/* * 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); } } }