/**
* 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 Feb 22, 2012
* Created by Andreas Prlic
*
* @since 3.0.2
*/
package org.biojava.nbio.structure.io.sifts;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.NodeList;
import org.xml.sax.SAXException;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.List;
public class SiftsXMLParser {
private final static Logger logger = LoggerFactory.getLogger(SiftsXMLParser.class);
Document dom;
List<SiftsEntity> entities;
static boolean debug = false;
public SiftsXMLParser(){
entities = new ArrayList<SiftsEntity>();
}
public List<SiftsEntity> getEntities(){
return entities;
}
public void parseXmlFile(InputStream is){
entities = new ArrayList<SiftsEntity>();
//get the factory
DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
try {
//Using factory get an instance of document builder
DocumentBuilder db = dbf.newDocumentBuilder();
//parse using builder to get DOM representation of the XML file
dom = db.parse(is);
parseDocument();
}catch(ParserConfigurationException pce) {
pce.printStackTrace();
}catch(SAXException se) {
se.printStackTrace();
}catch(IOException ioe) {
ioe.printStackTrace();
}
}
private void parseDocument(){
//get the root element
Element docEle = dom.getDocumentElement();
//get a nodelist of entities
NodeList nl = docEle.getElementsByTagName("entity");
if(nl != null && nl.getLength() > 0) {
for(int i = 0 ; i < nl.getLength();i++) {
//get the entity element
Element el = (Element)nl.item(i);
//get the Employee object
SiftsEntity e = getSiftsEntity(el);
//add it to list
entities.add(e);
}
}
}
/**
* <entity type="protein" entityId="A">
*/
private SiftsEntity getSiftsEntity(Element empEl) {
//for each <employee> element get text or int values of
//name ,id, age and name
String type = empEl.getAttribute("type");
String entityId = empEl.getAttribute("entityId");
//Create a new Employee with the value read from the xml nodes
SiftsEntity entity = new SiftsEntity(type,entityId);
// get nodelist of segments...
NodeList nl = empEl.getElementsByTagName("segment");
if(nl != null && nl.getLength() > 0) {
for(int i = 0 ; i < nl.getLength();i++) {
//get the entity element
Element el = (Element)nl.item(i);
SiftsSegment s = getSiftsSegment(el);
logger.debug("new segment: " + s);
entity.addSegment(s);
}
}
logger.debug("new SIFTS entity: " + entity);
return entity;
}
/** segId="4hhb_A_1_140" start="1" end="140"
*
* @param el
* @return
*/
private SiftsSegment getSiftsSegment(Element el) {
String segId = el.getAttribute("segId");
String start = el.getAttribute("start");
String end = el.getAttribute("end");
SiftsSegment seg = new SiftsSegment(segId,start,end);
if ( debug )
System.out.println("parsed " + seg);
// get nodelist of segments...
NodeList nl = el.getElementsByTagName("listResidue");
if(nl != null && nl.getLength() > 0) {
for(int i = 0 ; i < nl.getLength();i++) {
//get the entity element
Element listResidueEl = (Element)nl.item(i);
NodeList residueNodes = listResidueEl.getElementsByTagName("residue");
if(residueNodes != null && residueNodes.getLength() > 0) {
for(int j = 0 ; j < residueNodes.getLength();j++) {
Element residue = (Element) residueNodes.item(j);
SiftsResidue pos = getResidue(residue);
seg.addResidue(pos);
}
}
}
}
return seg;
}
/**
* <residue dbResNum="1" dbResName="THR">
<crossRefDb dbSource="PDB" dbVersion="20101103"
dbCoordSys="PDBresnum" dbAccessionId="1a4w" dbResNum="1H"
dbResName="THR" dbChainId="L"></crossRefDb>
<crossRefDb dbSource="UniProt" dbVersion="157-2"
dbCoordSys="UniProt" dbAccessionId="P00734"
dbResNum="328" dbResName="T"></crossRefDb>
<crossRefDb dbSource="SCOP" dbVersion="1.75"
dbCoordSys="PDBresnum" dbAccessionId="26083"
dbResNum="1H" dbResName="THR" dbChainId="L"></crossRefDb>
<residueDetail dbSource="MSD" property="Annotation">
Not_Observed</residueDetail>
</residue>
*/
private SiftsResidue getResidue(Element residue) {
SiftsResidue res = new SiftsResidue();
String dbResNumS = residue.getAttribute("dbResNum");
res.setNaturalPos(Integer.parseInt(dbResNumS));
String seqResName = residue.getAttribute("dbResName");
res.setSeqResName(seqResName);
boolean observed = true;
List<String> details = getTextValues(residue, "residueDetail");
if ( details != null && details.contains("Not_Observed")){
observed = false;
}
res.setNotObserved(! observed);
//else if ( detail != null && detail.trim().equalsIgnoreCase("Conflict")){
//
//}
NodeList nl = residue.getElementsByTagName("crossRefDb");
if(nl != null && nl.getLength() > 0) {
for(int i = 0 ; i < nl.getLength();i++) {
//get the entity element
Element crossRefEl = (Element)nl.item(i);
String dbSource = crossRefEl.getAttribute("dbSource");
String dbCoordSys = crossRefEl.getAttribute("dbCoordSys");
String dbAccessionId = crossRefEl.getAttribute("dbAccessionId");
String dbResNum = crossRefEl.getAttribute("dbResNum");
String dbResName = crossRefEl.getAttribute("dbResName");
String dbChainId = crossRefEl.getAttribute("dbChainId");
// System.out.println(dbSource + " " + dbCoordSys + " " + dbAccessionId + " " + dbResNum + " " + dbResName + " " + dbChainId);
if ( dbSource.equals("PDB") && ( dbCoordSys.equals("PDBresnum"))){
res.setPdbResNum(dbResNum);
res.setPdbResName(dbResName);
res.setChainId(dbChainId);
res.setPdbId(dbAccessionId);
} else if ( dbSource.equals("UniProt")){
res.setUniProtPos(Integer.parseInt(dbResNum));
res.setUniProtResName(dbResName);
res.setUniProtAccessionId(dbAccessionId);
}
}
}
return res;
}
/**
* I take a xml element and the tag name, look for the tag and get
* the text content
* i.e for <employee><name>John</name></employee> xml snippet if
* the Element points to employee node and tagName is 'name' I will return John
*/
@SuppressWarnings("unused")
private String getTextValue(Element ele, String tagName) {
String textVal = null;
NodeList nl = ele.getElementsByTagName(tagName);
if(nl != null && nl.getLength() > 0) {
Element el = (Element)nl.item(0);
textVal = el.getFirstChild().getNodeValue();
}
return textVal;
}
private List<String> getTextValues(Element ele, String tagName) {
List<String>values = new ArrayList<String>();
NodeList nl = ele.getElementsByTagName(tagName);
if(nl != null && nl.getLength() > 0) {
for ( int i = 0 ;i < nl.getLength() ; i ++) {
Element n = (Element) nl.item(i);
@SuppressWarnings("unused")
String k = n.getNodeName();
String val = n.getFirstChild().getNodeValue();
if ( val != null)
values.add(val);
}
}
return values;
}
}