Exemplo n.º 1
0
  public String induceRulesWithTestSet(double testSetPercent) throws DataFormatException {

    SystemVariables.getInstance()
        .appendToExperimentNotes("\\n* Total number of PSSM matches in positive sequences: ");
    // System.out.println("Total number of PSSM matches in positive sequences: ");
    ArrayList<Feature> posTrainingSet =
        regulatoryElementService.getRegulatoryElements(
            regulatoryRegionService.getPositiveRegulatoryRegions(),
            positiveCutOffScore,
            posATcomposition,
            posCGcomposition);

    SystemVariables.getInstance()
        .appendToExperimentNotes("\\n* Total number of PSSM matches in negative sequences: ");
    // System.out.println("Total number of PSSM matches in negative sequences: ");
    ArrayList<Feature> negTrainingSet =
        regulatoryElementService.getRegulatoryElements(
            regulatoryRegionService.getNegativeRegulatoryRegions(),
            negativeCutOffScore,
            negATcomposition,
            negCGcomposition);

    IlpService formatter = new IlpService(tempIlpJobDirName);
    formatter.createIlpFilesWithTestSet(
        regulatoryRegionService.getPositiveRegulatoryRegions(),
        regulatoryRegionService.getNegativeRegulatoryRegions(),
        posTrainingSet,
        negTrainingSet,
        testSetPercent);

    String ilpTheory = formatter.runILP();

    return ilpTheory;
  }
Exemplo n.º 2
0
  public IlpService createIlpFiles() throws DataFormatException {

    ArrayList<Feature> posRegElements =
        regulatoryElementService.getRegulatoryElements(
            regulatoryRegionService.getPositiveRegulatoryRegions(),
            positiveCutOffScore,
            posATcomposition,
            posCGcomposition);

    if (posRegElements == null) {
      posRegElements =
          regulatoryElementService.getRegulatoryElements(
              regulatoryRegionService.getPositiveRegulatoryRegions(),
              regulatoryRegionService.getNegativeRegulatoryRegions(),
              positiveCutOffScore);
    }

    // ***** Add statistics
    addMotifMatchingStatisticsToNotes("positive");
    SystemVariables.getInstance().setPosSeqRelElMatchesNum(posRegElements.size());

    ArrayList<Feature> negRegElements =
        regulatoryElementService.getRegulatoryElements(
            regulatoryRegionService.getNegativeRegulatoryRegions(),
            negativeCutOffScore,
            negATcomposition,
            negCGcomposition);

    if (negRegElements == null) {
      negRegElements =
          regulatoryElementService.getRegulatoryElements(
              regulatoryRegionService.getNegativeRegulatoryRegions(), null, negativeCutOffScore);
    }

    // ***** Add statistics
    addMotifMatchingStatisticsToNotes("negative");
    SystemVariables.getInstance().setNegSeqRelElMatchesNum(negRegElements.size());

    /*
    	System.out.println("\n Number of matches of pairs of matrices in jurkat and erythroid sequences");

    	String[] pwmPair = new String[]{"MA0055.1", "MA0152.1"};
    	System.out.println(pwmPair[0] + " and " + pwmPair[1]+" :\t" +
    			FeaturesTools.numSequencesContainingAll(pwmPair, posRegElements) + "\t"+
    			FeaturesTools.numSequencesContainingAll(pwmPair, negRegElements));

    	System.out.println("\nDistances between Gata and Ebox for positive sequences:");
    	FeaturesTools.printRegElDistances("Gata", "Ebox", posRegElements);
    */

    IlpService ilpService = new IlpService(tempIlpJobDirName);
    ilpService.createIlpFiles(
        regulatoryRegionService.getPositiveRegulatoryRegions(),
        regulatoryRegionService.getNegativeRegulatoryRegions(),
        posRegElements,
        negRegElements);

    return ilpService;
  }
  /* Generates regulatory regions for ILP positive examples.
   * Base of the sequence is random ACGT 0.25 : 0.25 : 0.25 : 0.25 composition,
   * cut-off score for finding PSSMs in model sequences is a default positive cut-off
   * C.elegans pwm are planted in the base sequence at random positions.
   *
   * @param int number of regions to be generates
   * @param String generic prefix for the name of regulatory sequence
   */
  private ArrayList<Feature> generateRegulatoryRegions(int numOfRegions, String regionNamePrefix)
      throws DataFormatException {
    ArrayList<Feature> regRegions = new ArrayList<Feature>();

    if (numOfRegions <= 0) {
      return regRegions;
    }

    // Generate probabilities based on C.elegans data
    // RegulatoryRegionService regRegionService =
    //	RegulatoryRegionServiceFactory.getService(RegulatoryRegionService.C_ELEGANS_DATA_SERVICE, 0,
    // 0);

    ArrayList<Feature> cElegansRegRegions = modelRegRegionService.getPositiveRegulatoryRegions();
    if (cElegansRegRegions == null) {
      throw new DataFormatException(
          "SyntheticRegRegionService: Unable to retrieve C.elegans regulatory regions to generate positive sequences.");
    }

    File pwmDir = new File(SystemVariables.getInstance().getString("C.elegans.PWMs.dir"));
    String tmpJobDir =
        SystemVariables.getInstance()
            .getString("temp.output.dir"); // TODO create a proper tmp job dir for experiments

    PatserRegElementService regElService = new PatserRegElementService(pwmDir, tmpJobDir);

    double cutOffScore = SystemVariables.getInstance().getPositivePatserCutOffScore();
    double atComposition = sequenceNtProbabilities[0] + sequenceNtProbabilities[3];
    double cgComposition = sequenceNtProbabilities[1] + sequenceNtProbabilities[2];
    ArrayList<Feature> regElements =
        regElService.getRegulatoryElements(
            cElegansRegRegions, cutOffScore, atComposition, cgComposition);

    ArrayList<RegulatoryElementPWM> regElementPWMs = regElService.getRegulatoryElementsPWMs();

    StatAnalyser stat = new StatAnalyser(regElements);

    for (int i = 0; i < numOfRegions; i++) {
      String sequence =
          generatePosExSequence(
              stat,
              regElementPWMs,
              cElegansRegRegions.get(0).getSequence().length(),
              cElegansRegRegions.size());
      regRegions.add(new Feature(regionNamePrefix + i, "gene", null, 0, 0, sequence, 0.0));
    }

    return regRegions;
  }
  @Override
  public void updateNumberOfPositiveRegRegions(int num) throws DataFormatException {
    // TODO check for empty regions
    // TODO test this
    int deltaSeqNum = num - positiveRegRegions.size();

    if (deltaSeqNum < 0) { // desired number of positive sequences is less than is available now
      for (int i = 0; i > deltaSeqNum; i--) {
        positiveRegRegions.remove(0);
      }
    } else { // desired number is more than available -> need to generate extra
      ArrayList<Feature> extraSimulatedGenes =
          FeaturesTools.generateSimulatedRegulatoryRegionsWithPositionalPSSMs(
              deltaSeqNum,
              regulatorySequenceLength,
              sequenceNtProbabilities,
              SystemVariables.getInstance().getPositivePatserCutOffScore(),
              POSITIVE_REGION_PREFIX,
              modelRegRegionService.getPositiveRegulatoryRegions(),
              modelRegElService);

