public boolean alterBlockOfCharacters(CharacterData data, int icStart, int icEnd) {
if (data == null) return false;
if (data instanceof MolecularData) {
MolecularData mData = (MolecularData) data;
mData.reverse(icStart, icEnd, true);
} else {
for (int it = 0; it < data.getNumTaxa(); it++)
for (int i = 0; i <= (icEnd - icStart) / 2 && icStart + i < icEnd - i; i++) {
data.tradeStatesBetweenCharacters(icStart + i, icEnd - i, it, true);
}
}
return true;
}
public boolean alterBlockInTaxon(CharacterData data, int icStart, int icEnd, int it) {
if (data == null) return false;
if (data instanceof MolecularData) {
MolecularData mData = (MolecularData) data;
mData.reverse(icStart, icEnd, it, false, true);
} else
for (int i = 0; i <= (icEnd - icStart) / 2 && icStart + i < icEnd - i; i++) {
data.tradeStatesBetweenCharacters(icStart + i, icEnd - i, it, true);
}
return true;
}
/*.................................................................................................................*/
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());
}
}
}
public Associable getTaxaInfo(CharacterData data, boolean makeIfNotPresent) {
if (makeIfNotPresent && taxaInfo == null) {
taxaInfo = new TaxaInfo(data.getNumTaxa(), data);
}
return taxaInfo;
}
/** 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;
}
