/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 * Created on 09.05.2004
 * @author Andreas Prlic
 *
 */

package org.biojava.bio.structure;

import java.util.Iterator;
import java.util.List;
import java.util.NoSuchElementException;


/** An iterator over all groups of a structure.
 * @author Andreas Prlic
 * @since 1.4
 * @version %I% %G%
 */

public class GroupIterator implements Iterator<Group> {
    
    Structure structure   ;
    int current_model_pos ;
    int current_chain_pos ;
    int current_group_pos ;
    
    /**
     * Constructs a GroupIterator object.
     *
     * @param struct  a Structure object
     */
    
    public GroupIterator (Structure struct) { 
        structure = struct     ;
        current_model_pos = 0  ;
        current_chain_pos = 0  ;
        current_group_pos = -1 ;
        
    } 
    
    
    /** needed to do a copy of iterator ... */
    private Structure getStructure() { return structure         ;}    
    private int  getModelPos()       { return current_model_pos ;}
    private void setModelPos(int pos){ current_model_pos = pos  ;}
    private int  getChainPos()       { return current_chain_pos ;}
    private void setChainPos(int pos){ current_chain_pos = pos  ;}
    private int  getGroupPos()       { return current_group_pos ;}
    private void setGroupPos(int pos){ current_group_pos = pos  ;}
    
    /**  Creates and returns a copy of this object. */
    public Object clone () {
        
        GroupIterator gr = new GroupIterator(this.getStructure()) ;
        gr.setModelPos(this.getModelPos());
        gr.setChainPos(this.getChainPos());
        gr.setGroupPos(this.getGroupPos());
        return gr ;
        
    }
    
    
    /** is there a group after the current one in the structure? */
    public boolean hasNext() {
        return hasSubGroup(current_model_pos,current_chain_pos , current_group_pos +1) ;
        //ArrayList model = structure.getModel(current_model_pos);
        //Chain     chain = model.getChain(current_chain_pos);
    }
    
    /** recursive method to determine if there is a next group. Helper
     * method for hasNext(). 
     * @see #hasNext
     */
    private boolean hasSubGroup(int tmp_model,int tmp_chain,int tmp_group){ 
        
        if ( tmp_model >= structure.nrModels()){
            return false;
        }
        
        List<Chain> model =  structure.getModel(tmp_model);
        
        if ( tmp_chain >= model.size() ){
            return hasSubGroup(tmp_model+1,0,0);
        }
        
        Chain     chain = (Chain)model.get(tmp_chain);
        
        if (tmp_group  >= chain.getAtomLength()){	   
            // start search at beginning of next chain.	    
            return hasSubGroup(tmp_model,tmp_chain+1,0);
        } else {
            return true;
        }
        
    }
    
    /** Get the model number of the current model.
     * 
     * @return the number of the model
     */
    public int getCurrentModel(){
        
        return current_model_pos;
    }
    
    /** Get the current Chain. Returns null if we are at the end of the iteration.
     * 
     * @return the Chain of the current position 
     */
    public Chain getCurrentChain(){
        if ( current_model_pos >= structure.nrModels()){
            return null;
        }
        
        List<Chain> model =  structure.getModel(current_model_pos);
        
        if ( current_chain_pos >= model.size() ){
            return null;
        }
        
        Chain     chain = (Chain)model.get(current_chain_pos);
        return chain;
        
    }
    
    /** get next Group.
     * @return next Group 
     * @throws NoSuchElementException ... 
     */
    public Group next()
    throws NoSuchElementException
    {
        
        return getNextGroup(current_model_pos,current_chain_pos,current_group_pos+1);
    }
    
    /** recursive method to retrieve the next group. Helper
     * method for gext(). 
     * @see #next
     */
    private Group getNextGroup(int tmp_model,int tmp_chain,int tmp_group)
    throws NoSuchElementException
    { 
        
        if ( tmp_model >= structure.nrModels()){
            throw new NoSuchElementException("arrived at end of structure!");
        }
        
        List<Chain> model = structure.getModel(tmp_model);
        
        if ( tmp_chain >= model.size() ){
            return getNextGroup(tmp_model+1,0,0);
        }
        
        Chain     chain = (Chain) model.get(tmp_chain);
        
        if (tmp_group  >= chain.getAtomLength()){	   
            // start search at beginning of next chain.	    
            return getNextGroup(tmp_model,tmp_chain+1,0);
        } else {
            current_model_pos = tmp_model;
            current_chain_pos = tmp_chain;
            current_group_pos = tmp_group;
            Group group = chain.getAtomGroup(current_group_pos);
            return group;
        }
        
    }
    
    /** does nothing .
     */
    public void remove() {
    }
    
    
    
}