/*.................................................................................................................*/
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);
}
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);
}
/*.................................................................................................................*/
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 int[] getTaxonNumberTranslation(Taxa taxa) {
int max = -1;
for (int it = 0; it < taxa.getNumTaxa(); it++) {
long translateNumber = getTaxonNumberInTree(taxa, it);
if (MesquiteLong.isCombinable(translateNumber) && translateNumber > max) {
max = (int) translateNumber;
}
}
int[] translate = new int[max + 1];
for (int it = 0; it < data.getNumTaxa(); it++) {
long translateNumber = getTaxonNumberInTree(taxa, it);
if (MesquiteLong.isCombinable(translateNumber) && translateNumber >= 0) {
translate[(int) translateNumber] = it;
}
}
return translate;
}
/*.................................................................................................................*/
public Tree getTrees(
TreeVector trees,
Taxa taxa,
MCharactersDistribution matrix,
long seed,
MesquiteDouble finalScore) {
if (!initializeGetTrees(CategoricalData.class, taxa, matrix)) return null;
setTNTSeed(seed);
isProtein = data instanceof ProteinData;
// David: if isDoomed() then module is closing down; abort somehow
// write data file
String tempDir =
MesquiteFileUtil.createDirectoryForFiles(
this, MesquiteFileUtil.IN_SUPPORT_DIR, "TNT", "-Run.");
if (tempDir == null) return null;
String dataFileName = "data.ss"; // replace this with actual file name?
String dataFilePath = tempDir + dataFileName;
FileInterpreterI exporter = ZephyrUtil.getFileInterpreter(this, "#InterpretTNT");
if (exporter == null) return null;
boolean fileSaved = false;
String translationTable = namer.getTranslationTable(taxa);
((InterpretHennig86Base) exporter).setTaxonNamer(namer);
fileSaved = ZephyrUtil.saveExportFile(this, exporter, dataFilePath, data, selectedTaxaOnly);
if (!fileSaved) return null;
String translationFileName = IOUtil.translationTableFileName;
setTaxonTranslation(taxa);
taxonNumberTranslation = getTaxonNumberTranslation(taxa);
namer.setNumberTranslationTable(taxonNumberTranslation);
setFileNames();
TaxaSelectionSet outgroupSet =
(TaxaSelectionSet) taxa.getSpecsSet(outgroupTaxSetString, TaxaSelectionSet.class);
int firstOutgroup = MesquiteInteger.unassigned;
if (outgroupSet != null) firstOutgroup = outgroupSet.firstBitOn();
formCommandFile(dataFileName, firstOutgroup);
logln("\n\nCommands given to TNT:");
logln(commands);
logln("");
MesquiteString arguments = new MesquiteString();
arguments.setValue(" proc " + commandsFileName);
String programCommand = externalProcRunner.getExecutableCommand();
int numInputFiles = 3;
String[] fileContents = new String[numInputFiles];
String[] fileNames = new String[numInputFiles];
for (int i = 0; i < numInputFiles; i++) {
fileContents[i] = "";
fileNames[i] = "";
}
fileContents[0] = MesquiteFile.getFileContentsAsString(dataFilePath);
fileNames[0] = dataFileName;
fileContents[1] = commands;
fileNames[1] = commandsFileName;
fileContents[2] = translationTable;
fileNames[2] = translationFileName;
// ----------//
boolean success =
runProgramOnExternalProcess(
programCommand, arguments, fileContents, fileNames, ownerModule.getName());
if (!isDoomed()) {
if (success) {
desuppressProjectPanelReset();
return retrieveTreeBlock(trees, finalScore); // here's where we actually process everything.
} else {
if (!beanWritten) postBean("unsuccessful [1]", false);
beanWritten = true;
}
}
desuppressProjectPanelReset();
if (data == null) data.decrementEditInhibition();
externalProcRunner.finalCleanup();
return null;
}