactory(new DefaultEditMenuFactory());
27 | registerMenuFactory(new DefaultHelpMenuFactory());
28 | }
29 | }
30 | }
--------------------------------------------------------------------------------
/src/jade/data/DataType.java:
--------------------------------------------------------------------------------
1 | package jade.data;
2 |
3 | public interface DataType {
4 | char UNKNOWN_CHARACTER = '?';
5 |
6 | char DEFAULT_GAP_CHARACTER = '-';
7 |
8 | /*
9 | * types of data
10 | */
11 | int BINARYDATATYPE = 0;
12 |
13 | int NUCLEOTIDEDATATYPE = 1;
14 |
15 | int NUMERICDATATYPE = 2;
16 |
17 | int CONTDATATYPE = 3;
18 |
19 | int UNKNOWN = 666;
20 |
21 | char[] SUGGESTED_GAP_CHARACTERS = { DEFAULT_GAP_CHARACTER, '_', '.' };
22 |
23 | int SUGGESTED_GAP_STATE = -2;
24 |
25 | int SUGGESTED_UNKNOWN_STATE = -1;
26 |
27 | String NUCLEOTIDE_DESCRIPTION = "nucleotide";
28 |
29 | String BINARY_DESCRIPTION = "binary";
30 |
31 | String GAP_BALANCED_DESCRIPTION = "gap balanced";
32 |
33 | String getDescription();
34 |
35 | int getState(char c);
36 |
37 | char getChar(int state);
38 |
39 | int getNumStates();
40 |
41 | char getSuggestedChar(char c);
42 |
43 | int getTypeID();
44 |
45 | boolean isUnknownState(int state);
46 |
47 | boolean isUnknownChar(char c);
48 |
49 | boolean hasGapCharacter();
50 |
51 | boolean isGapChar(char c);
52 |
53 | boolean isGapState(int state);
54 |
55 | int getSuggestedGapState();
56 |
57 | int getSuggestedUnknownState();
58 | }
59 |
--------------------------------------------------------------------------------
/src/jebl/gui/trees/treeviewer/decorators/AttributeBranchDecorator.java:
--------------------------------------------------------------------------------
1 | package jebl.gui.trees.treeviewer.decorators;
2 |
3 | import jebl.evolution.graphs.Node;
4 | import jebl.evolution.trees.Tree;
5 |
6 | import java.awt.*;
7 | import java.util.HashMap;
8 | import java.util.Map;
9 |
10 | /**
11 | * @author Andrew Rambaut
12 | * @version $Id: AttributeBranchDecorator.java 181 2006-01-23 17:31:10Z rambaut $
13 | */
14 | public class AttributeBranchDecorator implements BranchDecorator {
15 | public AttributeBranchDecorator(String attributeName, Map paintMap) {
16 | this.attributeName = attributeName;
17 | this.paintMap = paintMap;
18 | }
19 |
20 | public Paint getBranchPaint(Tree tree, Node node) {
21 | Paint paint = getPaint(node.getAttribute(attributeName));
22 | if (paint == null) return Color.BLACK;
23 | return paint;
24 | }
25 |
26 | protected Paint getPaint(Object value) {
27 | if (value != null) {
28 | return paintMap.get(value);
29 | }
30 | return null;
31 | }
32 |
33 | protected final String attributeName;
34 |
35 | protected Map paintMap = new HashMap();
36 | }
37 |
--------------------------------------------------------------------------------
/src/org/virion/jam/table/AdvancedTableUI.java:
--------------------------------------------------------------------------------
1 | package org.virion.jam.table;
2 |
3 | import javax.swing.plaf.basic.BasicTableUI;
4 | import javax.swing.event.MouseInputListener;
5 | import javax.swing.*;
6 | import java.awt.event.MouseEvent;
7 | import java.awt.*;
8 |
9 | /**
10 | * @author rambaut
11 | * Date: Oct 20, 2004
12 | * Time: 10:16:52 PM
13 | */
14 | public class AdvancedTableUI extends BasicTableUI {
15 |
16 | public void installUI(JComponent c) {
17 | super.installUI(c);
18 |
19 | if (org.virion.jam.mac.Utils.isMacOSX()) {
20 | c.setFont(new Font("Lucida Grande", Font.PLAIN, 9));
21 | }
22 | }
23 |
24 | protected MouseInputListener createMouseInputListener() {
25 | return new AdvancedTableUI.AdvancedMouseInputHandler();
26 | }
27 |
28 | class AdvancedMouseInputHandler extends MouseInputHandler {
29 | public void mousePressed(MouseEvent e) {
30 | Point origin = e.getPoint();
31 | int row = table.rowAtPoint(origin);
32 | int column = table.columnAtPoint(origin);
33 | if (row != -1 && column != -1) {
34 | if (table.isCellSelected(row, column)) {
35 | e.consume();
36 | }
37 | }
38 |
39 | super.mousePressed(e);
40 | }
41 | }
42 | }
43 |
--------------------------------------------------------------------------------
/src/jebl/evolution/graphs/Utils.java:
--------------------------------------------------------------------------------
1 | /*
2 | * Utils.java
3 | *
4 | * (c) 2005 JEBL Development Team
5 | *
6 | * This package is distributed under the
7 | * Lesser Gnu Public Licence (LGPL)
8 | */
9 | package jebl.evolution.graphs;
10 |
11 | /**
12 | * A collection of utility functions for graphs.
13 | *
14 | * @author Andrew Rambaut
15 | * @author Alexei Drummond
16 | *
17 | * @version $Id: Utils.java 185 2006-01-23 23:03:18Z rambaut $
18 | */
19 | public class Utils {
20 |
21 | /**
22 | * @param graph
23 | * @return true if the given graph is acyclic.
24 | */
25 | public boolean isAcyclical(Graph graph) {
26 | throw new UnsupportedOperationException("Not implemented yet");
27 | }
28 |
29 | /**
30 | * @param graph
31 | * @return true if the given graph is fully connected.
32 | */
33 | public boolean isConnected(Graph graph) {
34 | throw new UnsupportedOperationException("Not implemented yet");
35 | }
36 |
37 | /**
38 | * @param graph
39 | * @return true if the given graph is a tree, i.e. is acyclic
40 | * and fully connected.
41 | */
42 | public final boolean isTree(Graph graph) {
43 | return isAcyclical(graph) && isConnected(graph);
44 | }
45 | }
46 |
--------------------------------------------------------------------------------
/src/org/virion/jam/toolbar/ToolbarAction.java:
--------------------------------------------------------------------------------
1 | package org.virion.jam.toolbar;
2 |
3 | import javax.swing.*;
4 |
5 | /**
6 | * @author rambaut
7 | * Date: Oct 18, 2005
8 | * Time: 10:10:52 PM
9 | */
10 | public abstract class ToolbarAction extends AbstractAction {
11 |
12 | protected ToolbarAction(String label, String toolTipText, Icon icon) {
13 | this(label, toolTipText, icon, null, null);
14 | }
15 |
16 | protected ToolbarAction(String label, String toolTipText, Icon icon, Icon disabledIcon, Icon pressedIcon) {
17 | super(label, icon);
18 |
19 | this.label = label;
20 | this.toolTipText = toolTipText;
21 | this.icon = icon;
22 | this.disabledIcon = disabledIcon;
23 | this.pressedIcon = pressedIcon;
24 | }
25 |
26 | public String getLabel() {
27 | return label;
28 | }
29 |
30 | public Icon getIcon() {
31 | return icon;
32 | }
33 |
34 | public Icon getDisabledIcon() {
35 | return disabledIcon;
36 | }
37 |
38 | public Icon getPressedIcon() {
39 | return pressedIcon;
40 | }
41 |
42 | public String getToolTipText() {
43 | return toolTipText;
44 | }
45 |
46 | private String label;
47 | private String toolTipText;
48 | private Icon icon;
49 | private Icon disabledIcon;
50 | private Icon pressedIcon;
51 | }
52 |
--------------------------------------------------------------------------------
/src/jebl/gui/trees/treeviewer/painters/Painter.java:
--------------------------------------------------------------------------------
1 | package jebl.gui.trees.treeviewer.painters;
2 |
3 | import org.virion.jam.controlpanels.ControlsProvider;
4 |
5 | import java.awt.*;
6 | import java.awt.geom.Rectangle2D;
7 |
8 |
9 | /**
10 | * A painter draws a particular decoration onto the tree within a
11 | * rectangle.
12 | * @author Andrew Rambaut
13 | * @version $Id: Painter.java 595 2006-12-27 20:21:41Z pepster $
14 | */
15 | public interface Painter extends ControlsProvider {
16 |
17 | public enum Orientation {
18 | TOP,
19 | LEFT,
20 | BOTTOM,
21 | RIGHT
22 | }
23 |
24 | public enum Justification {
25 | FLUSH,
26 | LEFT,
27 | RIGHT,
28 | CENTER
29 | }
30 |
31 | boolean isVisible();
32 |
33 | //void calibrate(Graphics2D g2, T item);
34 |
35 | void calibrate(Graphics2D g2);
36 |
37 | // May change paint and stroke
38 | void paint(Graphics2D g2, T item, Justification justification, Rectangle2D bounds);
39 |
40 | double getWidth(Graphics2D g2, T item);
41 | double getPreferredHeight();
42 | double getHeightBound();
43 |
44 | void addPainterListener(PainterListener listener);
45 | void removePainterListener(PainterListener listener);
46 | }
47 |
--------------------------------------------------------------------------------
/src/org/virion/jam/controlpalettes/AbstractController.java:
--------------------------------------------------------------------------------
1 | package org.virion.jam.controlpalettes;
2 |
3 | import java.util.ArrayList;
4 | import java.util.List;
5 |
6 | /**
7 | * @author Andrew Rambaut
8 | * @author Alexei Drummond
9 | * @version $Id: AbstractController.java 363 2006-06-27 16:26:09Z rambaut $
10 | */
11 | public abstract class AbstractController implements Controller {
12 | /**
13 | * Add a ControllerListener to this controllers list of listeners
14 | * The main listener will be the ControlPalette itself which will use
15 | * this to resize the panels if the components changed
16 | *
17 | * @param listener
18 | */
19 | public void addControllerListener(ControllerListener listener) {
20 | listeners.add(listener);
21 | }
22 |
23 | /**
24 | * Remove a listener
25 | *
26 | * @param listener
27 | */
28 | public void removeControllerListener(ControllerListener listener) {
29 | listeners.remove(listener);
30 | }
31 |
32 | public void fireControllerChanged() {
33 | for (ControllerListener listener : listeners) {
34 | listener.controlsChanged();
35 | }
36 | }
37 |
38 | private final List listeners = new ArrayList();
39 | }
40 |
--------------------------------------------------------------------------------
/README.md:
--------------------------------------------------------------------------------
1 | phyutility
2 | ==========
3 | Phyutility (fyoo-til-i-te) is a command line program that performs simple analyses or modifications on both trees and data matrices. Makes use of JADE (PEBLS) and JEBL libraries. Please see the [NEWS] page for info concerning updates, etc.
4 |
5 | See [NEWS] and download the new release for amino acid acceptance in the concatenate and cleaning functions (use the -aa argument in -clean and -concat functions).
6 |
7 | *Please use this citation when using Phyutility* [http://bioinformatics.oxfordjournals.org/cgi/content/short/24/5/715 Smith, S. A. and Dunn, C. W. (2008) Phyutility: a phyloinformatics tool for trees, alignments, and molecular data. Bioinformatics. 24: 715-716]
8 |
9 | Currently it performs the following functions (to suggest another feature, submit an Issue and use the label Type-Enhancement) :
10 |
11 | *Trees*
12 |
13 | * rerooting
14 | * pruning
15 | * type conversion
16 | * consensus
17 | * leaf stability
18 | * lineage movement
19 | * tree support
20 |
21 | *Data Matrices*
22 |
23 | * concatenate alignments
24 | * genbank parsing
25 | * trimming alignments
26 | * search NCBI
27 | * fetch NCBI
28 |
29 | *please reroot your trees before performing the leaf stability, lineage movement, or consensus functions -- unrooted functions for these will be incorporated ASAP*
30 |
31 |
--------------------------------------------------------------------------------
/src/jebl/gui/trees/treecomponent/RootedTreePainter.java:
--------------------------------------------------------------------------------
1 | /*
2 | * RootedTreePainter.java
3 | *
4 | * (c) 2005 JEBL Development Team
5 | *
6 | * This package is distributed under the
7 | * Lesser Gnu Public Licence (LGPL)
8 | */
9 | package jebl.gui.trees.treecomponent;
10 |
11 | import jebl.evolution.graphs.Node;
12 | import jebl.evolution.trees.RootedTree;
13 |
14 | import java.awt.*;
15 | import java.awt.geom.Point2D;
16 |
17 | /**
18 | * @author Alexei Drummond
19 | *
20 | * @version $Id: RootedTreePainter.java 309 2006-05-02 08:22:06Z rambaut $
21 | */
22 | public interface RootedTreePainter {
23 |
24 | /**
25 | * Set line style
26 | */
27 | void setLineStyle(Stroke lineStroke, Paint linePaint);
28 |
29 | /**
30 | * Set hilight style
31 | */
32 | void setHilightStyle(Stroke hilightStroke, Paint hilightPaint);
33 |
34 | /**
35 | * Set label style.
36 | */
37 | void setLabelStyle(Font labelFont, Paint labelPaint);
38 |
39 | /**
40 | * Set hilight label style.
41 | */
42 | void setHilightLabelStyle(Font hilightLabelFont, Paint hilightLabelPaint);
43 |
44 | /**
45 | * Do the actual painting.
46 | */
47 | void paintTree(Graphics2D g, Dimension size, RootedTree tree);
48 |
49 | /**
50 | * Find the node under point. Returns -1 if not found.
51 | */
52 | public Node findNodeAtPoint(Point2D point);
53 |
54 | }
55 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/AlignLinearSpace.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align;
2 |
3 | import jebl.evolution.align.scores.Scores;
4 |
5 | abstract class AlignLinearSpace extends AlignSimple {
6 |
7 | float[][] F = null; // the matrices used to compute the alignment
8 |
9 | public AlignLinearSpace(Scores sub, float d) {
10 | super(sub, d);
11 | }
12 |
13 | /**
14 | * Performs the alignment. Abstract.
15 | *
16 | * @param seq1
17 | * @param seq2
18 | */
19 | public abstract void doAlignment(String seq1, String seq2);
20 |
21 | public void prepareAlignment(String sq1, String sq2) {
22 | this.n = sq1.length(); this.m = sq2.length();
23 | this.seq1 = strip(sq1); this.seq2 = strip(sq2);
24 | F = new float[2][m+1];
25 | }
26 |
27 | /**
28 | * Print matrix used to calculate this alignment.
29 | *
30 | * @param out Output to print to.
