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(); } }