/*.................................................................................................................*/
public void processAceFileWithoutContig(
DNAData data,
String processedAceFilePath,
AceFile ace,
String geneName,
MesquiteString fullName,
int it,
MesquiteString voucherCode) {
DNAData editedData = ChromaseqUtil.getEditedData(data);
DNAData originalData = ChromaseqUtil.getOriginalData(data);
Taxa taxa = data.getTaxa();
ace.processFailedContig(polyThreshold);
ace.setNameTranslation(fileNameTranslation);
ace.renameContigs(fullName.toString(), addFragName, geneName);
ace.setLowQualityToLowerCase(qualThresholdForLowerCase);
ace.writeToPropertiesFile(contigPropertiesFileBuffer, fullName.toString());
if (truncateMixedEnds) {
ace.trimMixedEnds(mixedEndThreshold, mixedEndWindow, qualThresholdForTrim, addPhrapFailures);
}
MesquiteFile.putFileContents(processedAceFilePath, ace.toString(processPolymorphisms), true);
ace.importSequence(
taxa,
editedData,
it,
originalData,
ChromaseqUtil.getQualityData(data),
ChromaseqUtil.getRegistryData(data),
singleTaxaBlock,
processPolymorphisms,
maxChar,
"",
true,
voucherCode);
}
/*.................................................................................................................*/
public Object getProgramArguments(
String dataFileName, String configFileName, boolean isPreflight) {
MesquiteString arguments = new MesquiteString();
if (externalProcRunner.isWindows()) arguments.setValue(" --batch " + configFileName);
else
arguments.setValue(
""); // GARLI command is very simple as all of the arguments are in the config file
return arguments;
}
/*.................................................................................................................*/
public void processAceFileWithContig(
CharacterData data,
MesquiteModule ownerModule,
String processedAceFilePath,
String fragmentDirPath,
AceFile ace,
SequenceUploader uploader,
String geneName,
MesquiteString fullName,
String baseName,
MesquiteString voucherCode,
int it) {
DNAData editedData = ChromaseqUtil.getEditedData(data);
DNAData originalData = ChromaseqUtil.getOriginalData(data);
Taxa taxa = data.getTaxa();
ace.setNameTranslation(fileNameTranslation);
ownerModule.log(ace.contigListForLog() + StringUtil.lineEnding());
if (processPolymorphisms) ace.processPolys(); // creates an additional CO that has polys in it
if (renameContigsInAceFiles) ace.renameContigs(fullName.toString(), addFragName, geneName);
ace.setLowQualityToLowerCase(qualThresholdForLowerCase);
ace.writeToPropertiesFile(contigPropertiesFileBuffer, fullName.toString());
if (truncateMixedEnds)
ace.trimMixedEnds(mixedEndThreshold, mixedEndWindow, qualThresholdForTrim, addPhrapFailures);
/* if (uploadResultsToDatabase && StringUtil.notEmpty(databaseURL)) {
uploader.uploadAceFileToServer(MesquiteXMLToLUtilities.getTOLPageDatabaseURL(databaseURL), ace, processPolymorphisms, qualThresholdForTrim);
}
*/
System.out.println("\n\nfasta file name: " + baseName + " ace file: " + ace);
MesquiteFile.putFileContents(
fragmentDirPath
+ MesquiteFile.fileSeparator
+ ChromaseqUtil.processedFastaFolder
+ MesquiteFile.fileSeparator
+ baseName
+ ".fas",
ace.toFASTAString(processPolymorphisms, qualThresholdForTrim),
true);
MesquiteFile.putFileContents(processedAceFilePath, ace.toString(processPolymorphisms), true);
ace.importSequence(
taxa,
editedData,
it,
originalData,
ChromaseqUtil.getQualityData(data),
ChromaseqUtil.getRegistryData(data),
singleTaxaBlock,
processPolymorphisms,
maxChar,
" contig ",
false,
voucherCode);
}
/** 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;
}
}
/*.................................................................................................................*/
private void recordSourceProject() {
MesquiteString s = new MesquiteString();
s.setValue(getProject().getHomeFileName());
if (!QueryDialogs.queryString(
containerOfModule(),
"Name to Stamp",
"Indicate source file name to stamp on matrix rows",
s)) return;
int numMatrices = getProject().getNumberCharMatrices();
NameReference sourceRef = NameReference.getNameReference("SourceFile");
for (int im = 0; im < numMatrices; im++) {
CharacterData data = getProject().getCharacterMatrix(im);
Taxa taxa = data.getTaxa();
Associable tInfo = data.getTaxaInfo(true);
boolean anySelected = taxa.anySelected();
for (int it = 0; it < taxa.getNumTaxa(); it++) {
if (data.hasDataForTaxon(it) && (!anySelected || taxa.getSelected(it)))
tInfo.setAssociatedObject(sourceRef, it, s.getValue());
}
}
}
/*.................................................................................................................*/
public Object doCommand(String commandName, String arguments, CommandChecker checker) {
if (checker.compare(
this.getClass(),
"Sets module supplying characters",
"[name of module]",
commandName,
"setCharacterSource")) {
CharacterObedSource newCharacterSourceTask;
if (hiringCondition != null)
newCharacterSourceTask =
(CharacterObedSource)
replaceCompatibleEmployee(
CharacterObedSource.class,
arguments,
characterSourceTask,
hiringCondition); // , "Source of characters"
else
newCharacterSourceTask =
(CharacterObedSource)
replaceEmployee(
CharacterObedSource.class,
arguments,
"Source of characters",
characterSourceTask);
if (newCharacterSourceTask != null) {
