GlycoVisitorCyclic.java

/*
*   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.io.Linucs;

import java.util.ArrayList;

import org.eurocarbdb.MolecularFramework.sugar.GlycoEdge;
import org.eurocarbdb.MolecularFramework.sugar.Monosaccharide;
import org.eurocarbdb.MolecularFramework.sugar.NonMonosaccharide;
import org.eurocarbdb.MolecularFramework.sugar.Substituent;
import org.eurocarbdb.MolecularFramework.sugar.Sugar;
import org.eurocarbdb.MolecularFramework.sugar.SugarUnitAlternative;
import org.eurocarbdb.MolecularFramework.sugar.SugarUnitCyclic;
import org.eurocarbdb.MolecularFramework.sugar.SugarUnitRepeat;
import org.eurocarbdb.MolecularFramework.sugar.UnvalidatedGlycoNode;
import org.eurocarbdb.MolecularFramework.util.traverser.GlycoTraverser;
import org.eurocarbdb.MolecularFramework.util.traverser.GlycoTraverserNodes;
import org.eurocarbdb.MolecularFramework.util.visitor.GlycoVisitor;
import org.eurocarbdb.MolecularFramework.util.visitor.GlycoVisitorException;

/**
* @author rene
*
*/
public class GlycoVisitorCyclic  implements GlycoVisitor
{
    private int m_iCyclic = 0;
    private ArrayList<Integer> m_aPositions = null;
    
    /**
     * @see org.eurocarbdb.MolecularFramework.util.visitor.GlycoVisitor#visit(org.eurocarbdb.MolecularFramework.sugar.Monosaccharide)
     */
    public void visit(Monosaccharide a_objMonosaccharid) throws GlycoVisitorException
    {
        // nothing to do
    }

    /**
     * @see org.glycomedb.MolecularFrameWork.util.visitor.GlycoVisitor#visit(org.eurocarbdb.MolecularFramework.sugar.NonMonosaccharides)
     */
    public void visit(NonMonosaccharide a_objResidue) throws GlycoVisitorException
    {
        // nothing to do
    }

    /**
     * @see org.eurocarbdb.MolecularFramework.util.visitor.GlycoVisitor#visit(org.eurocarbdb.MolecularFramework.sugar.SugarUnitRepeat)
     */
    public void visit(SugarUnitRepeat a_objRepeat) throws GlycoVisitorException
    {
        // nothing to do
    }

    /**
     * @see org.eurocarbdb.MolecularFramework.util.visitor.GlycoVisitor#visit(org.eurocarbdb.MolecularFramework.sugar.Substituent)
     */
    public void visit(Substituent a_objSubstituent) throws GlycoVisitorException
    {
        // nothing to do
    }

    /**
     * @see org.eurocarbdb.MolecularFramework.util.visitor.GlycoVisitor#visit(org.eurocarbdb.MolecularFramework.sugar.SugarUnitCyclic)
     */
    public void visit(SugarUnitCyclic a_objCyclic) throws GlycoVisitorException
    {
        this.m_iCyclic++;
        this.m_aPositions = a_objCyclic.getParentEdge().getGlycosidicLinkages().get(0).getChildLinkages();
    }

    /**
     * @see org.eurocarbdb.MolecularFramework.util.visitor.GlycoVisitor#visit(org.eurocarbdb.MolecularFramework.sugar.SugarUnitAlternative)
     */
    public void visit(SugarUnitAlternative a_objAlternative) throws GlycoVisitorException
    {
        // nothing to do
    }

    /**
     * @see org.eurocarbdb.MolecularFramework.util.visitor.GlycoVisitor#visit(org.eurocarbdb.MolecularFramework.sugar.UnvalidatedGlycoNode)
     */
    public void visit(UnvalidatedGlycoNode a_objUnvalidated) throws GlycoVisitorException
    {
        // nothing to do
    }

    /**
     * @see org.eurocarbdb.MolecularFramework.util.visitor.GlycoVisitor#visit(org.eurocarbdb.MolecularFramework.sugar.GlycoEdge)
     */
    public void visit(GlycoEdge a_objLinkage) throws GlycoVisitorException
    {
        // nothing to do        
    }

    /**
     * @see org.eurocarbdb.MolecularFramework.util.visitor.GlycoVisitor#start(org.eurocarbdb.MolecularFramework.sugar.Sugar)
     */
    public void start(Sugar a_objSugar) throws GlycoVisitorException
    {
        this.clear();
        GlycoTraverser t_objTraverser = this.getTraverser(this);
        t_objTraverser.traverseGraph(a_objSugar);
    }

    /**
     * @see org.eurocarbdb.MolecularFramework.util.visitor.GlycoVisitor#getTraverser(org.eurocarbdb.MolecularFramework.util.visitor.GlycoVisitor)
     */
    public GlycoTraverser getTraverser(GlycoVisitor a_objVisitor) throws GlycoVisitorException
    {
        return new GlycoTraverserNodes(this);
    }

    /**
     * @see org.eurocarbdb.MolecularFramework.util.visitor.GlycoVisitor#clear()
     */
    public void clear()
    {
        this.m_iCyclic = 0;
    }

    /**
     * @return
     */
    public int getCyclic() 
    {
        return this.m_iCyclic;
    }
    
    public ArrayList<Integer> getChildPosition()
    {
        return this.m_aPositions;
    }
}