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);
}
}
/**
* A request for the MesquiteModule to perform a command. It is passed two strings, the name of
* the command and the arguments. This should be overridden by any module that wants to respond to
* a command.
*/
public Object doCommand(String commandName, String arguments, CommandChecker checker) {
if (checker.compare(MesquiteModule.class, null, null, commandName, "paint")) {
MesquiteInteger io = new MesquiteInteger(0);
int column = MesquiteInteger.fromString(arguments, io);
int row = MesquiteInteger.fromString(arguments, io);
if (MesquiteInteger.isCombinable(row)) {
if (!MesquiteLong.isCombinable(currentColor)) removeColor(row, true);
else setColor(row, (int) currentColor);
}
} else if (checker.compare(
this.getClass(),
"Sets the color to be used to paint cells",
"[name of color]",
commandName,
"setColor")) {
int bc = ColorDistribution.standardColorNames.indexOf(parser.getFirstToken(arguments));
if (bc >= 0 && MesquiteLong.isCombinable(bc)) {
removeColor.setValue(false);
currentColor = bc;
savedColor = bc;
colorString = "Color " + ColorDistribution.standardColorNames.getValue(bc);
}
} else if (checker.compare(
this.getClass(),
"Sets the color of selected taxa",
"[name of color]",
commandName,
"setColorSelected")) {
int bc = ColorDistribution.standardColorNames.indexOf(parser.getFirstToken(arguments));
if (bc >= 0 && MesquiteLong.isCombinable(bc)) {
for (int it = 0; it < taxa.getNumTaxa(); it++) if (taxa.getSelected(it)) setColor(it, bc);
}
} else if (checker.compare(
this.getClass(), "Removes color from all the cells", null, commandName, "removeAllColor")) {
removeAllColor(true);
} else if (checker.compare(
this.getClass(),
"Sets the paint brush so that it removes colors from any cells touched",
null,
commandName,
"removeColor")) {
if (StringUtil.blank(arguments)) removeColor.setValue(!removeColor.getValue());
else removeColor.toggleValue(parser.getFirstToken(arguments));
if (removeColor.getValue()) {
colorString = "Remove color";
currentColor = MesquiteLong.unassigned;
} else {
colorString = "Color " + ColorDistribution.standardColorNames.getValue((int) currentColor);
currentColor = savedColor;
}
} else return super.doCommand(commandName, arguments, checker);
return null;
}
/*.................................................................................................................*/
public void fromString(String description, MesquiteInteger stringPos, int format) {
hasDefaultValues = false;
ParseUtil.getToken(description, stringPos); // RMatrix
ParseUtil.getToken(description, stringPos); // =
ParseUtil.getToken(description, stringPos); // (
for (int i = 0; i < getNumStates(); i++) {
String s = ParseUtil.getToken(description, stringPos);
if (s.equalsIgnoreCase(")") || StringUtil.blank(s)) return;
setStateFreq(i, MesquiteDouble.fromString(s));
}
checkNormality(getStateFrequencies());
}
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 + ") ***");
}
}
/*.................................................................................................................*/
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);
}
}