private void writeMetaStructure(XMLEventWriter writer, GAMObject go) {
XMLEventFactory efac = XMLEventFactory.newInstance();
/* create indent from 2 tabs */
String sIndent = " " + " ";
XMLEvent indent = efac.createDTD(sIndent);
XMLEvent startMetadata = efac.createStartElement("", "", "metadata");
XMLEvent endMetadata = efac.createEndElement("", "", "metadata");
String data = go.getType();
if (data == null) {
data = "";
}
XMLEvent startType = efac.createStartElement("", "", "type");
XMLEvent charsType = efac.createCharacters(data);
XMLEvent endType = efac.createEndElement("", "", "type");
data = go.getAuthor();
if (data == null) {
data = "";
}
XMLEvent startAuthor = efac.createStartElement("", "", "author");
XMLEvent charsAuthor = efac.createCharacters(data);
XMLEvent endAuthor = efac.createEndElement("", "", "author");
data = go.getOrganization();
if (data == null) {
data = "";
}
XMLEvent startOrganization = efac.createStartElement("", "", "organization");
XMLEvent charsOrganization = efac.createCharacters(data);
XMLEvent endOrganization = efac.createEndElement("", "", "organization");
data = go.getOrganism();
if (data == null) {
data = "";
}
XMLEvent startOrganism = efac.createStartElement("", "", "organism");
XMLEvent charsOrganism = efac.createCharacters(data);
XMLEvent endOrganism = efac.createEndElement("", "", "organism");
data = go.getStage();
if (data == null) {
data = "";
}
XMLEvent startDevelStage = efac.createStartElement("", "", "developmental_stage");
XMLEvent charsDevelStage = efac.createCharacters(data);
XMLEvent endDevelStage = efac.createEndElement("", "", "developmental_stage");
data = go.getDescription();
if (data == null) {
data = "";
}
XMLEvent startDescription = efac.createStartElement("", "", "description");
XMLEvent charsDescription = efac.createCharacters(data);
XMLEvent endDescription = efac.createEndElement("", "", "description");
Collection<XMLEvent> attrSampling = new ArrayList<XMLEvent>();
attrSampling.add(efac.createAttribute("pointdistX", String.valueOf(go.getPointDistX())));
attrSampling.add(efac.createAttribute("pointdistY", String.valueOf(go.getPointDistY())));
attrSampling.add(efac.createAttribute("stepsize", String.valueOf(go.getStepsize())));
attrSampling.add(efac.createAttribute("numberofpointsX", String.valueOf(go.getNumPointsX())));
attrSampling.add(efac.createAttribute("numberofpointsY", String.valueOf(go.getNumPointsY())));
String voxelSize = go.getVoxelSize();
if (voxelSize == null) {
voxelSize = "";
}
attrSampling.add(efac.createAttribute("voxelsize", voxelSize));
XMLEvent startSampling =
efac.createStartElement("", "", "sampling", attrSampling.iterator(), null);
XMLEvent endSampling = efac.createEndElement("", "", "sampling");
try {
/*<metadata>*/
writer.add(indent);
writer.add(startMetadata);
writer.add(newLine);
/*<type>*/
writer.add(indent);
writer.add(tab);
writer.add(startType);
writer.add(charsType);
writer.add(endType);
writer.add(newLine);
/*<author>*/
writer.add(indent);
writer.add(tab);
writer.add(startAuthor);
writer.add(charsAuthor);
writer.add(endAuthor);
writer.add(newLine);
/*<organization>*/
writer.add(indent);
writer.add(tab);
writer.add(startOrganization);
writer.add(charsOrganization);
writer.add(endOrganization);
writer.add(newLine);
/*<organism>*/
writer.add(indent);
writer.add(tab);
writer.add(startOrganism);
writer.add(charsOrganism);
writer.add(endOrganism);
writer.add(newLine);
/*<developmental_stage>*/
writer.add(indent);
writer.add(tab);
writer.add(startDevelStage);
writer.add(charsDevelStage);
writer.add(endDevelStage);
writer.add(newLine);
/*<description>*/
writer.add(indent);
writer.add(tab);
writer.add(startDescription);
writer.add(charsDescription);
writer.add(endDescription);
writer.add(newLine);
/*<sampling>*/
writer.add(indent);
writer.add(tab);
writer.add(startSampling);
writer.add(endSampling);
writer.add(newLine);
/*</metadata>*/
writer.add(indent);
writer.add(endMetadata);
writer.add(newLine);
} catch (XMLStreamException e) {
System.out.println("GAMLWriterV10::writerMetadata - error writing Metadata");
e.printStackTrace();
}
}
