CrossRingFragmentDictionary.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 $Date:: 2009-06-12 #$  
*/
/**
   @author Alessio Ceroni (a.ceroni@imperial.ac.uk)
*/

package org.eurocarbdb.application.glycanbuilder;

import java.io.*;
import java.util.*;
import java.awt.*;
import java.awt.geom.*;
import java.awt.image.*;
import javax.swing.*;

/**
   The dictionary of all cross ring fragments types available in the
   application. Information about cross ring fragment types is loaded
   at run time from a configuration file. The dictionary is a
   singleton and all information has class-wide access.

   @see CrossRingFragmentType   

   @author Alessio Ceroni (a.ceroni@imperial.ac.uk)
*/

public class CrossRingFragmentDictionary {
    
    static {
    dictionary = new Vector<CrossRingFragmentType>();
    }
    
    private static Vector<CrossRingFragmentType> dictionary;
        
    //---- init

    private CrossRingFragmentDictionary() {}

    /**
       Load the dictionary from a configuration file.
     */
    public static void loadDictionary(String filename) {
    // clear dict
    dictionary.clear();
    
    try {
        // open file
        java.net.URL file_url = CrossRingFragmentDictionary.class.getResource(filename);
        if( file_url==null )
        throw new FileNotFoundException(filename);
        BufferedReader is = new BufferedReader(new InputStreamReader(file_url.openStream()));
        
        // read dictionary
        String line;
        while( (line=is.readLine())!=null ) {
        line = TextUtils.trim(line);
        if( line.length()>0 && !line.startsWith("%") ) {
            CrossRingFragmentType toadd = new CrossRingFragmentType(line);
            dictionary.add(toadd);
        }
        }

        is.close();
    }
    catch(Exception e) {
        LogUtils.report(e);
        dictionary.clear();
    }
    }
      
    
    // --- Data access


    /**
       Get all cross ring fragment types available for the given residue.
     */
    public static Collection<CrossRingFragmentType> getCrossRingFragmentTypes(Residue r) {
    Vector<CrossRingFragmentType> ret = new Vector<CrossRingFragmentType>();
    for(CrossRingFragmentType crt : dictionary ) {
        if( crt.matches(r) ) 
        ret.add(crt);
    }
    return ret;
    }

    /**
       Get all A cross ring fragment types available for the given residue.
     */
    public static Collection<CrossRingFragmentType> getCrossRingFragmentTypesA(Residue r) {
    Vector<CrossRingFragmentType> ret = new Vector<CrossRingFragmentType>();
    for(CrossRingFragmentType crt : dictionary ) {
        if( crt.matches(r) && crt.isACleavage() ) 
        ret.add(crt);
    }
    return ret;
    }

    /**
       Get all X cross ring fragment types available for the given residue.
     */
    public static Collection<CrossRingFragmentType> getCrossRingFragmentTypesX(Residue r) {
    Vector<CrossRingFragmentType> ret = new Vector<CrossRingFragmentType>();
    for(CrossRingFragmentType crt : dictionary ) {
        if( crt.matches(r) && crt.isXCleavage() ) 
        ret.add(crt);
    }
    return ret;
    }

    /**
       Get a specific cross ring fragment type.
       @param fragment_type type of cross ring fragment (A/B)
       @param first_pos position of the first cleavage in the ring
       @param last_pos position of the second cleavage in the ring
       @param r residue for which the ring fragment is computed
     */
    public static CrossRingFragmentType getCrossRingFragmentType(char fragment_type, int first_pos, int last_pos, Residue r) {
    for(CrossRingFragmentType crt : dictionary ) {
        if( crt.matches(fragment_type,first_pos,last_pos,r) ) 
        return crt;
    }
    return null;
    }

    /**
       Create a new residue representing a specific cross ring fragment type.
       @param fragment_type type of cross ring fragment (A/B)
       @param first_pos position of the first cleavage in the ring
       @param last_pos position of the second cleavage in the ring
       @param r residue for which the ring fragment is computed
     */
    public static Residue newCrossRingFragment(char fragment_type, int first_pos, int last_pos, Residue r) throws Exception {
    if( r==null )
        throw new Exception("Cannot create a cross ring fragment without a residue");

    ResidueType type = getCrossRingFragmentType(fragment_type,first_pos,last_pos,r);
    if( type==null )
        throw new Exception("Invalid " + fragment_type + " cross-ring cleavage at positions " + first_pos + "," + last_pos + " of residue " + r.getTypeName());

    Residue ret = new Residue(type);
    ret.setCleavedResidue(r);
    return ret;
    }

        
    static Residue newFragment(String type_name, Residue cleaved) {
    if( type_name==null || cleaved==null )
        return null;

    if( !type_name.startsWith("#acleavage") && !type_name.startsWith("#xcleavage") ) 
        return null;

    Vector<String> tokens = TextUtils.tokenize(type_name,"_");
    char fragment_type = type_name.charAt(1);    
    int first_pos = Integer.parseInt(tokens.elementAt(1));
    int last_pos  = Integer.parseInt(tokens.elementAt(2));
    
    CrossRingFragmentType crt = getCrossRingFragmentType(fragment_type,first_pos,last_pos,cleaved);
    return (crt!=null ) ?new Residue(crt) :null;
    }
    
}