GlycoEdge.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.sugar;

import java.util.ArrayList;
import java.util.Iterator;

import org.eurocarbdb.MolecularFramework.util.visitor.GlycoVisitor;
import org.eurocarbdb.MolecularFramework.util.visitor.GlycoVisitorException;
import org.eurocarbdb.MolecularFramework.util.visitor.Visitable;

/**
* @author rene
*
*/
public class GlycoEdge implements Visitable
{
    private GlycoNode m_objParent = null;
    private GlycoNode m_objChild = null;
    private ArrayList<Linkage> m_aLinkages = new ArrayList<Linkage>(); 
    
    public void setParent(GlycoNode a_objParent)
    {
        this.m_objParent = a_objParent;
    }
    
    public void setChild(GlycoNode a_objChild)
    {
        this.m_objChild = a_objChild;
    }
    
    public GlycoNode getChild()
    {
        return this.m_objChild;
    }
    
    public GlycoNode getParent()
    {
        return this.m_objParent;
    }

    public void setGlycosidicLinkages(ArrayList<Linkage> a_aLinkages) throws GlycoconjugateException
    {
        if ( a_aLinkages == null )
        {
            throw new GlycoconjugateException("null is not a valide set of linkages.");
        }
        this.m_aLinkages.clear();
        for (Iterator<Linkage> t_iterLinkage = a_aLinkages.iterator(); t_iterLinkage.hasNext();)
        {
            this.addGlycosidicLinkage(t_iterLinkage.next());            
        }
        this.m_aLinkages = a_aLinkages;
    }
    
    public ArrayList<Linkage> getGlycosidicLinkages()
    {
        return this.m_aLinkages;
    }
    
    public boolean addGlycosidicLinkage(Linkage a_objLinkage) throws GlycoconjugateException
    {
        if ( a_objLinkage == null )
        {
            throw new GlycoconjugateException("null linkage is not allowed");
        }
        if ( !this.m_aLinkages.contains(a_objLinkage) )
        {
            return this.m_aLinkages.add(a_objLinkage);
        }
        return false;
    }
    
    public boolean removeGlycosidicLinkage(Linkage a_objLinkage)
    {
        if ( this.m_aLinkages.contains(a_objLinkage) )
        {
            return this.m_aLinkages.remove(a_objLinkage);
        }
        return false;
    }

    /**
     * @see org.eurocarbdb.MolecularFramework.util.visitor.Visitable#accept(org.eurocarbdb.MolecularFramework.util.visitor.GlycoVisitor)
     */
    public void accept(GlycoVisitor a_objVisitor) throws GlycoVisitorException 
    {
        a_objVisitor.visit(this);
    }

    /**
     * copy without parent and childs
     * @return
     * @throws GlycoconjugateException
     */
    public GlycoEdge copy() throws GlycoconjugateException 
    {
        GlycoEdge t_objCopy = new GlycoEdge();
        for (Iterator<Linkage> t_iterEdges = this.m_aLinkages.iterator(); t_iterEdges.hasNext();)
        {
            t_objCopy.addGlycosidicLinkage(t_iterEdges.next().copy());            
        }
        
        return t_objCopy;
    }
}