31 | */
32 | public void printf(Output out) {
33 | for (int j=0; j<=m; j++) {
34 | for (int i = 0; i < F.length; i++) {
35 | float[] f = F[i];
36 | out.print(padLeft(formatScore(f[j]), 5));
37 | }
38 | out.println();
39 | }
40 | }
41 |
42 | static void swap01(Object[] A) {
43 | Object tmp = A[1]; A[1] = A[0]; A[0] = tmp;
44 | }
45 | }
46 |
--------------------------------------------------------------------------------
/src/org/virion/jam/toolbar/GenericToolbarItem.java:
--------------------------------------------------------------------------------
1 | package org.virion.jam.toolbar;
2 |
3 | import javax.swing.*;
4 | import java.awt.*;
5 |
6 | /**
7 | * @author rambaut
8 | * Date: Oct 18, 2005
9 | * Time: 10:09:21 PM
10 | */
11 | public class GenericToolbarItem extends JPanel implements ToolbarItem {
12 |
13 | public GenericToolbarItem(String title, String toolTipText, JComponent component) {
14 | setLayout(new BorderLayout());
15 | add(component, BorderLayout.NORTH);
16 |
17 | label = new JLabel(title);
18 | label.setHorizontalAlignment(SwingConstants.CENTER);
19 | add(label, BorderLayout.SOUTH);
20 | setToolTipText(toolTipText);
21 | }
22 |
23 | public void setToolbarOptions(ToolbarOptions options) {
24 | switch (options.getDisplay()) {
25 | case ToolbarOptions.ICON_AND_TEXT:
26 | case ToolbarOptions.TEXT_ONLY:
27 | label.setVisible(true);
28 | break;
29 | case ToolbarOptions.ICON_ONLY:
30 | label.setVisible(false);
31 | break;
32 | }
33 | }
34 |
35 | public void setAction(Action action) {
36 | throw new UnsupportedOperationException("Method setAction() not supported in GenericToolBarItem");
37 | }
38 |
39 | private JLabel label;
40 | }
41 |
--------------------------------------------------------------------------------
/src/jade/lib/jade_reconstruct_area_PJNI.c:
--------------------------------------------------------------------------------
1 | #include
2 | #include "jade_reconstruct_area_PJNI.h"
3 | #include
4 | #include
5 |
6 | JNIEXPORT jdoubleArray JNICALL Java_jade_reconstruct_area_PJNI_matrixExp
7 | (JNIEnv *jenv, jobject obj, jdoubleArray arr,jint size){
8 | jdoubleArray ret = (*jenv)->NewDoubleArray(jenv,(jint)( size * size));
9 | double *OutData = (*jenv)->GetDoubleArrayElements(jenv,ret,JNI_FALSE);
10 | //double OutData [size*size];
11 | jdouble * at_data = (*jenv)->GetDoubleArrayElements(jenv, arr, NULL);
12 | int i,j;
13 | double a_data [size*size];
14 | for (i = 0; i < size*size; i++){
15 | a_data[i] = (double)at_data[i];
16 | }
17 | gsl_matrix_view m = gsl_matrix_view_array (a_data, (int)size, (int)size);
18 | gsl_mode_t mt = 0;
19 | gsl_matrix *ma = gsl_matrix_alloc (size,size);
20 | gsl_linalg_exponential_ss(&m.matrix, ma, mt);//m input, ma output
21 |
22 | int x = 0;
23 | for(i = 0; i < size; i++){
24 | for(j=0;jSetDoubleArrayRegion(jenv,ret,(jsize)0,(jsize)size*size,OutData);
31 | (*jenv)->ReleaseDoubleArrayElements(jenv,ret,OutData,0);
32 | (*jenv)->ReleaseDoubleArrayElements(jenv,arr,at_data,0);
33 | gsl_matrix_free (ma);
34 | return ret;
35 | }
36 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/SubstScoreMatrix.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | import jebl.evolution.sequences.SequenceType;
4 | import jebl.evolution.substmodel.RateMatrix;
5 |
6 | /**
7 | * @author Alexei Drummond
8 | *
9 | * @version $Id: SubstScoreMatrix.java 360 2006-06-22 07:42:48Z pepster $
10 | */
11 | public class SubstScoreMatrix extends Scores {
12 |
13 | SequenceType sequenceType;
14 | String alphabet;
15 |
16 | public SubstScoreMatrix(RateMatrix rateMatrix) {
17 |
18 | alphabet = SequenceType.Utils.getAlphabet(sequenceType);
19 |
20 | int m = alphabet.length();
21 |
22 | double[][] transProbs = new double[m][m];
23 | rateMatrix.getTransitionProbabilities(transProbs);
24 |
25 | buildScores(log(transProbs));
26 | }
27 |
28 | private float[][] log(double[][] values) {
29 |
30 | float[][] logValues = new float[values.length][values[0].length];
31 |
32 | for (int i = 0; i < values.length; i++) {
33 | for (int j = 0; j < values[i].length; j++) {
34 | logValues[i][j] = (float)Math.log(values[i][j]);
35 | }
36 | }
37 |
38 | return logValues;
39 | }
40 |
41 | public String getName() {
42 | return toString();
43 | }
44 |
45 | public String getAlphabet() {
46 | return alphabet;
47 | }
48 | }
49 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/AlignmentResult.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align;
2 |
3 | /**
4 | * @author Matt Kearse
5 | * @version $Id: AlignmentResult.java 650 2007-03-12 20:09:10Z twobeers $
6 | *
7 | * Used for representing the results of a sequence alignment. Basically just stores
8 | * an array representing whether or not each position in the alignment is a gap or not.
9 | */
10 | class AlignmentResult {
11 | int size;
12 | boolean values[];
13 | // true represents a character from the original sequence, and false represents a gap
14 | // for example:
15 | // original sequence: abcd
16 | // values: true, false, false, true, true, false, true
17 | // then the resulting alignment is: a--bc-d
18 |
19 | public AlignmentResult(int size) {
20 | this.size = 0;
21 | // TT: Wouldn't a BitSet be better?
22 | values =new boolean[size];
23 | }
24 |
25 | public void append(String result) {
26 | for (char character : result.toCharArray()) {
27 | if(character =='-')
28 | values [ size ++ ]= false;
29 | else
30 | values [ size ++ ] = true;
31 | }
32 | }
33 |
34 | public void print() {
35 | for (int i = 0; i < size; i++) {
36 | System.out.print(values[i] ? "X" : "-");
37 |
38 | }
39 | System.out.println ();
40 | }
41 | }
42 |
--------------------------------------------------------------------------------
/src/org/virion/jam/mac/MacHelpMenuFactory.java:
--------------------------------------------------------------------------------
1 | package org.virion.jam.mac;
2 |
3 | import org.virion.jam.framework.MenuFactory;
4 | import org.virion.jam.framework.AbstractFrame;
5 | import org.virion.jam.framework.Application;
6 | import org.virion.jam.framework.MenuBarFactory;
7 |
8 | import javax.swing.*;
9 | import java.awt.event.KeyEvent;
10 |
11 | /**
12 | * @author rambaut
13 | * Date: Dec 26, 2004
14 | * Time: 11:04:02 AM
15 | */
16 | public class MacHelpMenuFactory implements MenuFactory {
17 | public String getMenuName() {
18 | return "Help";
19 | }
20 |
21 | public void populateMenu(JMenu menu, AbstractFrame frame) {
22 |
23 | JMenuItem item;
24 |
25 | Application application = Application.getApplication();
26 |
27 | if (frame.getHelpAction() != null) {
28 | item = new JMenuItem(frame.getHelpAction());
29 | item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_SLASH, MenuBarFactory.MENU_MASK));
30 | menu.add(item);
31 |
32 | menu.addSeparator();
33 | }
34 |
35 | if (application.getHelpAction() != null) {
36 | item = new JMenuItem(application.getHelpAction());
37 | menu.add(item);
38 |
39 | menu.addSeparator();
40 | }
41 |
42 | if (application.getWebsiteAction() != null) {
43 | item = new JMenuItem("Website");
44 | }
45 | }
46 |
47 | public int getPreferredAlignment() {
48 | return RIGHT;
49 | }
50 |
51 | }
52 |
--------------------------------------------------------------------------------
/src/org/virion/jam/controlpanels/ControlsProvider.java:
--------------------------------------------------------------------------------
1 | package org.virion.jam.controlpanels;
2 |
3 | import java.util.List;
4 |
5 | /**
6 | * @author Andrew Rambaut
7 | * @version $Id: ControlsProvider.java 548 2006-11-30 01:43:31Z pepster $
8 | */
9 | public interface ControlsProvider {
10 | /**
11 | * Give the controls provider with a handle for the controlPalette object.
12 | *
13 | * @param controlPalette
14 | */
15 | void setControlPalette(ControlPalette controlPalette);
16 |
17 | /**
18 | * Get a list of Controls handled by this provider.
19 | *
20 | * @param detachPrimaryCheckbox When false, do nothing. When true, if controls have a "main" on/off switch
21 | * (implemented as a JCheckBox), that checkbox should not be included in the controls
22 | * panel but returned in {@link Controls#getPrimaryCheckbox}
23 | * @return A list of Controls
24 | */
25 | List getControls(boolean detachPrimaryCheckbox);
26 |
27 | /**
28 | * Give the provider some settings.
29 | *
30 | * @param settings
31 | */
32 | void setSettings(ControlsSettings settings);
33 |
34 | /**
35 | * Get the settings for a given Controls object.
36 | *
37 | * @param settings
38 | */
39 | void getSettings(ControlsSettings settings);
40 | }
41 |
--------------------------------------------------------------------------------
/src/org/virion/jam/framework/DefaultHelpMenuFactory.java:
--------------------------------------------------------------------------------
1 | /*
2 | * Copyright (c) 2005 Biomatters LTD. All Rights Reserved.
3 | */
4 | package org.virion.jam.framework;
5 |
6 | import javax.swing.*;
7 | import java.awt.event.KeyEvent;
8 |
9 | /**
10 | * @author rambaut
11 | * Date: Dec 26, 2004
12 | * Time: 11:02:20 AM
13 | */
14 | public class DefaultHelpMenuFactory implements MenuFactory {
15 | public String getMenuName() {
16 | return "Help";
17 | }
18 |
19 | public void populateMenu(JMenu menu, AbstractFrame frame) {
20 |
21 | menu.setMnemonic('H');
22 |
23 | JMenuItem item;
24 |
25 | Application application = Application.getApplication();
26 |
27 | item = new JMenuItem(application.getAboutAction());
28 | menu.add(item);
29 |
30 | if (frame.getHelpAction() != null) {
31 | item = new JMenuItem(frame.getHelpAction());
32 | item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_SLASH, MenuBarFactory.MENU_MASK));
33 | menu.add(item);
34 |
35 | menu.addSeparator();
36 | }
37 |
38 | if (application.getHelpAction() != null) {
39 | item = new JMenuItem(application.getHelpAction());
40 | menu.add(item);
41 |
42 | menu.addSeparator();
43 | }
44 |
45 | if (application.getWebsiteAction() != null) {
46 | item = new JMenuItem("Website");
47 | }
48 | }
49 |
50 | public int getPreferredAlignment() {
51 | return RIGHT;
52 | }
53 | }
54 |
--------------------------------------------------------------------------------
/src/jade/math/fRan.java:
--------------------------------------------------------------------------------
1 | package jade.math;
2 |
3 | import java.util.Random;
4 |
5 | public class fRan {
6 | public static double fRan(double d){
7 | int RAN_IA = 16807;
8 | int RAN_IM = 2147483647;
9 | double RAN_AM = (1.0/RAN_IM);
10 | int RAN_IQ = 127773;
11 | int RAN_IR = 2836;
12 | int RAN_NTAB =32;
13 | int RAN_NDIV =(1+(RAN_IM-1)/RAN_NTAB);
14 | double RAN_EPS = 1.2e-7;
15 | double RAN_RNMX =(1.0-RAN_EPS);
16 | long seed = (new Random()).nextLong();
17 |
18 | double temp;
19 | int j;
20 | long k;
21 | long iy = 0;
22 | long [] iv = new long[RAN_NTAB];
23 |
24 | if (seed <= 0 || iy == 0) {
25 | if (-(seed) < 1)
26 | seed = 1;
27 | else
28 | seed = -(seed);
29 | for (j = RAN_NTAB+7; j >= 0; j--) {
30 | k = (seed)/RAN_IQ;
31 | seed = RAN_IA*(seed-k*RAN_IQ)-RAN_IR*k;
32 | if (seed < 0)
33 | seed += RAN_IM;
34 | if (j < RAN_NTAB)
35 | iv[j] = seed;
36 | }
37 | iy = iv[0];
38 | }
39 | k = (seed)/RAN_IQ;
40 | seed = RAN_IA*(seed-k*RAN_IQ)-RAN_IR*k;
41 | if (seed < 0)
42 | seed += RAN_IM;
43 | j = (int)iy/RAN_NDIV;//(int)
44 | iy = iv[j];
45 | iv[j] = seed;
46 | if ((temp=RAN_AM*iy) > RAN_RNMX)
47 | return d*RAN_RNMX;
48 | else
49 | return d*temp;
50 | }
51 | public static void main(String [] args){
52 | for(int i=0;i<1000;i++){
53 | System.out.println((fRan.fRan(0.1)));
54 | }
55 | }
56 |
57 | }
58 |
--------------------------------------------------------------------------------
/src/org/virion/jam/demo/menus/DemoMenuFactory.java:
--------------------------------------------------------------------------------
1 | /*
2 | * Copyright (c) 2005 Your Corporation. All Rights Reserved.
3 | */
4 | package org.virion.jam.demo.menus;
5 |
6 | import org.virion.jam.framework.MenuFactory;
7 | import org.virion.jam.framework.AbstractFrame;
8 |
9 | import javax.swing.*;
10 |
11 | /**
12 | * @author rambaut
13 | * Date: Feb 24, 2005
14 | * Time: 5:12:11 PM
15 | */
16 | public class DemoMenuFactory implements MenuFactory {
17 |
18 | public static final String FIRST = "First";
19 | public static final String SECOND = "Second";
20 |
21 | public String getMenuName() {
22 | return "Demo";
23 | }
24 |
25 | public void populateMenu(JMenu menu, AbstractFrame frame) {
26 | JMenuItem item;
27 |
28 | if (frame instanceof DemoMenuHandler) {
29 | item = new JMenuItem(((DemoMenuHandler)frame).getFirstAction());
30 | menu.add(item);
31 |
32 | item = new JMenuItem(((DemoMenuHandler)frame).getSecondAction());
33 | menu.add(item);
34 | } else {
35 | item = new JMenuItem(FIRST);
36 | item.setEnabled(false);
37 | menu.add(item);
38 |
39 | item = new JMenuItem(SECOND);
40 | item.setEnabled(false);
41 | menu.add(item);
42 | }
43 |
44 | }
45 |
46 | public int getPreferredAlignment() {
47 | return LEFT;
48 | }
49 | }
50 |
--------------------------------------------------------------------------------
/src/org/virion/jam/util/SimpleListenerManager.java:
--------------------------------------------------------------------------------
1 | package org.virion.jam.util;
2 |
3 | import java.util.ArrayList;
4 | import java.util.List;
5 |
6 | /**
7 | * @author Richard Moir
8 | * @version $Id: SimpleListenerManager.java 636 2007-01-31 03:15:55Z matt_kearse $
9 | */
10 | public class SimpleListenerManager {
11 |
12 | private List listeners = new ArrayList();
13 |
14 | public SimpleListenerManager(SimpleListenerManager manager) {
15 | this.listeners = new ArrayList(manager.listeners);
16 | }
17 |
18 | public SimpleListenerManager() {
19 | }
20 |
21 | public synchronized void add(SimpleListener listener) {
22 | listeners.add(listener);
23 | }
24 |
25 | public synchronized void remove(SimpleListener listener) {
26 | listeners.remove(listener);
27 | }
28 |
29 |
30 | /**
31 | * calls {@link org.virion.jam.util.SimpleListener#objectChanged()} on all listeners added using
32 | * {@link #add(SimpleListener)} .
