f1f2OrientationTypes.put("R1R2", AlignmentTrack.OrientationType.RL);
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);