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();
    }
  }