      // generateRegulatoryRegions(deltaSeqNum, POSITIVE_REGION_PREFIX);

      negativeRegRegions.addAll(extraSimulatedGenes);
    }
  }
  private String createSequencesFile(ArrayList<Feature> regRegions) throws DataFormatException {
    if (regRegions == null) {
      throw new DataFormatException(
          "Can not create regulatory sequences file for PATSER. No regulatory regions were supplied.");
    }
    if (tempPatserOutputDir == null
        || tempPatserOutputDir.isEmpty()) { // in case the constructor workaround was used
      throw new DataFormatException(
          "Can not create regulatory sequences file for PATSER. No temporary output directory was set.");
    }

    String seqFileName =
        tempPatserOutputDir
            + SystemVariables.getInstance().getString("patser.tmp.seq.output.file.name")
            + System.currentTimeMillis();

    BufferedWriter writer = null;

    try {
      writer = new BufferedWriter(new FileWriter(seqFileName));

      for (Iterator<Feature> iterator = regRegions.iterator(); iterator.hasNext(); ) {
        Feature gene = (Feature) iterator.next();

        writer.write(gene.getId() + " \\" + gene.getSequence() + "\\\n");
      }

      writer.close();

    } catch (IOException e) {
      e.printStackTrace();
    }

    return seqFileName;
  }
  public SyntheticRegRegionService(int numOfPositiveRegRegions, int negExMultiplicationFactor)
      throws DataFormatException {

    modelRegRegionService = new CElegansRegRegionService(0);

    File pwmDir = new File(SystemVariables.getInstance().getString("C.elegans.PWMs.dir"));
    String tmpJobDir =
        SystemVariables.getInstance()
            .getString("temp.output.dir"); // TODO create a proper tmp job dir for experiments

    modelRegElService = new PatserRegElementService(pwmDir, tmpJobDir);

    if (modelRegRegionService.getPositiveRegulatoryRegions().size() > 0) {
      regulatorySequenceLength =
          modelRegRegionService.getPositiveRegulatoryRegions().get(0).getSequence().length();
    } else {
      throw new DataFormatException(
          "Model regulatory regions are empty. Can not model synthetic regions based on an empty regions.");
    }

    // TODO: remove - just for testing
    regulatorySequenceLength = 25;
    negativeRegRegions =
        FeaturesTools.generateSimulatedRegulatoryRegions(
            negExMultiplicationFactor * numOfPositiveRegRegions,
            regulatorySequenceLength,
            NEGATIVE_REGION_PREFIX,
            sequenceNtProbabilities);

    positiveRegRegions =
        FeaturesTools.generateSimulatedRegulatoryRegionsWithPositionalPSSMs(
            numOfPositiveRegRegions,
            regulatorySequenceLength,
            sequenceNtProbabilities,
            SystemVariables.getInstance().getPositivePatserCutOffScore(),
            POSITIVE_REGION_PREFIX,
            modelRegRegionService.getPositiveRegulatoryRegions(),
            modelRegElService);
    // this.generateRegulatoryRegions(numOfPositiveRegRegions, );

  }
Exemplo n.º 7
0
  /* Note: unsound method
   * Based on the statistics, collected when extracting motif matches by RegElementService,
   * collects text note of motif matching statistics, which will be added to ILP file.
   * This method has to be called immediately after RegElementService.getRegulatoryElements call,
   * since every such call overrides the pssmMatchStatistics in RegElementService
   *
   * @param sequenceKind - can only be "positive" or "negative", depending on the kind of sequences
   */
  private void addMotifMatchingStatisticsToNotes(String sequenceKind) throws DataFormatException {

    Hashtable<String, Double> pssmMatchStats = regulatoryElementService.getPssmMatchingStatistics();
    if (pssmMatchStats != null && !pssmMatchStats.isEmpty()) {

      SystemVariables.getInstance()
          .appendToExperimentNotes(
              "\\n* Number of PSSM matches in " + sequenceKind + " sequences: ");
      int numberOfRegions = 0;
      if ("positive".equals(sequenceKind)) {
        numberOfRegions = regulatoryRegionService.getPositiveRegulatoryRegions().size();
      } else {
        numberOfRegions = regulatoryRegionService.getNegativeRegulatoryRegions().size();
      }

      Enumeration<String> pssmMatchNames = pssmMatchStats.keys();
      int totalNumMatches = 0;
      String r_pssmNames = "";
      String r_matches = "";
      while (pssmMatchNames.hasMoreElements()) {
        String pssmName = pssmMatchNames.nextElement();
        double pssmStat = pssmMatchStats.get(pssmName);
        int numMatches = (int) (pssmStat * numberOfRegions);
        totalNumMatches = totalNumMatches + numMatches;

        r_pssmNames = r_pssmNames + "\'" + pssmName + "\', ";
        r_matches = r_matches + numMatches + ", ";
        SystemVariables.getInstance()
            .appendToExperimentNotes("\\n\\t" + pssmName + "\\t" + numMatches);
      }
      SystemVariables.getInstance()
          .appendToExperimentNotes("\\n Total number of matches: " + totalNumMatches);

      //			System.out.println("In positive sequences: ");
      //			System.out.println(r_pssmNames);
      //			System.out.println(r_matches);
    }
  }
Exemplo n.º 8
0
  /*
   * Runs ILP
   */
  public String induceRules() throws DataFormatException {

    IlpService ilpService = createIlpFiles();

    System.out.println("== Created all ILP files. Starting to induce.");

    //
    // ==> the star of the show
    //
    ilpService.runILP();

    // Overwrite temporary result html footer with the one that explains how to read a theory
    String htmlFooterFileName =
        tempIlpJobDirName + SystemVariables.getInstance().getString("html.footer.file.name");
    FileHandling.writeFile(htmlFooterFileName, FileHandling.getHTMLResultsFooter(true, true));

    return "Done";
  }
Exemplo n.º 9
0
  public Explorer(
      RegulatoryRegionService regRegionService,
      RegulatoryElementService regElService,
      String tempIlpJobDirName)
      throws DataFormatException {
    this.regulatoryRegionService = regRegionService;
    this.regulatoryElementService = regElService;
    this.tempIlpJobDirName = tempIlpJobDirName;

    positiveCutOffScore = SystemVariables.getInstance().getPositivePatserCutOffScore();
    negativeCutOffScore = SystemVariables.getInstance().getNegativePatserCutOffScore();

    ///////  Statistics
    SystemVariables.getInstance().cleanStatistics(); // clean old;

    SystemVariables.getInstance()
        .setPosSeqNum(regulatoryRegionService.getPositiveRegulatoryRegions().size());
    SystemVariables.getInstance()
        .setNegSeqNum(regulatoryRegionService.getNegativeRegulatoryRegions().size());

    SystemVariables.getInstance()
        .appendToExperimentNotes(
            "\\n* Number of positive sequences: "
                + regulatoryRegionService.getPositiveRegulatoryRegions().size());
    SystemVariables.getInstance()
        .appendToExperimentNotes(
            "\\n* Number of negative sequences: "
                + regulatoryRegionService.getNegativeRegulatoryRegions().size());