characterSourceTask = newCharacterSourceTask;
characterSourceTask.setHiringCommand(cstC);
charSourceName.setValue(characterSourceTask.getName());
resetContainingMenuBar();
parametersChanged();
return characterSourceTask;
} else {
discreetAlert(
"Unable to activate character source \""
+ arguments
+ "\" for use by "
+ employer.getName());
}
} else if (characterSourceTask != null) { // todo: temporary, for snapshot conversions
return characterSourceTask.doCommand(commandName, arguments, checker);
} else return super.doCommand(commandName, arguments, checker);
return null;
}
public void calculateNumber(Taxon taxon, MesquiteNumber result, MesquiteString resultString) {
if (result == null) return;
clearResultAndLastResult(result);
Taxa taxa = taxon.getTaxa();
int it = taxa.whichTaxonNumber(taxon);
if (taxa != currentTaxa || observedStates == null) {
observedStates = matrixSourceTask.getCurrentMatrix(taxa);
currentTaxa = taxa;
}
if (observedStates == null || !(observedStates.getParentData() instanceof DNAData)) return;
DNAData data = (DNAData) observedStates.getParentData();
int count = data.getAminoAcidNumbers(it, ProteinData.TER, countEvenIfOthers.getValue());
if (result != null) result.setValue(count);
if (resultString != null)
resultString.setValue(
"Number of stop codons in taxon " + observedStates.getName() + ": " + count);
saveLastResult(result);
saveLastResultString(resultString);
}
/*.................................................................................................................*/
public void reprocessAceFileDirectory(
MesquiteFile file, MesquiteModule ownerModule, DNAData data, int it) {
if (data == null || file == null) return;
String aceFileDirectoryPath =
ChromaseqUtil.getAceFileDirectory(file.getDirectoryName(), ownerModule, data, it);
File aceFileDirectory = new File(aceFileDirectoryPath);
boolean addFragName = false; // control of this?
int currentRead = -1;
String dataFilePath = MesquiteFile.composePath(data.getProject().getHomeDirectoryName(), "");
boolean addingPhrapFailures = false;
AceFile ace = null;
MesquiteProject project = data.getProject();
if (project == null) return;
String processedAceFilePath = "";
MesquiteString fullName = null;
MesquiteString voucherCode = null;
String geneName = ChromaseqUtil.getGeneName(data);
if (aceFileDirectory.isDirectory()) {
int numPhdFiles = getNumPhdFilesInDirectory(aceFileDirectory, aceFileDirectoryPath);
fileNameTranslation = new String[5][numPhdFiles];
fillNameTranslation(data, it, numPhdFiles);
String[] files = aceFileDirectory.list();
for (int i = 0;
i < files.length;
i++) { // going through the folders and finding the ace files
if (files[i] != null) {
String filePath = aceFileDirectoryPath + MesquiteFile.fileSeparator + files[i];
String infoFilePath =
aceFileDirectoryPath + MesquiteFile.fileSeparator + ChromaseqUtil.infoFileName;
File cFile = new File(filePath);
if (cFile.exists()) {
if (!cFile.isDirectory()) {
if (files[i].endsWith(ChromaseqUtil.processedACESuffix + ".ace")) {
// don't do anything
} else if (files[i].endsWith(".ace")
&& !files[i].startsWith(".")
&& !addingPhrapFailures) {
ownerModule.logln("Processing ACE file: " + files[i]);
String baseName =
files[i].substring(
0, files[i].length() - 4); // this is the name of the sequence
processedAceFilePath =
aceFileDirectoryPath
+ MesquiteFile.fileSeparator
+ baseName
+ ChromaseqUtil.processedACESuffix
+ ".ace";
ace =
new AceFile(
filePath,
processedAceFilePath,
dataFilePath,
dataFilePath,
ownerModule,
processPolymorphisms,
polyThreshold,
false);
if (ace == null) return;
ace.setBaseName(baseName);
fullName = new MesquiteString(baseName);
voucherCode = new MesquiteString();
ChromaseqInfoFile.processInfoFile(infoFilePath, fullName, voucherCode);
String fragmentDirPath =
StringUtil.getAllButLastItem(
StringUtil.getAllButLastItem(
aceFileDirectoryPath, MesquiteFile.fileSeparator),
MesquiteFile.fileSeparator);
ace.setLongSequenceName(fullName.toString());
if (ace.getNumContigs() >= 1) {
processAceFileWithContig(
data,
ownerModule,
processedAceFilePath,
fragmentDirPath,
ace,
null,
geneName,
fullName,
baseName,
voucherCode,
it);
} else {
ownerModule.logln(" ACE file contains no contigs!");
if (project != null) {
addingPhrapFailures = true;
i = 0;
ace.createEmptyContigs(
MesquiteFile.numFilesEndingWith(
aceFileDirectoryPath, files, ".phd.1")); // create an empty contig
ace.renameContigs(fullName.toString(), addFragName, geneName);
}
}
if (!addingPhrapFailures) ace.dispose();
} else if (files[i].endsWith(".phd.1") && addingPhrapFailures) {
ownerModule.logln(" Importing single-read Phred file " + files[i]);
currentRead++;
ace.addPhdFileAsSingleReadInContig(
currentRead,
aceFileDirectoryPath,
files[i],
processPolymorphisms,
polyThreshold);
}
}
}
}
}
}
if (addingPhrapFailures && ace != null) { // have to process AceFile that we have manually made
MesquiteFile.putFileContents(processedAceFilePath, ace.toString(processPolymorphisms), true);
if (project != null) {
processAceFileWithoutContig(
data, processedAceFilePath, ace, geneName, fullName, it, voucherCode);
}
ace.dispose();
}
}
/*.................................................................................................................*/
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;
}