33 | */
34 | public synchronized void fire() {
35 | for (SimpleListener simpleListener : listeners) {
36 | simpleListener.objectChanged();
37 | }
38 | }
39 |
40 | /**
41 | * Get the number of listeners (those added, but not yet removed)
42 | * @return
43 | */
44 | public synchronized int size () {
45 | return listeners.size ();
46 | }
47 | }
48 |
--------------------------------------------------------------------------------
/src/jade/math/BetaDistribution.java:
--------------------------------------------------------------------------------
1 | /*
2 | * BetaDistribution.java
3 | *
4 | * Created on August 9, 2005, 3:58 PM
5 | *
6 | * author: Stephen A. Smith
7 | */
8 |
9 | package jade.math;
10 |
11 | /**
12 | *
13 | * @author stephensmith
14 | */
15 | public class BetaDistribution implements ProbDistribution{
16 |
17 | /** Creates a new instance of BetaDistribution */
18 | public BetaDistribution( double shape1, double shape2) {
19 | alpha1 = shape1;
20 | alpha2 = shape2;
21 | norm = GammaFunction.logBeta(alpha1, alpha2);
22 | gamma1 = new GammaDistribution( alpha1, 1.0 );
23 | gamma2 = new GammaDistribution( alpha2, 1.0 );
24 | }
25 |
26 | public void setShape1(double shape1){
27 | alpha1 = shape1;
28 | }
29 | public void setShape2(double shape2){
30 | alpha2 = shape2;
31 | }
32 | public double getShape1(){ return alpha1; }
33 | public double getShape2(){ return alpha2; }
34 | public double getValue(){
35 | double y1 = gamma1.getValue();
36 | double y2 = gamma2.getValue();
37 | return y1 / (y1 + y2);
38 | }
39 |
40 | public double getPDF(double x){
41 | return x;
42 | }
43 |
44 | //private methods
45 | private double alpha1;
46 | private double alpha2;
47 | private double norm;
48 | private GammaDistribution gamma1;
49 | private GammaDistribution gamma2;
50 |
51 | }
52 |
--------------------------------------------------------------------------------
/src/jade/math/ExponentialDistribution.java:
--------------------------------------------------------------------------------
1 | /*
2 | * ExponentialDistribution.java
3 | *
4 | * Created on August 9, 2005, 3:24 PM
5 | *
6 | * author: Stephen A. Smith
7 | */
8 |
9 | package jade.math;
10 |
11 | import java.util.*;
12 | /**
13 | *
14 | * @author stephensmith
15 | */
16 | public class ExponentialDistribution implements ProbDistribution{
17 |
18 | /** Creates a new instance of ExponentialDistribution */
19 | public ExponentialDistribution() {
20 | }
21 | public ExponentialDistribution( double beta ){
22 | if(beta<=0)
23 | throw new IllegalArgumentException(" Exponential fall-off must be positive ( function was sent a negative value ) ");
24 | else
25 | this.beta = beta;
26 | }
27 | /**
28 | *@param beta the falloff value for the exponential distribution
29 | */
30 | public void setFallOff( double beta ){
31 | this.beta = beta;
32 | }
33 |
34 | public double getFallOff(){ return beta; }
35 |
36 | public double getValue(){
37 | return -beta * Math.log(r.nextDouble());
38 | }
39 |
40 | //
41 | //probability of finding something smaller than x
42 | //@return the intregral of the probability distribution function from 0 to x
43 | public double getPDF(double x){
44 | return (1/beta)*Math.exp(-(1/beta)*x);
45 | }
46 | private double beta;
47 | private Random r = new Random();
48 | }
49 |
--------------------------------------------------------------------------------
/src/jebl/evolution/sequences/Sequence.java:
--------------------------------------------------------------------------------
1 | /*
2 | * Sequence.java
3 | *
4 | * (c) 2002-2005 JEBL Development Core Team
5 | *
6 | * This package may be distributed under the
7 | * Lesser Gnu Public Licence (LGPL)
8 | */
9 | package jebl.evolution.sequences;
10 |
11 | import jebl.evolution.taxa.Taxon;
12 | import jebl.util.Attributable;
13 |
14 | /**
15 | * A biomolecular sequence.
16 | *
17 | * @author Andrew Rambaut
18 | * @author Alexei Drummond
19 | *
20 | * @version $Id: Sequence.java 365 2006-06-28 07:34:56Z pepster $
21 | */
22 | public interface Sequence extends Attributable, Comparable {
23 |
24 | /**
25 | * @return the taxon that this sequence represents (primarily used to match sequences with tree nodes)
26 | */
27 | Taxon getTaxon();
28 |
29 | /**
30 | * @return the type of symbols that this sequence is made up of.
31 | */
32 | SequenceType getSequenceType();
33 |
34 | /**
35 | * @return a string representing the sequence of symbols.
36 | */
37 | String getString();
38 |
39 | /**
40 | * @return an array of state objects.
41 | */
42 | State[] getStates();
43 |
44 | /**
45 | * @return an array of state indices.
46 | */
47 | byte[] getStateIndices();
48 |
49 | /**
50 | * @return the state at site.
51 | */
52 | State getState(int site);
53 |
54 | /**
55 | * Get the length of the sequence
56 | * @return the length
57 | */
58 | int getLength();
59 | }
60 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/AlignLinearSpaceAffine.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align;
2 |
3 | import jebl.evolution.align.scores.Scores;
4 |
5 | // Alignment with affine gap costs; smart linear-space algorithm
6 |
7 | abstract class AlignLinearSpaceAffine extends AlignAffine {
8 |
9 | float[][][] F; // the matrices used to compute the alignment
10 |
11 | public AlignLinearSpaceAffine(Scores sub, float openGapPenalty, float extendGapPenalty) {
12 | super(sub, openGapPenalty, extendGapPenalty);
13 | }
14 |
15 | /**
16 | * Performs the alignment. Abstract.
17 | *
18 | * @param sq1
19 | * @param sq2
20 | */
21 | public abstract void doAlignment(String sq1, String sq2);
22 |
23 | public void prepareAlignment(String sq1, String sq2) {
24 | this.n = sq1.length(); this.m = sq2.length();
25 | this.seq1 = sq1;
26 | this.seq2 = sq2;
27 | F = new float[3][2][m+1];
28 | }
29 |
30 | /**
31 | * Print matrix used to calculate this alignment.
32 | *
33 | * @param out Output to print to.
34 | */
35 | public void printf(Output out) {
36 | for (int k=0; k<3; k++) {
37 | out.println("F[" + k + "]:");
38 | for (int j=0; j<=m; j++) {
39 | for (int i=0; i {
26 |
27 | /**
28 | * This can be used to read one tree at a time in a loop:
29 | *
30 | * List trees = new ArrayList();
31 | * while (hasTree()) {
32 | * trees.add(importNextTree());
33 | * }
34 | *
35 | * return whether another tree is available.
36 | */
37 | boolean hasTree() throws IOException, ImportException;
38 |
39 | /**
40 | * Import a single tree
41 | * @return the tree
42 | * @throws IOException
43 | * @throws ImportException
44 | */
45 | Tree importNextTree() throws IOException, ImportException;
46 |
47 | /**
48 | * Import all the trees
49 | * @return the list of trees
50 | * @throws IOException
51 | * @throws ImportException
52 | * Any type of tree is fine.
53 | */
54 | List importTrees() throws IOException, ImportException;
55 | }
56 |
--------------------------------------------------------------------------------
/src/jebl/evolution/sequences/NucleotideState.java:
--------------------------------------------------------------------------------
1 | /*
2 | * NucleotideState.java
3 | *
4 | * (c) 2002-2005 JEBL Development Core Team
5 | *
6 | * This package may be distributed under the
7 | * Lesser Gnu Public Licence (LGPL)
8 | */
9 | package jebl.evolution.sequences;
10 |
11 | /**
12 | * @author Andrew Rambaut
13 | * @author Alexei Drummond
14 | *
15 | * @version $Id: NucleotideState.java 267 2006-03-21 02:36:55Z twobeers $
16 | */
17 | public final class NucleotideState extends State {
18 |
19 | NucleotideState(String name, String stateCode, int index) {
20 | super(name, stateCode, index);
21 | }
22 |
23 | NucleotideState(String name, String stateCode, int index, NucleotideState[] ambiguities) {
24 | super(name, stateCode, index, ambiguities);
25 | }
26 |
27 | public int compareTo(Object o) {
28 | // throws ClassCastException on across-class comparison
29 | NucleotideState that = (NucleotideState) o;
30 | return super.compareTo(that);
31 | }
32 |
33 | // we do not need to override equals because there is only one
34 | // unique instance of each nucleotide state - i.e. we can use ==
35 | /*
36 | public boolean equals(Object o) {
37 | if (!(o instanceof NucleotideState))
38 | return false;
39 | return super.equals(o);
40 | } */
41 |
42 | public int hashCode() {
43 | return 23 * super.hashCode() + 17;
44 | }
45 |
46 | public boolean isGap() {
47 | return this == Nucleotides.GAP_STATE;
48 | }
49 | }
50 |
--------------------------------------------------------------------------------
/src/jebl/evolution/io/FastaExporter.java:
--------------------------------------------------------------------------------
1 | /*
2 | * Copyright (c) 2005 JEBL Development team. All Rights Reserved.
3 | */
4 |
5 | package jebl.evolution.io;
6 |
7 | import jebl.evolution.sequences.Sequence;
8 | import jebl.evolution.taxa.Taxon;
9 |
10 | import java.io.IOException;
11 | import java.io.PrintWriter;
12 | import java.io.Writer;
13 | import java.util.List;
14 | import java.util.Collection;
15 |
16 | /**
17 | * Class for exporting a fasta file format.
18 | *
19 | * @author Andrew Rambaut
20 | * @author Alexei Drummond
21 | * @version $Id: FastaExporter.java 442 2006-09-05 21:59:20Z matt_kearse $
22 | */
23 | public class FastaExporter implements SequenceExporter {
24 |
25 | /**
26 | * Constructor
27 | */
28 | public FastaExporter(Writer writer) {
29 | this.writer = new PrintWriter(writer);
30 | }
31 |
32 | /**
33 | * export alignment or set of sequences.
34 | */
35 | public void exportSequences(Collection sequences) throws IOException {
36 | for (Sequence sequence : sequences) {
37 | final Taxon taxon = sequence.getTaxon();
38 | String desc = (String) sequence.getAttribute(FastaImporter.descriptionPropertyName);
39 | if(desc== null) desc = (String) taxon.getAttribute(FastaImporter.descriptionPropertyName);
40 | writer.println(">" + taxon.getName().replace(' ','_') + ((desc != null) ? (" " + desc) : ""));
41 | writer.println(sequence.getString());
42 | }
43 | }
44 |
45 | private final PrintWriter writer;
46 | }
47 |
--------------------------------------------------------------------------------
/src/org/virion/jam/table/WholeNumberCellEditor.java:
--------------------------------------------------------------------------------
1 | package org.virion.jam.table;
2 |
3 | import org.virion.jam.components.WholeNumberField;
4 |
5 | import javax.swing.*;
6 | import java.awt.*;
7 | import java.awt.event.ActionEvent;
8 | import java.awt.event.ActionListener;
9 |
10 |
11 | public class WholeNumberCellEditor extends DefaultCellEditor {
12 |
13 | private WholeNumberField editor;
14 |
15 | public WholeNumberCellEditor(int minValue, int maxValue) {
16 | super(new WholeNumberField(minValue, maxValue));
17 |
18 | editor = (WholeNumberField) getComponent();
19 |
20 | setClickCountToStart(2); //This is usually 1 or 2.
21 |
22 | // Must do this so that editing stops when appropriate.
23 | editor.addActionListener(new ActionListener() {
24 | public void actionPerformed(ActionEvent e) {
25 | fireEditingStopped();
26 | }
27 | });
28 | }
29 |
30 | protected void fireEditingStopped() {
31 | super.fireEditingStopped();
32 | }
33 |
34 | public Object getCellEditorValue() {
35 | return editor.getValue();
36 | }
37 |
38 | public Component getTableCellEditorComponent(JTable table,
39 | Object value,
40 | boolean isSelected,
41 | int row,
42 | int column) {
43 | editor.setValue(((Integer) value).intValue());
44 | return editor;
45 | }
46 | }
--------------------------------------------------------------------------------
/src/jebl/math/MultivariateFunction.java:
--------------------------------------------------------------------------------
1 | // MultivariateFunction.java
2 | //
3 | // (c) 2006- JEBL development team
4 | //
5 | // based on LGPL code from the Phylogenetic Analysis Library (PAL),
6 | // http://www.cebl.auckland.ac.nz/pal-project/
7 | // which is (c) 1999-2001 PAL Development Core Team
8 | //
9 | // This package may be distributed under the
10 | // terms of the Lesser GNU General Public License (LGPL)
11 |
12 | package jebl.math;
13 |
14 |
15 | /**
16 | * interface for a function of several variables
17 | *
18 | * @author Korbinian Strimmer
19 | */
20 | public interface MultivariateFunction
21 | {
22 | /**
23 | * compute function value
24 | *
25 | * @param argument function argument (vector)
26 | *
27 | * @return function value
28 | */
29 | double evaluate(double[] argument);
30 |
31 |
32 | /**
33 | * get number of arguments
34 | *
35 | * @return number of arguments
36 | */
37 | int getNumArguments();
38 |
39 | /**
40 | * get lower bound of argument n
41 | *
42 | * @param n argument number
43 | *
44 | * @return lower bound
45 | */
46 | double getLowerBound(int n);
47 |
48 | /**
49 | * get upper bound of argument n
50 | *
51 | * @param n argument number
52 | *
53 | * @return upper bound
54 | */
55 | double getUpperBound(int n);
56 |
57 | /**
58 | * @return an Orthogonal Hints object that can be used by Orthogonal based optimisers
59 | * to get information about the function
60 | * @return if no such information just return null!
61 | */
62 | OrthogonalHints getOrthogonalHints();
63 |
64 |
65 | }
66 |
--------------------------------------------------------------------------------
/src/org/virion/jam/table/RealNumberCellEditor.java:
--------------------------------------------------------------------------------
1 | package org.virion.jam.table;
2 |
3 | import org.virion.jam.components.RealNumberField;
4 |
5 | import javax.swing.*;
6 | import java.awt.*;
7 | import java.awt.event.ActionEvent;
8 | import java.awt.event.ActionListener;
9 |
10 |
11 | public class RealNumberCellEditor extends DefaultCellEditor {
12 |
13 | private RealNumberField editor;
14 |
15 | public RealNumberCellEditor(double minValue, double maxValue) {
16 | super(new RealNumberField(minValue, maxValue));
17 |
18 | editor = (RealNumberField) getComponent();
19 |
20 | setClickCountToStart(2); //This is usually 1 or 2.
21 |
22 | // Must do this so that editing stops when appropriate.
