/*.................................................................................................................*/
public void processSingleXMLPreference(String tag, String content) {
if ("bootStrapReps".equalsIgnoreCase(tag)) bootstrapreps = MesquiteInteger.fromString(content);
if ("mxram".equalsIgnoreCase(tag)) mxram = MesquiteInteger.fromString(content);
if ("convertGapsToMissing".equalsIgnoreCase(tag))
convertGapsToMissing = MesquiteBoolean.fromTrueFalseString(content);
if ("resamplingAllConsensusTrees".equalsIgnoreCase(tag))
resamplingAllConsensusTrees = MesquiteBoolean.fromTrueFalseString(content);
if ("harvestOnlyStrictConsensus".equalsIgnoreCase(tag))
harvestOnlyStrictConsensus = MesquiteBoolean.fromTrueFalseString(content);
if ("searchStyle".equalsIgnoreCase(tag)) searchStyle = MesquiteInteger.fromString(content);
if ("searchArguments".equalsIgnoreCase(tag))
searchArguments = StringUtil.cleanXMLEscapeCharacters(content);
if ("bootstrapSearchArguments".equalsIgnoreCase(tag))
bootstrapSearchArguments = StringUtil.cleanXMLEscapeCharacters(content);
if ("otherOptions".equalsIgnoreCase(tag))
otherOptions = StringUtil.cleanXMLEscapeCharacters(content);
// parallel, etc.
preferencesSet = true;
}
/*.................................................................................................................*/
public void processSingleXMLPreference(String tag, String content) {
if ("availMemory".equalsIgnoreCase(tag)) availMemory = MesquiteInteger.fromString(content);
super.processSingleXMLPreference(tag, content);
}
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 boolean queryOptions() {
if (!okToInteractWithUser(
CAN_PROCEED_ANYWAY,
"Querying Options")) // Debugg.println needs to check that options set well enough to
// proceed anyway
return true;
boolean closeWizard = false;
if ((MesquiteTrunk.isMacOSXBeforeSnowLeopard()) && MesquiteDialog.currentWizard == null) {
CommandRecord cRec = null;
cRec = MesquiteThread.getCurrentCommandRecordDefIfNull(null);
if (cRec != null) {
cRec.requestEstablishWizard(true);
closeWizard = true;
}
}
MesquiteInteger buttonPressed = new MesquiteInteger(1);
queryOptionsDialog =
new ExtensibleDialog(
containerOfModule(),
"TNT Options & Locations",
buttonPressed); // MesquiteTrunk.mesquiteTrunk.containerOfModule()
// queryOptionsDialog.addLabel("TNT - Options and Locations");
String helpString =
"This module will prepare a matrix for TNT, and ask TNT do to an analysis. A command-line version of TNT must be installed. "
+ "You can ask it to do a bootstrap analysis or not. "
+ "Mesquite will read in the trees found by TNT. ";
queryOptionsDialog.appendToHelpString(helpString);
queryOptionsDialog.setHelpURL(zephyrRunnerEmployer.getProgramURL());
MesquiteTabbedPanel tabbedPanel = queryOptionsDialog.addMesquiteTabbedPanel();
tabbedPanel.addPanel("TNT Program Details", true);
externalProcRunner.addItemsToDialogPanel(queryOptionsDialog);
Checkbox parallelCheckBox =
queryOptionsDialog.addCheckBox("use PVM for parallel processing", parallel);
parallelCheckBox.addItemListener(this);
IntegerField slavesField =
queryOptionsDialog.addIntegerField(
"Number of Slaves", numSlaves, 4, 0, MesquiteInteger.infinite);
IntegerField maxRamField =
queryOptionsDialog.addIntegerField("mxram value", mxram, 4, 0, MesquiteInteger.infinite);
tabbedPanel.addPanel("Search Options", true);
Choice searchStyleChoice = null;
if (bootstrapAllowed)
searchStyleChoice =
queryOptionsDialog.addPopUpMenu(
"Type of search/resampling:",
new String[] {
"Regular Search",
"Bootstrap",
"Jackknife",
"Symmetric Resampled",
"Poisson Bootstrap"
},
searchStyle);
queryOptionsDialog.addLabel("Regular Search Commands");
