Example #1
0
  /**
   * Annotates a block of values of a heatmap.plus SVG file by giving them an id and row/column
   * attributes. A heatmap.plus can contain up to three 'blocks': row annotations, column
   * annotations and the matrix.
   *
   * @param nRow number of rows of this block
   * @param nCol number of columns of this block
   * @param blockId value of the id attribute to give elements in this block
   * @throws XMLStreamException
   */
  private void annotateHeatMapBlock(
      int nRow, int nCol, String blockId, XMLEventWriter writer, XMLEventReader reader)
      throws XMLStreamException {
    int counter = 0;
    int nPath = nRow * nCol;
    int currentRow = nRow; // elements drawn from bottom to top, so start counting at last row
    int currentCol = 1;
    while (counter < nPath) {
      XMLEvent event = (XMLEvent) reader.next();
      if (event.isStartElement() && event.asStartElement().getName().getLocalPart().equals(PATH)) {
        // make a new start element with the same attributes plus the extra annotations
        @SuppressWarnings("unchecked")
        Iterator<Attribute> attributes = event.asStartElement().getAttributes();

        StartElement newSe = eventFactory.createStartElement(new QName(PATH), attributes, null);
        writer.add(newSe);
        writer.add(eventFactory.createAttribute(ID, blockId));
        writer.add(eventFactory.createAttribute(new QName("row"), Integer.toString(currentRow)));
        writer.add(eventFactory.createAttribute(new QName("col"), Integer.toString(currentCol)));

        currentRow--;
        if (currentRow == 0) {
          // finished one column, reset currentRow and increment currentCol
          currentRow = nRow;
          currentCol++;
        }
        counter++;
      } else {
        // write the rest untouched
        writer.add(event);
      }
    }
  }
Example #2
0
  /**
   * Can annotate SVG heatmap.plus charts made by R. Reads and writes using StAX, adding row and col
   * attributes to <path> elements corresponding to data points in the heatmap. All indexes can be
   * calculated using nRow, nCol, nRowAnnotations and nColAnnotations.
   *
   * @param chart
   * @throws FactoryConfigurationError
   * @throws XMLStreamException
   * @throws FileNotFoundException
   */
  public void annotateHeatMap(HeatMapChart chart)
      throws XMLStreamException, FactoryConfigurationError, FileNotFoundException {
    XMLEventReader reader =
        XMLInputFactory.newInstance().createXMLEventReader(new FileInputStream(inFile));

    OutputStream os = new FileOutputStream(outFile);
    XMLEventWriter writer = XMLOutputFactory.newInstance().createXMLEventWriter(os);

    // get values from HeatMapChart
    int nRow = chart.getData().getRowTargets().size();
    int nCol = chart.getData().getColumnTargets().size();

    // TODO get from HeatMapChart:
    int nRowAnnotations = 0;
    int nColAnnotations = 0;

    // skip the headers and <def> bit until we reach <g id="">
    while (true) {
      XMLEvent event = (XMLEvent) reader.next();
      if (event.isStartElement()) {
        StartElement se = event.asStartElement();
        if (se.getName().getLocalPart().equals(G) && se.getAttributeByName(ID) != null) {
          LOG.info("<g id=\"\"> reached");
          writer.add(event);
          break;
        }
      }
      writer.add(event);
    }

    // annotation begins here
    // ROW ANNOTATIONS
    if (nRowAnnotations > 0) {
      LOG.info("parsing " + nRowAnnotations + " row annotations");
      annotateHeatMapBlock(nRow, nRowAnnotations, "rowAnnotation", writer, reader);
    }

    // COLUMN ANNOTATIONS
    if (nColAnnotations > 0) {
      LOG.info("parsing " + nColAnnotations + " col annotations");
      annotateHeatMapBlock(nColAnnotations, nCol, "colAnnotatation", writer, reader);
    }

    // MATRIX ANNOTATIONS
    LOG.info("parsing " + (nRow * nCol) + " matrix values");
    annotateHeatMapBlock(nRow, nCol, "matrix", writer, reader);

    // COLUMN NAMES
    LOG.info("parsing " + nCol + " column names");
    int counter = 0;
    while (counter < nCol) {
      XMLEvent event = (XMLEvent) reader.next();
      if (event.isStartElement() && event.asStartElement().getName().getLocalPart().equals(G)) {

        @SuppressWarnings("unchecked")
        Iterator<Attribute> attributes = event.asStartElement().getAttributes();

        StartElement newSe = eventFactory.createStartElement(new QName(G), attributes, null);
        writer.add(newSe);
        writer.add(eventFactory.createAttribute(ID, "colName"));
        writer.add(eventFactory.createAttribute(new QName("col"), Integer.toString(counter + 1)));

        counter++;
      } else {
        writer.add(event);
      }
    }

    // ROW NAMES
    LOG.info("parsing " + nRow + " row names");
    counter = 0;
    while (counter < nRow) {
      XMLEvent event = (XMLEvent) reader.next();
      if (event.isStartElement() && event.asStartElement().getName().getLocalPart().equals(G)) {

        @SuppressWarnings("unchecked")
        Iterator<Attribute> attributes = event.asStartElement().getAttributes();

        StartElement newSe = eventFactory.createStartElement(new QName(G), attributes, null);
        writer.add(newSe);
        writer.add(eventFactory.createAttribute(ID, "rowName"));
        writer.add(
            eventFactory.createAttribute(new QName("row"), Integer.toString(nRow - counter)));
        counter++;

      } else {
        writer.add(event);
      }
    }

    // finish rest of file
    while (reader.hasNext()) {
      XMLEvent event = (XMLEvent) reader.next();
      if (event.isEndElement()) {
        // close the <g id=""> tag, right before the </svg> end element
        if (event.asEndElement().getName().getLocalPart().equals("svg")) {
          EndElement newEe = eventFactory.createEndElement(new QName(G), null);
          writer.add(newEe);
        }
      }
      writer.add(event);
    }

    writer.close();
  }