23 | editor.addActionListener(new ActionListener() {
24 | public void actionPerformed(ActionEvent e) {
25 | fireEditingStopped();
26 | }
27 | });
28 | }
29 |
30 | protected void fireEditingStopped() {
31 | super.fireEditingStopped();
32 | }
33 |
34 | public Object getCellEditorValue() {
35 | return editor.getValue();
36 | }
37 |
38 | public Component getTableCellEditorComponent(JTable table,
39 | Object value,
40 | boolean isSelected,
41 | int row,
42 | int column) {
43 | editor.setValue(((Double) value).doubleValue());
44 | return editor;
45 | }
46 | }
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/Pam100.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | public class Pam100 extends AminoAcidScores {
4 |
5 | private final float[][] residueScores = {
6 |
7 | /* A R N D C Q E G H I L K M F P S T W Y V */
8 | { 4},
9 | { -3, 7},
10 | { -1, -2, 5},
11 | { -1, -4, 3, 5},
12 | { -3, -5, -5, -7, 9},
13 | { -2, 1, -1, 0, -8, 6},
14 | { 0, -3, 1, 4, -8, 2, 5},
15 | { 1, -5, -1, -1, -5, -3, -1, 5},
16 | { -3, 1, 2, -1, -4, 3, -1, -4, 7},
17 | { -2, -3, -3, -4, -3, -4, -3, -5, -4, 6},
18 | { -3, -5, -4, -6, -8, -2, -5, -6, -3, 1, 6},
19 | { -3, 2, 1, -1, -8, 0, -1, -3, -2, -3, -4, 5},
20 | { -2, -1, -4, -5, -7, -2, -4, -4, -4, 1, 3, 0, 9},
21 | { -5, -6, -5, -8, -7, -7, -8, -6, -3, 0, 0, -7, -1, 8},
22 | { 1, -1, -2, -3, -4, -1, -2, -2, -1, -4, -4, -3, -4, -6, 7},
23 | { 1, -1, 1, -1, -1, -2, -1, 0, -2, -3, -4, -1, -3, -4, 0, 4},
24 | { 1, -3, 0, -2, -4, -2, -2, -2, -3, 0, -3, -1, -1, -5, -1, 2, 5},
25 | { -7, 1, -5, -9, -9, -7, -9, -9, -4, -7, -3, -6, -6, -1, -7, -3, -7, 12},
26 | { -4, -6, -2, -6, -1, -6, -5, -7, -1, -3, -3, -6, -5, 4, -7, -4, -4, -2, 9},
27 | { 0, -4, -3, -4, -3, -3, -3, -3, -3, 3, 0, -4, 1, -3, -3, -2, 0, -9, -4, 5}};
28 |
29 | public Pam100() { buildScores(residueScores); }
30 | }
31 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/Pam110.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | public class Pam110 extends AminoAcidScores {
4 |
5 | private final float[][] residueScores = {
6 |
7 | /* A R N D C Q E G H I L K M F P S T W Y V */
8 | { 3},
9 | { -3, 7},
10 | { -1, -1, 4},
11 | { -1, -4, 2, 5},
12 | { -3, -4, -5, -7, 9},
13 | { -1, 1, 0, 1, -7, 6},
14 | { 0, -3, 1, 4, -7, 2, 5},
15 | { 1, -4, 0, 0, -5, -3, -1, 5},
16 | { -3, 1, 2, 0, -4, 3, -1, -4, 7},
17 | { -1, -3, -2, -3, -3, -3, -3, -4, -4, 6},
18 | { -3, -4, -4, -6, -8, -2, -5, -6, -3, 1, 6},
19 | { -3, 2, 1, -1, -7, 0, -1, -3, -2, -3, -4, 5},
20 | { -2, -1, -3, -5, -7, -1, -3, -4, -4, 1, 3, 0, 8},
21 | { -4, -5, -4, -7, -6, -6, -7, -5, -3, 0, 0, -7, -1, 8},
22 | { 1, -1, -2, -3, -4, 0, -2, -2, -1, -4, -4, -3, -4, -6, 6},
23 | { 1, -1, 1, -1, -1, -2, -1, 0, -2, -3, -4, -1, -2, -4, 0, 3},
24 | { 1, -2, 0, -1, -3, -2, -2, -2, -3, 0, -3, -1, -1, -4, -1, 2, 5},
25 | { -7, 1, -5, -8, -9, -6, -9, -8, -4, -7, -3, -5, -6, -1, -7, -3, -6, 12},
26 | { -4, -5, -2, -5, -1, -6, -5, -7, -1, -2, -3, -5, -5, 4, -7, -3, -3, -2, 8},
27 | { 0, -4, -3, -4, -3, -3, -3, -2, -3, 3, 1, -4, 1, -3, -2, -2, 0, -8, -4, 5}};
28 |
29 | public Pam110() { buildScores(residueScores); }
30 | }
31 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/Pam120.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | public class Pam120 extends AminoAcidScores {
4 |
5 | private final float[][] residueScores = {
6 |
7 | /* A R N D C Q E G H I L K M F P S T W Y V */
8 | { 3},
9 | { -3, 6},
10 | { -1, -1, 4},
11 | { 0, -3, 2, 5},
12 | { -3, -4, -5, -7, 9},
13 | { -1, 1, 0, 1, -7, 6},
14 | { 0, -3, 1, 3, -7, 2, 5},
15 | { 1, -4, 0, 0, -4, -3, -1, 5},
16 | { -3, 1, 2, 0, -4, 3, -1, -4, 7},
17 | { -1, -2, -2, -3, -3, -3, -3, -4, -4, 6},
18 | { -3, -4, -4, -5, -7, -2, -4, -5, -3, 1, 5},
19 | { -2, 2, 1, -1, -7, 0, -1, -3, -2, -3, -4, 5},
20 | { -2, -1, -3, -4, -6, -1, -3, -4, -4, 1, 3, 0, 8},
21 | { -4, -5, -4, -7, -6, -6, -7, -5, -3, 0, 0, -7, -1, 8},
22 | { 1, -1, -2, -3, -4, 0, -2, -2, -1, -3, -3, -2, -3, -5, 6},
23 | { 1, -1, 1, 0, 0, -2, -1, 1, -2, -2, -4, -1, -2, -3, 1, 3},
24 | { 1, -2, 0, -1, -3, -2, -2, -1, -3, 0, -3, -1, -1, -4, -1, 2, 4},
25 | { -7, 1, -4, -8, -8, -6, -8, -8, -3, -6, -3, -5, -6, -1, -7, -2, -6, 12},
26 | { -4, -5, -2, -5, -1, -5, -5, -6, -1, -2, -2, -5, -4, 4, -6, -3, -3, -2, 8},
27 | { 0, -3, -3, -3, -3, -3, -3, -2, -3, 3, 1, -4, 1, -3, -2, -2, 0, -8, -3, 5}};
28 |
29 | public Pam120() { buildScores(residueScores); }
30 | }
31 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/Pam130.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | public class Pam130 extends AminoAcidScores {
4 |
5 | private final float[][] residueScores = {
6 |
7 | /* A R N D C Q E G H I L K M F P S T W Y V */
8 | { 3},
9 | { -3, 6},
10 | { 0, -1, 4},
11 | { 0, -3, 2, 5},
12 | { -3, -4, -4, -6, 9},
13 | { -1, 1, 0, 1, -6, 5},
14 | { 0, -3, 1, 3, -6, 2, 5},
15 | { 1, -4, 0, 0, -4, -2, -1, 5},
16 | { -2, 1, 2, 0, -4, 3, 0, -3, 7},
17 | { -1, -2, -2, -3, -3, -3, -2, -4, -3, 5},
18 | { -3, -4, -3, -5, -7, -2, -4, -5, -3, 1, 5},
19 | { -2, 2, 1, -1, -6, 0, -1, -3, -1, -2, -4, 5},
20 | { -2, -1, -3, -4, -6, -1, -3, -4, -3, 2, 3, 0, 8},
21 | { -4, -5, -4, -7, -5, -6, -6, -5, -2, 0, 1, -6, -1, 7},
22 | { 1, -1, -1, -2, -3, 0, -2, -2, -1, -3, -3, -2, -3, -5, 6},
23 | { 1, -1, 1, 0, 0, -1, -1, 1, -2, -2, -4, -1, -2, -3, 1, 3},
24 | { 1, -2, 0, -1, -3, -2, -1, -1, -2, 0, -2, 0, -1, -4, -1, 2, 4},
25 | { -6, 1, -4, -7, -8, -6, -8, -7, -3, -6, -2, -5, -5, -1, -6, -2, -6, 12},
26 | { -4, -5, -2, -5, -1, -5, -5, -6, 0, -2, -2, -5, -4, 4, -6, -3, -3, -1, 8},
27 | { 0, -3, -3, -3, -2, -3, -3, -2, -3, 3, 1, -4, 1, -2, -2, -2, 0, -7, -3, 5}};
28 |
29 | public Pam130() { buildScores(residueScores); }
30 | }
31 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/Pam140.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | public class Pam140 extends AminoAcidScores {
4 |
5 | private final float[][] residueScores = {
6 |
7 | /* A R N D C Q E G H I L K M F P S T W Y V */
8 | { 3},
9 | { -2, 6},
10 | { 0, -1, 3},
11 | { 0, -3, 2, 4},
12 | { -2, -4, -4, -6, 9},
13 | { -1, 1, 0, 1, -6, 5},
14 | { 0, -2, 1, 3, -6, 2, 4},
15 | { 1, -4, 0, 0, -4, -2, -1, 5},
16 | { -2, 1, 2, 0, -4, 3, 0, -3, 6},
17 | { -1, -2, -2, -3, -3, -3, -2, -4, -3, 5},
18 | { -2, -4, -3, -5, -7, -2, -4, -5, -2, 1, 5},
19 | { -2, 3, 1, -1, -6, 0, -1, -3, -1, -2, -3, 5},
20 | { -2, -1, -2, -4, -6, -1, -3, -3, -3, 2, 3, 0, 7},
21 | { -4, -5, -4, -6, -5, -5, -6, -5, -2, 0, 1, -6, -1, 7},
22 | { 1, -1, -1, -2, -3, 0, -1, -1, -1, -3, -3, -2, -3, -5, 6},
23 | { 1, -1, 1, 0, 0, -1, -1, 1, -1, -2, -3, -1, -2, -3, 1, 3},
24 | { 1, -2, 0, -1, -3, -2, -1, -1, -2, 0, -2, 0, -1, -4, 0, 2, 4},
25 | { -6, 1, -4, -7, -8, -5, -8, -7, -3, -6, -2, -4, -5, -1, -6, -2, -5, 12},
26 | { -4, -5, -2, -5, -1, -5, -4, -6, 0, -2, -2, -5, -4, 4, -6, -3, -3, -1, 8},
27 | { 0, -3, -2, -3, -2, -2, -2, -2, -3, 3, 1, -3, 1, -2, -2, -2, 0, -7, -3, 5}};
28 |
29 | public Pam140() { buildScores(residueScores); }
30 | }
31 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/Pam150.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | public class Pam150 extends AminoAcidScores {
4 |
5 | private final float[][] residueScores = {
6 |
7 | /* A R N D C Q E G H I L K M F P S T W Y V */
8 | { 3},
9 | { -2, 6},
10 | { 0, -1, 3},
11 | { 0, -2, 2, 4},
12 | { -2, -4, -4, -6, 9},
13 | { -1, 1, 0, 1, -6, 5},
14 | { 0, -2, 1, 3, -6, 2, 4},
15 | { 1, -3, 0, 0, -4, -2, -1, 4},
16 | { -2, 1, 2, 0, -3, 3, 0, -3, 6},
17 | { -1, -2, -2, -3, -2, -3, -2, -3, -3, 5},
18 | { -2, -3, -3, -5, -6, -2, -4, -4, -2, 1, 5},
19 | { -2, 3, 1, -1, -6, 0, -1, -2, -1, -2, -3, 4},
20 | { -1, -1, -2, -3, -5, -1, -2, -3, -3, 2, 3, 0, 7},
21 | { -4, -4, -4, -6, -5, -5, -6, -5, -2, 0, 1, -6, -1, 7},
22 | { 1, -1, -1, -2, -3, 0, -1, -1, -1, -3, -3, -2, -3, -5, 6},
23 | { 1, -1, 1, 0, 0, -1, -1, 1, -1, -2, -3, -1, -2, -3, 1, 2},
24 | { 1, -2, 0, -1, -3, -1, -1, -1, -2, 0, -2, 0, -1, -3, 0, 1, 4},
25 | { -6, 1, -4, -7, -7, -5, -7, -7, -3, -5, -2, -4, -5, -1, -6, -2, -5, 12},
26 | { -3, -4, -2, -4, 0, -4, -4, -5, 0, -2, -2, -4, -3, 5, -5, -3, -3, -1, 8},
27 | { 0, -3, -2, -3, -2, -2, -2, -2, -3, 3, 1, -3, 1, -2, -2, -1, 0, -6, -3, 4}};
28 |
29 | public Pam150() { buildScores(residueScores); }
30 | }
31 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/Pam160.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | public class Pam160 extends AminoAcidScores {
4 |
5 | private final float[][] residueScores = {
6 |
7 | /* A R N D C Q E G H I L K M F P S T W Y V */
8 | { 2},
9 | { -2, 6},
10 | { 0, -1, 3},
11 | { 0, -2, 2, 4},
12 | { -2, -3, -4, -5, 9},
13 | { -1, 1, 0, 1, -5, 5},
14 | { 0, -2, 1, 3, -5, 2, 4},
15 | { 1, -3, 0, 0, -3, -2, 0, 4},
16 | { -2, 1, 2, 0, -3, 2, 0, -3, 6},
17 | { -1, -2, -2, -3, -2, -2, -2, -3, -3, 5},
18 | { -2, -3, -3, -4, -6, -2, -3, -4, -2, 2, 5},
19 | { -2, 3, 1, 0, -5, 0, -1, -2, -1, -2, -3, 4},
20 | { -1, -1, -2, -3, -5, -1, -2, -3, -3, 2, 3, 0, 7},
21 | { -3, -4, -3, -6, -5, -5, -5, -4, -2, 0, 1, -5, 0, 7},
22 | { 1, -1, -1, -2, -3, 0, -1, -1, -1, -2, -3, -2, -2, -4, 5},
23 | { 1, -1, 1, 0, 0, -1, 0, 1, -1, -2, -3, -1, -2, -3, 1, 2},
24 | { 1, -1, 0, -1, -2, -1, -1, -1, -2, 0, -2, 0, -1, -3, 0, 1, 3},
25 | { -5, 1, -4, -6, -7, -5, -7, -7, -3, -5, -2, -4, -4, -1, -5, -2, -5, 12},
26 | { -3, -4, -2, -4, 0, -4, -4, -5, 0, -2, -2, -4, -3, 5, -5, -3, -3, -1, 8},
27 | { 0, -3, -2, -3, -2, -2, -2, -2, -2, 3, 1, -3, 1, -2, -2, -1, 0, -6, -3, 4}};
28 |
29 | public Pam160() { buildScores(residueScores); }
30 | }
31 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/Pam170.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | public class Pam170 extends AminoAcidScores {
4 |
5 | private final float[][] residueScores = {
6 |
7 | /* A R N D C Q E G H I L K M F P S T W Y V */
8 | { 3},
9 | { -3, 8},
10 | { 0, -1, 4},
11 | { 0, -3, 3, 6},
12 | { -3, -5, -5, -7, 13},
13 | { -1, 1, 0, 2, -8, 6},
14 | { 0, -2, 2, 5, -8, 3, 6},
15 | { 1, -4, 0, 0, -5, -2, 0, 6},
16 | { -3, 2, 2, 0, -5, 4, 0, -4, 9},
17 | { -1, -3, -3, -4, -3, -3, -3, -4, -4, 7},
18 | { -3, -4, -4, -6, -9, -2, -5, -6, -3, 2, 7},
19 | { -2, 4, 1, -1, -8, 0, -1, -3, -1, -3, -4, 6},
20 | { -2, -1, -3, -4, -7, -1, -3, -4, -4, 2, 4, 1, 10},
21 | { -5, -6, -5, -8, -6, -7, -8, -6, -3, 1, 1, -8, 0, 10},
22 | { 1, -1, -1, -2, -4, 0, -1, -2, -1, -3, -4, -2, -3, -6, 8},
23 | { 2, -1, 1, 0, 0, -1, -1, 1, -2, -2, -4, -1, -2, -4, 1, 3},
24 | { 2, -2, 0, -1, -3, -2, -1, -1, -2, 0, -3, 0, -1, -5, 0, 2, 5},
25 | { -8, 2, -5, -9,-10, -7,-10, -9, -4, -7, -3, -5, -6, -1, -8, -3, -7, 18},
26 | { -5, -6, -3, -6, 0, -6, -6, -7, 0, -2, -2, -6, -4, 7, -7, -4, -4, -1, 12},
27 | { 0, -4, -3, -4, -3, -3, -3, -2, -3, 5, 2, -4, 2, -2, -2, -2, 0, -9, -4, 6}};
28 |
29 | public Pam170() { buildScores(residueScores); }
30 | }
31 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/Pam180.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | public class Pam180 extends AminoAcidScores {
4 |
