/*
* EuroCarbDB, a framework for carbohydrate bioinformatics
*
* Copyright (c) 2006-2009, Eurocarb project, or third-party contributors as
* indicated by the @author tags or express copyright attribution
* statements applied by the authors.
*
* This copyrighted material is made available to anyone wishing to use, modify,
* copy, or redistribute it subject to the terms and conditions of the GNU
* Lesser General Public License, as published by the Free Software Foundation.
* A copy of this license accompanies this distribution in the file LICENSE.txt.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
* for more details.
*
* Last commit: $Rev: 1210 $ by $Author: glycoslave $ on $Date:: 2009-06-12 #$
*/
/**
@author Alessio Ceroni (a.ceroni@imperial.ac.uk)
*/
package org.eurocarbdb.application.glycoworkbench.plugin;
import org.eurocarbdb.application.glycoworkbench.*;
import org.eurocarbdb.application.glycanbuilder.*;
import java.util.*;
import org.w3c.dom.*;
import org.xml.sax.SAXException;
import org.xml.sax.Attributes;
public class StructureType implements FragmentSource {
//
String database = "";
String type = "";
String source = "";
String structure = "";
//--
public StructureType() {
}
public StructureType(String d, String t, String s, String g) {
database = "" + d;
type = "" + t;
source = "" + s;
structure = "" + g.split("\\$")[0]; // remove mass opt
}
public StructureType(String init) throws Exception {
Vector<String> tokens = TextUtils.tokenize(init,"\t");
if( tokens.size()!=4 )
throw new Exception("Invalid string format: " + init);
database = tokens.elementAt(0);
type = tokens.elementAt(1);
source = tokens.elementAt(2);
structure = tokens.elementAt(3).split("\\$")[0]; // remove mass opt;
}
public boolean equals(Object o) {
if( o==null || !(o instanceof StructureType) )
return false;
StructureType other = (StructureType)o;
return (other.database.equals(this.database) &&
other.type.equals(this.type) &&
other.source.equals(this.source) &&
other.structure.equals(this.structure));
}
public int hashCode() {
return database.hashCode() + type.hashCode() + source.hashCode() + structure.hashCode();
}
public StructureType clone(String dict_name) {
if( database==null || database.length()==0 || database.equals("unknown") )
return new StructureType(dict_name,type,source,structure);
else
return new StructureType(database,type,source,structure);
}
public String getDatabase() {
return database;
}
public String getType() {
return type;
}
public void setType(String t) {
type = t;
}
public String getSource() {
return source;
}
public void setSource(String s) {
source = s;
}
public String getStructure() {
return structure;
}
public void setStructure(String s) {
structure = s;
}
public boolean merge(StructureType other) {
if( other==null )
return false;
if( !other.structure.equals(this.structure) )
return false;
boolean changed = false;
if( !other.type.equals("unknown") && !TextUtils.tokenize(type,",").contains(other.type) ) {
if( type.equals("unknown") )
type = other.type;
else
type += ", " + other.type;
changed = true;
}
if( !other.source.equals("unknown") && !TextUtils.tokenize(source,",").contains(other.source) ) {
if( source.equals("unknown") )
source = other.source;
else
source += ", " + other.source;
changed = true;
}
return changed;
}
public FragmentEntry generateFragmentEntry(MassOptions mass_opt) throws Exception {
Glycan g = generateStructure(mass_opt);
FragmentEntry ret = new FragmentEntry();
ret.fragment = g;
ret.name = getDescription();
ret.mass = g.computeMass();
ret.mz_ratio = g.getChargesAndExchanges().computeMZ(ret.mass);
ret.structure = structure;
ret.source = this;
return ret;
}
public Glycan generateStructure(ProfilerOptions opt) throws Exception {
Glycan ret = Glycan.fromString(structure,new MassOptions());
ret.setMassOptions(opt.getMassOptions());
return ret;
}
public Glycan generateStructure(MassOptions mass_opt) throws Exception {
Glycan ret = Glycan.fromString(structure,new MassOptions());
ret.setMassOptions(mass_opt);
return ret;
}
public Glycan generateStructure() throws Exception {
return generateStructure(new MassOptions(MassOptions.NO_DERIVATIZATION));
}
public String getDescription() {
StringBuilder desc = new StringBuilder();
if( !type.equals("unknown") )
desc.append(type);
if( !source.equals("unknown") ) {
if( desc.length()>0 )
desc.append(": ");
desc.append(source);
}
if( !source.equals("unknown") ) {
if( desc.length()>0 )
desc.append(' ');
desc.append('(');
desc.append(database);
desc.append(')');
}
return desc.toString();
}
static public StructureType fromString(String str) throws Exception {
String[] tokens = str.split("\t");
if( tokens.length!=4 )
throw new Exception("Invalid format");
StructureType ret = new StructureType();
ret.database = tokens[0];
ret.type = tokens[1];
ret.source = tokens[2];
ret.structure = tokens[3];
return ret;
}
public String toString() {
return database + "\t" + type + "\t" + source + "\t" + structure;
}
static public StructureType fromXML(Node st_node) throws Exception {
StructureType ret = new StructureType();
// read values
ret.database = XMLUtils.getAttribute(st_node,"database");
if( ret.database==null )
ret.database = "";
ret.type = XMLUtils.getAttribute(st_node,"type");
if( ret.type==null )
ret.type = "";
ret.source = XMLUtils.getAttribute(st_node,"source");
if( ret.source==null )
ret.source = "";
ret.structure = XMLUtils.getAttribute(st_node,"structure");
if( ret.structure==null )
ret.structure = "";
return ret;
}
public Element toXML(Document document) {
if( document==null )
return null;
// create root node
Element st_node = document.createElement("StructureType");
// set values
st_node.setAttribute("database", "" + database);
st_node.setAttribute("type", "" + type);
st_node.setAttribute("source", "" + source);
st_node.setAttribute("structure", "" + structure);
return st_node;
}
public static class SAXHandler extends SAXUtils.ObjectTreeHandler {
public boolean isElement(String namespaceURI, String localName, String qName) {
return qName.equals(getNodeElementName());
}
public static String getNodeElementName() {
return "StructureType";
}
protected void initContent(String namespaceURI, String localName, String qName, Attributes atts) throws SAXException {
super.initContent(namespaceURI,localName,qName,atts);
StructureType ret = new StructureType();
ret.database = stringAttribute(atts,"database","");
ret.type = stringAttribute(atts,"type","");
ret.source = stringAttribute(atts,"source","");
ret.structure = stringAttribute(atts,"structure","");
object = ret;
}
}
}