    SystemVariables.getInstance()
        .appendToExperimentNotes(
            "\\n* Patser cut-off score for positive sequences: " + positiveCutOffScore);
    SystemVariables.getInstance()
        .appendToExperimentNotes(
            "\\n* Patser cut-off score for negative sequences: " + negativeCutOffScore);

    double[] posNtComposition =
        FeaturesTools.getNucleotideComposition(
            regulatoryRegionService.getPositiveRegulatoryRegions());
    posATcomposition = posNtComposition[0] + posNtComposition[3];
    posCGcomposition = posNtComposition[1] + posNtComposition[2];
    SystemVariables.getInstance()
        .appendToExperimentNotes(
            "\\n* A:T and C:G composition of positive sequences: "
                + posATcomposition
                + " "
                + posCGcomposition);

    SystemVariables.getInstance().setPosATcomposition(posATcomposition);
    SystemVariables.getInstance().setPosCGcomposition(posCGcomposition);

    double[] negNtComposition =
        FeaturesTools.getNucleotideComposition(
            regulatoryRegionService.getNegativeRegulatoryRegions());
    negATcomposition = negNtComposition[0] + negNtComposition[3];
    negCGcomposition = negNtComposition[1] + negNtComposition[2];
    SystemVariables.getInstance()
        .appendToExperimentNotes(
            "\\n* A:T and C:G composition of negative sequences: "
                + negATcomposition
                + " "
                + negCGcomposition);

    SystemVariables.getInstance().setNegATcomposition(negATcomposition);
    SystemVariables.getInstance().setNegCGcomposition(negCGcomposition);
  }
  /* Parses and saves an input stream of several PWMs. Each PWM is saved
   * in separate file (for Patser)
   * Expected input stream format:
   * > matrixName
   * A | 10 20 30
   * C | 20 0 ...
   */
  public static void savePwmFiles(String dirName, String pwmsStr)
      throws DataFormatException, IOException {

    int maxPwmNum = Integer.parseInt(SystemVariables.getInstance().getString("regEl.max.pwm.num"));

    String line = null;
    String pwmName = "";
    int pwmLineCount = 0;
    int pwmColNum = -1;
    String pwmString = "";
    StringTokenizer stMain = new StringTokenizer(pwmsStr, "\n\r");
    int currPwmNum = 0;

    while (stMain.hasMoreTokens()) {
      line = stMain.nextToken();
      line = line.trim();

      if (!(line.matches("\\s*"))) { // ignore blank lines

        if (pwmName.isEmpty()) { // expecting and annotated line

          StringTokenizer st = new StringTokenizer(line, " \t");
          String token = st.nextToken();

          // Check for the line to start with ">" and read the first token after it. The rest of the
          // line is ignored
          if (!">".equals(token)) {
            throw new DataFormatException(
                "Supplied PSSM(s) are not in the correct format. Each PSSM should be preceded by a line starting with \"> pssm_name\"");
          }

          if (st.hasMoreTokens()) {
            pwmName = st.nextToken().trim();
          } else {
            throw new DataFormatException(
                "Supplied PSSM(s) are not in the correct format. PSSM name should follow \">\".");
          }

        } else { // expecting a pwm line

          if (line.matches("[ACGT][\\t ]+\\|([\\t ]+[0-9]+)+")) {

            int currColNum = line.split("[\\t ]+").length;
            if (pwmColNum < 0) {
              pwmColNum = currColNum;
            } else {
              if (currColNum != pwmColNum) {
                throw new DataFormatException(
                    "Supplied PSSM(s) are not in the correct format. Unequal length of rows in one PSSM.");
              }
            }

            pwmString = pwmString + line + "\n";
            pwmLineCount++;

          } else {
            throw new DataFormatException("Supplied PSSM(s) are not in the correct format. ");
          }
        }

        if (!pwmName.isEmpty() && pwmLineCount == 4) { // got all the info for writing a matrix

          currPwmNum++;

          //					if (currPwmNum > maxPwmNum){
          //						throw new DataFormatException("Number of biological markers (PSSMs) has exceeded
          // the limit of " +
          //								maxPwmNum + ".");
          //					}

          BufferedWriter writer = new BufferedWriter(new FileWriter(dirName + pwmName + ".matrix"));

          writer.write(pwmString);

          writer.close();

          pwmName = "";
          pwmLineCount = 0;
          pwmColNum = -1;
          pwmString = "";
        }
      }
    }
  }
  // TODO: faze it out - now I use Hash as above. Make sure that the score
  public ArrayList<RegulatoryElementPWM> getRegulatoryElementsPWMs() throws DataFormatException {
    String pwmLineRegEx1 = "[ACGTacgt][ \t]*\\|([ \t]*\\d+)+[ \t]*";
    String pwmLineRegEx2 = "[ACGTacgt][ \t]*\\[([ \t]*\\d+)+[ \t]*\\][ \t]*";

    ArrayList<RegulatoryElementPWM> pwms = new ArrayList<RegulatoryElementPWM>();

    // *** Get file names of all matrixes
    final String[] matrixFileNames = new File(matrixFilesDir).list();

    if (matrixFileNames == null) {
      throw new DataFormatException(
          "Patser Regulatory Element Service has no PSSMs associated with it.");
    }

    for (int i = 0; i < matrixFileNames.length; i++) {
      // Only read files with .matrix extension
      if (!matrixFileNames[i].endsWith(SystemVariables.getInstance().getString("pwm.extension"))) {
        continue;
      }

      RegulatoryElementPWM currPwmObj = new RegulatoryElementPWM();
      String tfbsName = matrixFileNames[i].substring(0, matrixFileNames[i].length() - 7);
      currPwmObj.setName(tfbsName);

      BufferedReader bufferedReader = null;

      try {
        // for Mac
        bufferedReader =
            new BufferedReader(new FileReader(matrixFilesDir + "/" + matrixFileNames[i]));

        // bufferedReader = new BufferedReader(new FileReader(matrixFilesDir + matrixFileNames[i]));

        String line = null;
        int[][] pwmArr = null;

        int j = -1;
        while (null != (line = bufferedReader.readLine())) {

          if (line.matches(pwmLineRegEx1) || line.matches(pwmLineRegEx2)) {

            j++;
            if (j > 3)
              throw new DataFormatException(
                  "Error parsing matrix file <"
                      + tfbsName
                      + ".matrix>. Unexpected line in the file. File should contain only one matrix.");

            line = line.replaceAll("[ACGTacgt\\|\\[\\]]", ""); // remove everything but the numbers

            StringTokenizer strTok = new StringTokenizer(line);

            int lengthOfPwm = strTok.countTokens();

            if (pwmArr == null) {
              pwmArr = new int[lengthOfPwm][4];
            }

            if (lengthOfPwm != pwmArr.length)
              throw new DataFormatException(
                  "Error parsing matrix file <" + tfbsName + ".matrix>. Matrix is unbalanced.");

            int k = -1;
            while (strTok.hasMoreElements()) {
              k++;
              String token = strTok.nextToken();
              pwmArr[k][j] = Integer.parseInt(token);
            }
          }
        }

        currPwmObj.setPwm(pwmArr);

