/*
* 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/
*
*/
package org.biojava.bio.seq.io.agave;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
/**
* xrefs
*
* @author Hanning Ni Doubletwist Inc
* @author Greg Cox
*/
public class AGAVEXrefs{
private List db_ids ;
private List xrefs ;
/** add @param id **/
public void addDbId(AGAVEDbId id)
{
if( db_ids == null )
db_ids = new ArrayList(1) ;
db_ids .add( id ) ;
}
/** add @param xref **/
public void addXref(AGAVEXref xref)
{
if( xrefs == null )
xrefs = new ArrayList(1) ;
xrefs.add( xref ) ;
}
/** return a set of DbId **/
public Iterator getDbIds()
{
return db_ids.iterator() ;
}
/** return a set of AGAVEXref **/
public Iterator getXrefs()
{
return xrefs.iterator() ;
}
/**
* @param indent the leading space
* @param indent_unit the unit of indenting for xml format
*
**/
public String toString(String indent, String indent_unit)
{
StringBuffer tmp = new StringBuffer();
tmp.append(indent + "" + "\n" );
Iterator it = db_ids.iterator() ;
while( it.hasNext() )
{
tmp.append( ((AGAVEDbId)it.next()).toString(indent + indent_unit, indent_unit) ) ;
}
it = xrefs.iterator() ;
while( it.hasNext() )
{
tmp.append( ((AGAVEXref)it.next()).toString(indent + indent_unit, indent_unit) ) ;
}
tmp.append(indent + "" + "\n" );
return tmp.substring(0) ;
}
/** the agave xml representation of xrefs **/
public String toString()
{
StringBuffer tmp = new StringBuffer();
tmp.append( "" + "\n" );
Iterator it = db_ids.iterator() ;
while( it.hasNext() )
{
tmp.append(it.next().toString() ) ;
}
it = xrefs.iterator() ;
while( it.hasNext() )
{
tmp.append(it.next().toString() ) ;
}
tmp.append("" + "\n" );
return tmp.substring(0) ;
}
}