public static boolean checkNoContigAceFiles(CharacterData data, MesquiteModule ownerModule) {
DNAData editedData = ChromaseqUtil.getEditedData(data);
if (editedData == null) return false;
int count = 0;
boolean resave = false;
boolean warn = false;
for (int it = 0; it < editedData.getNumTaxa(); it++)
if (AceFile.hasAceFilePath(editedData, it)) {
if (!AceFile.hasAceFile(ownerModule, editedData, it)) {}
AceFile ace = AceFile.getAceFile(ownerModule, editedData, it);
if (ace != null) {
if (ace.getNumContigs() <= 0 || ace.getContig(0).getNumBases() == 0) {
if (!warn
&& !AlertDialog.query(
ownerModule.containerOfModule(),
"Reprocess and save file?",
"Some of the contigs need to be reprocessed, which will"
+ " alter the modified .ace files produced by Phrap and Chromaseq. To be compatible with these altered .ace files, the Mesquite file "
+ "would then need to be re-saved. If instead you choose not to reprocess contigs, they will not be fully editable in Chromaseq.",
"Reprocess and Save",
"Do not reprocess",
-1)) {
return false;
} else resave = true;
warn = true;
ChromaseqUtil.setReprocessContig(editedData, it);
}
}
count++;
}
return resave;
}
/*.................................................................................................................*/
public static boolean hasDisconnectedAceFiles(CharacterData data, MesquiteModule ownerModule) {
DNAData editedData = ChromaseqUtil.getEditedData(data);
if (editedData == null) return true;
for (int it = 0; it < editedData.getNumTaxa(); it++)
if (AceFile.hasAceFilePath(editedData, it)
&& !AceFile.hasAceFile(ownerModule, editedData, it)) {
// boolean db = AceFile.hasAceFile(ownerModule, editedData,it);
return true;
}
return false;
}
public static boolean processNoContigAceFiles(CharacterData data, MesquiteModule ownerModule) {
DNAData editedData = ChromaseqUtil.getEditedData(data);
if (editedData == null) return false;
boolean changed = false;
MesquiteFile file = data.getProject().getHomeFile();
int count = 0;
int originalChars = editedData.getNumChars();
for (int it = 0; it < editedData.getNumTaxa(); it++)
if (ChromaseqUtil.reprocessContig(editedData, it)) {
AceDirectoryProcessor aceDirProcessor = new AceDirectoryProcessor();
aceDirProcessor.reprocessAceFileDirectory(file, ownerModule, editedData, it);
count++;
}
if (count > 0) {
editedData.getTaxa().notifyListeners(ownerModule, new Notification(ownerModule.PARTS_ADDED));
MesquiteMessage.discreetNotifyUser(
"Some of the contigs have been reprocessed; this will be lost permanently unless you resave the file.");
changed = true;
}
if (originalChars < editedData.getNumChars())
editedData.notifyListeners(ownerModule, new Notification(ownerModule.PARTS_ADDED));
else if (originalChars > editedData.getNumChars())
editedData.notifyListeners(ownerModule, new Notification(ownerModule.PARTS_DELETED));
ChromaseqUtil.removeAssociatedObjects(editedData, ChromaseqUtil.reprocessContigRef);
return changed;
}
/*.................................................................................................................*/
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 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 fillNameTranslation(DNAData editedData, int it, int numReads) {
Associable as = editedData.getTaxaInfo(false);
if (as == null) return;
String[] fileNames =
ChromaseqUtil.getStringsAssociated(as, ChromaseqUtil.origReadFileNamesRef, it);
String[] primerNames =
ChromaseqUtil.getStringsAssociated(as, ChromaseqUtil.primerForEachReadNamesRef, it);
String[] sampleCodes =
ChromaseqUtil.getStringsAssociated(as, ChromaseqUtil.sampleCodeNamesRef, it);
for (int i = 0; i < numReads; i++) {
if (fileNames == null) {
if (i == 0)
MesquiteMessage.warnProgrammer(
"fileNames NULL in AceDirectoryProcess.fileNameTranslation");
} else if (i * 2 + 1 < fileNames.length) {
fileNameTranslation[0][i] = fileNames[i * 2];
fileNameTranslation[1][i] = fileNames[i * 2 + 1];
} else
MesquiteMessage.warnProgrammer(
"fileNames.length too small in AceDirectoryProcess.fileNameTranslation: fileNames.length = "
+ fileNames.length
+ ", numReads: "
+ numReads);
if (primerNames == null) {
if (i == 0)
MesquiteMessage.warnProgrammer(
"primerNames NULL in AceDirectoryProcess.fileNameTranslation");
} else if (i * 2 + 1 < primerNames.length) fileNameTranslation[2][i] = primerNames[i * 2 + 1];
else
MesquiteMessage.warnProgrammer(
"primerNames.length too small in AceDirectoryProcess.fileNameTranslation: primerNames.length = "
+ primerNames.length
+ ", numReads: "
+ numReads);
if (sampleCodes == null) {
if (i == 0)
MesquiteMessage.warnProgrammer(
"sampleCodes NULL in AceDirectoryProcess.fileNameTranslation");
} else if (i * 3 + 2 < sampleCodes.length) {
fileNameTranslation[3][i] = sampleCodes[i * 3 + 1];
fileNameTranslation[4][i] = sampleCodes[i * 3 + 2];
} else
MesquiteMessage.warnProgrammer(
"sampleCodes.length too small in AceDirectoryProcess.fileNameTranslation: sampleCodes.length = "
+ sampleCodes.length
+ ", numReads: "
+ numReads);
}
}
/*.................................................................................................................*/
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();
}
}