/**
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
* Created on Aug 30, 2011
* Created by Andreas Prlic
*
* @since 3.0.2
*/
package org.biojava.nbio.structure.scop.server;
import org.biojava.nbio.structure.domain.pdp.Domain;
import org.biojava.nbio.structure.scop.ScopDescription;
import org.biojava.nbio.structure.scop.ScopDomain;
import org.biojava.nbio.structure.scop.ScopNode;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.Marshaller;
import javax.xml.bind.Unmarshaller;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.PrintStream;
import java.util.List;
import java.util.SortedSet;
import java.util.TreeSet;
/** Utility classes for the XML serialization and de-serialization of SCOP.
*
* @author Andreas Prlic
* @since 3.0.2
*
*/
public class XMLUtil {
static JAXBContext jaxbContextScopDescription;
static {
try {
jaxbContextScopDescription= JAXBContext.newInstance(ScopDescription.class);
} catch (JAXBException e){
throw new RuntimeException("Could not initialize JAXB context", e);
}
}
static JAXBContext jaxbContextScopDomain;
static {
try {
jaxbContextScopDomain= JAXBContext.newInstance(ScopDomain.class);
} catch (JAXBException e){
throw new RuntimeException("Could not initialize JAXB context", e);
}
}
static JAXBContext jaxbContextScopNode;
static {
try {
jaxbContextScopNode= JAXBContext.newInstance(ScopNode.class);
} catch (JAXBException e){
throw new RuntimeException("Could not initialize JAXB context", e);
}
}
static JAXBContext jaxbContextDomains;
static {
try {
jaxbContextDomains= JAXBContext.newInstance(TreeSet.class);
} catch (JAXBException e){
throw new RuntimeException("Could not initialize JAXB context", e);
}
}
static JAXBContext jaxbContextStringSortedSet;
static {
try {
jaxbContextStringSortedSet= JAXBContext.newInstance(TreeSetStringWrapper.class);
} catch (JAXBException e){
throw new RuntimeException("Could not initialize JAXB context", e);
}
}
static JAXBContext jaxbContextComments;
static {
try {
jaxbContextComments = JAXBContext.newInstance(ListStringWrapper.class);
} catch( JAXBException e){
throw new RuntimeException("Could not initialize JAXB context", e);
}
}
public static String getScopDescriptionXML(ScopDescription desc){
return converScopDescription(desc);
}
public static ScopDescription getScopDescriptionFromXML(String xml){
ScopDescription job = null;
try {
Unmarshaller un = jaxbContextScopDescription.createUnmarshaller();
ByteArrayInputStream bais = new ByteArrayInputStream(xml.getBytes());
job = (ScopDescription) un.unmarshal(bais);
} catch (JAXBException e){
throw new RuntimeException("Could not parse from XML", e);
}
return job;
}
private static String converScopDescription(ScopDescription desc) {
ByteArrayOutputStream baos = new ByteArrayOutputStream();
PrintStream ps = new PrintStream(baos);
try {
Marshaller m = jaxbContextScopDescription.createMarshaller();
m.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
m.marshal( desc, ps);
} catch (JAXBException e){
throw new RuntimeException("Could not parse from XML", e);
}
return baos.toString();
}
public static String getScopDescriptionsXML(List<ScopDescription> descriptions){
ScopDescriptions container = new ScopDescriptions();
container.setScopDescription(descriptions);
return container.toXML();
}
public static String getCommentsXML(List<String> comments ){
ByteArrayOutputStream baos = new ByteArrayOutputStream();
PrintStream ps = new PrintStream(baos);
try {
Marshaller m = jaxbContextComments.createMarshaller();
m.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
ListStringWrapper wrapper = new ListStringWrapper();
wrapper.setData(comments);
m.marshal( wrapper, ps);
} catch (JAXBException e){
throw new RuntimeException("Could not parse from XML", e);
}
return baos.toString();
}
public static List<String> getCommentsFromXML(String xml){
List<String> comments = null;
try {
Unmarshaller un = jaxbContextComments.createUnmarshaller();
ByteArrayInputStream bais = new ByteArrayInputStream(xml.getBytes());
ListStringWrapper wrapper = (ListStringWrapper) un.unmarshal(bais);
