001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 */
021package org.biojava.bio.seq.io.agave;
022import java.util.ArrayList;
023import java.util.Iterator;
024import java.util.List;
025
026/**
027 * xref
028 * @author Hanning Ni    Doubletwist Inc
029 * @author Greg Cox
030*/
031public class AGAVEXref {
032    private AGAVEDbId id ;
033    private List xrefs ;
034    private String rel ;
035    public void setDbId( AGAVEDbId id )
036    {
037        this.id = id ;
038    }
039    public void addProp(AGAVEProperty prop)
040    {
041        if( xrefs  == null )
042            xrefs = new ArrayList(1) ;
043        xrefs.add( prop );
044    }
045    public void setRel(String rel)
046    {
047        this.rel = rel ;
048    }
049    public String getRel()
050    {
051        return rel  ;
052    }
053    public AGAVEDbId getDbId()
054    {
055        return id ;
056    }
057    public Iterator getXrefProps()
058    {
059        return xrefs.iterator() ;
060    }
061
062    /** return the agave xml representation of this instance **/
063    public String toString(String indent, String indent_unit)
064    {
065       StringBuffer tmp = new StringBuffer();
066       tmp.append(indent +  "<xref");
067       if( rel != rel )
068           tmp.append(" relationship=\"" + rel + "\"") ;
069       tmp.append( ">" + "\n") ;
070       tmp.append( id.toString(indent + indent_unit, indent_unit) ) ;
071       Iterator it = xrefs.iterator() ;
072       while( it.hasNext() )
073       {
074           tmp.append( ((AGAVEProperty)it.next()).toString(indent + indent_unit, indent_unit) ) ;
075       }
076       tmp.append(indent + "</xref>" + "\n" );
077       return tmp.substring(0) ;
078    }
079    /** return the agave xml representation of this instance **/
080    public String toString()
081    {
082       StringBuffer tmp = new StringBuffer();
083       tmp.append( "<xref");
084       if( rel != rel )
085           tmp.append(" relationship=\"" + rel + "\"") ;
086       tmp.append( ">" + "\n") ;
087       tmp.append( id ) ;
088       Iterator it = xrefs.iterator() ;
089       while( it.hasNext() )
090       {
091           tmp.append( it.next().toString() ) ;
092       }
093       tmp.append("</xref>" + "\n" );
094       return tmp.toString() ;
095    }
096}