      } catch (FileNotFoundException ex) {
        ex.printStackTrace();
      } catch (IOException ex) {
        ex.printStackTrace();
      } finally {
        try {
          if (bufferedReader != null) bufferedReader.close();
        } catch (IOException ex) {
          ex.printStackTrace();
        }
      }

      pwms.add(currPwmObj);
    } // matrix for

    return pwms;
  }
  /* Reads the PSSM directory (saved in this instance) with a number of files that contain PSSMs and creates a Hashmap of
   * these PSSMs keyed by name.
   *  - Each pwm file should have a .matrix extension. "." are permitted in the name (i.e. ma.123.my.matrix is acceptable)
   *  - Each file should have only one pwm in it.
   *  - No "> pmw.." lines accepted in a file. I.e nothing but the actual matrix should be present in a file
   *  - pwms can be of 2 formats: A | 1 2 3... or A [ 1 2 3]...
   *  - blank lines are permitted in the file
   */
  private Hashtable<String, int[][]> readPssmsFromFileSystem() throws DataFormatException {
    Hashtable<String, int[][]> resultPssms = new Hashtable<String, int[][]>();

    String pssmLineRegEx1 = "[ACGTacgt][ \t]*\\|([ \t]*\\d+)+[ \t]*";
    String pssmLineRegEx2 = "[ACGTacgt][ \t]*\\[([ \t]*\\d+)+[ \t]*\\][ \t]*";

    // *** Get file names of all matrixes
    final String[] matrixFileNames = new File(matrixFilesDir).list();

    for (int i = 0; i < matrixFileNames.length; i++) {
      // Only read files with .matrix extension
      if (!matrixFileNames[i].endsWith(SystemVariables.getInstance().getString("pwm.extension"))) {
        continue;
      }

      String pssmName = matrixFileNames[i].substring(0, matrixFileNames[i].length() - 7);

      BufferedReader bufferedReader = null;

      try {
        // for Mac
        bufferedReader =
            new BufferedReader(new FileReader(matrixFilesDir + "/" + matrixFileNames[i]));

        // bufferedReader = new BufferedReader(new FileReader(matrixFilesDir + matrixFileNames[i]));

        String line = null;
        int[][] pssmMatrix = null;

        int j = -1;
        while (null != (line = bufferedReader.readLine())) {

          if (line.matches(pssmLineRegEx1) || line.matches(pssmLineRegEx2)) {

            j++;
            if (j > 3)
              throw new DataFormatException(
                  "Error parsing matrix file <"
                      + pssmName
                      + ".matrix>. Unexpected line in the file. File should contain only one matrix.");

            line = line.replaceAll("[ACGTacgt\\|\\[\\]]", ""); // remove everything but the numbers

            StringTokenizer strTok = new StringTokenizer(line);

            int lengthOfPwm = strTok.countTokens();

            if (pssmMatrix == null) {
              pssmMatrix = new int[lengthOfPwm][4];
            }

            if (lengthOfPwm != pssmMatrix.length)
              throw new DataFormatException(
                  "Error parsing matrix file <" + pssmName + ".matrix>. Matrix is unbalanced.");

            int k = -1;
            while (strTok.hasMoreElements()) {
              k++;
              String token = strTok.nextToken();
              pssmMatrix[k][j] = Integer.parseInt(token);
            }
          }
        }

        resultPssms.put(pssmName, pssmMatrix);

      } catch (FileNotFoundException ex) {
        ex.printStackTrace();
      } catch (IOException ex) {
        ex.printStackTrace();
      } finally {
        try {
          if (bufferedReader != null) bufferedReader.close();
        } catch (IOException ex) {
          ex.printStackTrace();
        }
      }
    } // matrix for

    return resultPssms;
  }
public class PatserRegElementService implements RegulatoryElementService {

  private String patserInstallDirName =
      SystemVariables.getInstance().getString("patser.install.dir");
  private String matrixFilesDir;
  private String tempPatserOutputDir;
  private Hashtable<String, Double>
      pssmMatchingStats; // keeps track of number of PSSM matches in all sequences / by # of
  // sequences
  private Hashtable<String, int[][]> pssms; // hashed by name

  /*
   * @param pwmDir	name of the directory, which contains one or more pwm files
   */
  public PatserRegElementService(File pwmDir, String tempJobDir) throws DataFormatException {

    if (tempJobDir != null && !tempJobDir.isEmpty()) { // workaround for the web interface bean:
      // to load example data we only need pwm dir to extract pwm info
      this.tempPatserOutputDir = FileHandling.createTempPatserOutputDirectory(tempJobDir);
    }
    this.matrixFilesDir = pwmDir.getAbsolutePath(); // TODO
  }

  /* Parses a string with multiple PWMs and writes each pwm in an individual, Patser-approved file
   * in a standard pwm directory, created inside a temporary directory specified.
   *
   * @param pmws	String with one or more PWMs. The format of the String is:
   * 				> pmwName
   * 				A | 10 20 1		 or		A [10 20 1]
   * 				C | 0 22 ...			C [0 22 ...]
   *
   * @param tempJobDir	name of a temporary directory for the whole Module Inducer run.
   * 						A new directory will be created inside this directory to hold
   * 						all the pwm files.
   */
  public PatserRegElementService(String pwms, String tempJobDir)
      throws DataFormatException, IOException {

    this.tempPatserOutputDir = FileHandling.createTempPatserOutputDirectory(tempJobDir);

    this.matrixFilesDir = FileHandling.createTempPwmDirectory(tempPatserOutputDir);
    savePwmFiles(matrixFilesDir, pwms);
    // matrixFilesDir = (new File(matrixFilesDir)).getAbsolutePath(); //TODO stupid windows hack

  }

  private String createSequencesFile(ArrayList<Feature> regRegions) throws DataFormatException {
    if (regRegions == null) {
      throw new DataFormatException(
          "Can not create regulatory sequences file for PATSER. No regulatory regions were supplied.");
    }
    if (tempPatserOutputDir == null
        || tempPatserOutputDir.isEmpty()) { // in case the constructor workaround was used
      throw new DataFormatException(
          "Can not create regulatory sequences file for PATSER. No temporary output directory was set.");
    }

    String seqFileName =
        tempPatserOutputDir
            + SystemVariables.getInstance().getString("patser.tmp.seq.output.file.name")
            + System.currentTimeMillis();

    BufferedWriter writer = null;

    try {
      writer = new BufferedWriter(new FileWriter(seqFileName));

      for (Iterator<Feature> iterator = regRegions.iterator(); iterator.hasNext(); ) {
        Feature gene = (Feature) iterator.next();

        writer.write(gene.getId() + " \\" + gene.getSequence() + "\\\n");
      }

      writer.close();

    } catch (IOException e) {
      e.printStackTrace();
    }

    return seqFileName;
  }

  /* Finds regulatory elements in regulatory sequences
   * @param regRegions - list of regulatory regions in which to look for the reg. elements
   * @param cutOffScore - minimum score cut off (-ls option in Patser). Matches with lower
   * 						score will not be accepted
   */
  public ArrayList<Feature> getRegulatoryElements(
      ArrayList<Feature> regRegions, double cutOffScore, double atComposition, double cgComposition)
      throws DataFormatException {
    /* Verified:
     * When Patser matches an "R" sequence (reverse complement), it reports a start position in the
     * original sequence of the reverse complement of a PSSM.
     */

