/*.................................................................................................................*/
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;
}
/*.................................................................................................................*/
void getArguments(
MultipartEntityBuilder builder,
StringBuffer sb,
String fileName,
String LOCproteinModel,
String LOCdnaModel,
String LOCotherOptions,
int LOCbootstrapreps,
int LOCbootstrapSeed,
int LOCnumRuns,
String LOCoutgroupTaxSetString,
String LOCMultipleModelFile,
boolean preflight) {
if (builder == null) return;
/*
if (preflight)
arguments += " -n preflight.out ";
else
arguments += " -s " + fileName + " -n file.out ";
*/
if (isProtein) {
if (StringUtil.blank(LOCproteinModel))
addArgument(builder, sb, "vparam.protein_opts_", "PROTGAMMAJTT");
else addArgument(builder, sb, "vparam.protein_opts_", LOCproteinModel);
} else if (StringUtil.blank(LOCdnaModel))
addArgument(builder, sb, "vparam.dna_gtrcat_", "GTRGAMMA");
else addArgument(builder, sb, "vparam.dna_gtrcat_", "GTRGAMMA");
// builder.addTextBody("vparam.dna_gtrcat_",LOCdnaModel);
/*
if (StringUtil.notEmpty(LOCMultipleModelFile))
arguments += " -q " + ShellScriptUtil.protectForShellScript(LOCMultipleModelFile);
if (!StringUtil.blank(LOCotherOptions))
arguments += " " + LOCotherOptions;
*/
addArgument(builder, sb, "vparam.provide_parsimony_seed_", "1");
addArgument(builder, sb, "vparam.parsimony_seed_val_", "" + randomIntSeed);
if (bootstrapOrJackknife()) {
if (LOCbootstrapreps > 0) {
addArgument(builder, sb, "vparam.choose_bootstrap_", "b");
addArgument(builder, sb, "vparam.bootstrap_value_", "" + LOCbootstrapreps);
addArgument(builder, sb, "vparam.seed_value_", "" + LOCbootstrapSeed);
// addArgument(builder, sb, "vparam.bootstrap_",""+LOCbootstrapreps);
// addArgument(builder, sb, "vparam.mulparambootstrap_seed_",""+LOCbootstrapSeed);
} else Debugg.println("TOO FEW BOOTSTRAP REPS");
} else {
addArgument(builder, sb, "vparam.specify_runs_", "1");
addArgument(builder, sb, "vparam.altrun_number_", "" + LOCnumRuns);
// if (RAxML814orLater)
// addArgument(builder, sb, "vparam.mesquite_output_","1");
}
TaxaSelectionSet outgroupSet = null;
if (!StringUtil.blank(LOCoutgroupTaxSetString)) {
outgroupSet =
(TaxaSelectionSet) taxa.getSpecsSet(LOCoutgroupTaxSetString, TaxaSelectionSet.class);
if (outgroupSet != null)
addArgument(builder, sb, "vparam.outgroup_", outgroupSet.getStringList(",", true));
arguments += " -o " + outgroupSet.getStringList(",", true);
}
}