searchField = queryOptionsDialog.addTextAreaSmallFont(searchArguments, 7, 80);
searchScriptPathField =
queryOptionsDialog.addTextField(
"Path to TNT run file containing search commands", searchScriptPath, 40);
Button browseSearchScriptPathButton =
queryOptionsDialog.addAListenedButton("Browse...", null, this);
browseSearchScriptPathButton.setActionCommand("browseSearchScript");
harvestOnlyStrictConsensusBox =
queryOptionsDialog.addCheckBox("only acquire strict consensus", harvestOnlyStrictConsensus);
queryOptionsDialog.addHorizontalLine(1);
// Checkbox doBootstrapBox = queryOptionsDialog.addCheckBox("do bootstrapping", doBootstrap);
if (bootstrapAllowed) {
bootStrapRepsField =
queryOptionsDialog.addIntegerField(
"Resampling Replicates", bootstrapreps, 8, 0, MesquiteInteger.infinite);
queryOptionsDialog.addLabel("Resampling Search Commands");
bootstrapSearchField =
queryOptionsDialog.addTextAreaSmallFont(bootstrapSearchArguments, 7, 80);
bootSearchScriptPathField =
queryOptionsDialog.addTextField(
"Path to TNT run file containing search commands for resampled",
bootSearchScriptPath,
30);
Button browseBootSearchScriptPathButton =
queryOptionsDialog.addAListenedButton("Browse...", null, this);
browseSearchScriptPathButton.setActionCommand("browseBootSearchScript");
resamplingAllConsensusTreesBox =
queryOptionsDialog.addCheckBox(
"allow TNT to calculate consensus tree", !resamplingAllConsensusTrees);
}
adjustDialogText();
queryOptionsDialog.addHorizontalLine(1);
queryOptionsDialog.addNewDialogPanel();
useDefaultsButton = queryOptionsDialog.addAListenedButton("Set to Defaults", null, this);
useDefaultsButton.setActionCommand("setToDefaults");
tabbedPanel.addPanel("Other Options", true);
convertGapsBox =
queryOptionsDialog.addCheckBox(
"convert gaps to missing (to avoid gap=extra state)", convertGapsToMissing);
queryOptionsDialog.addHorizontalLine(1);
queryOptionsDialog.addLabel("Post-Search TNT Commands");
otherOptionsField = queryOptionsDialog.addTextAreaSmallFont(otherOptions, 7, 80);
queryOptionsDialog.addHorizontalLine(1);
queryOptionsDialog.addNewDialogPanel();
useDefaultsOtherOptionsButton =
queryOptionsDialog.addAListenedButton("Set to Defaults", null, this);
useDefaultsOtherOptionsButton.setActionCommand("setToDefaultsOtherOptions");
tabbedPanel.cleanup();
queryOptionsDialog.nullifyAddPanel();
queryOptionsDialog.completeAndShowDialog("Search", "Cancel", null, null);
if (buttonPressed.getValue() == 0) {
boolean infererOK = (treeInferer == null || treeInferer.optionsChosen());
if (externalProcRunner.optionsChosen() && infererOK) {
if (bootstrapAllowed) {
bootstrapreps = bootStrapRepsField.getValue();
bootstrapSearchArguments = bootstrapSearchField.getText();
bootSearchScriptPath = bootSearchScriptPathField.getText();
harvestOnlyStrictConsensus = harvestOnlyStrictConsensusBox.getState();
resamplingAllConsensusTrees = !resamplingAllConsensusTreesBox.getState();
searchStyle = searchStyleChoice.getSelectedIndex();
}
numSlaves = slavesField.getValue();
otherOptions = otherOptionsField.getText();
convertGapsToMissing = convertGapsBox.getState();
parallel = parallelCheckBox.getState();
// doBootstrap = doBootstrapBox.getState();
searchArguments = searchField.getText();
searchScriptPath = searchScriptPathField.getText();
mxram = maxRamField.getValue();
storeRunnerPreferences();
}
}
queryOptionsDialog.dispose();
if (closeWizard) MesquiteDialog.closeWizard();
return (buttonPressed.getValue() == 0);
}
/*.................................................................................................................*/
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");
}
}