Examples of PaletteColorTable

org.broad.igv.ui.color.PaletteColorTable
A lookup table mapping symbols (strings) -> color. Can be initiated with our without a palette. If a palette is used colors are selected sequentially from the palette as needed until it is exhausted.
@author jrobinso @date Feb 26, 2010

Examples of org.broad.igv.ui.color.PaletteColorTable

    public MutationLegendPanel() {
        init();
    }


    private void init() {
        PaletteColorTable prefTable = PreferenceManager.getInstance().getMutationColorScheme();
        colorTable = new PaletteColorTable();
        for (String key : prefTable.getKeys()) {
            colorTable.put(key, prefTable.get(key));
        }
    }

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Examples of org.broad.igv.ui.color.PaletteColorTable

    /**
     * Open the user preferences dialog
     */
    public void edit() {


        PaletteColorTable ct = PreferenceManager.getInstance().getMutationColorScheme();
        ColorMapEditor editor = new ColorMapEditor(IGV.getMainFrame(), ct.getColorMap());
        editor.setVisible(true);


        Map<String, Color> changedColors = editor.getChangedColors();
        if (!changedColors.isEmpty()) {
            for (Map.Entry<String, Color> entry : changedColors.entrySet()) {
                ct.put(entry.getKey(), entry.getValue());
            }
            String colorTableString = ct.getMapAsString();
            PreferenceManager.getInstance().put(PreferenceManager.MUTATION_COLOR_TABLE, colorTableString);
            reloadPreferences();
        }


    }

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Examples of org.broad.igv.ui.color.PaletteColorTable


    public synchronized void setModel(XYDataModel dataModel) {


        this.dataModel = dataModel;


        colorTable = new PaletteColorTable(ColorUtilities.getPalette("Set 1"));
        double minX = Double.MAX_VALUE;
        double maxX = -minX;
        double minY = minX;
        double maxY = maxX;

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Examples of org.broad.igv.ui.color.PaletteColorTable

            boolean useColor = true;
            if (useColor) {
                ColorTable ct = colorTables.get(attKey);
                if (ct == null) {
                    ColorPalette palette = ColorUtilities.getNextPalette();
                    ct = new PaletteColorTable(palette);
                    colorTables.put(attKey, ct);
                }
                c = ct.get(attValue);
            } else {
                c = ColorUtilities.randomDesaturatedColor(0.5f);

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Examples of org.broad.igv.ui.color.PaletteColorTable

                String.valueOf(showAllHeatmapFeauresCB.isSelected()));
    }




    private void chooseMutationColorsButtonActionPerformed(ActionEvent e) {
        PaletteColorTable ct = PreferenceManager.getInstance().getMutationColorScheme();
        ColorMapEditor editor = new ColorMapEditor(IGV.getMainFrame(), ct.getColorMap());
        editor.setVisible(true);


        Map<String, Color> changedColors = editor.getChangedColors();
        if (!changedColors.isEmpty()) {
            for (Map.Entry<String, Color> entry : changedColors.entrySet()) {
                ct.getColorMap().put(entry.getKey(), entry.getValue());
            }
            String mapString = ct.getMapAsString();
            PreferenceManager.getInstance().put(PreferenceManager.MUTATION_COLOR_TABLE, mapString);
        }
    }

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Examples of org.broad.igv.ui.color.PaletteColorTable


        if (renderOptions.getColorOption() == ColorOption.BISULFITE) {
            setExperimentType(ExperimentType.BISULFITE);
        }


        readNamePalette = new PaletteColorTable(ColorUtilities.getDefaultPalette());


        // Register track
        if (!Globals.isHeadless()) {
            IGV.getInstance().addAlignmentTrackEventListener(this);
        }

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Examples of org.broad.igv.ui.color.PaletteColorTable

     */
    public synchronized PaletteColorTable getMutationColorScheme() {
        if (mutationColorScheme == null) {
            String colorTableString = get(MUTATION_COLOR_TABLE);
            if (colorTableString != null) {
                PaletteColorTable pallete = new PaletteColorTable();
                pallete.restoreMapFromString(colorTableString);
                mutationColorScheme = pallete;
            } else {
                mutationColorScheme = getLegacyMutationColorScheme();
            }
        }

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Examples of org.broad.igv.ui.color.PaletteColorTable

        String spliceSiteColor = get(MUTATION_SPLICE_SITE_COLOR_KEY);
        String synonymousColor = get(MUTATION_SYNONYMOUS_COLOR_KEY);
        String targetedRegionColor = get(MUTATION_TARGETED_REGION_COLOR_KEY);
        String unknownColor = get(MUTATION_UNKNOWN_COLOR_KEY);


        PaletteColorTable colorTable = new PaletteColorTable();
        if ((indelColor != null) && (missenseColor != null) && (nonsenseColor != null) &&
                (spliceSiteColor != null) &&
                (synonymousColor != null) &&
                (targetedRegionColor != null) &&
                (unknownColor != null)) {


            Color color1 = ColorUtilities.stringToColor(indelColor);
            colorTable.put("Indel", color1);


            Color color2 = ColorUtilities.stringToColor(missenseColor);
            colorTable.put("Missense", color2);


            Color color3 = ColorUtilities.stringToColor(nonsenseColor);
            colorTable.put("Nonsense", color3);


            Color color4 = ColorUtilities.stringToColor(spliceSiteColor);
            colorTable.put("Splice_site", color4);


            Color color5 = ColorUtilities.stringToColor(synonymousColor);
            colorTable.put("Synonymous", color5);


            Color color6 = ColorUtilities.stringToColor(targetedRegionColor);
            colorTable.put("Targeted_Region", color6);


            Color color7 = ColorUtilities.stringToColor(unknownColor);
            colorTable.put("Unknown", color7);


            // Nicos extensions
            String[] nicosCats = {"Truncating", "Non-coding_Transcript", "Other_AA_changing", "Other_likely_neutral"};
            for (String cat : nicosCats) {
                String key = "MUTATION_" + cat + "_COLOR";
                colorTable.put(cat, ColorUtilities.stringToColor(get(key)));
            }
        }


        return colorTable;
    }

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Examples of org.broad.igv.ui.color.PaletteColorTable

        f1f2OrientationTypes.put("F2F1", AlignmentTrack.OrientationType.RL);
    }


    private void initializeTagColors() {
        ColorPalette palette = ColorUtilities.getPalette("Pastel 1");  // TODO let user choose
        readGroupColors = new PaletteColorTable(palette);
        sampleColors = new PaletteColorTable(palette);
        tagValueColors = new PaletteColorTable(palette);


        typeToColorMap = new HashMap<AlignmentTrack.OrientationType, Color>(5);
        typeToColorMap.put(AlignmentTrack.OrientationType.LL, LL_COLOR);
        typeToColorMap.put(AlignmentTrack.OrientationType.LR, LR_COLOR);
        typeToColorMap.put(AlignmentTrack.OrientationType.RL, RL_COLOR);

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