/**
* 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);
}
}
}
@Override
public Scenario parse(InputStream inputStream)
throws IOException, SAXException, ParserConfigurationException {
OutputStream output = new ByteArrayOutputStream();
JsonXMLConfig config = new JsonXMLConfigBuilder().autoArray(true).prettyPrint(false).build();
try {
/* Create source (XML). */
XMLEventReader reader = XMLInputFactory.newInstance().createXMLEventReader(inputStream);
// XMLStreamReader reader = XMLInputFactory.newInstance().createXMLStreamReader(inputStream);
// Source source = new StAXSource(reader);
/* Create result (JSON). */
XMLEventWriter writer = new JsonXMLOutputFactory(config).createXMLEventWriter(output);
// XMLStreamWriter writer = new JsonXMLOutputFactory(config).createXMLStreamWriter(output);
// Result result = new StAXResult(writer);
/*
* Copy events from reader to writer.
*/
writer.add(reader);
/* Copy source to result via "identity transform". */
// TransformerFactory.newInstance().newTransformer().transform(source, result);
} catch (XMLStreamException e) {
e.printStackTrace();
} finally {
/* As per StAX specification, XMLStreamReader/Writer.close()
doesn't close
the underlying stream. */
output.close();
inputStream.close();
}
/*
try {
json = xmlToJson(inputStream);
} catch (JSONException e) {
e.printStackTrace();
}
String jsonString = json.toString();
System.out.println(jsonString);
GenericDocument genericDocument = new GenericDocument();
genericDocument.setJson(jsonString);
*/
GenericDocument genericDocument = new GenericDocument();
String json = output.toString();
genericDocument.setJson(json);
return genericDocument;
}
/**
* 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();
}