private void writeMetaSections(XMLEventWriter writer, GAMObject go) {
XMLEventFactory efac = XMLEventFactory.newInstance();
/* create indent from 2 tabs */
String sIndent = " " + " ";
XMLEvent indent = efac.createDTD(sIndent);
XMLEvent startMetadata = efac.createStartElement("", "", "meta");
XMLEvent endMetadata = efac.createEndElement("", "", "meta");
String data = String.valueOf(go.getFirstNum());
if (data == null) {
data = "";
}
XMLEvent startFirst = efac.createStartElement("", "", "firstnum");
XMLEvent charsFirst = efac.createCharacters(data);
XMLEvent endFirst = efac.createEndElement("", "", "firstnum");
data = String.valueOf(go.getLastNum());
if (data == null) {
data = "";
}
XMLEvent startLast = efac.createStartElement("", "", "lastnum");
XMLEvent charsLast = efac.createCharacters(data);
XMLEvent endLast = efac.createEndElement("", "", "lastnum");
data = go.getSectionType();
if (data == null) {
data = "";
}
XMLEvent startType = efac.createStartElement("", "", "type");
XMLEvent charsType = efac.createCharacters(data);
XMLEvent endType = efac.createEndElement("", "", "type");
data = go.getSectionFormat();
if (data == null) {
data = "";
}
XMLEvent startFormat = efac.createStartElement("", "", "format");
XMLEvent charsFormat = efac.createCharacters(data);
XMLEvent endFormat = efac.createEndElement("", "", "format");
data = go.getStackFileName();
if (data == null) {
data = "";
}
XMLEvent startStackFile = efac.createStartElement("", "", "stack_file");
XMLEvent charsStackFile = efac.createCharacters(data);
XMLEvent endStackFile = efac.createEndElement("", "", "stack_file");
try {
/*<metadata>*/
writer.add(indent);
writer.add(startMetadata);
writer.add(newLine);
/*<firstnum>*/
writer.add(indent);
writer.add(tab);
writer.add(startFirst);
writer.add(charsFirst);
writer.add(endFirst);
writer.add(newLine);
/*<lastnum>*/
writer.add(indent);
writer.add(tab);
writer.add(startLast);
writer.add(charsLast);
writer.add(endLast);
writer.add(newLine);
/*<type>*/
writer.add(indent);
writer.add(tab);
writer.add(startType);
writer.add(charsType);
writer.add(endType);
writer.add(newLine);
/*<format>*/
writer.add(indent);
writer.add(tab);
writer.add(startFormat);
writer.add(charsFormat);
writer.add(endFormat);
writer.add(newLine);
/*<stack_file>*/
writer.add(indent);
writer.add(tab);
writer.add(startStackFile);
writer.add(charsStackFile);
writer.add(endStackFile);
writer.add(newLine);
/*</metadata>*/
writer.add(indent);
writer.add(endMetadata);
writer.add(newLine);
} catch (XMLStreamException e) {
System.out.println("GAMLWriterV10::writerMetaSections - error writing Metadata");
e.printStackTrace();
}
}
private void writeSections(XMLEventWriter writer, GAMObject go) {
XMLEventFactory efac = XMLEventFactory.newInstance();
/* create indent from 2 tabs */
String sIndent = " " + " ";
XMLEvent indent = efac.createDTD(sIndent);
String section_format = go.getSectionFormat();
if (section_format == null) {
section_format = "JPEG";
}
String section_type = go.getSectionType();
if (section_type == null) {
section_type = "sequence_image";
}
XMLEvent startSections = efac.createStartElement("", "", "sections");
XMLEvent endSections = efac.createEndElement("", "", "sections");
XMLEvent attrFirstnum = efac.createAttribute("firstnum", String.valueOf(go.getFirstNum()));
XMLEvent attrLastnum = efac.createAttribute("lastnum", String.valueOf(go.getLastNum()));
XMLEvent attrSectionType = efac.createAttribute("type", section_type);
XMLEvent attrSectionFormat = efac.createAttribute("format", section_format);
XMLEvent startSection = efac.createStartElement("", "", "section");
XMLEvent endSection = efac.createEndElement("", "", "section");
XMLEvent startStack = efac.createStartElement("", "", "stack");
XMLEvent endStack = efac.createEndElement("", "", "stack");
XMLEvent attrNumber;
XMLEvent attrSrc;
Set<Entry<Integer, TDRSection>> sections = go.getSections().entrySet();
Iterator<Entry<Integer, TDRSection>> it = sections.iterator();
try {
/* sequence images or stack image? */
if (section_type == null || section_type.equalsIgnoreCase("sequence_image")) {
