コード例 #1
0
ファイル: PeakMLParser.java プロジェクト: joewandy/HDP-Align
  private static SetInfo parseSet(Node parent) throws XmlParserException {
    String id = "";
    String type = "";
    String measurementids = null;

    NodeList nodes = parent.getChildNodes();
    Vector<SetInfo> sets = new Vector<SetInfo>();
    for (int nodeid = 0; nodeid < nodes.getLength(); ++nodeid) {
      Node node = nodes.item(nodeid);
      if (node.getNodeType() != Node.ELEMENT_NODE) continue;

      Element element = (Element) node;
      if (element.getTagName().equals("id")) id = element.getTextContent();
      else if (element.getTagName().equals("set")) sets.add(parseSet(element));
      else if (element.getTagName().equals("type")) type = element.getTextContent();
      else if (element.getTagName().equals("measurementids"))
        measurementids = element.getTextContent();
    }

    // create the set
    SetInfo set = new SetInfo(id, Integer.parseInt(type));
    if (measurementids != null) {
      int mids[] = ByteArray.toIntArray(Base64.decode(measurementids), ByteArray.ENDIAN_LITTLE, 32);
      for (int mid : mids) set.addMeasurementID(mid);
    }

    // add the children
    for (SetInfo s : sets) set.addChild(s);

    return set;
  }
コード例 #2
0
ファイル: PeakMLParser.java プロジェクト: joewandy/HDP-Align
  private static PeakData<? extends Peak> parsePeakData(Node parent) throws XmlParserException {
    // get the attributes
    Node typeattribute = parent.getAttributes().getNamedItem(PeakMLWriter.TYPE);
    if (typeattribute == null) throw new XmlParserException("Failed to locate a type attribute.");
    Node sizeattribute = parent.getAttributes().getNamedItem(PeakMLWriter.SIZE);
    if (sizeattribute == null) throw new XmlParserException("Failed to locate a size attribute.");

    int size = Integer.parseInt(sizeattribute.getNodeValue());
    String type = typeattribute.getNodeValue();

    // create the arrays
    int scanids[] = null;
    int patternids[] = null;
    int measurementids[] = null;
    double masses[] = null;
    double intensities[] = null;
    double retentiontimes[] = null;

    // retrieve all the data
    NodeList nodes = parent.getChildNodes();
    for (int nodeid = 0; nodeid < nodes.getLength(); ++nodeid) {
      Node node = nodes.item(nodeid);
      if (node.getNodeType() != Node.ELEMENT_NODE) continue;

      Element element = (Element) node;
      if (element.getTagName().equals("scanids"))
        scanids =
            ByteArray.toIntArray(
                Base64.decode(element.getTextContent()), ByteArray.ENDIAN_LITTLE, 32);
      else if (element.getTagName().equals("patternids"))
        patternids =
            ByteArray.toIntArray(
                Base64.decode(element.getTextContent()), ByteArray.ENDIAN_LITTLE, 32);
      else if (element.getTagName().equals("measurementids"))
        measurementids =
            ByteArray.toIntArray(
                Base64.decode(element.getTextContent()), ByteArray.ENDIAN_LITTLE, 32);
      else if (element.getTagName().equals("masses"))
        masses =
            ByteArray.toDoubleArray(
                Base64.decode(element.getTextContent()), ByteArray.ENDIAN_LITTLE, 32);
      else if (element.getTagName().equals("intensities"))
        intensities =
            ByteArray.toDoubleArray(
                Base64.decode(element.getTextContent()), ByteArray.ENDIAN_LITTLE, 32);
      else if (element.getTagName().equals("retentiontimes"))
        retentiontimes =
            ByteArray.toDoubleArray(
                Base64.decode(element.getTextContent()), ByteArray.ENDIAN_LITTLE, 32);
    }

    // create the PeakData instance
    if (type.equals("centroid"))
      return new PeakData<Centroid>(
          Centroid.factory,
          size,
          scanids,
          patternids,
          measurementids,
          masses,
          intensities,
          retentiontimes);
    return null;
  }