5 | private final float[][] residueScores = {
6 |
7 | /* A R N D C Q E G H I L K M F P S T W Y V */
8 | { 3},
9 | { -3, 8},
10 | { 0, -1, 4},
11 | { 0, -3, 3, 5},
12 | { -3, -5, -5, -7, 13},
13 | { -1, 1, 0, 2, -7, 6},
14 | { 0, -2, 2, 4, -7, 3, 5},
15 | { 1, -4, 0, 0, -5, -2, 0, 6},
16 | { -2, 2, 2, 0, -4, 4, 0, -3, 8},
17 | { -1, -3, -3, -3, -3, -3, -3, -4, -4, 6},
18 | { -3, -4, -4, -6, -8, -2, -5, -6, -3, 2, 7},
19 | { -2, 4, 1, 0, -7, 0, -1, -3, -1, -3, -4, 6},
20 | { -2, -1, -3, -4, -7, -1, -3, -4, -3, 2, 4, 1, 9},
21 | { -5, -6, -5, -8, -6, -6, -7, -6, -3, 1, 1, -7, 0, 10},
22 | { 1, -1, -1, -2, -4, 0, -1, -1, -1, -3, -4, -2, -3, -6, 8},
23 | { 1, -1, 1, 0, 0, -1, -1, 1, -2, -2, -4, -1, -2, -4, 1, 3},
24 | { 2, -2, 0, -1, -3, -2, -1, -1, -2, 0, -3, 0, -1, -4, 0, 2, 4},
25 | { -8, 2, -5, -9,-10, -6, -9, -9, -4, -7, -3, -5, -6, 0, -7, -3, -7, 18},
26 | { -5, -6, -2, -6, 0, -6, -6, -7, 0, -2, -2, -6, -4, 7, -7, -4, -4, -1, 11},
27 | { 0, -4, -3, -3, -3, -3, -3, -2, -3, 5, 2, -4, 2, -2, -2, -2, 0, -8, -4, 6}};
28 |
29 | public Pam180() { buildScores(residueScores); }
30 | }
31 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/Pam190.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | public class Pam190 extends AminoAcidScores {
4 |
5 | private final float[][] residueScores = {
6 |
7 | /* A R N D C Q E G H I L K M F P S T W Y V */
8 | { 3},
9 | { -2, 8},
10 | { 0, -1, 3},
11 | { 0, -2, 3, 5},
12 | { -3, -5, -5, -7, 13},
13 | { -1, 1, 1, 2, -7, 6},
14 | { 0, -2, 2, 4, -7, 3, 5},
15 | { 1, -4, 0, 0, -4, -2, 0, 6},
16 | { -2, 2, 2, 0, -4, 3, 0, -3, 8},
17 | { -1, -3, -2, -3, -3, -3, -3, -4, -3, 6},
18 | { -3, -4, -4, -5, -8, -2, -4, -5, -3, 2, 7},
19 | { -2, 4, 1, 0, -7, 1, -1, -3, -1, -3, -4, 6},
20 | { -2, -1, -3, -4, -7, -1, -3, -4, -3, 2, 4, 1, 9},
21 | { -5, -6, -4, -7, -6, -6, -7, -6, -2, 1, 2, -7, 0, 10},
22 | { 1, 0, -1, -2, -4, 0, -1, -1, -1, -3, -3, -2, -3, -6, 7},
23 | { 1, -1, 1, 0, 0, -1, 0, 1, -1, -2, -4, 0, -2, -4, 1, 3},
24 | { 2, -2, 0, -1, -3, -1, -1, -1, -2, 0, -2, 0, -1, -4, 0, 2, 4},
25 | { -7, 2, -5, -8, -9, -6, -9, -9, -3, -7, -3, -5, -6, 0, -7, -3, -6, 18},
26 | { -4, -5, -2, -5, 0, -5, -5, -7, 0, -2, -2, -6, -4, 7, -6, -4, -3, -1, 11},
27 | { 0, -3, -3, -3, -3, -3, -3, -2, -3, 4, 2, -3, 2, -2, -2, -2, 0, -8, -3, 6}};
28 |
29 | public Pam190() { buildScores(residueScores); }
30 | }
31 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/Pam200.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | public class Pam200 extends AminoAcidScores {
4 |
5 | private final float[][] residueScores = {
6 |
7 | /* A R N D C Q E G H I L K M F P S T W Y V */
8 | { 3},
9 | { -2, 7},
10 | { 0, 0, 3},
11 | { 0, -2, 3, 5},
12 | { -3, -4, -5, -6, 12},
13 | { -1, 1, 1, 2, -7, 5},
14 | { 0, -2, 2, 4, -7, 3, 5},
15 | { 1, -4, 0, 0, -4, -2, 0, 6},
16 | { -2, 2, 2, 0, -4, 3, 0, -3, 8},
17 | { -1, -2, -2, -3, -3, -3, -3, -3, -3, 6},
18 | { -2, -4, -4, -5, -7, -2, -4, -5, -3, 2, 7},
19 | { -2, 4, 1, 0, -7, 1, 0, -2, -1, -2, -4, 6},
20 | { -2, -1, -2, -4, -6, -1, -3, -4, -3, 2, 4, 1, 8},
21 | { -4, -5, -4, -7, -6, -6, -7, -6, -2, 1, 2, -7, 0, 10},
22 | { 1, 0, -1, -2, -4, 0, -1, -1, -1, -3, -3, -2, -3, -6, 7},
23 | { 1, -1, 1, 0, 0, -1, 0, 1, -1, -2, -4, 0, -2, -4, 1, 2},
24 | { 1, -1, 0, 0, -3, -1, -1, 0, -2, 0, -2, 0, -1, -4, 0, 2, 4},
25 | { -7, 2, -5, -8, -9, -6, -9, -8, -3, -6, -2, -4, -5, 0, -7, -3, -6, 18},
26 | { -4, -5, -2, -5, 0, -5, -5, -6, 0, -2, -2, -5, -3, 7, -6, -3, -3, -1, 11},
27 | { 0, -3, -2, -3, -2, -3, -2, -2, -3, 4, 2, -3, 2, -2, -2, -1, 0, -8, -3, 5}};
28 |
29 | public Pam200() { buildScores(residueScores); }
30 | }
31 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/Pam210.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | public class Pam210 extends AminoAcidScores {
4 |
5 | private final float[][] residueScores = {
6 |
7 | /* A R N D C Q E G H I L K M F P S T W Y V */
8 | { 2},
9 | { -2, 7},
10 | { 0, 0, 3},
11 | { 0, -2, 2, 5},
12 | { -2, -4, -4, -6, 12},
13 | { -1, 1, 1, 2, -6, 5},
14 | { 0, -2, 2, 4, -6, 3, 5},
15 | { 1, -3, 0, 0, -4, -2, 0, 5},
16 | { -2, 2, 2, 1, -4, 3, 0, -3, 8},
17 | { -1, -2, -2, -3, -3, -3, -2, -3, -3, 5},
18 | { -2, -4, -3, -5, -7, -2, -4, -5, -2, 2, 7},
19 | { -2, 4, 1, 0, -6, 1, 0, -2, 0, -2, -3, 5},
20 | { -1, -1, -2, -3, -6, -1, -3, -3, -3, 2, 4, 1, 8},
21 | { -4, -5, -4, -7, -5, -6, -6, -5, -2, 1, 2, -6, 0, 10},
22 | { 1, 0, -1, -1, -3, 0, -1, -1, 0, -3, -3, -2, -3, -5, 7},
23 | { 1, 0, 1, 0, 0, -1, 0, 1, -1, -2, -3, 0, -2, -4, 1, 2},
24 | { 1, -1, 0, 0, -3, -1, -1, 0, -2, 0, -2, 0, -1, -4, 0, 2, 3},
25 | { -7, 2, -5, -8, -9, -6, -8, -8, -3, -6, -2, -4, -5, 0, -7, -3, -6, 18},
26 | { -4, -5, -2, -5, 0, -5, -5, -6, 0, -1, -1, -5, -3, 7, -6, -3, -3, -1, 11},
27 | { 0, -3, -2, -3, -2, -2, -2, -2, -3, 4, 2, -3, 2, -2, -2, -1, 0, -7, -3, 5}};
28 |
29 | public Pam210() { buildScores(residueScores); }
30 | }
31 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/Pam220.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | public class Pam220 extends AminoAcidScores {
4 |
5 | private final float[][] residueScores = {
6 |
7 | /* A R N D C Q E G H I L K M F P S T W Y V */
8 | { 2},
9 | { -2, 7},
10 | { 0, 0, 3},
11 | { 0, -2, 2, 4},
12 | { -2, -4, -4, -6, 12},
13 | { -1, 1, 1, 2, -6, 5},
14 | { 0, -1, 2, 4, -6, 3, 4},
15 | { 1, -3, 0, 0, -4, -2, 0, 5},
16 | { -2, 2, 2, 1, -4, 3, 1, -3, 7},
17 | { -1, -2, -2, -3, -3, -2, -2, -3, -3, 5},
18 | { -2, -3, -3, -5, -7, -2, -4, -5, -2, 2, 6},
19 | { -1, 4, 1, 0, -6, 1, 0, -2, 0, -2, -3, 5},
20 | { -1, -1, -2, -3, -6, -1, -2, -3, -3, 2, 4, 1, 8},
21 | { -4, -5, -4, -6, -5, -5, -6, -5, -2, 1, 2, -6, 0, 10},
22 | { 1, 0, -1, -1, -3, 0, -1, -1, 0, -2, -3, -1, -2, -5, 7},
23 | { 1, 0, 1, 0, 0, -1, 0, 1, -1, -2, -3, 0, -2, -4, 1, 2},
24 | { 1, -1, 0, 0, -3, -1, -1, 0, -2, 0, -2, 0, -1, -4, 0, 2, 3},
25 | { -6, 2, -4, -8, -8, -5, -8, -8, -3, -6, -2, -4, -5, 0, -6, -3, -6, 17},
26 | { -4, -5, -2, -5, 0, -5, -5, -6, 0, -1, -1, -5, -3, 7, -6, -3, -3, 0, 11},
27 | { 0, -3, -2, -3, -2, -2, -2, -2, -3, 4, 2, -3, 2, -2, -1, -1, 0, -7, -3, 5}};
28 |
29 | public Pam220() { buildScores(residueScores); }
30 | }
31 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/Pam230.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | public class Pam230 extends AminoAcidScores {
4 |
5 | private final float[][] residueScores = {
6 |
7 | /* A R N D C Q E G H I L K M F P S T W Y V */
8 | { 2},
9 | { -2, 7},
10 | { 0, 0, 2},
11 | { 0, -2, 2, 4},
12 | { -2, -4, -4, -6, 12},
13 | { -1, 1, 1, 2, -6, 5},
14 | { 0, -1, 1, 4, -6, 3, 4},
15 | { 1, -3, 0, 1, -4, -1, 0, 5},
16 | { -2, 2, 2, 1, -4, 3, 1, -2, 7},
17 | { -1, -2, -2, -3, -2, -2, -2, -3, -3, 5},
18 | { -2, -3, -3, -4, -7, -2, -4, -4, -2, 2, 6},
19 | { -1, 4, 1, 0, -6, 1, 0, -2, 0, -2, -3, 5},
20 | { -1, -1, -2, -3, -6, -1, -2, -3, -2, 2, 4, 0, 7},
21 | { -4, -5, -4, -6, -5, -5, -6, -5, -2, 1, 2, -6, 0, 9},
22 | { 1, 0, -1, -1, -3, 0, -1, -1, 0, -2, -3, -1, -2, -5, 6},
23 | { 1, 0, 1, 0, 0, -1, 0, 1, -1, -2, -3, 0, -2, -3, 1, 2},
24 | { 1, -1, 0, 0, -2, -1, -1, 0, -2, 0, -2, 0, -1, -3, 0, 2, 3},
25 | { -6, 2, -4, -7, -8, -5, -8, -7, -3, -6, -2, -4, -5, 0, -6, -3, -6, 17},
26 | { -4, -5, -2, -5, 0, -4, -5, -6, 0, -1, -1, -5, -3, 7, -5, -3, -3, 0, 10},
27 | { 0, -3, -2, -2, -2, -2, -2, -2, -2, 4, 2, -3, 2, -1, -1, -1, 0, -7, -3, 5}};
28 |
29 | public Pam230() { buildScores(residueScores); }
30 | }
31 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/Pam240.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | public class Pam240 extends AminoAcidScores {
4 |
5 | private final float[][] residueScores = {
6 |
7 | /* A R N D C Q E G H I L K M F P S T W Y V */
8 | { 2},
9 | { -2, 6},
10 | { 0, 0, 2},
11 | { 0, -1, 2, 4},
12 | { -2, -4, -4, -5, 12},
13 | { 0, 1, 1, 2, -6, 4},
14 | { 0, -1, 1, 4, -6, 3, 4},
15 | { 1, -3, 0, 1, -4, -1, 0, 5},
16 | { -1, 2, 2, 1, -4, 3, 1, -2, 7},
17 | { -1, -2, -2, -2, -2, -2, -2, -3, -3, 5},
18 | { -2, -3, -3, -4, -6, -2, -3, -4, -2, 2, 6},
19 | { -1, 3, 1, 0, -6, 1, 0, -2, 0, -2, -3, 5},
20 | { -1, 0, -2, -3, -5, -1, -2, -3, -2, 2, 4, 0, 7},
21 | { -4, -5, -4, -6, -5, -5, -6, -5, -2, 1, 2, -5, 0, 9},
22 | { 1, 0, -1, -1, -3, 0, -1, -1, 0, -2, -3, -1, -2, -5, 6},
23 | { 1, 0, 1, 0, 0, -1, 0, 1, -1, -1, -3, 0, -2, -3, 1, 2},
24 | { 1, -1, 0, 0, -2, -1, 0, 0, -1, 0, -2, 0, -1, -3, 0, 1, 3},
25 | { -6, 2, -4, -7, -8, -5, -7, -7, -3, -5, -2, -4, -4, 0, -6, -3, -5, 17},
26 | { -4, -4, -2, -4, 0, -4, -4, -5, 0, -1, -1, -5, -3, 7, -5, -3, -3, 0, 10},
27 | { 0, -3, -2, -2, -2, -2, -2, -1, -2, 4, 2, -3, 2, -1, -1, -1, 0, -6, -3, 4}};
28 |
29 | public Pam240() { buildScores(residueScores); }
30 | }
31 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/Pam250.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | public class Pam250 extends AminoAcidScores {
4 |
5 | private final float[][] residueScores = {
6 |
7 | /* A R N D C Q E G H I L K M F P S T W Y V */
8 | { 2},
9 | { -2, 6},
10 | { 0, 0, 2},
11 | { 0, -1, 2, 4},
12 | { -2, -4, -4, -5, 12},
13 | { 0, 1, 1, 2, -5, 4},
14 | { 0, -1, 1, 3, -5, 2, 4},
15 | { 1, -3, 0, 1, -3, -1, 0, 5},
16 | { -1, 2, 2, 1, -3, 3, 1, -2, 6},
17 | { -1, -2, -2, -2, -2, -2, -2, -3, -2, 5},
18 | { -2, -3, -3, -4, -6, -2, -3, -4, -2, 2, 6},
19 | { -1, 3, 1, 0, -5, 1, 0, -2, 0, -2, -3, 5},
20 | { -1, 0, -2, -3, -5, -1, -2, -3, -2, 2, 4, 0, 6},
21 | { -3, -4, -3, -6, -4, -5, -5, -5, -2, 1, 2, -5, 0, 9},
22 | { 1, 0, 0, -1, -3, 0, -1, 0, 0, -2, -3, -1, -2, -5, 6},
23 | { 1, 0, 1, 0, 0, -1, 0, 1, -1, -1, -3, 0, -2, -3, 1, 2},
24 | { 1, -1, 0, 0, -2, -1, 0, 0, -1, 0, -2, 0, -1, -3, 0, 1, 3},
25 | { -6, 2, -4, -7, -8, -5, -7, -7, -3, -5, -2, -3, -4, 0, -6, -2, -5, 17},
26 | { -3, -4, -2, -4, 0, -4, -4, -5, 0, -1, -1, -4, -2, 7, -5, -3, -3, 0, 10},
27 | { 0, -2, -2, -2, -2, -2, -2, -1, -2, 4, 2, -2, 2, -1, -1, -1, 0, -6, -2, 4}};
28 |
29 | public Pam250() { buildScores(residueScores); }
30 | }
31 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/Blosum55.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | public class Blosum55 extends AminoAcidScores {
4 |
5 | private final float[][] residueScores = {
6 |
7 | /* A R N D C Q E G H I L K M F P S T W Y V */
8 | { 5},
9 | { -2, 8},
10 | { -2, -1, 8},
11 | { -2, -2, 2, 8},
12 | { 0, -4, -3, -4, 13},
13 | { -1, 1, 0, 0, -4, 7},
14 | { -1, 0, 0, 2, -4, 2, 7},
15 | { 0, -3, 0, -2, -3, -2, -3, 8},
16 | { -2, 0, 1, -1, -4, 1, -1, -2, 11},
17 | { -2, -4, -4, -4, -2, -4, -4, -5, -4, 6},
18 | { -2, -3, -4, -5, -2, -3, -4, -5, -3, 2, 6},
19 | { -1, 3, 0, -1, -4, 2, 1, -2, 0, -4, -3, 6},
20 | { -1, -2, -3, -4, -2, 0, -3, -3, -2, 2, 3, -2, 8},
21 | { -3, -3, -4, -5, -3, -4, -4, -4, -1, 0, 1, -4, 0, 9},
22 | { -1, -3, -2, -2, -3, -1, -1, -3, -3, -3, -4, -1, -3, -5, 10},
23 | { 2, -1, 1, 0, -1, 0, 0, 0, -1, -3, -3, 0, -2, -3, -1, 5},
24 | { 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -2, -1, -1, -3, -1, 2, 6},
25 | { -4, -3, -5, -5, -4, -2, -3, -3, -3, -3, -3, -4, -2, 2, -5, -4, -3, 15},
