public void processCompletedOutputFiles(String[] outputFilePaths) {
if (outputFilePaths.length > 1 && !StringUtil.blank(outputFilePaths[1])) {
ZephyrUtil.copyLogFile(this, "TNT", outputFilePaths[1]);
}
if (outputFilePaths.length > 2 && !StringUtil.blank(outputFilePaths[2])) {
ZephyrUtil.copyOutputText(this, outputFilePaths[2], commands);
}
}
/*.................................................................................................................*/
public Tree retrieveTreeBlock(TreeVector treeList, MesquiteDouble finalScore) {
logln("Preparing to receive TNT trees.");
boolean success = false;
taxa = treeList.getTaxa();
// TODO finalScore.setValue(finalValue);
suppressProjectPanelReset();
CommandRecord oldCR = MesquiteThread.getCurrentCommandRecord();
CommandRecord scr = new CommandRecord(true);
MesquiteThread.setCurrentCommandRecord(scr);
// define file paths and set tree files as needed.
setFileNames();
String[] outputFilePaths = externalProcRunner.getOutputFilePaths();
String treeFilePath = outputFilePaths[OUT_TREEFILE];
taxonNumberTranslation = getTaxonNumberTranslation(taxa);
namer.setNumberTranslationTable(taxonNumberTranslation);
runFilesAvailable();
// read in the tree files
success = false;
Tree t = null;
MesquiteBoolean readSuccess = new MesquiteBoolean(false);
// TreeVector tv = new TreeVector(taxa);
if (bootstrapOrJackknife()) {
if (resamplingAllConsensusTrees)
t =
ZephyrUtil.readTNTTreeFile(
this,
treeList,
taxa,
treeFilePath,
"TNT " + getResamplingKindName() + " Rep",
0,
readSuccess,
false,
false,
null,
namer); // set first tree number as 0 as will remove the first one later.
else
t =
ZephyrUtil.readTNTTreeFile(
this,
treeList,
taxa,
treeFilePath,
"TNT " + getResamplingKindName() + " Majority Rule Tree",
1,
readSuccess,
false,
false,
freqRef,
namer);
} else
t =
ZephyrUtil.readTNTTreeFile(
this,
treeList,
taxa,
treeFilePath,
"TNTTree",
1,
readSuccess,
false,
harvestOnlyStrictConsensus,
null,
namer);
success = t != null;
if (success && bootstrapOrJackknife() && resamplingAllConsensusTrees) {
t = t.cloneTree();
treeList.removeElementAt(0, false); // get rid of first one as this is the bootstrap tree
}
MesquiteThread.setCurrentCommandRecord(oldCR);
success = readSuccess.getValue();
if (!success) {
logln("Execution of TNT unsuccessful [2]");
if (!beanWritten) postBean("unsuccessful [2]", false);
beanWritten = true;
} else {
if (!beanWritten) postBean("successful", false);
beanWritten = true;
}
desuppressProjectPanelReset();
if (data != null) data.decrementEditInhibition();
// manager.deleteElement(tv); // get rid of temporary tree block
externalProcRunner.finalCleanup();
if (success) return t;
return null;
}
/*.................................................................................................................*/
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;
}
