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Viewing changes to src/figtree/treeviewer/decorators/ParsimonyBranchDecorator.java

  • Committer: Bazaar Package Importer
  • Author(s): Andreas Tille
  • Date: 2011-02-21 08:17:38 UTC
  • Revision ID: james.westby@ubuntu.com-20110221081738-80pe2ulo8rg7up10
Tags: upstream-1.3.1
Import upstream version 1.3.1

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src/figtree/treeviewer/decorators/ParsimonyBranchDecorator.java
 
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package figtree.treeviewer.decorators;
 
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import jebl.evolution.trees.Tree;
 
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import jebl.evolution.graphs.Node;
 
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import jebl.evolution.alignments.Pattern;
 
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import jebl.evolution.parsimony.ParsimonyCriterion;
 
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import jebl.evolution.parsimony.FitchParsimony;
 
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import jebl.evolution.sequences.State;
 
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import jebl.evolution.sequences.Nucleotides;
 
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import jebl.evolution.sequences.SequenceType;
 
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import jebl.evolution.sequences.AminoAcids;
 
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import java.util.ArrayList;
 
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import java.util.List;
 
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import java.awt.*;
 
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/**
 
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 * @author Andrew Rambaut
 
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 * @author Alexei Drummond
 
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 * @version $Id: ParsimonyBranchDecorator.java,v 1.4 2006/08/27 15:17:36 rambaut Exp $
 
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 */
 
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public class ParsimonyBranchDecorator {
 
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    public ParsimonyBranchDecorator(Pattern pattern) {
 
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        List<Pattern> patterns = new ArrayList<Pattern>();
 
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        patterns.add(pattern);
 
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        parsimony = new FitchParsimony(patterns, true);
 
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        if (pattern.getSequenceType() == SequenceType.NUCLEOTIDE) {
 
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            paints = new Paint[Nucleotides.getStateCount()];
 
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            paints[Nucleotides.A_STATE.getIndex()] = Color.RED;
 
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            paints[Nucleotides.C_STATE.getIndex()] = Color.BLUE;
 
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            paints[Nucleotides.G_STATE.getIndex()] = Color.BLACK;
 
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            paints[Nucleotides.T_STATE.getIndex()] = Color.GREEN;
 
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            paints[Nucleotides.R_STATE.getIndex()] = Color.MAGENTA;
 
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            paints[Nucleotides.Y_STATE.getIndex()] = Color.DARK_GRAY;
 
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            paints[Nucleotides.M_STATE.getIndex()] = Color.DARK_GRAY;
 
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            paints[Nucleotides.W_STATE.getIndex()] = Color.DARK_GRAY;
 
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            paints[Nucleotides.S_STATE.getIndex()] = Color.DARK_GRAY;
 
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            paints[Nucleotides.K_STATE.getIndex()] = Color.DARK_GRAY;
 
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            paints[Nucleotides.B_STATE.getIndex()] = Color.DARK_GRAY;
 
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            paints[Nucleotides.D_STATE.getIndex()] = Color.DARK_GRAY;
 
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            paints[Nucleotides.H_STATE.getIndex()] = Color.DARK_GRAY;
 
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            paints[Nucleotides.V_STATE.getIndex()] = Color.DARK_GRAY;
 
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            paints[Nucleotides.N_STATE.getIndex()] = Color.GRAY;
 
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            paints[Nucleotides.UNKNOWN_STATE.getIndex()] = Color.GRAY;
 
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            paints[Nucleotides.GAP_STATE.getIndex()] = Color.GRAY;
 
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        } else if (pattern.getSequenceType() == SequenceType.AMINO_ACID) {
 
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            paints = new Paint[AminoAcids.getStateCount()];
 
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            paints[AminoAcids.A_STATE.getIndex()] = new Color(204, 255, 255);
 
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            paints[AminoAcids.C_STATE.getIndex()] = new Color(0, 255, 255);
 
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            paints[AminoAcids.D_STATE.getIndex()] = new Color(255, 204, 153);
 
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            paints[AminoAcids.E_STATE.getIndex()] = new Color(255, 204, 0);
 
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            paints[AminoAcids.F_STATE.getIndex()] = new Color(0, 204, 255);
 
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            paints[AminoAcids.G_STATE.getIndex()] = new Color(0, 255, 0);
 
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            paints[AminoAcids.H_STATE.getIndex()] = new Color(255, 255, 153);
 
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            paints[AminoAcids.I_STATE.getIndex()] = new Color(0, 0, 128);
 
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            paints[AminoAcids.K_STATE.getIndex()] = new Color(198, 66, 0);
 
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            paints[AminoAcids.L_STATE.getIndex()] = new Color(51, 102, 255);
 
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            paints[AminoAcids.M_STATE.getIndex()] = new Color(153, 204, 255);
 
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            paints[AminoAcids.N_STATE.getIndex()] = new Color(255, 153, 0);
 
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            paints[AminoAcids.P_STATE.getIndex()] = new Color(255, 255, 0);
 
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            paints[AminoAcids.Q_STATE.getIndex()] = new Color(255, 102, 0);
 
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            paints[AminoAcids.R_STATE.getIndex()] = new Color(230, 6, 6);
 
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            paints[AminoAcids.S_STATE.getIndex()] = new Color(204, 255, 153);
 
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            paints[AminoAcids.T_STATE.getIndex()] = new Color(0, 255, 153);
 
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            paints[AminoAcids.V_STATE.getIndex()] = new Color(0, 0, 255);
 
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            paints[AminoAcids.W_STATE.getIndex()] = new Color(204, 153, 255);
 
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            paints[AminoAcids.Y_STATE.getIndex()] = new Color(204, 255, 204);
 
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            paints[AminoAcids.B_STATE.getIndex()] = Color.DARK_GRAY;
 
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            paints[AminoAcids.Z_STATE.getIndex()] = Color.DARK_GRAY;
 
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            paints[AminoAcids.X_STATE.getIndex()] = Color.GRAY;
 
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            paints[AminoAcids.UNKNOWN_STATE.getIndex()] = Color.GRAY;
 
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            paints[AminoAcids.STOP_STATE.getIndex()] = Color.GRAY;
 
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            paints[AminoAcids.GAP_STATE.getIndex()] = Color.GRAY;
 
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        } else {
 
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            throw new IllegalArgumentException("Unsupported sequence type");
 
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        }
 
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    }
 
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    public Paint getBranchPaint(Tree tree, Node node) {
 
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        State[] states = parsimony.getStates(tree, node);
 
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        return paints[states[0].getIndex()];
 
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    }
 
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    private final ParsimonyCriterion parsimony;
 
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    private final Paint[] paints;
 
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}
 
 
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