/*
* 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 $Date:: 2009-06-12 #$
*/
/**
*
*/
package org.eurocarbdb.MolecularFramework.util.traverser;
import java.util.ArrayList;
import java.util.Iterator;
import org.eurocarbdb.MolecularFramework.sugar.GlycoEdge;
import org.eurocarbdb.MolecularFramework.sugar.GlycoGraph;
import org.eurocarbdb.MolecularFramework.sugar.GlycoNode;
import org.eurocarbdb.MolecularFramework.sugar.GlycoconjugateException;
import org.eurocarbdb.MolecularFramework.util.visitor.GlycoVisitor;
import org.eurocarbdb.MolecularFramework.util.visitor.GlycoVisitorException;
/**
* Traverser travers a sugar tree. Expects a connected tree otherwise a exception is thrown.
* Each residue ist touched only one time. Traverser supports
* ENTER,for residues and ENTER for linkages. Traversing of linkages
* in no order.
* Internal repeat is not touched. Descent into subunits.
*
* @author rene
*
*/
public class GlycoTraverserTreeSingle extends GlycoTraverser
{
public GlycoTraverserTreeSingle(GlycoVisitor a_objVisitor) throws GlycoVisitorException
{
super(a_objVisitor);
}
/**
* @see de.glycosciences.MolecularFrameWork.util.SugarTraverser#traverse(de.glycosciences.MolecularFrameWork.sugar.Residue)
*/
@Override
public void traverse(GlycoNode a_objResidue) throws GlycoVisitorException
{
// callback before subtree
this.m_iState = GlycoTraverser.ENTER;
a_objResidue.accept(this.m_objVisitor);
// traverse subtree
for (Iterator<GlycoEdge> t_iterLinkages = a_objResidue.getChildEdges().iterator(); t_iterLinkages.hasNext();)
{
GlycoEdge t_linkChild = t_iterLinkages.next();
//t_linkChild.accept(this.m_objVisitor);
this.traverse(t_linkChild);
}
}
/**
* @see de.glycosciences.MolecularFrameWork.util.SugarTraverser#traverse(de.glycosciences.MolecularFrameWork.Linkage)
*/
@Override
public void traverse(GlycoEdge a_objLinkage) throws GlycoVisitorException
{
// callback of the function before subtree
this.m_iState = GlycoTraverser.ENTER;
a_objLinkage.accept(this.m_objVisitor);
// traverse subtree
this.traverse(a_objLinkage.getChild());
}
/**
* @see de.glycosciences.MolecularFrameWork.util.SugarTraverser#traverseGraph(de.glycosciences.MolecularFrameWork.sugar.Sugar)
*/
@Override
public void traverseGraph(GlycoGraph a_objSugar) throws GlycoVisitorException
{
ArrayList<GlycoNode> t_aRoot;
try
{
t_aRoot = a_objSugar.getRootNodes();
if ( t_aRoot.size() != 1 )
{
throw new GlycoVisitorException("Not a connected sugar.");
}
this.traverse(t_aRoot.get(0));
}
catch (GlycoconjugateException e)
{
throw new GlycoVisitorException(e.getMessage(),e);
}
}
}