26 | { -2, -2, -2, -3, -3, -1, -2, -4, 2, -1, -1, -2, -1, 4, -4, -2, -2, 3, 9},
27 | { 0, -3, -4, -4, -1, -3, -3, -4, -4, 4, 1, -3, 1, -1, -3, -2, 0, -4, -2, 5}};
28 |
29 | public Blosum55() { buildScores(residueScores); }
30 | }
31 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/Blosum60.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | public class Blosum60 extends AminoAcidScores {
4 |
5 | private final float[][] residueScores = {
6 |
7 | /* A R N D C Q E G H I L K M F P S T W Y V */
8 | { 4},
9 | { -1, 5},
10 | { -1, 0, 6},
11 | { -2, -1, 1, 6},
12 | { 0, -3, -2, -3, 9},
13 | { -1, 1, 0, 0, -3, 5},
14 | { -1, 0, 0, 2, -3, 2, 5},
15 | { 0, -2, 0, -1, -2, -2, -2, 6},
16 | { -2, 0, 1, -1, -3, 1, 0, -2, 7},
17 | { -1, -3, -3, -3, -1, -3, -3, -3, -3, 4},
18 | { -1, -2, -3, -3, -1, -2, -3, -4, -3, 2, 4},
19 | { -1, 2, 0, -1, -3, 1, 1, -1, -1, -3, -2, 4},
20 | { -1, -1, -2, -3, -1, 0, -2, -2, -1, 1, 2, -1, 5},
21 | { -2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6},
22 | { -1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7},
23 | { 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4},
24 | { 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 4},
25 | { -3, -3, -4, -4, -2, -2, -3, -2, -2, -2, -2, -3, -1, 1, -4, -3, -2, 10},
26 | { -2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 6},
27 | { 0, -2, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4}};
28 |
29 | public Blosum60() { buildScores(residueScores); }
30 | }
31 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/Blosum62.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | public class Blosum62 extends AminoAcidScores {
4 |
5 | private final float[][] residueScores = {
6 |
7 | /* A R N D C Q E G H I L K M F P S T W Y V */
8 | { 4},
9 | { -1, 5},
10 | { -2, 0, 6},
11 | { -2, -2, 1, 6},
12 | { 0, -3, -3, -3, 9},
13 | { -1, 1, 0, 0, -3, 5},
14 | { -1, 0, 0, 2, -4, 2, 5},
15 | { 0, -2, 0, -1, -3, -2, -2, 6},
16 | { -2, 0, 1, -1, -3, 0, 0, -2, 8},
17 | { -1, -3, -3, -3, -1, -3, -3, -4, -3, 4},
18 | { -1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4},
19 | { -1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5},
20 | { -1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5},
21 | { -2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6},
22 | { -1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7},
23 | { 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4},
24 | { 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5},
25 | { -3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11},
26 | { -2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7},
27 | { 0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4}};
28 |
29 | public Blosum62() { buildScores(residueScores); }
30 | }
31 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/Blosum65.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | public class Blosum65 extends AminoAcidScores {
4 |
5 | private final float[][] residueScores = {
6 |
7 | /* A R N D C Q E G H I L K M F P S T W Y V */
8 | { 4},
9 | { -1, 6},
10 | { -2, 0, 6},
11 | { -2, -2, 1, 6},
12 | { 0, -4, -3, -4, 9},
13 | { -1, 1, 0, 0, -3, 6},
14 | { -1, 0, 0, 2, -4, 2, 5},
15 | { 0, -2, -1, -1, -3, -2, -2, 6},
16 | { -2, 0, 1, -1, -3, 1, 0, -2, 8},
17 | { -1, -3, -3, -3, -1, -3, -3, -4, -3, 4},
18 | { -2, -2, -4, -4, -1, -2, -3, -4, -3, 2, 4},
19 | { -1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -3, 5},
20 | { -1, -2, -2, -3, -2, 0, -2, -3, -2, 1, 2, -2, 6},
21 | { -2, -3, -3, -4, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6},
22 | { -1, -2, -2, -2, -3, -1, -1, -2, -2, -3, -3, -1, -3, -4, 8},
23 | { 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -3, 0, -2, -2, -1, 4},
24 | { 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5},
25 | { -3, -3, -4, -5, -2, -2, -3, -3, -2, -2, -2, -3, -2, 1, -4, -3, -3, 10},
26 | { -2, -2, -2, -3, -2, -2, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7},
27 | { 0, -3, -3, -3, -1, -2, -3, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4}};
28 |
29 | public Blosum65() { buildScores(residueScores); }
30 | }
31 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/Blosum70.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | public class Blosum70 extends AminoAcidScores {
4 |
5 | private final float[][] residueScores = {
6 |
7 | /* A R N D C Q E G H I L K M F P S T W Y V */
8 | { 4},
9 | { -2, 6},
10 | { -2, -1, 6},
11 | { -2, -2, 1, 6},
12 | { -1, -4, -3, -4, 9},
13 | { -1, 1, 0, -1, -3, 6},
14 | { -1, 0, 0, 1, -4, 2, 5},
15 | { 0, -3, -1, -2, -3, -2, -2, 6},
16 | { -2, 0, 0, -1, -4, 1, 0, -2, 8},
17 | { -2, -3, -4, -4, -1, -3, -4, -4, -4, 4},
18 | { -2, -3, -4, -4, -2, -2, -3, -4, -3, 2, 4},
19 | { -1, 2, 0, -1, -4, 1, 1, -2, -1, -3, -3, 5},
20 | { -1, -2, -2, -3, -2, 0, -2, -3, -2, 1, 2, -2, 6},
21 | { -2, -3, -3, -4, -2, -3, -4, -4, -1, 0, 0, -3, 0, 6},
22 | { -1, -2, -2, -2, -3, -2, -1, -3, -2, -3, -3, -1, -3, -4, 8},
23 | { 1, -1, 0, 0, -1, 0, 0, -1, -1, -3, -3, 0, -2, -3, -1, 4},
24 | { 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -2, -1, -1, -2, -1, 1, 5},
25 | { -3, -3, -4, -5, -3, -2, -4, -3, -2, -3, -2, -3, -2, 1, -4, -3, -3, 11},
26 | { -2, -2, -2, -4, -3, -2, -3, -4, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7},
27 | { 0, -3, -3, -4, -1, -2, -3, -4, -3, 3, 1, -3, 1, -1, -3, -2, 0, -3, -2, 4}};
28 |
29 | public Blosum70() { buildScores(residueScores); }
30 | }
31 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/Blosum75.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | public class Blosum75 extends AminoAcidScores {
4 |
5 | private final float[][] residueScores = {
6 |
7 | /* A R N D C Q E G H I L K M F P S T W Y V */
8 | { 4},
9 | { -2, 6},
10 | { -2, -1, 6},
11 | { -2, -2, 1, 6},
12 | { -1, -4, -3, -4, 9},
13 | { -1, 1, 0, -1, -3, 6},
14 | { -1, 0, -1, 1, -5, 2, 5},
15 | { 0, -3, -1, -2, -3, -2, -3, 6},
16 | { -2, 0, 0, -1, -4, 1, 0, -2, 8},
17 | { -2, -3, -4, -4, -1, -3, -4, -5, -4, 4},
18 | { -2, -3, -4, -4, -2, -3, -4, -4, -3, 1, 4},
19 | { -1, 2, 0, -1, -4, 1, 1, -2, -1, -3, -3, 5},
20 | { -1, -2, -3, -4, -2, 0, -2, -3, -2, 1, 2, -2, 6},
21 | { -3, -3, -4, -4, -2, -4, -4, -4, -2, 0, 0, -4, 0, 6},
22 | { -1, -2, -3, -2, -4, -2, -1, -3, -2, -3, -3, -1, -3, -4, 8},
23 | { 1, -1, 0, -1, -1, 0, 0, -1, -1, -3, -3, 0, -2, -3, -1, 5},
24 | { 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -2, -1, -1, -2, -1, 1, 5},
25 | { -3, -3, -4, -5, -3, -2, -4, -3, -2, -3, -2, -4, -2, 1, -5, -3, -3, 11},
26 | { -2, -2, -3, -4, -3, -2, -3, -4, 2, -2, -1, -2, -2, 3, -4, -2, -2, 2, 7},
27 | { 0, -3, -3, -4, -1, -2, -3, -4, -4, 3, 1, -3, 1, -1, -3, -2, 0, -3, -2, 4}};
28 |
29 | public Blosum75() { buildScores(residueScores); }
30 | }
31 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/Blosum80.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | public class Blosum80 extends AminoAcidScores {
4 |
5 | private final float[][] residueScores = {
6 |
7 | /* A R N D C Q E G H I L K M F P S T W Y V */
8 | { 7},
9 | { -3, 9},
10 | { -3, -1, 9},
11 | { -3, -3, 2, 10},
12 | { -1, -6, -5, -7, 13},
13 | { -2, 1, 0, -1, -5, 9},
14 | { -2, -1, -1, 2, -7, 3, 8},
15 | { 0, -4, -1, -3, -6, -4, -4, 9},
16 | { -3, 0, 1, -2, -7, 1, 0, -4, 12},
17 | { -3, -5, -6, -7, -2, -5, -6, -7, -6, 7},
18 | { -3, -4, -6, -7, -3, -4, -6, -7, -5, 2, 6},
19 | { -1, 3, 0, -2, -6, 2, 1, -3, -1, -5, -4, 8},
20 | { -2, -3, -4, -6, -3, -1, -4, -5, -4, 2, 3, -3, 9},
21 | { -4, -5, -6, -6, -4, -5, -6, -6, -2, -1, 0, -5, 0, 10},
22 | { -1, -3, -4, -3, -6, -3, -2, -5, -4, -5, -5, -2, -4, -6, 12},
23 | { 2, -2, 1, -1, -2, -1, -1, -1, -2, -4, -4, -1, -3, -4, -2, 7},
24 | { 0, -2, 0, -2, -2, -1, -2, -3, -3, -2, -3, -1, -1, -4, -3, 2, 8},
25 | { -5, -5, -7, -8, -5, -4, -6, -6, -4, -5, -4, -6, -3, 0, -7, -6, -5, 16},
26 | { -4, -4, -4, -6, -5, -3, -5, -6, 3, -3, -2, -4, -3, 4, -6, -3, -3, 3, 11},
27 | { -1, -4, -5, -6, -2, -4, -4, -6, -5, 4, 1, -4, 1, -2, -4, -3, 0, -5, -3, 7}};
28 |
29 | public Blosum80() { buildScores(residueScores); }
30 | }
31 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/Blosum85.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | public class Blosum85 extends AminoAcidScores {
4 |
5 | private final float[][] residueScores = {
6 |
7 | /* A R N D C Q E G H I L K M F P S T W Y V */
8 | { 5},
9 | { -2, 6},
10 | { -2, -1, 7},
11 | { -2, -2, 1, 7},
12 | { -1, -4, -4, -5, 9},
13 | { -1, 1, 0, -1, -4, 6},
14 | { -1, -1, -1, 1, -5, 2, 6},
15 | { 0, -3, -1, -2, -4, -3, -3, 6},
16 | { -2, 0, 0, -2, -5, 1, -1, -3, 8},
17 | { -2, -4, -4, -5, -2, -4, -4, -5, -4, 5},
18 | { -2, -3, -4, -5, -2, -3, -4, -5, -3, 1, 4},
19 | { -1, 2, 0, -1, -4, 1, 0, -2, -1, -3, -3, 6},
20 | { -2, -2, -3, -4, -2, 0, -3, -4, -3, 1, 2, -2, 7},
21 | { -3, -4, -4, -4, -3, -4, -4, -4, -2, -1, 0, -4, -1, 7},
22 | { -1, -2, -3, -2, -4, -2, -2, -3, -3, -4, -4, -2, -3, -4, 8},
23 | { 1, -1, 0, -1, -2, -1, -1, -1, -1, -3, -3, -1, -2, -3, -1, 5},
24 | { 0, -2, 0, -2, -2, -1, -1, -2, -2, -1, -2, -1, -1, -3, -2, 1, 5},
25 | { -3, -4, -5, -6, -4, -3, -4, -4, -3, -3, -3, -5, -2, 0, -5, -4, -4, 11},
26 | { -3, -3, -3, -4, -3, -2, -4, -5, 2, -2, -2, -3, -2, 3, -4, -2, -2, 2, 7},
27 | { -1, -3, -4, -4, -1, -3, -3, -4, -4, 3, 0, -3, 0, -1, -3, -2, 0, -3, -2, 5}};
28 |
29 | public Blosum85() { buildScores(residueScores); }
30 | }
31 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/Blosum90.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | public class Blosum90 extends AminoAcidScores {
4 |
5 | private final float[][] residueScores = {
6 |
7 | /* A R N D C Q E G H I L K M F P S T W Y V */
8 | { 5},
9 | { -2, 6},
10 | { -2, -1, 7},
11 | { -3, -3, 1, 7},
12 | { -1, -5, -4, -5, 9},
13 | { -1, 1, 0, -1, -4, 7},
14 | { -1, -1, -1, 1, -6, 2, 6},
15 | { 0, -3, -1, -2, -4, -3, -3, 6},
16 | { -2, 0, 0, -2, -5, 1, -1, -3, 8},
17 | { -2, -4, -4, -5, -2, -4, -4, -5, -4, 5},
18 | { -2, -3, -4, -5, -2, -3, -4, -5, -4, 1, 5},
19 | { -1, 2, 0, -1, -4, 1, 0, -2, -1, -4, -3, 6},
20 | { -2, -2, -3, -4, -2, 0, -3, -4, -3, 1, 2, -2, 7},
21 | { -3, -4, -4, -5, -3, -4, -5, -5, -2, -1, 0, -4, -1, 7},
22 | { -1, -3, -3, -3, -4, -2, -2, -3, -3, -4, -4, -2, -3, -4, 8},
23 | { 1, -1, 0, -1, -2, -1, -1, -1, -2, -3, -3, -1, -2, -3, -2, 5},
24 | { 0, -2, 0, -2, -2, -1, -1, -3, -2, -1, -2, -1, -1, -3, -2, 1, 6},
25 | { -4, -4, -5, -6, -4, -3, -5, -4, -3, -4, -3, -5, -2, 0, -5, -4, -4, 11},
26 | { -3, -3, -3, -4, -4, -3, -4, -5, 1, -2, -2, -3, -2, 3, -4, -3, -2, 2, 8},
27 | { -1, -3, -4, -5, -2, -3, -3, -5, -4, 3, 0, -3, 0, -2, -3, -2, -1, -3, -3, 5}};
28 |
29 | public Blosum90() { buildScores(residueScores); }
30 | }
31 |
--------------------------------------------------------------------------------
/src/jade/math/PrecisionCalculator.java:
--------------------------------------------------------------------------------
1 | package jade.math;
2 |
3 | public final class PrecisionCalculator {
4 |