    ///// Patser parameters :
    // double cutOffScore = SystemVariables.getInstance().getString("");

    ArrayList<Feature> tfbsHits = new ArrayList<Feature>();

    // *** Write genes into file acceptable by PATSER
    final String seqFileName = createSequencesFile(regRegions);

    // *** Get file names of all matrixes
    final String[] matrixFileNames = new File(matrixFilesDir).list();

    pssmMatchingStats = new Hashtable<String, Double>();

    for (int i = 0; i < matrixFileNames.length; i++) {
      // Only read files with .matrix extension
      if (!matrixFileNames[i].endsWith(SystemVariables.getInstance().getString("pwm.extension"))) {
        continue;
      }
      // *** Run PATSER tool and extract tfbs info from its output
      try {
        Runtime rt = Runtime.getRuntime();
        // Process pr = rt.exec("cmd /c dir");
        // Process pr = rt.exec("pwd");
        File patserDir = new File(patserInstallDirName);

        Process pr;

        if (System.getProperty("os.name").startsWith("Mac")) {

          final String cmd =
              "./patser-v3e -A a:t "
                  + atComposition
                  + " c:g "
                  + cgComposition
                  + " -b 1 -c -d1 -ls "
                  + cutOffScore
                  + " -p -s -m "
                  + matrixFilesDir
                  + "/"
                  + matrixFileNames[i]
                  + " -f "
                  + seqFileName;

          pr = rt.exec(new String[] {"/bin/sh", "-c", cmd}, null, patserDir);
          // pr = rt.exec(cmd);

          // pr = rt.exec( new String[] { "patser-v3e", "-A", "a:t 0.25 c:g 0.25", "-b", "1", "-c",
          // "-d1", "-ls", "7", "-p", "-s", "-m", matrixFileNames[i], "-f", seqFileName } );

        } else { // i.e. Windows
          String patserCommand;
          // Stupid windows hack
          if (matrixFilesDir.endsWith("/")) {
            patserCommand =
                "cmd /c patser-v3e -A a:t "
                    + atComposition
                    + " c:g "
                    + cgComposition
                    + " -b 1 -c -d1 -ls "
                    + cutOffScore
                    + " -p -s -m \""
                    + matrixFilesDir
                    + matrixFileNames[i]
                    + "\" -f \""
                    + seqFileName
                    + "\"";
          } else {
            patserCommand =
                "cmd /c patser-v3e -A a:t "
                    + atComposition
                    + " c:g "
                    + cgComposition
                    + " -b 1 -c -d1 -ls "
                    + cutOffScore
                    + " -p -s -m \""
                    + matrixFilesDir
                    + "\\"
                    + matrixFileNames[i]
                    + "\" -f \""
                    + seqFileName
                    + "\"";
          }

          //					String patserCommand = "cmd /c patser-v3e -A a:t 0.25 c:g 0.25 -b 1 -c -d1 -ls 7 -p
          // -s"
          //						+ " -m " + matrixFilesDir + matrixFileNames[i]  + " -f " + seqFileName;

          pr = rt.exec(patserCommand, new String[] {"PATH=C:/cygwin/bin"}, patserDir);
        }

        BufferedReader input = new BufferedReader(new InputStreamReader(pr.getInputStream()));

        String line = null;
        String pssmName = matrixFileNames[i].substring(0, matrixFileNames[i].length() - 7);
        int hits = 0;
        String lastGeneName = "";
        // TODO

        String word;
        // Read the input and filter out matrix hits data
        while ((line = input.readLine()) != null) {
          // System.out.println(line);

          if (line.contains("position=") && line.contains("score=")) { // result line
            Feature regElement = new Feature("TF_binding_site");
            // Set tfbs name, but filter the .matrix extension
            regElement.setName(pssmName);
            // hit.setNameAttribute(matrixFileNames[i]);

            StringTokenizer st = new StringTokenizer(line);
            // first one is the name
            word = st.nextToken();
            regElement.setParent(word);

            while (st.hasMoreTokens()) {
              word = st.nextToken();
              if (word.equals("position=")) {
                word = st.nextToken();
                if (word.endsWith("C")) {
                  regElement.setStrand("R");
                  word = word.substring(0, word.indexOf("C"));
                } else {
                  regElement.setStrand("D");
                }
                regElement.setStartPosition(Integer.parseInt(word));
              } else if (word.equals("score=")) {
                word = st.nextToken();
                regElement.setScore(Double.parseDouble(word));
              } else if (word.equals("sequence=")) {
                word = st.nextToken();
                regElement.setSequence(word);
                // Now that we have TFBS sequence, we can set the end position of TFBS:
                regElement.setEndPosition(regElement.getStartPosition() + word.length());
              }
            } // end of tokenizer

            // This is to calculate statistics of PSSM hits
            // if (!lastGeneName.equals(regElement.getParent())){
            hits++;
            lastGeneName = regElement.getParent();
            // }

            tfbsHits.add(regElement);
          }
        } // end of reading patser input

        pssmMatchingStats.put(pssmName, (double) hits / regRegions.size());

        // int exitVal = pr.waitFor();
        // System.out.println("Exited with error code " + exitVal);

      } catch (IOException e) {
        e.printStackTrace();
        throw new DataFormatException("PATSER execution failed. ");
      }
    }

    File seqFile = new File(seqFileName);
    seqFile.delete();
    /*
    		// add begin and end of sequence "fake" matches, or markers; like ^ and $ for begin and ed sequence in regEx
    		// this is for ILP to be able to induce rules with begin and end of sequence (distance, etc.)
    		for (Iterator<Feature> iterator = regRegions.iterator(); iterator.hasNext();) {
    			Feature feature = (Feature) iterator.next();
    			// markers are place before the sequence begins and after it ends
    			tfbsHits.add(new Feature("generic_marker", "begin", feature.getId(), "D", 0, 0, 0.0));
    			tfbsHits.add(new Feature("generic_marker", "end", feature.getId(), "D", feature.getSequence().length()+2, feature.getSequence().length()+2, 0.0));
    		}
    */
    if (tfbsHits.isEmpty()) {
      throw new DataFormatException("PATSER did not locate any motifs in the data.");
    }

    return tfbsHits;
  }

  /* Statistics for the last Patser run. With every getRegulatoryElements() run it gets overwritten.
   *
   * (non-Javadoc)
   * @see ca.uottawa.okorol.bioinf.ModuleInducer.interfaces.RegulatoryElementService#getPssmMatchingStatistics()
   */
  public Hashtable<String, Double> getPssmMatchingStatistics() {
    return pssmMatchingStats;
  }

