/*.................................................................................................................*/ 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(); } }