/** Called to operate on the CharacterData blocks. Returns true if taxa altered */
public boolean operateOnDatas(ListableVector datas, MesquiteTable table) {
boolean anyExcluded = false;
for (int im = 0; im < datas.size(); im++) {
CharacterData data = (CharacterData) datas.elementAt(im);
if (data.numCharsCurrentlyIncluded() < data.getNumChars()) anyExcluded = true;
}
if (anyExcluded) queryOptions();
if (getProject() != null) getProject().incrementProjectWindowSuppression();
for (int im = 0; im < datas.size(); im++) {
CharacterData data = (CharacterData) datas.elementAt(im);
CharacterData starter = data.makeCharacterData(data.getMatrixManager(), data.getTaxa());
starter.addToFile(
getProject().getHomeFile(), getProject(), findElementManager(CharacterData.class));
boolean success =
starter.concatenate(data, false, duplicateExcludedCharacters, false, false, false, false);
if (success) {
starter.setName(datas.getUniqueName(data.getName() + " (duplicate)"));
}
}
if (getProject() != null) getProject().decrementProjectWindowSuppression();
resetAllMenuBars();
return true;
}
/*.................................................................................................................*/
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;
}