GlycoCTGlycoNodeComparator.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.GlycoCT;

import java.util.Comparator;


import org.eurocarbdb.MolecularFramework.sugar.GlycoNode;
import org.eurocarbdb.MolecularFramework.util.analytical.misc.GlycoVisitorCountNodeType;
import org.eurocarbdb.MolecularFramework.util.visitor.GlycoVisitorCountBranchingPoints;
import org.eurocarbdb.MolecularFramework.util.visitor.GlycoVisitorCountLongestBranch;
import org.eurocarbdb.MolecularFramework.util.visitor.GlycoVisitorCountResidueTerminal;
import org.eurocarbdb.MolecularFramework.util.visitor.GlycoVisitorException;

public class GlycoCTGlycoNodeComparator implements  Comparator<GlycoNode> {


    public int compare(GlycoNode r1, GlycoNode r2) {

        // First criterion: RESIDUE COUNT
        if (ResidueCount(r1,r2)!=0)
        {
            return (ResidueCount(r1,r2));
        }             

        // Second criterion: LONGEST BRANCH
        if (LongestBranch(r1,r2)!=0){
            return (LongestBranch(r1,r2));
        }    
        // Third criterion: TERMINAL RESIDUE COUNT
        if (TerminalResidue(r1,r2)!=0){
            return (TerminalResidue(r1,r2));
        } 
        // Fourth criterion: BRANCHING POINTS COUNT
        if (BranchingCount(r1,r2)!=0){
            return (BranchingCount(r1,r2));
        }         
        //Last criterion: ALPHANUM SORT OF REMAINING GLYCO - CT
        if (AlphaNum(r1,r2)!=0){
            return (AlphaNum(r1,r2));
        } 

        // Not able to discrimate subgraphs
        return 0;
    }

    private int BranchingCount(GlycoNode r1, GlycoNode r2) {
        int t_g1LongestBranch=0;
        int t_g2LongestBranch=0;

        GlycoVisitorCountBranchingPoints t_oLongest = new  GlycoVisitorCountBranchingPoints();
        try {
            t_oLongest.start(r1);
            t_g1LongestBranch = t_oLongest.getBranchingPointsCountResidue();
            t_oLongest.clear();
            t_oLongest.start(r2);
            t_g2LongestBranch = t_oLongest.getBranchingPointsCountResidue();

            if (t_g1LongestBranch < t_g2LongestBranch){
                return -1;
            }
            else if (t_g1LongestBranch > t_g2LongestBranch){
                return 1;
            }            
        } catch (GlycoVisitorException e) {
            e.printStackTrace();
        }        
        return 0;
    }

    private int TerminalResidue(GlycoNode r1, GlycoNode r2) {
        int t_g1LongestBranch=0;
        int t_g2LongestBranch=0;

        GlycoVisitorCountResidueTerminal t_oLongest = new  GlycoVisitorCountResidueTerminal();
        try {
            t_oLongest.start(r1);
            t_g1LongestBranch = t_oLongest.getTerminalCountResidue();

            t_oLongest.start(r2);
            t_g2LongestBranch = t_oLongest.getTerminalCountResidue();

            if (t_g1LongestBranch < t_g2LongestBranch){
                return -1;
            }
            else if (t_g1LongestBranch > t_g2LongestBranch){
                return 1;
            }            
        } catch (GlycoVisitorException e) {
            e.printStackTrace();
        }        
        return 0;
    }

    private int AlphaNum(GlycoNode r1, GlycoNode r2) {
        String t_g1StringGlycoCT="";
        String t_g2StringGlycoCT="";

        SugarExporterGlycoCTCondensed t_objGlycoCTExporter = new SugarExporterGlycoCTCondensed();
        try {
            t_objGlycoCTExporter.start(r1);
        } catch (GlycoVisitorException e) {
            e.printStackTrace();
        }                
        t_g1StringGlycoCT=t_objGlycoCTExporter.getHashCode();
        t_objGlycoCTExporter.clear();
        try {
            t_objGlycoCTExporter.start(r2);
        } catch (GlycoVisitorException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }                
        t_g2StringGlycoCT=t_objGlycoCTExporter.getHashCode();    

        return (t_g2StringGlycoCT.compareTo(t_g1StringGlycoCT));
    }

    private int LongestBranch (GlycoNode r1, GlycoNode r2) {
        int t_g1LongestBranch=0;
        int t_g2LongestBranch=0;

        GlycoVisitorCountLongestBranch t_oLongest = new  GlycoVisitorCountLongestBranch();
        try {
            t_oLongest.start(r1);
            t_g1LongestBranch = t_oLongest.getLongestBranchResidue();

            t_oLongest.start(r2);
            t_g2LongestBranch = t_oLongest.getLongestBranchResidue();

            if (t_g1LongestBranch < t_g2LongestBranch){
                return -1;
            }
            else if (t_g1LongestBranch > t_g2LongestBranch){
                return 1;
            }            
        } catch (GlycoVisitorException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }        
        return 0;

    }
    private int ResidueCount (GlycoNode r1, GlycoNode r2) 
    {
        int t_g1LongestBranch=0;
        int t_g2LongestBranch=0;

        GlycoVisitorCountNodeType t_oLongest = new  GlycoVisitorCountNodeType();
        try {
            t_oLongest.start(r1);
            t_g1LongestBranch = 
                t_oLongest.getMonosaccharideCount()+
                t_oLongest.getNonMonosaccharideCount()+
                t_oLongest.getSubstituentCount()+
                t_oLongest.getAlternativeNodeCount();
            t_oLongest.clear();

            t_oLongest.start(r2);            
            t_g2LongestBranch = t_oLongest.getMonosaccharideCount()+
            t_oLongest.getNonMonosaccharideCount()+
            t_oLongest.getSubstituentCount()+
            t_oLongest.getAlternativeNodeCount();

            if (t_g1LongestBranch < t_g2LongestBranch){
                return -1;
            }
            else if (t_g1LongestBranch > t_g2LongestBranch){
                return 1;
            }            
        } catch (GlycoVisitorException e) {
            e.printStackTrace();
        }        
        return 0;

    }


}