/*
* 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 Jun 1, 2010
* Author: Jianjiong Gao
*
*/
package org.biojava.nbio.protmod.io;
import org.biojava.nbio.protmod.*;
import org.w3c.dom.Document;
import org.w3c.dom.NamedNodeMap;
import org.w3c.dom.Node;
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.*;
/**
*
* @author Jianjiong Gao
* @since 3.0
*/
public final class ProteinModificationXmlReader {
/**
* This is a utility class and thus cannot be instantialized.
*/
private ProteinModificationXmlReader() {}
/**
* Read protein modifications from XML file and register them.
* @param isXml {@link InputStream} of the XML file.
* @throws IOException if failed to read the XML file.
* @throws ParserConfigurationException if parse errors occur.
* @throws SAXException the {@link DocumentBuilder} cannot be created.
*/
public static void registerProteinModificationFromXml(InputStream isXml)
throws IOException, ParserConfigurationException, SAXException {
if (isXml==null) {
throw new IllegalArgumentException("Null argument.");
}
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder = factory.newDocumentBuilder();
Document doc = builder.parse(isXml);
NodeList modNodes = doc.getElementsByTagName("Entry");
int modSize = modNodes.getLength();
List<Node> nodes;
for (int iMod=0; iMod<modSize; iMod++) {
Node modNode = modNodes.item(iMod);
Map<String,List<Node>> infoNodes = getChildNodes(modNode);
// ID
nodes = infoNodes.get("Id");
if (nodes==null || nodes.size()!=1) {
throw new RuntimeException("Each modification must have exact " +
"one <Id> field.");
}
String id = nodes.get(0).getTextContent();
// modification category
nodes = infoNodes.get("Category");
if (nodes==null || nodes.size()!=1) {
throw new RuntimeException("Each modification must have exact " +
"one <Category> field. See Modification "+id+".");
}
ModificationCategory cat = ModificationCategory.getByLabel(
nodes.get(0).getTextContent());
if (cat==null) {
throw new RuntimeException(nodes.get(0).getTextContent()+
" is not defined as an modification category." +
" See Modification "+id+".");
}
// occurrence type
nodes = infoNodes.get("Occurrence");
if (nodes==null || nodes.size()!=1) {
throw new RuntimeException("Each modification must have exact " +
"one <Occurrence> field. See Modification "+id+".");
}
ModificationOccurrenceType occType = ModificationOccurrenceType
.getByLabel(nodes.get(0).getTextContent());
if (occType==null) {
throw new RuntimeException(nodes.get(0).getTextContent()+
" is not defined as an modification occurence type." +
" See Modification "+id+".");
}
// condition
ModificationCondition condition = null;
{
nodes = infoNodes.get("Condition");
if (nodes==null || nodes.size()!=1) {
throw new RuntimeException("Each modification must have exact " +
"one <Condition> field. See Modification "+id+".");
}
Node compsNode = nodes.get(0);
// keep track of the labels of component indices
Map<String,Integer> mapLabelComp = new HashMap<String,Integer>();
Map<String,List<Node>> compInfoNodes = getChildNodes(compsNode);
// components
List<Node> compNodes = compInfoNodes.get("Component");
int sizeComp = compNodes.size();
List<Component> comps = new ArrayList<Component>(sizeComp);
for (int iComp=0; iComp<sizeComp; iComp++) {
Node compNode = compNodes.get(iComp);
// comp label
NamedNodeMap compNodeAttrs = compNode.getAttributes();
Node labelNode = compNodeAttrs.getNamedItem("component");
if (labelNode==null) {
throw new RuntimeException("Each component must have a label." +
" See Modification "+id+".");
}
String label = labelNode.getTextContent();
if (mapLabelComp.containsKey(label)) {
throw new RuntimeException("Each component must have a unique label." +
" See Modification "+id+".");
}
// comp PDBCC ID
Set<String> compIds = new HashSet<String>();
List<Node> compIdNodes = getChildNodes(compNode).get("Id");
if (compIdNodes!=null) {
for (Node compIdNode : compIdNodes) {
NamedNodeMap compIdNodeAttr = compIdNode.getAttributes();
Node compIdSource = compIdNodeAttr.getNamedItem("source");
if (compIdSource!=null && compIdSource.getTextContent().equals("PDBCC")) {
String strComps = compIdNode.getTextContent();
if (strComps.isEmpty()) {
throw new RuntimeException("Empty component." +
" See Modification "+id+".");
}
compIds.addAll(Arrays.asList(strComps.split(",")));
}
}
}
if (compIds.isEmpty()) {
throw new RuntimeException("Each component must have a PDBCC ID." +
" See Modification "+id+".");
}
// terminal
boolean nTerminal = false;
boolean cTerminal = false;
List<Node> compTermNode = getChildNodes(compNode).get("Terminal");
if (compTermNode!=null) {
if (compTermNode.size()!=1) {
throw new RuntimeException("Only one <Terminal> condition is allowed for " +
"each component. See Modification "+id+".");
}
String nc = compTermNode.get(0).getTextContent();
if (nc.equals("N")) {
nTerminal = true;
} else if (nc.equals("C")) {
cTerminal = true;
} else {
throw new RuntimeException("Only N or C is allowed for <Terminal>." +
" See Modification "+id+".");
}
}
// register
