src/org/gel/mauve/color/MultiplicityTypeColorScheme.java

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package org.gel.mauve.color;

import java.awt.Color;

import org.gel.mauve.BaseViewerModel;
import org.gel.mauve.ColorScheme;
import org.gel.mauve.Genome;
import org.gel.mauve.Match;

public class MultiplicityTypeColorScheme implements ColorScheme {

        public void apply (BaseViewerModel model) {
                if (model.getSequenceCount () > 62) {
                        throw new RuntimeException (
                                        " Can't color by multiplicity type with more than 62 sequences.");
                }

                double mult_range = Math.pow (2, model.getSequenceCount ());

                for (int matchI = 0; matchI < model.getMatchCount (); matchI++) {
                        Match cur_match = model.getMatch (matchI);

                        // color the match based on its multiplicity.
                        long color_type = 0;
                        for (int seqI = 0; seqI < model.getSequenceCount (); seqI++) {
                                Genome g = model.getGenomeByViewingIndex (seqI);
                                color_type <<= 1;
                                if (cur_match.getStart (g) != Match.NO_MATCH) {
                                        color_type |= 1;
                                }
                        }
                        double hue = (double) color_type / mult_range;
                        cur_match.color = Color.getHSBColor ((float) hue, MATCH_SAT,
                                        MATCH_BRIGHT);
                }
        }

        public String toString () {
                return "Multiplicity type";
        }

}

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