Exemplo n.º 1
0
  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;
  }
Exemplo n.º 2
0
  /*.................................................................................................................*/
  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);
  }