Component comp = Component.of(compIds, nTerminal, cTerminal);
comps.add(comp);
mapLabelComp.put(label, comps.size()-1);
}
// bonds
List<Node> bondNodes = compInfoNodes.get("Bond");
List<ModificationLinkage> linkages = null;
if (bondNodes!=null) {
int sizeBonds = bondNodes.size();
linkages = new ArrayList<ModificationLinkage>(sizeBonds);
for (int iBond=0; iBond<sizeBonds; iBond++) {
Node bondNode = bondNodes.get(iBond);
Map<String,List<Node>> bondChildNodes = getChildNodes(bondNode);
if (bondChildNodes==null) {
throw new RuntimeException("Each bond must contain two atoms" +
" See Modification "+id+".");
}
List<Node> atomNodes = bondChildNodes.get("Atom");
if (atomNodes==null || atomNodes.size()!=2) {
throw new RuntimeException("Each bond must contain two atoms" +
" See Modification "+id+".");
}
// atom 1
NamedNodeMap atomNodeAttrs = atomNodes.get(0).getAttributes();
Node compNode = atomNodeAttrs.getNamedItem("component");
if (compNode==null) {
throw new RuntimeException("Each atom must on a component." +
" See Modification "+id+".");
}
String labelComp1 = compNode.getTextContent();
int iComp1 = mapLabelComp.get(labelComp1);
Node labelNode = atomNodeAttrs.getNamedItem("atom");
String labelAtom1 = labelNode==null?null:labelNode.getTextContent();
String atom1 = atomNodes.get(0).getTextContent();
if (atom1.isEmpty()) {
throw new RuntimeException("Each atom must have a name. Please use wildcard * if unknown." +
" See Modification "+id+".");
}
List<String> potentialAtoms1 = Arrays.asList(atom1.split(","));
// atom 2
atomNodeAttrs = atomNodes.get(1).getAttributes();
compNode = atomNodeAttrs.getNamedItem("component");
if (compNode==null) {
throw new RuntimeException("Each atom must on a component." +
" See Modification "+id+".");
}
String labelComp2 = compNode.getTextContent();
int iComp2 = mapLabelComp.get(labelComp2);
labelNode = atomNodeAttrs.getNamedItem("atom");
String labelAtom2 = labelNode==null?null:labelNode.getTextContent();
String atom2 = atomNodes.get(1).getTextContent();
if (atom2.isEmpty()) {
throw new RuntimeException("Each atom must have a name. Please use wildcard * if unknown." +
" See Modification "+id+".");
}
List<String> potentialAtoms2 = Arrays.asList(atom2.split(","));
// add linkage
ModificationLinkage linkage = new ModificationLinkage(comps,
iComp1, potentialAtoms1, labelAtom1,
iComp2, potentialAtoms2, labelAtom2);
linkages.add(linkage);
}
}
condition = new ModificationConditionImpl(comps, linkages);
} // end of condition
ProteinModificationImpl.Builder modBuilder =
new ProteinModificationImpl.Builder(id, cat, occType, condition);
// description
nodes = infoNodes.get("Description");
if (nodes!=null && !nodes.isEmpty()) {
modBuilder.setDescription(nodes.get(0).getTextContent());
}
// cross references
nodes = infoNodes.get("CrossReference");
if (nodes!=null) {
for (Node node:nodes) {
Map<String,List<Node>> xrefInfoNodes = getChildNodes(node);
// source
List<Node> xrefNode = xrefInfoNodes.get("Source");
if (xrefNode==null || xrefNode.size()!=1) {
throw new RuntimeException("Error in XML file: " +
"a cross reference must contain exactly one <Source> field." +
" See Modification "+id+".");
}
String xrefDb = xrefNode.get(0).getTextContent();
// id
xrefNode = xrefInfoNodes.get("Id");
if (xrefNode==null || xrefNode.size()!=1) {
throw new RuntimeException("Error in XML file: " +
"a cross reference must contain exactly one <Id> field." +
" See Modification "+id+".");
}
String xrefId = xrefNode.get(0).getTextContent();
// name
String xrefName = null;
xrefNode = xrefInfoNodes.get("Name");
if (xrefNode!=null && !xrefNode.isEmpty()) {
xrefName = xrefNode.get(0).getTextContent();
}
if (xrefDb.equals("PDBCC")) {
modBuilder.setPdbccId(xrefId).setPdbccName(xrefName);
} else if (xrefDb.equals("RESID")) {
modBuilder.setResidId(xrefId).setResidName(xrefName);
} else if (xrefDb.equals("PSI-MOD")) {
modBuilder.setPsimodId(xrefId).setPsimodName(xrefName);
}
}
} // end of cross references
// formula
nodes = infoNodes.get("Formula");
if (nodes!=null && !nodes.isEmpty()) {
modBuilder.setFormula(nodes.get(0).getTextContent());
}
// keywords
nodes = infoNodes.get("Keyword");
if (nodes!=null && !nodes.isEmpty()) {
for (Node node : nodes) {
modBuilder.addKeyword(node.getTextContent());
}
}
ProteinModificationRegistry.register(modBuilder.build());
}
}
/**
* Utility method to group child nodes by their names.
* @param parent parent node.
* @return Map from name to child nodes.
*/
private static Map<String,List<Node>> getChildNodes(Node parent) {
if (parent==null)
return Collections.emptyMap();
Map<String,List<Node>> children = new HashMap<String,List<Node>>();
NodeList nodes = parent.getChildNodes();
int nNodes = nodes.getLength();
for (int i=0; i<nNodes; i++) {
Node node = nodes.item(i);
if (node.getNodeType()!=Node.ELEMENT_NODE)
continue;
String name = node.getNodeName();
List<Node> namesakes = children.get(name);
if (namesakes==null) {
namesakes = new ArrayList<Node>();
children.put(name, namesakes);
}
namesakes.add(node);
}
return children;
}
}