/* .......................................... DNAData .................................................. */
public long getTaxonNumberInTree(Taxa taxa, int it) {
Associable tInfo = getTaxaInfo(data, true);
if (tInfo != null) {
return (int) tInfo.getAssociatedLong(TNTtoAnalyze, it);
}
return -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());
}
}
}
/* .......................................... MolecularData .................................................. */
public void setTaxonNumberInTree(Taxa taxa, int it, int value) {
Associable tInfo = getTaxaInfo(data, true);
if (tInfo != null) {
tInfo.setAssociatedLong(TNTtoAnalyze, it, value);
}
}