/*.................................................................................................................*/
public void actionPerformed(ActionEvent e) {
if (e.getActionCommand().equalsIgnoreCase("setToDefaults")) {
setDefaultTNTCommandsSearchOptions();
searchField.setText(searchArguments);
bootstrapSearchField.setText(bootstrapSearchArguments);
harvestOnlyStrictConsensusBox.setState(harvestOnlyStrictConsensus);
resamplingAllConsensusTreesBox.setState(!resamplingAllConsensusTrees);
bootStrapRepsField.setValue(bootstrapreps);
} else if (e.getActionCommand().equalsIgnoreCase("setToDefaultsOtherOptions")) {
setDefaultTNTCommandsOtherOptions();
otherOptionsField.setText(otherOptions);
convertGapsBox.setState(convertGapsToMissing);
} else if (e.getActionCommand().equalsIgnoreCase("browseSearchScript")
&& searchScriptPathField != null) {
MesquiteString directoryName = new MesquiteString();
MesquiteString fileName = new MesquiteString();
String path =
MesquiteFile.openFileDialog("Choose Search Script File", directoryName, fileName);
if (StringUtil.notEmpty(path)) searchScriptPathField.setText(path);
} else if (e.getActionCommand().equalsIgnoreCase("browseBootSearchScript")
&& bootSearchScriptPathField != null) {
MesquiteString directoryName = new MesquiteString();
MesquiteString fileName = new MesquiteString();
String path =
MesquiteFile.openFileDialog(
"Choose Resampling Search Script File", directoryName, fileName);
if (StringUtil.notEmpty(path)) bootSearchScriptPathField.setText(path);
}
}
/** monitors the run. */
public boolean monitorAndCleanUpShell() {
lastModified = null;
boolean stillGoing = true;
if (outputFilePaths != null) {
lastModified = new long[outputFilePaths.length];
LongArray.deassignArray(lastModified);
}
if (!StringUtil.blank(
runningFilePath)) // is file at runningFilePath; watch for its disappearance
while (MesquiteFile.fileExists(runningFilePath) && stillGoing) {
processOutputFiles();
try {
Thread.sleep(sleepTime);
} catch (InterruptedException e) {
MesquiteMessage.notifyProgrammer(
"InterruptedException in shell script executed by " + name);
return false;
}
stillGoing = watcher == null || watcher.continueShellProcess(proc);
}
if (outputFileProcessor != null)
outputFileProcessor.processCompletedOutputFiles(outputFilePaths);
return true;
}
/*................................................................................................*/
public boolean startJob(String arguments, Object condition, boolean hiredByName) {
addMenuItem("Directory for Sample Trees From Directory...", makeCommand("setDirPath", this));
fillerTasks = new Vector();
if (!MesquiteThread
.isScripting()) { // enclosed in conditional to avoid hiring query when opening file; should
// be handled by snapshot/doCommand when file is opened.
String directoryPath =
MesquiteFile.chooseDirectory(
"Choose directory containing tree files:",
previousDirectory); // MesquiteFile.saveFileAsDialog("Base name for files (files will
// be named <name>1.nex, <name>2.nex, etc.)", baseName);
if (StringUtil.blank(directoryPath)) { // TODO: clean this up?
return false;
} else {
directory = new File(directoryPath);
previousDirectory = directory.getParent();
if (directory.exists() && directory.isDirectory()) {
return hireFillers(directoryPath);
}
}
}
return true; // Add something to make sure directory paths are set up correctly, when not
// scripting...
}
/**
* executes a shell script at "scriptPath". If runningFilePath is not blank and not null, then
* Mesquite will create a file there that will serve as a flag to Mesquite that the script is
* running.