  /* Returns PSSMs used in this Patser instance, keyed by name
   */
  public Hashtable<String, int[][]> getPssms() throws DataFormatException {
    if (pssms == null || pssms.isEmpty()) {
      pssms = readPssmsFromFileSystem();
    }

    return pssms;
  }

  /* Reads the PSSM directory (saved in this instance) with a number of files that contain PSSMs and creates a Hashmap of
   * these PSSMs keyed by name.
   *  - Each pwm file should have a .matrix extension. "." are permitted in the name (i.e. ma.123.my.matrix is acceptable)
   *  - Each file should have only one pwm in it.
   *  - No "> pmw.." lines accepted in a file. I.e nothing but the actual matrix should be present in a file
   *  - pwms can be of 2 formats: A | 1 2 3... or A [ 1 2 3]...
   *  - blank lines are permitted in the file
   */
  private Hashtable<String, int[][]> readPssmsFromFileSystem() throws DataFormatException {
    Hashtable<String, int[][]> resultPssms = new Hashtable<String, int[][]>();

    String pssmLineRegEx1 = "[ACGTacgt][ \t]*\\|([ \t]*\\d+)+[ \t]*";
    String pssmLineRegEx2 = "[ACGTacgt][ \t]*\\[([ \t]*\\d+)+[ \t]*\\][ \t]*";

    // *** Get file names of all matrixes
    final String[] matrixFileNames = new File(matrixFilesDir).list();

    for (int i = 0; i < matrixFileNames.length; i++) {
      // Only read files with .matrix extension
      if (!matrixFileNames[i].endsWith(SystemVariables.getInstance().getString("pwm.extension"))) {
        continue;
      }

      String pssmName = matrixFileNames[i].substring(0, matrixFileNames[i].length() - 7);

      BufferedReader bufferedReader = null;

      try {
        // for Mac
        bufferedReader =
            new BufferedReader(new FileReader(matrixFilesDir + "/" + matrixFileNames[i]));

        // bufferedReader = new BufferedReader(new FileReader(matrixFilesDir + matrixFileNames[i]));

        String line = null;
        int[][] pssmMatrix = null;

        int j = -1;
        while (null != (line = bufferedReader.readLine())) {

          if (line.matches(pssmLineRegEx1) || line.matches(pssmLineRegEx2)) {

            j++;
            if (j > 3)
              throw new DataFormatException(
                  "Error parsing matrix file <"
                      + pssmName
                      + ".matrix>. Unexpected line in the file. File should contain only one matrix.");

            line = line.replaceAll("[ACGTacgt\\|\\[\\]]", ""); // remove everything but the numbers

            StringTokenizer strTok = new StringTokenizer(line);

            int lengthOfPwm = strTok.countTokens();

            if (pssmMatrix == null) {
              pssmMatrix = new int[lengthOfPwm][4];
            }

            if (lengthOfPwm != pssmMatrix.length)
              throw new DataFormatException(
                  "Error parsing matrix file <" + pssmName + ".matrix>. Matrix is unbalanced.");

            int k = -1;
            while (strTok.hasMoreElements()) {
              k++;
              String token = strTok.nextToken();
              pssmMatrix[k][j] = Integer.parseInt(token);
            }
          }
        }

        resultPssms.put(pssmName, pssmMatrix);

      } catch (FileNotFoundException ex) {
        ex.printStackTrace();
      } catch (IOException ex) {
        ex.printStackTrace();
      } finally {
        try {
          if (bufferedReader != null) bufferedReader.close();
        } catch (IOException ex) {
          ex.printStackTrace();
        }
      }
    } // matrix for

    return resultPssms;
  }

  /*
   * (non-Javadoc)
   * @see ca.uottawa.okorol.bioinf.ModuleInducer.interfaces.RegulatoryElementService#getRegulatoryElementsPWMs()
   *
   * Reads a directory with a number of files that contain pwms and creates an ArrayList of pwm objects.
   *  - Each pwm file should have a .matrix extension. "." are permitted in the name (i.e. ma.123.my.matrix is acceptable)
   *  - Each file should have only one pwm in it.
   *  - No "> pmw.." lines accepted in a file. I.e nothing but the actual matrix should be present in a file
   *  - pwms can be of 2 formats: A | 1 2 3... or A [ 1 2 3]...
   *  - blank lines are permitted in the file
   *  -
   */
  // TODO: faze it out - now I use Hash as above. Make sure that the score
  public ArrayList<RegulatoryElementPWM> getRegulatoryElementsPWMs() throws DataFormatException {
    String pwmLineRegEx1 = "[ACGTacgt][ \t]*\\|([ \t]*\\d+)+[ \t]*";
    String pwmLineRegEx2 = "[ACGTacgt][ \t]*\\[([ \t]*\\d+)+[ \t]*\\][ \t]*";

    ArrayList<RegulatoryElementPWM> pwms = new ArrayList<RegulatoryElementPWM>();

    // *** Get file names of all matrixes
    final String[] matrixFileNames = new File(matrixFilesDir).list();

    if (matrixFileNames == null) {
      throw new DataFormatException(
          "Patser Regulatory Element Service has no PSSMs associated with it.");
    }

    for (int i = 0; i < matrixFileNames.length; i++) {
      // Only read files with .matrix extension
      if (!matrixFileNames[i].endsWith(SystemVariables.getInstance().getString("pwm.extension"))) {
        continue;
      }

      RegulatoryElementPWM currPwmObj = new RegulatoryElementPWM();
      String tfbsName = matrixFileNames[i].substring(0, matrixFileNames[i].length() - 7);
      currPwmObj.setName(tfbsName);

      BufferedReader bufferedReader = null;

      try {
        // for Mac
        bufferedReader =
            new BufferedReader(new FileReader(matrixFilesDir + "/" + matrixFileNames[i]));

        // bufferedReader = new BufferedReader(new FileReader(matrixFilesDir + matrixFileNames[i]));

        String line = null;
        int[][] pwmArr = null;

        int j = -1;
        while (null != (line = bufferedReader.readLine())) {

          if (line.matches(pwmLineRegEx1) || line.matches(pwmLineRegEx2)) {

            j++;
            if (j > 3)
              throw new DataFormatException(
                  "Error parsing matrix file <"
                      + tfbsName
                      + ".matrix>. Unexpected line in the file. File should contain only one matrix.");

            line = line.replaceAll("[ACGTacgt\\|\\[\\]]", ""); // remove everything but the numbers

            StringTokenizer strTok = new StringTokenizer(line);

            int lengthOfPwm = strTok.countTokens();

            if (pwmArr == null) {
              pwmArr = new int[lengthOfPwm][4];
            }

            if (lengthOfPwm != pwmArr.length)
              throw new DataFormatException(
                  "Error parsing matrix file <" + tfbsName + ".matrix>. Matrix is unbalanced.");

            int k = -1;
            while (strTok.hasMoreElements()) {
              k++;
              String token = strTok.nextToken();
              pwmArr[k][j] = Integer.parseInt(token);
            }
          }
        }

        currPwmObj.setPwm(pwmArr);

      } catch (FileNotFoundException ex) {
        ex.printStackTrace();
      } catch (IOException ex) {
        ex.printStackTrace();
      } finally {
        try {
          if (bufferedReader != null) bufferedReader.close();
        } catch (IOException ex) {
          ex.printStackTrace();
        }
      }

      pwms.add(currPwmObj);
    } // matrix for

    return pwms;
  }

  /* Parses and saves an input stream of several PWMs. Each PWM is saved
   * in separate file (for Patser)
   * Expected input stream format:
   * > matrixName
   * A | 10 20 30
   * C | 20 0 ...
   */
  public static void savePwmFiles(String dirName, String pwmsStr)
      throws DataFormatException, IOException {

    int maxPwmNum = Integer.parseInt(SystemVariables.getInstance().getString("regEl.max.pwm.num"));