comments = wrapper.getData();
} catch (JAXBException e){
throw new RuntimeException("Could not parse from XML", e);
}
return comments;
}
public static String getScopNodeXML(ScopNode scopNode){
ByteArrayOutputStream baos = new ByteArrayOutputStream();
PrintStream ps = new PrintStream(baos);
try {
Marshaller m = jaxbContextScopNode.createMarshaller();
m.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
m.marshal( scopNode, ps);
} catch (JAXBException e){
throw new RuntimeException("Could not parse from XML", e);
}
return baos.toString();
}
public static ScopNode getScopNodeFromXML(String xml){
ScopNode job = null;
try {
Unmarshaller un = jaxbContextScopNode.createUnmarshaller();
ByteArrayInputStream bais = new ByteArrayInputStream(xml.getBytes());
job = (ScopNode) un.unmarshal(bais);
} catch (JAXBException e){
throw new RuntimeException("Could not parse from XML", e);
}
return job;
}
public static String getScopNodesXML(List<ScopNode> nodes) {
ScopNodes container = new ScopNodes();
container.setScopNode(nodes);
return container.toXML();
}
public static String getScopDomainXML(ScopDomain domain){
ByteArrayOutputStream baos = new ByteArrayOutputStream();
PrintStream ps = new PrintStream(baos);
try {
Marshaller m = jaxbContextScopDomain.createMarshaller();
m.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
m.marshal( domain, ps);
} catch (JAXBException e){
throw new RuntimeException("Could not serialize to XML", e);
}
return baos.toString();
}
public static ScopDomain getScopDomainFromXML(String xml){
ScopDomain job = null;
try {
Unmarshaller un = jaxbContextScopDomain.createUnmarshaller();
ByteArrayInputStream bais = new ByteArrayInputStream(xml.getBytes());
job = (ScopDomain) un.unmarshal(bais);
} catch (JAXBException e){
throw new RuntimeException("Could not serialize to XML", e);
}
return job;
}
public static String getScopDomainsXML(List<ScopDomain> domains) {
ScopDomains container = new ScopDomains();
container.setScopDomain(domains);
return container.toXML();
}
public static String getDomainsXML(SortedSet<Domain> domains){
ByteArrayOutputStream baos = new ByteArrayOutputStream();
PrintStream ps = new PrintStream(baos);
try {
Marshaller m = jaxbContextDomains.createMarshaller();
m.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
m.marshal( domains, ps);
} catch (JAXBException e){
throw new RuntimeException("Could not serialize to XML", e);
}
return baos.toString();
}
@SuppressWarnings("unchecked")
public static SortedSet<Domain> getDomainsFromXML(String xml) {
SortedSet<Domain> domains = null;
try {
Unmarshaller un = jaxbContextDomains.createUnmarshaller();
ByteArrayInputStream bais = new ByteArrayInputStream(xml.getBytes());
domains = (SortedSet<Domain>) un.unmarshal(bais);
} catch (JAXBException e){
throw new RuntimeException("Could not serialize to XML", e);
}
return domains;
}
public static String getDomainRangesXML(SortedSet<String> domainRanges){
if ( ! (domainRanges instanceof TreeSet)) {
throw new IllegalArgumentException("SortedSet needs to be a TreeSet!");
}
TreeSet<String> data = (TreeSet<String>)domainRanges;
ByteArrayOutputStream baos = new ByteArrayOutputStream();
PrintStream ps = new PrintStream(baos);
try {
Marshaller m = jaxbContextStringSortedSet.createMarshaller();
m.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);
TreeSetStringWrapper wrapper = new TreeSetStringWrapper();
wrapper.setData(data);
m.marshal( wrapper, ps);
} catch (JAXBException e){
throw new RuntimeException("Could not serialize to XML", e);
}
return baos.toString();
}
public static SortedSet<String> getDomainRangesFromXML(String xml){
SortedSet<String> domains = null;
try {
Unmarshaller un = jaxbContextStringSortedSet.createUnmarshaller();
ByteArrayInputStream bais = new ByteArrayInputStream(xml.getBytes());
TreeSetStringWrapper wrapper = (TreeSetStringWrapper) un.unmarshal(bais);
domains = wrapper.getData();
} catch (JAXBException e){
throw new RuntimeException("Could not serialize to XML", e);
}
return domains;
}
}