*/
public boolean executeInShell() {
proc = null;
try {
ShellScriptUtil.setScriptFileToBeExecutable(scriptPath);
if (!StringUtil.blank(runningFilePath)) {
if (StringUtil.blank(runningFileMessage))
MesquiteFile.putFileContents(runningFilePath, "Script running...", true);
else MesquiteFile.putFileContents(runningFilePath, runningFileMessage, true);
if (appendRemoveCommand && MesquiteFile.fileExists(runningFilePath))
MesquiteFile.appendFileContents(
scriptPath,
StringUtil.lineEnding() + ShellScriptUtil.getRemoveCommand(runningFilePath),
true); // append remove command to guarantee that the runningFile is deleted
// +StringUtil.lineEnding()+ShellScriptUtil.getExitCommand()
}
proc = ShellScriptUtil.executeScript(scriptPath, visibleTerminal);
} catch (IOException e) {
MesquiteMessage.warnProgrammer("IOException in shell script executed by " + name);
return false;
}
return true;
}
public void runFilesAvailable(int fileNum) {
String[] logFileNames = getLogFileNames();
if ((progIndicator != null && progIndicator.isAborted()) || logFileNames == null) return;
String[] outputFilePaths = new String[logFileNames.length];
outputFilePaths[fileNum] = externalProcRunner.getOutputFilePath(logFileNames[fileNum]);
String filePath = outputFilePaths[fileNum];
if (fileNum == 0
&& outputFilePaths.length > 0
&& !StringUtil.blank(outputFilePaths[0])
&& !bootstrapOrJackknife()) { // tree file
if (ownerModule instanceof NewTreeProcessor) {
String treeFilePath = filePath;
if (taxa != null) {
TaxaSelectionSet outgroupSet =
(TaxaSelectionSet) taxa.getSpecsSet(outgroupTaxSetString, TaxaSelectionSet.class);
((NewTreeProcessor) ownerModule).newTreeAvailable(treeFilePath, outgroupSet);
} else ((NewTreeProcessor) ownerModule).newTreeAvailable(treeFilePath, null);
}
} else if (fileNum == 1
&& outputFilePaths.length > 1
&& !StringUtil.blank(outputFilePaths[1])
&& !bootstrapOrJackknife()) { // log file
if (MesquiteFile.fileExists(filePath)) {
String s = MesquiteFile.getFileLastContents(filePath);
if (!StringUtil.blank(s))
if (progIndicator != null) {
parser.setString(s);
String rep = parser.getFirstToken(); // generation number
logln("");
if (MesquiteInteger.isNumber(rep)) {
int numReps = MesquiteInteger.fromString(rep) + 1;
progIndicator.setText(
"Replicate: " + numReps); // + ", ln L = " + parser.getNextToken());
if (bootstrapOrJackknife()) {
logln("Replicate " + numReps + " of " + bootstrapreps);
}
logln("Replicate " + numReps + " of " + totalNumHits);
progIndicator.spin();
double timePerRep = 0;
if (MesquiteInteger.isCombinable(numReps) && numReps > 0) {
timePerRep = timer.timeSinceVeryStartInSeconds() / numReps; // this is time per rep
}
int timeLeft = 0;
if (bootstrapOrJackknife()) {
timeLeft = (int) ((bootstrapreps - numReps) * timePerRep);
} else {
String token = parser.getNextToken(); // algorithm
token = parser.getNextToken(); // Tree
token = parser.getNextToken(); // Score
String best = parser.getNextToken(); // Best
logln(" Score " + token + "; best found so far " + best);
timeLeft = (int) ((totalNumHits - numReps) * timePerRep);
}
logln(
" Running time so far "
+ StringUtil.secondsToHHMMSS((int) timer.timeSinceVeryStartInSeconds())
+ ", approximate time remaining "
+ StringUtil.secondsToHHMMSS(timeLeft));
}
}
count++;
} else if (MesquiteTrunk.debugMode) logln("*** File does not exist (" + filePath + ") ***");
}
}
/*.................................................................................................................*/
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 formCommandFile(String dataFileName, int firstOutgroup) {
if (parallel) {
commands = "";
}
commands += getTNTCommand("mxram " + mxram);
commands += getTNTCommand("report+0/1/0");
commands += getTNTCommand("log " + logFileName);