    String line = null;
    String pwmName = "";
    int pwmLineCount = 0;
    int pwmColNum = -1;
    String pwmString = "";
    StringTokenizer stMain = new StringTokenizer(pwmsStr, "\n\r");
    int currPwmNum = 0;

    while (stMain.hasMoreTokens()) {
      line = stMain.nextToken();
      line = line.trim();

      if (!(line.matches("\\s*"))) { // ignore blank lines

        if (pwmName.isEmpty()) { // expecting and annotated line

          StringTokenizer st = new StringTokenizer(line, " \t");
          String token = st.nextToken();

          // Check for the line to start with ">" and read the first token after it. The rest of the
          // line is ignored
          if (!">".equals(token)) {
            throw new DataFormatException(
                "Supplied PSSM(s) are not in the correct format. Each PSSM should be preceded by a line starting with \"> pssm_name\"");
          }

          if (st.hasMoreTokens()) {
            pwmName = st.nextToken().trim();
          } else {
            throw new DataFormatException(
                "Supplied PSSM(s) are not in the correct format. PSSM name should follow \">\".");
          }

        } else { // expecting a pwm line

          if (line.matches("[ACGT][\\t ]+\\|([\\t ]+[0-9]+)+")) {

            int currColNum = line.split("[\\t ]+").length;
            if (pwmColNum < 0) {
              pwmColNum = currColNum;
            } else {
              if (currColNum != pwmColNum) {
                throw new DataFormatException(
                    "Supplied PSSM(s) are not in the correct format. Unequal length of rows in one PSSM.");
              }
            }

            pwmString = pwmString + line + "\n";
            pwmLineCount++;

          } else {
            throw new DataFormatException("Supplied PSSM(s) are not in the correct format. ");
          }
        }

        if (!pwmName.isEmpty() && pwmLineCount == 4) { // got all the info for writing a matrix

          currPwmNum++;

          //					if (currPwmNum > maxPwmNum){
          //						throw new DataFormatException("Number of biological markers (PSSMs) has exceeded
          // the limit of " +
          //								maxPwmNum + ".");
          //					}

          BufferedWriter writer = new BufferedWriter(new FileWriter(dirName + pwmName + ".matrix"));

          writer.write(pwmString);

          writer.close();

          pwmName = "";
          pwmLineCount = 0;
          pwmColNum = -1;
          pwmString = "";
        }
      }
    }
  }

  public static void savePwmFiles(String dirName, InputStream in)
      throws DataFormatException, IOException {
    StringBuffer out = new StringBuffer();
    byte[] b = new byte[4096];

    for (int n; (n = in.read(b)) != -1; ) {
      out.append(new String(b, 0, n));
    }

    savePwmFiles(dirName, out.toString());
  }
  /* Phased out. Insted, convert the InputStream to a String and use a method for String
  	public static void savePwmFiles(String dirName, InputStream in) throws DataFormatException, IOException{

  		BufferedReader input = new BufferedReader(new InputStreamReader(in));

  		String line = null;
  		String pwmName = "";
  		int pwmLineCount = 0;
  		int pwmColNum = -1;
  		String pwmString = "";

  		while ((line = input.readLine()) != null) {

  			if (!(line.matches("\\s*"))){ //ignore blank lines

  				if (pwmName.isEmpty()) { // expecting and annotated line

  					StringTokenizer st = new StringTokenizer(line, " \t");
  					String token = st.nextToken();

  					// Check for the line to start with ">" and read the first token after it. The rest of the line is ignored
  					if (!">".equals(token)){
  						throw new DataFormatException("Supplied PSSM(s) are not in the correct format. Each PSSM should be preceded by a line starting with \"> pssm_name\"");
  					}

  					if (st.hasMoreTokens()){
  						pwmName = st.nextToken();
  					}else {
  						throw new DataFormatException("Supplied PSSM(s) are not in the correct format. PSSM name should follow \">\".");
  					}

  				} else { //expecting a pwm line

  					if (line.matches("[ACGT][\\t ]+\\|([\\t ]+[0-9]+)+")){

  						int currColNum = line.split("[\\t ]+").length;
  						if (pwmColNum < 0){
  							pwmColNum = currColNum;
  						} else {
  							if (currColNum != pwmColNum){
  								throw new DataFormatException("Supplied PSSM(s) are not in the correct format. Unequal length of rows in one PSSM.");
  							}
  						}

  						pwmString = pwmString + line + "\n";
  						pwmLineCount++;

  					} else {
  						throw new DataFormatException("Supplied PSSM(s) are not in the correct format. ");
  					}
  				}

  				if (!pwmName.isEmpty() && pwmLineCount == 4){ // got all the info for writing a matrix

  					BufferedWriter writer = new BufferedWriter(new FileWriter(dirName + pwmName + ".matrix"));

  					writer.write(pwmString);

  					writer.close();

  					pwmName = "";
  					pwmLineCount = 0;
  					pwmColNum = -1;
  					pwmString = "";

  				}

  			}
  		}

  	}
  */

  /* Parses and saves an input stream of several PWMs. Each PWM is saved
   * in separate file (for Patser)
   * Expected input stream format:
   * > matrixName
   * A [ 10 20 30 ]
   * C [ 20 0 ...
   *
   * Converted files should be of format A | 10 20 10...
   */
  public static void saveAndConvertPwmFiles(String dirName, InputStream in)
      throws DataFormatException, IOException {

    BufferedReader input = new BufferedReader(new InputStreamReader(in));

    String line = null;
    String pwmName = "";
    int pwmLineCount = 0;
    String pwmString = "";

    while ((line = input.readLine()) != null) {

      if (!(line.matches("\\s*"))) { // ignore blank lines

        if (pwmName.isEmpty()) { // expecting and annotated line

          if (!line.startsWith(">")) {
            throw new DataFormatException(
                "PWM sequence is not in the correct format. Each PWM should be preceded by a line starting with \"> pwmName\"");
          }

          line = line.substring(1);

          StringTokenizer st = new StringTokenizer(line, " \t");

          if (st.hasMoreTokens()) {
            pwmName = st.nextToken();
          } else {
            throw new DataFormatException(
                "PWM sequence is not in the correct format. PWM name should follow \">\".");
          }

        } else { // expecting a pwm line

          // if (line.matches("[ACGT][\\t ]+\\|([\\t ]+[0-9]+)+")){

          line = line.replace('[', '|');
          int len = line.length();
          line = line.substring(0, len - 1);
          pwmString = pwmString + line + "\n";
          pwmLineCount++;

          // } else {
          //	throw new DataFormatException("At least one of the PWMs is not in the correct format.
          // ");
          // }
        }

        if (!pwmName.isEmpty() && pwmLineCount == 4) { // got all the info for writing a matrix

          BufferedWriter writer = new BufferedWriter(new FileWriter(dirName + pwmName + ".matrix"));

          writer.write(pwmString);

          writer.close();

          pwmName = "";
          pwmLineCount = 0;
          pwmString = "";
        }
      }
    }
  }

