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 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 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 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 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);
}