commands += getTNTCommand("p " + dataFileName);
commands += getTNTCommand("vversion");
if (MesquiteInteger.isCombinable(firstOutgroup) && firstOutgroup >= 0)
commands += getTNTCommand("outgroup " + firstOutgroup);
if (bootstrapOrJackknife()) {
if (parallel) {
commands += indentTNTCommand("ptnt begin parallelRun " + numSlaves + "/ram x 2 = ");
}
if (StringUtil.notEmpty(bootSearchScriptPath)) {
String script = MesquiteFile.getFileContentsAsString(bootSearchScriptPath);
if (StringUtil.notEmpty(script)) commands += script;
} else
commands += StringUtil.lineEnding() + bootstrapSearchArguments + StringUtil.lineEnding();
String saveTreesString = "";
if (resamplingAllConsensusTrees) saveTreesString = " savetrees ";
String bootSearchString = " [xmult; bb]";
bootSearchString = "";
if (parallel) {
int numRepsPerSlave = bootstrapreps / numSlaves;
if (numRepsPerSlave * numSlaves < bootstrapreps) numRepsPerSlave++;
if (searchStyle == BOOTSTRAPSEARCH)
commands +=
getTNTCommand(
"resample boot cut 50 "
+ saveTreesString
+ " replications "
+ numRepsPerSlave
+ " [xmult; bb] savetrees"); // + getComDelim();
else if (searchStyle == JACKKNIFESEARCH)
commands +=
getTNTCommand(
"resample jak cut 50 "
+ saveTreesString
+ " replications "
+ numRepsPerSlave
+ " [xmult; bb] savetrees"); // + getComDelim();
else if (searchStyle == SYMSEARCH)
commands +=
getTNTCommand(
"resample sym cut 50 "
+ saveTreesString
+ " replications "
+ numRepsPerSlave
+ " [xmult; bb] savetrees"); // + getComDelim();
else if (searchStyle == POISSONSEARCH)
commands +=
getTNTCommand(
"resample poisson cut 50 "
+ saveTreesString
+ " replications "
+ numRepsPerSlave
+ " [xmult; bb] savetrees"); // + getComDelim();
commands += getTNTCommand("return");
commands += getTNTCommand("ptnt wait parallelRun");
commands += getTNTCommand("ptnt get parallelRun");
} else {
if (!resamplingAllConsensusTrees) {
commands += getTNTCommand("macro=");
commands += getTNTCommand("ttags =");
}
commands += getTNTCommand("tsave *" + treeFileName);
if (bootstrapAllowed) {
if (searchStyle == BOOTSTRAPSEARCH)
commands +=
getTNTCommand(
"resample boot "
+ saveTreesString
+ " replications "
+ bootstrapreps
+ bootSearchString); // + getComDelim();
else if (searchStyle == JACKKNIFESEARCH)
commands +=
getTNTCommand(
"resample jak cut 50 "
+ saveTreesString
+ " replications "
+ bootstrapreps
+ bootSearchString); // + getComDelim();
else if (searchStyle == SYMSEARCH)
commands +=
getTNTCommand(
"resample sym cut 50 "
+ saveTreesString
+ " replications "
+ bootstrapreps
+ bootSearchString); // + getComDelim();
else if (searchStyle == POISSONSEARCH)
commands +=
getTNTCommand(
"resample poisson cut 50 "
+ saveTreesString
+ " replications "
+ bootstrapreps
+ bootSearchString); // + getComDelim();
}
if (!resamplingAllConsensusTrees) commands += getTNTCommand("save *");
else commands += getTNTCommand("save");
commands += getTNTCommand("tsave/");
if (!resamplingAllConsensusTrees) {
commands += getTNTCommand("ttags -/");
commands += getTNTCommand("macro-");
}
}
// commands += getTNTCommand("proc/") ;
commands += getTNTCommand("log/");
// if (!parallel)
commands += getTNTCommand("quit");
} else {
// commands += getTNTCommand("tsave !5 " + treeFileName) ; // if showing intermediate trees
commands += getTNTCommand("tsave *" + treeFileName);
if (StringUtil.notEmpty(searchScriptPath)) {
String script = MesquiteFile.getFileContentsAsString(searchScriptPath);
if (StringUtil.notEmpty(script)) commands += script;
} else commands += searchArguments;
commands += otherOptions;
if (harvestOnlyStrictConsensus) commands += getTNTCommand("nelsen *");
commands += getTNTCommand("save");
commands += getTNTCommand("log/");
commands += getTNTCommand("tsave/");
commands += getTNTCommand("quit");
}
}