/*.................................................................................................................*/
public void setTaxonTranslation(Taxa taxa) {
int countTaxa = 0;
for (int it = 0; it < data.getNumTaxa(); it++)
if ((!selectedTaxaOnly || taxa.getSelected(it)) && (data.hasDataForTaxon(it, false))) {
setTaxonNumberInTree(taxa, it, countTaxa);
countTaxa++;
} else setTaxonNumberInTree(taxa, it, -1);
}
/*.................................................................................................................*/
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());
}
}
}