/*.................................................................................................................*/ 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); } }
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"); } }