private void writeContours(XMLEventWriter writer, XMLEvent indent, TDRStructure structure) {
XMLEventFactory efac = XMLEventFactory.newInstance();
Collection<XMLEvent> attrContour = new ArrayList<XMLEvent>();
XMLEvent startContour;
XMLEvent endContour = efac.createEndElement("", "", "contour");
Vector<TDRContour> contours = structure.getContours();
Iterator<TDRContour> it = contours.iterator();
try {
while (it.hasNext()) {
TDRContour contour = it.next();
String section = String.valueOf(contour.getSection().getNumber());
String startpoint = contour.get_startpoint_x() + "," + contour.get_startpoint_y();
String offset = String.valueOf(contour.get_offset());
String numpoints = String.valueOf(contour.get_numpoints());
/* prepare contour's attributes */
attrContour.clear(); /*clear existing attributes*/
attrContour.add(efac.createAttribute("section", section));
attrContour.add(efac.createAttribute("startpoint", startpoint));
attrContour.add(efac.createAttribute("offset", offset));
attrContour.add(efac.createAttribute("numpoints", numpoints));
startContour = efac.createStartElement("", "", "contour", attrContour.iterator(), null);
/*<contour>*/
writer.add(indent);
writer.add(startContour);
writer.add(endContour);
writer.add(newLine);
}
} catch (XMLStreamException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
private void writeStructures(XMLEventWriter writer, GAMObject go) {
XMLEventFactory efac = XMLEventFactory.newInstance();
/* create indent from 2 tabs */
String sIndent = " " + " ";
XMLEvent indent = efac.createDTD(sIndent);
XMLEvent startStructures = efac.createStartElement("", "", "structures");
XMLEvent endStructures = efac.createEndElement("", "", "structures");
Collection<XMLEvent> attrStructure = new ArrayList<XMLEvent>();
XMLEvent startStructure;
XMLEvent endStructure = efac.createEndElement("", "", "structure");
XMLEvent startBoundingbox = efac.createStartElement("", "", "boundingbox");
XMLEvent attrMin, attrMax;
XMLEvent endBoundingbox = efac.createEndElement("", "", "boundingbox");
XMLEvent startSurfacemodel = efac.createStartElement("", "", "surfacemodel");
XMLEvent attrSurfaceSrc;
XMLEvent endSurfacemodel = efac.createEndElement("", "", "surfacemodel");
XMLEvent startContourmodel = efac.createStartElement("", "", "contourmodel");
XMLEvent attrContourSrc;
XMLEvent endControumodel = efac.createEndElement("", "", "contourmodel");
Collection<XMLEvent> attrContour = new ArrayList<XMLEvent>();
XMLEvent startContour;
XMLEvent endContour = efac.createEndElement("", "", "contour");
Set<Entry<String, TDRStructure>> structures = go.getStructures().entrySet();
if (structures == null) {
/* no 3D structure */
return;
}
Iterator<Entry<String, TDRStructure>> it = structures.iterator();
try {
/*<structures>*/
writer.add(indent);
writer.add(startStructures);
writer.add(newLine);
while (it.hasNext()) {
Entry<String, TDRStructure> s = (Entry<String, TDRStructure>) it.next();
TDRStructure structure = s.getValue();
String label = structure.getLabel();
String name = structure.getName();
String type = structure.getType();
Color c = structure.getColor();
String color = c.getRed() + "," + c.getGreen() + "," + c.getBlue();
/* prepare structure's attributes */
attrStructure.clear(); /*clear existing attributes*/
attrStructure.add(efac.createAttribute("label", label));
attrStructure.add(efac.createAttribute("name", name));
attrStructure.add(efac.createAttribute("type", type));
attrStructure.add(efac.createAttribute("color", color));
startStructure =
efac.createStartElement("", "", "structure", attrStructure.iterator(), null);
/* prepare boundingbox's attributes */
String min = structure.getMinBB();
String max = structure.getMaxBB();
attrMin = efac.createAttribute("min", min);
attrMax = efac.createAttribute("max", max);
/*
* prepare SRC attribute for surface and contour model
*
* local version: ObjectLoadingStr = ""
* server version: ObjectLoadingStr = "ObjectLoadingServlet"
* + "biolobj_name=" + tdro.getName()
* + "?image=";
* */
/* prepare <surfacemodel>'s attribute */
String surfaceSrc = structure.getSurfaceModel();
if (surfaceSrc == null || surfaceSrc.trim().equalsIgnoreCase("")) {
surfaceSrc = "";
} else {
surfaceSrc = ObjectLoadingStr + surfaceSrc;
}
attrSurfaceSrc = efac.createAttribute("src", surfaceSrc);
/* prepare <contourmodel>'s attribute */
String contourSrc = structure.getContourModel();
if (contourSrc == null || contourSrc.trim().equalsIgnoreCase("")) {
contourSrc = "";
} else {
contourSrc = ObjectLoadingStr + contourSrc;
}
attrContourSrc = efac.createAttribute("src", contourSrc);
/*<structure>*/
writer.add(indent);
writer.add(tab);
writer.add(startStructure);
writer.add(newLine);
/*<tags>*/
Vector<String> tags = structure.getTags();
if (tags.size() > 0) {
String sIndent2 = sIndent + " " + " ";
XMLEvent indent2 = efac.createDTD(sIndent2);
writeTags(writer, indent2, tags);
}
/*<annotations>*/
Properties annotations = structure.getAnnotations();
if (annotations.size() > 0) {
String sIndent2 = sIndent + " " + " ";
XMLEvent indent2 = efac.createDTD(sIndent2);
writeAnnotations(writer, indent2, annotations);
}
/*<boundingbox>*/
writer.add(indent);
writer.add(tab);
writer.add(tab);
writer.add(startBoundingbox);
writer.add(attrMin);
writer.add(attrMax);
writer.add(endBoundingbox);
writer.add(newLine);
/*<surfacemodel>*/
if (surfaceSrc != "") {
writer.add(indent);
writer.add(tab);
writer.add(tab);
writer.add(startSurfacemodel);
writer.add(attrSurfaceSrc);
writer.add(endSurfacemodel);
writer.add(newLine);
}
if (contourSrc != "") {
/*<contourmodel>*/
writer.add(indent);
writer.add(tab);
writer.add(tab);
writer.add(startContourmodel);
writer.add(attrContourSrc);
writer.add(newLine);
/*<contour>*/
String sIndent2 = sIndent + " " + " " + " ";
XMLEvent indent2 = efac.createDTD(sIndent2);
writeContours(writer, indent2, structure);
/*</contourmodel>*/
writer.add(indent);
writer.add(tab);
writer.add(tab);
writer.add(endControumodel);
writer.add(newLine);
}
/*</structure>*/
writer.add(indent);
writer.add(tab);
writer.add(endStructure);
writer.add(newLine);
}
/*</structures>*/
writer.add(indent);
writer.add(endStructures);
writer.add(newLine);
} catch (XMLStreamException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
