/* .......................................... DNAData .................................................. */
public long getTaxonNumberInTree(Taxa taxa, int it) {
Associable tInfo = getTaxaInfo(data, true);
if (tInfo != null) {
return (int) tInfo.getAssociatedLong(TNTtoAnalyze, it);
}
return -1;
}
/**
* 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 getExplanationForRow(int ic) {
if (observedStates != null && observedStates.getParentData() != null) {
captureCharacterDataFromObservedStates();
Associable tInfo = data.getTaxaInfo(false);
if (tInfo == null) return null;
return "Notes: " + tInfo.toString(ic);
}
return null;
}
/*.................................................................................................................*/
void zapData(CharacterData data, int it) {
Taxa taxa = data.getTaxa();
if (it < 0 || it >= taxa.getNumTaxa()) return;
Associable tInfo = data.getTaxaInfo(false);
int myColumn = -1;
if (getEmployer() instanceof ListModule) {
myColumn = ((ListModule) getEmployer()).getMyColumn(this);
}
if (tInfo != null) tInfo.deassignAssociated(it);
for (int ic = 0; ic < data.getNumChars(); ic++) data.deassign(ic, it);
data.notifyListeners(this, new Notification(MesquiteListener.DATA_CHANGED));
outputInvalid();
parametersChanged();
}
/*.................................................................................................................*/
private void recordSourceProject() {
MesquiteString s = new MesquiteString();
s.setValue(getProject().getHomeFileName());
if (!QueryDialogs.queryString(
containerOfModule(),
"Name to Stamp",
"Indicate source file name to stamp on matrix rows",
s)) return;
int numMatrices = getProject().getNumberCharMatrices();
NameReference sourceRef = NameReference.getNameReference("SourceFile");
for (int im = 0; im < numMatrices; im++) {
CharacterData data = getProject().getCharacterMatrix(im);
Taxa taxa = data.getTaxa();
Associable tInfo = data.getTaxaInfo(true);
boolean anySelected = taxa.anySelected();
for (int it = 0; it < taxa.getNumTaxa(); it++) {
if (data.hasDataForTaxon(it) && (!anySelected || taxa.getSelected(it)))
tInfo.setAssociatedObject(sourceRef, it, s.getValue());
}
}
}
String getNote(int row) {
if (tInfo == null) return null;
Object obj = tInfo.getAssociatedObject(MolecularData.genBankNumberRef, row);
if (obj == null || !(obj instanceof String)) return null;
return (String) obj;
}
void setNote(int row, String s) {
if (tInfo == null) return;
tInfo.setAssociatedObject(MolecularData.genBankNumberRef, row, s);
}
/* .......................................... MolecularData .................................................. */
public void setTaxonNumberInTree(Taxa taxa, int it, int value) {
Associable tInfo = getTaxaInfo(data, true);
if (tInfo != null) {
tInfo.setAssociatedLong(TNTtoAnalyze, it, value);
}
}