  @Override
  public ArrayList<Feature> getRegulatoryElements(
      ArrayList<Feature> regRegions, ArrayList<Feature> backgroundRegRegions, double cutOffScore)
      throws DataFormatException {
    throw new DataFormatException("This method is not applicable to Patser Service");
  }
}
  /* Finds regulatory elements in regulatory sequences
   * @param regRegions - list of regulatory regions in which to look for the reg. elements
   * @param cutOffScore - minimum score cut off (-ls option in Patser). Matches with lower
   * 						score will not be accepted
   */
  public ArrayList<Feature> getRegulatoryElements(
      ArrayList<Feature> regRegions, double cutOffScore, double atComposition, double cgComposition)
      throws DataFormatException {
    /* Verified:
     * When Patser matches an "R" sequence (reverse complement), it reports a start position in the
     * original sequence of the reverse complement of a PSSM.
     */

    ///// Patser parameters :
    // double cutOffScore = SystemVariables.getInstance().getString("");

    ArrayList<Feature> tfbsHits = new ArrayList<Feature>();

    // *** Write genes into file acceptable by PATSER
    final String seqFileName = createSequencesFile(regRegions);

    // *** Get file names of all matrixes
    final String[] matrixFileNames = new File(matrixFilesDir).list();

    pssmMatchingStats = new Hashtable<String, Double>();

    for (int i = 0; i < matrixFileNames.length; i++) {
      // Only read files with .matrix extension
      if (!matrixFileNames[i].endsWith(SystemVariables.getInstance().getString("pwm.extension"))) {
        continue;
      }
      // *** Run PATSER tool and extract tfbs info from its output
      try {
        Runtime rt = Runtime.getRuntime();
        // Process pr = rt.exec("cmd /c dir");
        // Process pr = rt.exec("pwd");
        File patserDir = new File(patserInstallDirName);

        Process pr;

        if (System.getProperty("os.name").startsWith("Mac")) {

          final String cmd =
              "./patser-v3e -A a:t "
                  + atComposition
                  + " c:g "
                  + cgComposition
                  + " -b 1 -c -d1 -ls "
                  + cutOffScore
                  + " -p -s -m "
                  + matrixFilesDir
                  + "/"
                  + matrixFileNames[i]
                  + " -f "
                  + seqFileName;

          pr = rt.exec(new String[] {"/bin/sh", "-c", cmd}, null, patserDir);
          // pr = rt.exec(cmd);

          // pr = rt.exec( new String[] { "patser-v3e", "-A", "a:t 0.25 c:g 0.25", "-b", "1", "-c",
          // "-d1", "-ls", "7", "-p", "-s", "-m", matrixFileNames[i], "-f", seqFileName } );

        } else { // i.e. Windows
          String patserCommand;
          // Stupid windows hack
          if (matrixFilesDir.endsWith("/")) {
            patserCommand =
                "cmd /c patser-v3e -A a:t "
                    + atComposition
                    + " c:g "
                    + cgComposition
                    + " -b 1 -c -d1 -ls "
                    + cutOffScore
                    + " -p -s -m \""
                    + matrixFilesDir
                    + matrixFileNames[i]
                    + "\" -f \""
                    + seqFileName
                    + "\"";
          } else {
            patserCommand =
                "cmd /c patser-v3e -A a:t "
                    + atComposition
                    + " c:g "
                    + cgComposition
                    + " -b 1 -c -d1 -ls "
                    + cutOffScore
                    + " -p -s -m \""
                    + matrixFilesDir
                    + "\\"
                    + matrixFileNames[i]
                    + "\" -f \""
                    + seqFileName
                    + "\"";
          }

          //					String patserCommand = "cmd /c patser-v3e -A a:t 0.25 c:g 0.25 -b 1 -c -d1 -ls 7 -p
          // -s"
          //						+ " -m " + matrixFilesDir + matrixFileNames[i]  + " -f " + seqFileName;

          pr = rt.exec(patserCommand, new String[] {"PATH=C:/cygwin/bin"}, patserDir);
        }

        BufferedReader input = new BufferedReader(new InputStreamReader(pr.getInputStream()));

        String line = null;
        String pssmName = matrixFileNames[i].substring(0, matrixFileNames[i].length() - 7);
        int hits = 0;
        String lastGeneName = "";
        // TODO

        String word;
        // Read the input and filter out matrix hits data
        while ((line = input.readLine()) != null) {
          // System.out.println(line);

          if (line.contains("position=") && line.contains("score=")) { // result line
            Feature regElement = new Feature("TF_binding_site");
            // Set tfbs name, but filter the .matrix extension
            regElement.setName(pssmName);
            // hit.setNameAttribute(matrixFileNames[i]);

            StringTokenizer st = new StringTokenizer(line);
            // first one is the name
            word = st.nextToken();
            regElement.setParent(word);

            while (st.hasMoreTokens()) {
              word = st.nextToken();
              if (word.equals("position=")) {
                word = st.nextToken();
                if (word.endsWith("C")) {
                  regElement.setStrand("R");
                  word = word.substring(0, word.indexOf("C"));
                } else {
                  regElement.setStrand("D");
                }
                regElement.setStartPosition(Integer.parseInt(word));
              } else if (word.equals("score=")) {
                word = st.nextToken();
                regElement.setScore(Double.parseDouble(word));
              } else if (word.equals("sequence=")) {
                word = st.nextToken();
                regElement.setSequence(word);
                // Now that we have TFBS sequence, we can set the end position of TFBS:
                regElement.setEndPosition(regElement.getStartPosition() + word.length());
              }
            } // end of tokenizer

            // This is to calculate statistics of PSSM hits
            // if (!lastGeneName.equals(regElement.getParent())){
            hits++;
            lastGeneName = regElement.getParent();
            // }

            tfbsHits.add(regElement);
          }
        } // end of reading patser input

        pssmMatchingStats.put(pssmName, (double) hits / regRegions.size());

        // int exitVal = pr.waitFor();
        // System.out.println("Exited with error code " + exitVal);

      } catch (IOException e) {
        e.printStackTrace();
        throw new DataFormatException("PATSER execution failed. ");
      }
    }

    File seqFile = new File(seqFileName);
    seqFile.delete();
    /*
    		// add begin and end of sequence "fake" matches, or markers; like ^ and $ for begin and ed sequence in regEx
    		// this is for ILP to be able to induce rules with begin and end of sequence (distance, etc.)
    		for (Iterator<Feature> iterator = regRegions.iterator(); iterator.hasNext();) {
    			Feature feature = (Feature) iterator.next();
    			// markers are place before the sequence begins and after it ends
    			tfbsHits.add(new Feature("generic_marker", "begin", feature.getId(), "D", 0, 0, 0.0));
    			tfbsHits.add(new Feature("generic_marker", "end", feature.getId(), "D", feature.getSequence().length()+2, feature.getSequence().length()+2, 0.0));
    		}
    */
    if (tfbsHits.isEmpty()) {
      throw new DataFormatException("PATSER did not locate any motifs in the data.");
    }

    return tfbsHits;
  }