5 | /** Radix used by floating-point numbers. */
6 | private final static int radix = computeRadix();
7 |
8 | /** Largest positive value which, when added to 1.0, yields 0 */
9 | private final static double machinePrecision = computeMachinePrecision();
10 |
11 | /** Typical meaningful precision for numerical calculations. */
12 | private final static double defaultNumericalPrecision = Math
13 | .sqrt(machinePrecision);
14 |
15 | private static int computeRadix() {
16 | int radix = 0;
17 | double a = 1.0d;
18 | double tmp1, tmp2;
19 | do {
20 | a += a;
21 | tmp1 = a + 1.0d;
22 | tmp2 = tmp1 - a;
23 | } while (tmp2 - 1.0d != 0.0d);
24 | double b = 1.0d;
25 | while (radix == 0) {
26 | b += b;
27 | tmp1 = a + b;
28 | radix = (int) (tmp1 - a);
29 | }
30 | return radix;
31 | }
32 |
33 | private static double computeMachinePrecision() {
34 | double floatingRadix = getRadix();
35 | double inverseRadix = 1.0d / floatingRadix;
36 | double machinePrecision = 1.0d;
37 | double tmp = 1.0d + machinePrecision;
38 | while (tmp - 1.0d != 0.0d) {
39 | machinePrecision *= inverseRadix;
40 | tmp = 1.0d + machinePrecision;
41 | }
42 | return machinePrecision;
43 | }
44 |
45 | public static int getRadix() {
46 | return radix;
47 | }
48 |
49 | public static double getMachinePrecision() {
50 | return machinePrecision;
51 | }
52 |
53 | public static double defaultNumericalPrecision() {
54 | return defaultNumericalPrecision;
55 | }
56 |
57 | }
58 |
--------------------------------------------------------------------------------
/src/jebl/evolution/distances/DistanceMatrix.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.distances;
2 |
3 | import jebl.evolution.taxa.Taxon;
4 |
5 | import java.util.Collection;
6 | import java.util.List;
7 |
8 | /**
9 | * @author Andrew Rambaut
10 | * @author Alexei Drummond
11 | * @version $Id: DistanceMatrix.java 186 2006-01-24 00:41:22Z pepster $
12 | */
13 | public interface DistanceMatrix {
14 |
15 | /**
16 | * Gets the size of the matrix (which is square), i.e., number of rows or columns.
17 | * @return the size
18 | */
19 | int getSize();
20 |
21 | /**
22 | * @return the list of taxa that the state values correspond to.
23 | */
24 | List getTaxa();
25 |
26 | /**
27 | * Gets the distance at a particular row and column
28 | * @param row the row index
29 | * @param column the column index
30 | * @return the distance
31 | */
32 | double getDistance(int row, int column);
33 |
34 | /**
35 | * Gets the distance between 2 taxa
36 | * @param taxonRow
37 | * @param taxonColumn
38 | * @return the distance
39 | */
40 | double getDistance(Taxon taxonRow, Taxon taxonColumn);
41 |
42 | /**
43 | * Gets a sub-matrix for only those taxa in the collection (all
44 | * of which should be present in this matrix).
45 | * @param taxa
46 | * @return the new submatrix
47 | */
48 | DistanceMatrix getSubmatrix(Collection taxa);
49 |
50 | /**
51 | * Gets a 2-dimensional array containing the distances
52 | * @return the distances
53 | */
54 | double[][] getDistances();
55 | }
--------------------------------------------------------------------------------
/src/jebl/evolution/io/NewickExporter.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.io;
2 |
3 | import jebl.evolution.trees.Tree;
4 | import jebl.evolution.trees.Utils;
5 | import jebl.evolution.trees.RootedTree;
6 |
7 | import java.io.Writer;
8 | import java.io.IOException;
9 | import java.io.BufferedWriter;
10 | import java.util.Collection;
11 |
12 | /**
13 | * @author Andrew Rambaut
14 | * @author Alexei Drummond
15 | * @version $Id: NewickExporter.java 429 2006-08-26 18:17:39Z rambaut $
16 | */
17 | public class NewickExporter implements TreeExporter {
18 | public NewickExporter(Writer writer) {
19 | this.writer = writer;
20 | }
21 |
22 | /**
23 | * Export a single tree
24 | *
25 | * @param tree
26 | * @throws java.io.IOException
27 | */
28 | public void exportTree(Tree tree) throws IOException {
29 | writeTree(tree);
30 | }
31 |
32 | /**
33 | * Export a collection of trees
34 | *
35 | * @param trees
36 | * @throws java.io.IOException
37 | */
38 | public void exportTrees(Collection trees) throws IOException {
39 | for (Tree tree : trees) {
40 | writeTreeMine(tree);
41 | }
42 | }
43 |
44 | private void writeTree(Tree tree) throws IOException {
45 | writer.write(Utils.toNewick(Utils.rootTheTree(tree)));
46 | }
47 |
48 | /*
49 | * edit for FileWriter
50 | */
51 | private void writeTreeMine(Tree tree) throws IOException {
52 | writer.write(Utils.toNewick(Utils.rootTheTree(tree))+";\n");
53 | }
54 |
55 | private final Writer writer;
56 | }
57 |
--------------------------------------------------------------------------------
/src/jebl/evolution/characters/Character.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.characters;
2 |
3 | import jebl.evolution.taxa.*;
4 | import java.util.*;
5 |
6 | /**
7 | * @author Stephen A. Smith
8 | *
9 | */
10 | public interface Character{
11 |
12 | /**
13 | * set the name of the character
14 | * @param name the name of the character
15 | */
16 | public void setName(String name);
17 |
18 | /**
19 | * return the name of the character
20 | * @return the name of the character
21 | */
22 | public String getName();
23 |
24 | /**
25 | * set the description of the character
26 | * @param desc the description of the character
27 | */
28 | public void setDesc(String desc);
29 |
30 | /**
31 | * return the description of the character
32 | * @return the description of the character
33 | */
34 | public String getDesc();
35 |
36 | /**
37 | * return the CharacterType of the character
38 | * @return the CharacterType of the character
39 | */
40 | public CharacterType getType();
41 |
42 | /**
43 | * add a taxon with this character
44 | * @param taxon the taxon to add containing the character
45 | */
46 | public void addTaxon(Taxon taxon);
47 |
48 | /**
49 | * get a value for a taxon containing the character
50 | * @param taxon the taxon to get the value for
51 | * @return the Object value of the character for the given taxon
52 | */
53 | public Object getValue(Taxon taxon);
54 |
55 | /**
56 | * get a Set of all the taxa for this character
57 | * @return a Set containing all of the taxa for this character
58 | */
59 | public Set getTaxa();
60 | }
61 |
--------------------------------------------------------------------------------
/src/jebl/evolution/sequences/AminoAcidState.java:
--------------------------------------------------------------------------------
1 | /*
2 | * AminoAcidState.java
3 | *
4 | * (c) 2002-2005 JEBL Development Core Team
5 | *
6 | * This package may be distributed under the
7 | * Lesser Gnu Public Licence (LGPL)
8 | */
9 | package jebl.evolution.sequences;
10 |
11 | /**
12 | * @author Andrew Rambaut
13 | * @author Alexei Drummond
14 | *
15 | * @version $Id: AminoAcidState.java 267 2006-03-21 02:36:55Z twobeers $
16 | */
17 | public final class AminoAcidState extends State {
18 |
19 | AminoAcidState(String name, String stateCode, int index) {
20 | super(name, stateCode, index);
21 | }
22 |
23 | AminoAcidState(String name, String stateCode, int index, AminoAcidState[] ambiguities) {
24 | super(name, stateCode, index, ambiguities);
25 | }
26 |
27 | public int compareTo(Object o) {
28 | // throws ClassCastException on across-class comparison
29 | AminoAcidState that = (AminoAcidState) o;
30 | return super.compareTo(that);
31 | }
32 |
33 | // we do not need to override equals because there is only one
34 | // unique instance of each nucleotide state - i.e. we can use ==
35 | /*
36 | public boolean equals(Object o) {
37 | if (!(o instanceof AminoAcidState))
38 | return false;
39 | return super.equals(o);
40 | }*/
41 |
42 | public int hashCode() {
43 | return 7 * super.hashCode() + 23;
44 | }
45 |
46 | public boolean isGap() {
47 | return this == AminoAcids.GAP_STATE;
48 | }
49 |
50 | public boolean isStop() {
51 | return this == AminoAcids.STOP_STATE;
52 | }
53 | }
54 |
--------------------------------------------------------------------------------
/src/jebl/evolution/trees/BaseNode.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.trees;
2 |
3 | import jebl.evolution.graphs.Node;
4 | import jebl.util.AttributableHelper;
5 |
6 | import java.util.Collections;
7 | import java.util.Map;
8 | import java.util.Set;
9 |
10 | /**
11 | * Common implementation of Attributable interface used by Nodes.
12 | *
13 | * @author Joseph Heled
14 | * @version $Id: BaseNode.java 295 2006-04-14 14:59:10Z rambaut $
15 | *
16 | */
17 |
18 | abstract class BaseNode implements Node {
19 | // Attributable IMPLEMENTATION
20 |
21 | public void setAttribute(String name, Object value) {
22 | if (helper == null) {
23 | helper = new AttributableHelper();
24 | }
25 | helper.setAttribute(name, value);
26 | }
27 |
28 | public Object getAttribute(String name) {
29 | if (helper == null) {
30 | return null;
31 | }
32 | return helper.getAttribute(name);
33 | }
34 |
35 | public void removeAttribute(String name) {
36 | if( helper != null ) {
37 | helper.removeAttribute(name);
38 | }
39 | }
40 |
41 | public Set getAttributeNames() {
42 | if (helper == null) {
43 | return Collections.emptySet();
44 | }
45 | return helper.getAttributeNames();
46 | }
47 |
48 | public Map getAttributeMap() {
49 | if (helper == null) {
50 | return Collections.emptyMap();
51 | }
52 | return helper.getAttributeMap();
53 | }
54 |
55 | // PRIVATE members
56 |
57 | private AttributableHelper helper = null;
58 | }
--------------------------------------------------------------------------------
/src/org/xml/sax/SAXNotRecognizedException.java:
--------------------------------------------------------------------------------
1 | // SAXNotRecognizedException.java - unrecognized feature or value.
2 | // http://www.saxproject.org
3 | // Written by David Megginson
4 | // NO WARRANTY! This class is in the Public Domain.
5 | // $Id: SAXNotRecognizedException.java,v 1.7 2002/01/30 21:13:48 dbrownell Exp $
6 |
7 | package org.xml.sax;
8 |
9 |
10 | /**
11 | * Exception class for an unrecognized identifier.
12 | *
13 | *
14 | * This module, both source code and documentation, is in the
15 | * Public Domain, and comes with NO WARRANTY.
16 | * See http://www.saxproject.org
17 | * for further information.
18 | *
19 | *
20 | * An XMLReader will throw this exception when it finds an
21 | * unrecognized feature or property identifier; SAX applications and
22 | * extensions may use this class for other, similar purposes.
23 | *
24 | * @since SAX 2.0
25 | * @author David Megginson
26 | * @version 2.0.1 (sax2r2)
27 | * @see org.xml.sax.SAXNotSupportedException
28 | */
29 | public class SAXNotRecognizedException extends SAXException
30 | {
31 |
32 | /**
33 | * Default constructor.
34 | */
35 | public SAXNotRecognizedException ()
36 | {
37 | super();
38 | }
39 |
40 |
41 | /**
42 | * Construct a new exception with the given message.
43 | *
44 | * @param message The text message of the exception.
