/**
* Gets background color for cell for row ic. Override it if you want to change the color from the
* default.
*/
public Color getBackgroundColorOfCell(int it, boolean selected) {
if (observedStates == null) {
doCalcs();
if (observedStates == null) return null;
}
if (observedStates.getParentData() != null) {
captureCharacterDataFromObservedStates();
Associable tInfo = data.getTaxaInfo(false);
NameReference genBankColor = NameReference.getNameReference("genbankcolor");
Object obj = tInfo.getAssociatedObject(genBankColor, it); // not saved to file
if (obj instanceof Color) return (Color) obj;
}
if (bits == null || it < 0 || it > bits.getSize()) return null;
String note = getNote(it);
if (selected) {
if (bits.isBitOn(it)) return ColorDistribution.darkGreen;
else return ColorDistribution.darkRed;
} else if (bits.isBitOn(it)) {
if (StringUtil.blank(note)) return ColorDistribution.veryLightGreen;
if (!(note.equalsIgnoreCase("x"))) return ColorDistribution.lightGreenYellowish;
return ColorDistribution.lightGreenYellow;
} else {
if (StringUtil.blank(note)) return ColorDistribution.brown;
if (!(note.equalsIgnoreCase("x"))) {
return Color.red;
}
return ColorDistribution.lightRed;
}
}
public String getStringForTaxon(int it) {
String note = getNote(it);
if (note != null) return note;
if (observedStates == null) doCalcs();
if (bits == null || it < 0 || it > bits.getSize()) return "?";
if (bits.isBitOn(it)) return "Yes";
else return "No Data";
}
public void doCalcs() {
if (bits != null) bits.clearAllBits();
if (taxa == null) return;
if (bits == null) bits = new Bits(taxa.getNumTaxa());
else bits.resetSize(taxa.getNumTaxa());
if (observedStates == null) {
tInfo = null;
observedStates = matrixSourceTask.getCurrentMatrix(taxa);
if (observedStates != null) {
captureCharacterDataFromObservedStates();
if (data != null) tInfo = data.getTaxaInfo(true);
}
}
if (observedStates == null) return;
for (int it = 0; it < taxa.getNumTaxa(); it++) {
if (hasData(it)) bits.setBit(it);
}
}
