/*.................................................................................................................*/
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 Object doCommand(String commandName, String arguments, CommandChecker checker) {
if (checker.compare(
this.getClass(), "Returns the matrix source", null, commandName, "getMatrixSource")) {
return matrixSourceTask;
} else if (checker.compare(
this.getClass(), "Copies the data for selected taxon", null, commandName, "copyData")) {
if (observedStates == null) return null;
CharacterData data = observedStates.getParentData();
if (data == null) return null;
int it = MesquiteInteger.fromString(parser.getFirstToken(arguments));
if (MesquiteInteger.isCombinable(it)) {
StringBuffer sb = new StringBuffer();
data.copyDataFromRowIntoBuffer(it, sb);
if (StringUtil.notEmpty(sb.toString())) {
localCopyDataClipboard = sb.toString();
localCopyData = data;
localCopyDataTaxon = data.getTaxa().getTaxonName(it);
} else {
localCopyDataClipboard = null;
localCopyData = null;
localCopyDataTaxon = null;
}
}
return null;
} else if (checker.compare(
this.getClass(), "Pastes the data for selected taxon", null, commandName, "pasteData")) {
if (observedStates == null) return null;
CharacterData data = observedStates.getParentData();
if (data == null) return null;
int it = MesquiteInteger.fromString(parser.getFirstToken(arguments));
if (MesquiteInteger.isCombinable(it) && StringUtil.notEmpty(localCopyDataClipboard)) {
data.pasteDataFromStringIntoTaxon(it, localCopyDataClipboard);
}
return null;
} else if (checker.compare(
this.getClass(),
"Pastes the data for selected taxon",
null,
commandName,
"deleteDataTouched")) {
if (observedStates == null) return null;
CharacterData data = observedStates.getParentData();
if (data == null) return null;
int it = MesquiteInteger.fromString(parser.getFirstToken(arguments));
Debugg.println("prepare to delete row: " + it);
if (MesquiteInteger.isCombinable(it)) {
if (!AlertDialog.query(
containerOfModule(),
"Delete Data?",
"Are you sure you want to delete the data for taxon "
+ data.getTaxa().getTaxonName(it)
+ " in the matrix \""
+ data.getName()
+ "\"",
"No",
"Yes")) {
zapData(data, it);
}
}
return null;
} else if (checker.compare(
this.getClass(), "Deletes the data for selected taxa", null, commandName, "deleteData")) {
if (observedStates == null) return null;
captureCharacterDataFromObservedStates();
if (data == null) return null;
if (!AlertDialog.query(
containerOfModule(),
"Delete Data?",
"Are you sure you want to delete the data for these taxa in the matrix \""
+ data.getName()
+ "\"",
"No",
"Yes")) zapData(data);
return null;
} else if (checker.compare(
this.getClass(),
"deleteds () and anything between",
null,
commandName,
"deletePrepended")) {
if (observedStates == null || taxa == null) return null;
boolean anySelected = taxa.anySelected();
int myColumn = -1;
if (getEmployer() instanceof ListModule) {
myColumn = ((ListModule) getEmployer()).getMyColumn(this);
if (table != null)
anySelected = anySelected || table.anyCellSelectedInColumnAnyWay(myColumn);
}
for (int it = 0; it < taxa.getNumTaxa(); it++) {
if ((!anySelected || selected(taxa, it, myColumn))) {
String note = getNote(it);
while (!StringUtil.blank(note) && note.indexOf("(") >= 0) {
int start = note.indexOf("(");
int end = note.indexOf(")");
String firstBit = "";
if (start > 0) firstBit = note.substring(0, start);
note = firstBit + note.substring(end + 1, note.length());
}
setNote(it, note);
}
}
outputInvalid();
parametersChanged();
return null;
} else if (checker.compare(this.getClass(), "deletes *", null, commandName, "deleteStar")) {
if (observedStates == null || taxa == null) return null;
boolean anySelected = taxa.anySelected();
int myColumn = -1;
if (getEmployer() instanceof ListModule) {
myColumn = ((ListModule) getEmployer()).getMyColumn(this);
if (table != null)
anySelected = anySelected || table.anyCellSelectedInColumnAnyWay(myColumn);
}
for (int it = 0; it < taxa.getNumTaxa(); it++) {
if ((!anySelected || selected(taxa, it, myColumn))) {
String note = getNote(it);
while (!StringUtil.blank(note) && note.indexOf("*") >= 0) {
int start = note.indexOf("*");
String firstBit = "";
if (start > 0) firstBit = note.substring(0, start);
note = firstBit + note.substring(start + 1, note.length());
}
setNote(it, note);
}
}
outputInvalid();
parametersChanged();
return null;
} else if (checker.compare(
this.getClass(),
"Prepends to the note the sequence length (including N\'s and ?\'s) for the selected taxa",
null,
commandName,
"prependLength")) {
if (observedStates == null || taxa == null) return null;
boolean anySelected = taxa.anySelected();
int myColumn = -1;
if (getEmployer() instanceof ListModule) {
myColumn = ((ListModule) getEmployer()).getMyColumn(this);
if (table != null)
anySelected = anySelected || table.anyCellSelectedInColumnAnyWay(myColumn);
}
for (int it = 0; it < taxa.getNumTaxa(); it++) {
if (hasData(it) && (!anySelected || selected(taxa, it, myColumn))) {
String note = getNote(it);
if (StringUtil.blank(note)) note = "(" + sequenceLength(it) + ")";
else note = "(" + sequenceLength(it) + ") " + note;
setNote(it, note);
}
}
outputInvalid();
parametersChanged();
return null;
} else if (checker.compare(
this.getClass(),
"Prepends to the note the number of non-missing sites (not including N\'s and ?\'s) for the selected taxa",
null,
commandName,
"prependNumSites")) {
if (observedStates == null || taxa == null) return null;
boolean anySelected = taxa.anySelected();
int myColumn = -1;
if (getEmployer() instanceof ListModule) {
myColumn = ((ListModule) getEmployer()).getMyColumn(this);
if (table != null)
anySelected = anySelected || table.anyCellSelectedInColumnAnyWay(myColumn);
}
for (int it = 0; it < taxa.getNumTaxa(); it++) {
if (hasData(it) && (!anySelected || selected(taxa, it, myColumn))) {
String note = getNote(it);
if (StringUtil.blank(note)) note = "(" + numSites(it) + ")";
else note = "(" + numSites(it) + ") " + note;
setNote(it, note);
}
}
outputInvalid();
parametersChanged();
return null;
} else if (checker.compare(
this.getClass(),
"Deletes the notes for the selected taxa",
null,
commandName,
"deleteAnnotation")) {
if (observedStates == null || taxa == null) return null;
boolean anySelected = taxa.anySelected();
int myColumn = -1;
if (getEmployer() instanceof ListModule) {
myColumn = ((ListModule) getEmployer()).getMyColumn(this);
if (table != null)
anySelected = anySelected || table.anyCellSelectedInColumnAnyWay(myColumn);
}
for (int it = 0; it < taxa.getNumTaxa(); it++) {
if (hasData(it) && (!anySelected || selected(taxa, it, myColumn))) {
setNote(it, null);
}
}
outputInvalid();
parametersChanged();
return null;
} else return super.doCommand(commandName, arguments, checker);
}
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 + ") ***");
}
}