/*.................................................................................................................*/
public Object doCommand(String commandName, String arguments, CommandChecker checker) {
if (checker.compare(
this.getClass(),
"Sets the number of trees included in each tree block",
"[number of trees]",
commandName,
"setNumberTrees")) {
MesquiteInteger pos = new MesquiteInteger(0);
int newNum = MesquiteInteger.fromFirstToken(arguments, pos);
if (!MesquiteInteger.isCombinable(newNum))
newNum =
MesquiteInteger.queryInteger(
containerOfModule(),
"Set Number of Trees",
"Number of Trees:",
numTrees,
0,
MesquiteInteger.infinite);
if (newNum > 0 && newNum != numTrees) {
numTrees = newNum;
parametersChanged();
}
} else if (checker.compare(
this.getClass(),
"Returns the module supplying trees",
"[name of module]",
commandName,
"getTreeFiller")) {
return fillerTask;
} else return super.doCommand(commandName, arguments, checker);
return null;
}
/** Called to alter data in all cells */
public boolean operateOnData(CharacterData data) {
if (!(data instanceof ContinuousData)) return false;
ContinuousData cData = (ContinuousData) data;
int numItems = cData.getNumItems();
String[] items = new String[numItems];
for (int i = 0; i < items.length; i++) {
if (StringUtil.blank(cData.getItemName(i))) items[i] = "(unnamed)";
else items[i] = cData.getItemName(i);
}
int d =
ListDialog.queryList(
containerOfModule(),
"Rename item",
"Rename item:",
MesquiteString.helpString,
items,
0);
if (!MesquiteInteger.isCombinable(d) || d < 0 || d >= numItems) return false;
else {
String s =
MesquiteString.queryString(
containerOfModule(), "Rename Item", "New name for " + items[d], items[d]);
if (StringUtil.blank(s)) return false;
cData.setItemReference(d, NameReference.getNameReference(s));
return true;
}
}
/**
* 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;
}
/** queryies the user to choose a tree and returns an integer of the tree chosen */
public int queryUserChoose(Taxa taxa, String forMessage) {
int ic = MesquiteInteger.unassigned;
int numBlocks = getNumberOfTreeBlocks(taxa);
if (MesquiteInteger.isCombinable(numBlocks)) {
String[] s = new String[numBlocks];
for (int i = 0; i < numBlocks; i++) {
s[i] = getTreeBlockNameString(taxa, i);
}
if (forMessage == null) {
forMessage = "Choose tree block";
}
return ListDialog.queryList(
containerOfModule(), "Choose tree block", forMessage, MesquiteString.helpString, s, 0);
} else {
if (forMessage == null) {
forMessage = "Number of tree block to be used";
}
int r = MesquiteInteger.queryInteger(containerOfModule(), "Choose tree block", forMessage, 1);
if (MesquiteInteger.isCombinable(r)) return MesquiteTree.toInternal(r);
else return r;
}
}
/*.................................................................................................................*/
public Object doCommand(String commandName, String arguments, CommandChecker checker) {
if (checker.compare(
this.getClass(),
"Sets the number of randomly chosen taxa to exclude",
"[number]",
commandName,
"setNumberExcluded")) {
int s = MesquiteInteger.fromString(parser.getFirstToken(arguments));
if (!MesquiteInteger.isCombinable(s)) {
s =
MesquiteInteger.queryInteger(
containerOfModule(),
"Number of taxa to exclude",
"Enter the number of randomly chosen taxa to exclude",
numExcluded);
}
if (MesquiteInteger.isCombinable(s)) {
numExcluded = s;
parametersChanged();
}
} else return super.doCommand(commandName, arguments, checker);
return null;
}
/*.................................................................................................................*/
public boolean startJob(String arguments, Object condition, boolean hiredByName) {
if (!MesquiteThread.isScripting()) {
int s =
MesquiteInteger.queryInteger(
containerOfModule(),
"Number of taxa to exclude",
"Enter the number of randomly chosen taxa to exclude",
numExcluded);
if (MesquiteInteger.isCombinable(s)) numExcluded = s;
else return false;
}
addMenuItem("Number of Taxa Excluded...", makeCommand("setNumberExcluded", this));
return true;
}
/**
* Called to provoke any necessary initialization. This helps prevent the module's intialization
* queries to the user from happening at inopportune times (e.g., while a long chart calculation
* is in mid-progress)
*/
public void initialize(Taxa taxa) {
setPreferredTaxa(taxa);
fillerTask.initialize(taxa);
if (!fillerTask.hasLimitedTrees(taxa)) {
if (!MesquiteThread.isScripting() && !nTreesSet) {
int n =
MesquiteInteger.queryInteger(
containerOfModule(),
"Trees per block?",
"How many trees to include per tree block?",
numTrees);
if (MesquiteInteger.isCombinable(n) && n > 0) numTrees = n;
nTreesSet = true;
}
}
ntreesItem.setEnabled(!fillerTask.hasLimitedTrees(taxa));
MesquiteTrunk.resetMenuItemEnabling();
}
/*.................................................................................................................*/
public Object doCommand(String commandName, String arguments, CommandChecker checker) {
if (checker.compare(
this.getClass(),
"Sets the number of trees included in each tree block",
"[number of trees]",
commandName,
"setNumberTrees")) {
MesquiteInteger pos = new MesquiteInteger(0);
int newNum = MesquiteInteger.fromFirstToken(arguments, pos);
if (!MesquiteInteger.isCombinable(newNum))
newNum =
MesquiteInteger.queryInteger(
containerOfModule(),
"Set Number of Trees",
"Number of Trees:",
numTrees,
0,
MesquiteInteger.infinite);
if (newNum > 0 && newNum != numTrees) {
numTrees = newNum;
parametersChanged();
}
} else if (checker.compare(
this.getClass(),
"Sets the module supplying trees",
"[name of module]",
commandName,
"setTreeFiller")) {
TreeBlockFiller temp =
(TreeBlockFiller)
replaceEmployee(
TreeBlockFiller.class, arguments, "Source of trees for tree blocks", fillerTask);
if (temp != null) {
fillerTask = temp;
initialize(preferredTaxa);
parametersChanged(); // ?
}
return temp;
} else return super.doCommand(commandName, arguments, checker);
return null;
}
/**
* Called to provoke any necessary initialization. This helps prevent the module's intialization
* queries to the user from happening at inopportune times (e.g., while a long chart calculation
* is in mid-progress)
*/
public void initialize(Taxa taxa) {
setPreferredTaxa(taxa);
fillerTask.initialize(taxa);
if (!fillerTask.hasLimitedTrees(taxa)) {
if (!MesquiteThread.isScripting() && !nTreesSet) {
int n =
MesquiteInteger.queryInteger(
containerOfModule(),
"Trees per block?",
"How many trees to include per tree block?",
numTrees);
if (MesquiteInteger.isCombinable(n) && n > 0) numTrees = n;
nTreesSet = true;
}
}
if (enableNumTreesChoice() && ntreesItem == null)
ntreesItem = addMenuItem("Number of Trees...", makeCommand("setNumberTrees", this));
if (ntreesItem != null && fillerTask != null)
ntreesItem.setEnabled(!fillerTask.hasLimitedTrees(taxa));
MesquiteTrunk.resetMenuItemEnabling();
}
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 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");
}
}