/*.................................................................................................................*/
public boolean transformTree(AdjustableTree tree, MesquiteString resultString, boolean notify) {
Taxa taxa = tree.getTaxa();
// counting how many excluded
int count = 0;
for (int i = 0; i < taxa.getNumTaxa(); i++) {
if (!tree.taxonInTree(i)) count++;
}
if (count == 0) {
discreetAlert(
"The tree contains all of the taxa available in the block of taxa. There are none available to be added");
return true;
}
// getting list of excluded
ListableVector excluded = new ListableVector(count);
count = 0;
for (int i = 0; i < taxa.getNumTaxa(); i++) {
if (!tree.taxonInTree(i)) {
excluded.addElement(taxa.getTaxon(i), false);
}
}
// presenting choice
Listable[] toInclude =
ListDialog.queryListMultiple(
containerOfModule(),
"Add taxa to tree",
"Select taxa to be added to the tree",
MesquiteString.helpString,
"Add",
false,
excluded,
null);
if (toInclude == null || toInclude.length == 0) return true;
for (int i = 0; i < toInclude.length; i++) {
int taxon = taxa.whichTaxonNumber((Taxon) toInclude[i]);
tree.graftTaxon(taxon, tree.getRoot(), false);
}
if (notify && tree instanceof Listened)
((Listened) tree)
.notifyListeners(this, new Notification(MesquiteListener.BRANCHES_REARRANGED));
return true;
}
public void calculateNumber(Taxon taxon, MesquiteNumber result, MesquiteString resultString) {
if (result == null) return;
clearResultAndLastResult(result);
Taxa taxa = taxon.getTaxa();
int it = taxa.whichTaxonNumber(taxon);
if (taxa != currentTaxa || observedStates == null) {
observedStates = matrixSourceTask.getCurrentMatrix(taxa);
currentTaxa = taxa;
}
if (observedStates == null || !(observedStates.getParentData() instanceof DNAData)) return;
DNAData data = (DNAData) observedStates.getParentData();
int count = data.getAminoAcidNumbers(it, ProteinData.TER, countEvenIfOthers.getValue());
if (result != null) result.setValue(count);
if (resultString != null)
resultString.setValue(
"Number of stop codons in taxon " + observedStates.getName() + ": " + count);
saveLastResult(result);
saveLastResultString(resultString);
}