45 | */
46 | public SAXNotRecognizedException (String message)
47 | {
48 | super(message);
49 | }
50 |
51 | }
52 |
53 | // end of SAXNotRecognizedException.java
54 |
--------------------------------------------------------------------------------
/src/org/virion/jam/framework/AuxilaryFrame.java:
--------------------------------------------------------------------------------
1 | /**
2 | * AuxilaryFrame.java
3 | */
4 |
5 | package org.virion.jam.framework;
6 |
7 | import javax.swing.*;
8 |
9 | public class AuxilaryFrame extends AbstractFrame {
10 |
11 | private DocumentFrame documentFrame;
12 | private JPanel contentsPanel;
13 |
14 | public AuxilaryFrame(DocumentFrame documentFrame) {
15 | super();
16 |
17 | this.documentFrame = documentFrame;
18 | this.contentsPanel = null;
19 | }
20 |
21 | public AuxilaryFrame(DocumentFrame documentFrame,
22 | JPanel contentsPanel) {
23 | super();
24 |
25 | this.documentFrame = documentFrame;
26 | setContentsPanel(contentsPanel);
27 | }
28 |
29 | public void setContentsPanel(JPanel contentsPanel) {
30 | this.contentsPanel = contentsPanel;
31 | getContentPane().add(contentsPanel);
32 | pack();
33 | }
34 |
35 | public DocumentFrame getDocumentFrame() {
36 | return documentFrame;
37 | }
38 |
39 | protected void initializeComponents() {
40 | }
41 |
42 | public boolean requestClose() {
43 | return true;
44 | }
45 |
46 | public JComponent getExportableComponent() {
47 | return contentsPanel;
48 | }
49 |
50 | @SuppressWarnings({"deprecation"})
51 | public void doCloseWindow() {
52 | hide();
53 | }
54 |
55 | public Action getSaveAction() {
56 | return documentFrame.getSaveAction();
57 | }
58 |
59 | public Action getSaveAsAction() {
60 | return documentFrame.getSaveAsAction();
61 | }
62 |
63 | }
64 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/scores/Blosum45.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align.scores;
2 |
3 | public class Blosum45 extends AminoAcidScores {
4 |
5 | private final float[][] residueScores = {
6 |
7 | /* A R N D C Q E G H I L K M F P S T W Y V */
8 | { 5},
9 | { -2, 7},
10 | { -1, 0, 6},
11 | { -2, -1, 2, 7},
12 | { -1, -3, -2, -3, 12},
13 | { -1, 1, 0, 0, -3, 6},
14 | { -1, 0, 0, 2, -3, 2, 6},
15 | { 0, -2, 0, -1, -3, -2, -2, 7},
16 | { -2, 0, 1, 0, -3, 1, 0, -2, 10},
17 | { -1, -3, -2, -4, -3, -2, -3, -4, -3, 5},
18 | { -1, -2, -3, -3, -2, -2, -2, -3, -2, 2, 5},
19 | { -1, 3, 0, 0, -3, 1, 1, -2, -1, -3, -3, 5},
20 | { -1, -1, -2, -3, -2, 0, -2, -2, 0, 2, 2, -1, 6},
21 | { -2, -2, -2, -4, -2, -4, -3, -3, -2, 0, 1, -3, 0, 8},
22 | { -1, -2, -2, -1, -4, -1, 0, -2, -2, -2, -3, -1, -2, -3, 9},
23 | { 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -3, -1, -2, -2, -1, 4},
24 | { 0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -1, -1, 2, 5},
25 | { -2, -2, -4, -4, -5, -2, -3, -2, -3, -2, -2, -2, -2, 1, -3, -4, -3, 15},
26 | { -2, -1, -2, -2, -3, -1, -2, -3, 2, 0, 0, -1, 0, 3, -3, -2, -1, 3, 8},
27 | { 0, -2, -3, -3, -1, -3, -3, -3, -3, 3, 1, -2, 1, 0, -3, -1, 0, -3, -1, 5}};
28 |
29 | public Blosum45() { buildScores(residueScores); }
30 |
31 | public String getName() { return "Blosum45"; }
32 | }
33 |
--------------------------------------------------------------------------------
/src/jebl/evolution/trees/BaseEdge.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.trees;
2 |
3 | import jebl.evolution.graphs.Node;
4 | import jebl.evolution.graphs.Edge;
5 | import jebl.util.AttributableHelper;
6 |
7 | import java.util.Set;
8 | import java.util.Collections;
9 | import java.util.Map;
10 |
11 | /**
12 | * Common implementation of Attributable interface used by Nodes.
13 | *
14 | * @author Joseph Heled
15 | * @version $Id: BaseEdge.java 295 2006-04-14 14:59:10Z rambaut $
16 | *
17 | */
18 |
19 | abstract class BaseEdge implements Edge {
20 | // Attributable IMPLEMENTATION
21 |
22 | public void setAttribute(String name, Object value) {
23 | if (helper == null) {
24 | helper = new AttributableHelper();
25 | }
26 | helper.setAttribute(name, value);
27 | }
28 |
29 | public Object getAttribute(String name) {
30 | if (helper == null) {
31 | return null;
32 | }
33 | return helper.getAttribute(name);
34 | }
35 |
36 | public void removeAttribute(String name) {
37 | if( helper != null ) {
38 | helper.removeAttribute(name);
39 | }
40 | }
41 |
42 | public Set getAttributeNames() {
43 | if (helper == null) {
44 | return Collections.emptySet();
45 | }
46 | return helper.getAttributeNames();
47 | }
48 |
49 | public Map getAttributeMap() {
50 | if (helper == null) {
51 | return Collections.emptyMap();
52 | }
53 | return helper.getAttributeMap();
54 | }
55 |
56 | // PRIVATE members
57 |
58 | private AttributableHelper helper = null;
59 | }
60 |
--------------------------------------------------------------------------------
/src/jade/reconstruct/discrete/P.java:
--------------------------------------------------------------------------------
1 | package jade.reconstruct.discrete;
2 |
3 | /*
4 | * currently does not take into account assymetrical rates
5 | * to do so, just need to do something with b
6 | */
7 |
8 | public class P {
9 | public P(int size) {
10 | this.size = size;
11 | this.a = 0.1;
12 | this.b = 0.1;
13 |
14 | }
15 |
16 | public P(int size, double a, double b) {
17 | this.size = size;
18 | this.a = a;
19 | this.b = b;
20 | System.out.println(size);
21 | }
22 |
23 | public double[][] getP(double time) {
24 | double[][] p = new double[2][2];
25 | p = new double[size][size];
26 | for (int i = 0; i < size; i++) {
27 | for (int j = 0; j < size; j++) {
28 | if (i == j) {
29 | p[i][j] = (1.0 / size)
30 | + ((size - 1) / Double.valueOf(size))
31 | * (Math.exp(-(size * a * time)));
32 | } else {
33 | p[i][j] = (1.0 / size) - (1.0 / size)
34 | * (Math.exp(-(size * a * time)));
35 | }
36 | }
37 | }
38 | P = p;
39 | return p;
40 | }
41 |
42 | public void setRates(double a) {
43 | this.a = a;
44 | this.b = a;
45 | }
46 |
47 | public void setRates(double a, double b) {
48 | this.a = a;
49 | this.b = b;
50 | }
51 |
52 | public void printP() {
53 | for (int i = 0; i < size; i++) {
54 | for (int j = 0; j < size; j++) {
55 | System.out.print(P[i][j] + "\t");
56 | }
57 | System.out.println();
58 | }
59 |
60 | }
61 |
62 | public static void main(String[] args) {
63 | P p = new P(2);
64 | p.getP(1);
65 | p.printP();
66 | }
67 |
68 | private double[][] P;
69 |
70 | private double a;
71 |
72 | private double b;
73 |
74 | private int size;
75 | }
76 |
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/src/jade/math/ContinuedFraction.java:
--------------------------------------------------------------------------------
1 | /*
2 | * ContinuedFraction.java
3 | *
4 | * Created on August 19, 2005, 12:31 PM
5 | *
6 | * author: Stephen A. Smith
7 | */
8 |
9 | package jade.math;
10 |
11 | /**
12 | *
13 | * @author stephensmith
14 | */
15 | public abstract class ContinuedFraction extends IterativeProcess{
16 |
17 | /** Creates a new instance of ContinuedFraction */
18 | public ContinuedFraction() {
19 | }
20 |
21 | protected abstract void computeFactorsAt(int n);
22 |
23 | public double evaluateIteration(){
24 | computeFactorsAt(getIterations());
25 | denominator = 1/limitedSmallValue(factors[0]*denominator+factors[1]);
26 | numerator = limitedSmallValue(factors[0]/numerator+factors[1]);
27 | double delta = numerator * denominator;
28 | result *=delta;
29 | return Math.abs(delta-1);
30 | }
31 |
32 | public double getResult(){ return result; }
33 |
34 | public void initializeIterations(){
35 | numerator = limitedSmallValue(initialValue());
36 | denominator = 0;
37 | result = numerator;
38 | return;
39 | }
40 |
41 | protected abstract double initialValue();
42 |
43 | private double limitedSmallValue(double r){
44 | return Math.abs(r)
13 | * This module, both source code and documentation, is in the
14 | * Public Domain, and comes with NO WARRANTY.
15 | * See http://www.saxproject.org
16 | * for further information.
17 | *
18 | *
19 | * An XMLReader will throw this exception when it recognizes a
20 | * feature or property identifier, but cannot perform the requested
21 | * operation (setting a state or value). Other SAX2 applications and
22 | * extensions may use this class for similar purposes.
23 | *
24 | * @since SAX 2.0
25 | * @author David Megginson
26 | * @version 2.0.1 (sax2r2)
27 | * @see org.xml.sax.SAXNotRecognizedException
28 | */
29 | public class SAXNotSupportedException extends SAXException
30 | {
31 |
32 | /**
33 | * Construct a new exception with no message.
34 | */
35 | public SAXNotSupportedException ()
36 | {
37 | super();
38 | }
39 |
40 |
41 | /**
42 | * Construct a new exception with the given message.
43 | *
44 | * @param message The text message of the exception.
45 | */
46 | public SAXNotSupportedException (String message)
47 | {
48 | super(message);
49 | }
50 |
51 | }
52 |
53 | // end of SAXNotSupportedException.java
54 |
--------------------------------------------------------------------------------
/src/jebl/evolution/align/MaximalSegmentPair.java:
--------------------------------------------------------------------------------
1 | package jebl.evolution.align;
2 |
3 | import jebl.evolution.align.scores.Scores;
4 |
5 | /**
6 | * @author Alexei Drummond
7 | *
8 | * @version $Id: MaximalSegmentPair.java 185 2006-01-23 23:03:18Z rambaut $
9 | */
10 | public class MaximalSegmentPair extends AlignSimple {
11 |
12 | public MaximalSegmentPair(Scores sub) {
13 | super(sub, Integer.MAX_VALUE);
14 | }
15 |
16 | /**
17 | * @param sq1
18 | * @param sq2
19 | */
20 | public final void doAlignment(String sq1, String sq2) {
21 |
22 | super.prepareAlignment(sq1, sq2);
23 |
24 | int n = this.n, m = this.m;
25 | float[][] score = sub.score;
26 | int maxi = n, maxj = m;
27 | float maxval = Float.NEGATIVE_INFINITY;
28 | float val;
29 | for (int i=1; i<=n; i++) {
30 | for (int j=1; j<=m; j++) {
31 | float s = score[seq1.charAt(i-1)][seq2.charAt(j-1)];
32 | val = max(0.0f, F[i-1][j-1]+s);
33 | F[i][j] = val;
34 | if (val == 0.0f) {
35 | B[i][j].setTraceback(-1,-1);
36 | } else {
37 | B[i][j].setTraceback(i-1, j-1);
38 | }
39 | if (val > maxval) {
40 | maxval = val;
41 | maxi = i; maxj = j;
42 | }
43 | }
44 | }
45 | B0 = new TracebackSimple(maxi, maxj);
46 | }
47 |
48 | public final Traceback next(Traceback tb) {
49 |
50 | Traceback next = super.next(tb);
51 | if (next != null) {
52 | if (next.i - tb.i != next.j - tb.j) return null;
53 | }
54 | return next;
55 | }
56 | }
57 |
--------------------------------------------------------------------------------
/src/org/virion/jam/controlpanels/Controls.java:
--------------------------------------------------------------------------------
1 | package org.virion.jam.controlpanels;
2 |
3 | import javax.swing.*;
4 |
5 | /**
6 | * @author Andrew Rambaut
7 | * @version $Id: Controls.java 276 2006-03-23 00:37:40Z pepster $
8 | */
9 | public class Controls {
10 |
11 |
12 | public Controls(String title, JPanel panel, boolean isVisible) {
13 | this(title, panel, isVisible, false, null);
14 | }
15 |
16 | /**
17 | * @param title
18 | * @param panel
19 | * @param isVisible
20 | * @param isPinned
21 | * @param primaryCheckbox the "main" on/off toggle, if any.
22 | */
23 | public Controls(String title, JPanel panel, boolean isVisible, boolean isPinned, JCheckBox primaryCheckbox) {
24 | this.title = title;
25 | this.panel = panel;
26 | this.isVisible = isVisible;
27 | this.isPinned = isPinned;
28 | this.primaryCheckbox = primaryCheckbox;
29 | }
30 |
31 | public String getTitle() {
32 | return title;
33 | }
34 |
35 | public JPanel getPanel() {
36 | return panel;
37 | }
38 |
39 | public boolean isVisible() {
40 | return isVisible;
41 | }
42 |
43 | public void setVisible(boolean visible) {
44 | isVisible = visible;
45 | }
46 |
47 | public boolean isPinned() {
48 | return isPinned;
49 | }
50 |
51 | public void setPinned(boolean pinned) {
52 | isPinned = pinned;
53 | }
54 |
55 | public JCheckBox getPrimaryCheckbox() {
56 | return primaryCheckbox;
57 | }
58 |
59 | private String title;
60 | private JPanel panel;
61 | private JCheckBox primaryCheckbox;
62 | private boolean isVisible;
63 |
64 | private boolean isPinned;
65 | }
66 |
--------------------------------------------------------------------------------
/src/org/virion/jam/framework/DefaultEditMenuFactory.java:
--------------------------------------------------------------------------------
1 | /*
2 | * Copyright (c) 2005 Biomatters LTD. All Rights Reserved.
3 | */
4 | package org.virion.jam.framework;
5 |
6 | import javax.swing.*;
7 | import java.awt.event.KeyEvent;
8 |
9 | /**
10 | * @author rambaut
11 | * Date: Dec 26, 2004
12 | * Time: 11:01:40 AM
13 | *
14 | * @version $Id: DefaultEditMenuFactory.java 183 2006-01-23 21:29:48Z rambaut $
15 | */
16 | public class DefaultEditMenuFactory implements MenuFactory {
17 | public String getMenuName() {
18 | return "Edit";
19 | }
20 |
21 | public void populateMenu(JMenu menu, AbstractFrame frame) {
22 |
23 | JMenuItem item;
24 |
25 | menu.setMnemonic('E');
26 |
27 | item = new JMenuItem(frame.getCutAction());
28 | item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_X, MenuBarFactory.MENU_MASK));
29 | menu.add(item);
30 |
31 | item = new JMenuItem(frame.getCopyAction());
32 | item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_C, MenuBarFactory.MENU_MASK));
33 | menu.add(item);
34 |
35 | item = new JMenuItem(frame.getPasteAction());
36 | item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_V, MenuBarFactory.MENU_MASK));
37 | menu.add(item);
38 |
39 | item = new JMenuItem(frame.getDeleteAction());
40 | menu.add(item);
41 |
42 | item = new JMenuItem(frame.getSelectAllAction());
43 | item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_A, MenuBarFactory.MENU_MASK));
44 | menu.add(item);
45 |
46 | menu.addSeparator();
47 |
48 | item = new JMenuItem(frame.getFindAction());
49 | item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F, MenuBarFactory.MENU_MASK));
50 | menu.add(item);
51 |
52 | }
53 |
54 | public int getPreferredAlignment() {
55 | return LEFT;
56 | }
57 | }
58 |
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