Package org.broad.igv

Examples of org.broad.igv.PreferenceManager

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    public GWASTrack(ResourceLocator locator, String id, String name, GWASData gData, GWASParser parser) {


        super(locator, id, name);

        PreferenceManager prefs = PreferenceManager.getInstance();

        // Set range from 0 to highest value rounded to greater integer
        int maxValue = (int) Math.ceil(gData.getMaxValue());
        super.setDataRange(new DataRange(0, (maxValue / 2), maxValue));


        // Get default values
        super.setHeight(prefs.getAsInt(PreferenceManager.GWAS_TRACK_HEIGHT));

        this.minPointSize = prefs.getAsInt(PreferenceManager.GWAS_MIN_POINT_SIZE);
        this.maxPointSize = prefs.getAsInt(PreferenceManager.GWAS_MAX_POINT_SIZE);

        this.primaryColor = ColorUtilities.stringToColor(prefs.get(PreferenceManager.GWAS_PRIMARY_COLOR));
        this.secondaryColor = ColorUtilities.stringToColor(prefs.get(PreferenceManager.GWAS_SECONDARY_COLOR));
        this.singleColor = prefs.getAsBoolean(PreferenceManager.GWAS_SINGLE_COLOR);
        this.alternatingColors = prefs.getAsBoolean(PreferenceManager.GWAS_ALTERNATING_COLORS);
        this.useChrColors = prefs.getAsBoolean(PreferenceManager.GWAS_USE_CHR_COLORS);
        this.showAxis = prefs.getAsBoolean(PreferenceManager.GWAS_SHOW_AXIS);

        this.gData = gData;
        this.parser = parser;

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    private TreeSet<Shape> arcsByEnd;
    private HashMap<Shape, Alignment> curveMap;

    private static void setNucleotideColors() {

        PreferenceManager prefs = PreferenceManager.getInstance();

        nucleotideColors = new HashMap();

        Color a = ColorUtilities.stringToColor(prefs.get(PreferenceManager.SAM_COLOR_A),  Color.green);
        Color c = ColorUtilities.stringToColor(prefs.get(PreferenceManager.SAM_COLOR_C),  Color.blue);
        Color t = ColorUtilities.stringToColor(prefs.get(PreferenceManager.SAM_COLOR_T),  Color.red);
        Color g = ColorUtilities.stringToColor(prefs.get(PreferenceManager.SAM_COLOR_G),  Color.gray);
        Color n = ColorUtilities.stringToColor(prefs.get(PreferenceManager.SAM_COLOR_N),  Color.gray);

        nucleotideColors.put('A', a);
        nucleotideColors.put('a', a);
        nucleotideColors.put('C', c);
        nucleotideColors.put('c', c);
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Related Classes of org.broad.igv.PreferenceManager

  • com.iontorrent.views.FlowSignalDistributionPanel
  • org.broad.igv.gwas.DescriptionCache
  • org.broad.igv.gwas.GWASTrack
  • org.broad.igv.renderer.ContinuousColorScale
  • org.broad.igv.renderer.DataRenderer
  • org.broad.igv.renderer.SequenceRenderer
  • org.broad.igv.renderer.SpliceJunctionRenderer
  • org.broad.igv.renderer.XYPlotRenderer
  • org.broad.igv.sam.AlignmentDataManager$DownsampleOptions
  • org.broad.igv.sam.AlignmentRenderer
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