/*<sections>: in case of SEQUENCE images */
writer.add(indent);
writer.add(startSections);
writer.add(attrFirstnum);
writer.add(attrLastnum);
writer.add(attrSectionType);
writer.add(attrSectionFormat);
writer.add(newLine);
while (it.hasNext()) {
Entry<Integer, TDRSection> section = (Entry<Integer, TDRSection>) it.next();
String number = String.valueOf(section.getKey());
/* local version: ObjectLoadingStr = ""
* server version: ObjectLoadingStr = "ObjectLoadingServlet"
* + "biolobj_name=" + tdro.getName()
* + "?image=";
* */
String src = ObjectLoadingStr + section.getValue().getImageFileName();
attrNumber = efac.createAttribute("number", number);
attrSrc = efac.createAttribute("src", src);
/*<section>*/
writer.add(indent);
writer.add(tab);
writer.add(startSection);
writer.add(attrNumber);
writer.add(attrSrc);
writer.add(endSection);
writer.add(newLine);
}
/*<sections>*/
writer.add(indent);
writer.add(endSections);
writer.add(newLine);
} else {
/*<sections>: in case of STACK images */
writer.add(indent);
writer.add(startSections);
writer.add(attrFirstnum);
writer.add(attrLastnum);
writer.add(attrSectionType);
writer.add(attrSectionFormat);
writer.add(newLine);
/* local version: ObjectLoadingStr = ""
* server version: ObjectLoadingStr = "ObjectLoadingServlet"
* + "biolobj_name=" + tdro.getName()
* + "?image=";
* */
String src = ObjectLoadingStr + go.getStackFileName();
attrSrc = efac.createAttribute("src", src);
/*<stack>*/
writer.add(indent);
writer.add(tab);
writer.add(startStack);
writer.add(attrSrc);
writer.add(endStack);
writer.add(newLine);
/*<sections>*/
writer.add(indent);
writer.add(endSections);
writer.add(newLine);
}
} catch (XMLStreamException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
@Override
public void write(GAMObject go) {
try {
XMLEventFactory efac = XMLEventFactory.newInstance();
XMLEvent startDoc = efac.createStartDocument("UTF-8", "1.0");
XMLEvent endDoc = efac.createEndDocument();
XMLEvent startGAML = efac.createStartElement("", "", "gaml");
XMLEvent attrVersion = efac.createAttribute("version", "1.0");
XMLEvent endGAML = efac.createEndElement("", "", "gaml");
XMLEvent startServer = efac.createStartElement("", "", "server");
String server = go.getServer();
if (server == null) {
server = "";
}
XMLEvent charServer = efac.createCharacters(server);
XMLEvent endServer = efac.createEndElement("", "", "server");
XMLEvent startModel = efac.createStartElement("", "", "model");
XMLEvent attrName = efac.createAttribute("name", go.getName());
XMLEvent endModel = efac.createEndElement("", "", "model");
/*<?xml version="1.0" encoding="UTF-8"?>*/
writer.add(startDoc);
writer.add(newLine);
/*<gaml>*/
writer.add(startGAML);
writer.add(attrVersion);
writer.add(newLine);
/*<server>*/
writer.add(tab);
writer.add(startServer);
writer.add(charServer);
writer.add(endServer);
writer.add(newLine);
/*<model>*/
writer.add(tab);
writer.add(startModel);
writer.add(attrName);
writer.add(newLine);
/*<meta>*/
writeMetaModel(writer, go);
/*<tags>*/
Vector<String> tags = go.getTags();
if (tags.size() > 0) {
String sIndent2 = " " + " ";
XMLEvent indent2 = efac.createDTD(sIndent2);
writeTags(writer, indent2, tags);
}
/*<annotations>*/
Properties annotations = go.getAnnotations();
if (annotations.size() > 0) {
String sIndent2 = " " + " ";
XMLEvent indent2 = efac.createDTD(sIndent2);
writeAnnotations(writer, indent2, annotations);
}
/*<sections>*/
if (go.getSections().size() > 0) {
writeSections(writer, go);
}
/*<structures>*/
if (go.getStructures().size() > 0) {
writeStructures(writer, go);
}
/*</model>*/
writer.add(tab);
writer.add(endModel);
writer.add(newLine);
/*<user-annotations>*/
Properties userAnnotations = go.getUserAnnotations();
if (userAnnotations.size() > 0) {
String sIndent1 = " ";
XMLEvent indent1 = efac.createDTD(sIndent1);
writeUserAnnotations(writer, indent1, userAnnotations);
}
/*</gaml>*/
writer.add(endGAML);
writer.add(newLine);
writer.add(endDoc);
writer.flush();
} catch (XMLStreamException e) {
System.out.println("GAMLWriterV10::write - error writing GAM");
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();
}
}
