/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
*/
package MCview;

import jalview.datamodel.*;

import java.io.*;

import java.util.*;
import java.awt.Color;


public class PDBfile extends jalview.io.AlignFile {
    public Vector chains;
    public String id;

    public PDBfile(String inFile, String inType) throws IOException
    {
        super(inFile, inType);
    }

    public String print()
    {
      return null;
    }

    public void parse() throws IOException
    {
        chains = new Vector();

        PDBChain tmpchain;
        String line;
        boolean modelFlag = false;
        boolean terFlag = false;


        int index = 0;
        while((line = nextLine())!=null)
        {
           if (line.indexOf("HEADER") == 0)
           {
             id = line.substring(62, 67).trim();
             continue;
           }

           if(line.indexOf("MODEL")==0)
             modelFlag = true;

           if(line.indexOf("TER")==0)
             terFlag = true;

           if(modelFlag && line.indexOf("ENDMDL")==0)
             break;

           if (    line.indexOf("ATOM")==0
               || (line.indexOf("HETATM")==0 && !terFlag)
             )
            {
              terFlag = false;


              //Jalview is only interested in CA bonds????
              if (!line.substring(12, 15).trim().equals("CA"))
              {
                continue;
              }

              Atom tmpatom = new Atom(line);
              tmpchain = findChain(tmpatom.chain);
              if (tmpchain != null)
              {
                tmpchain.atoms.addElement(tmpatom);
              }
              else
              {
                tmpchain = new PDBChain(tmpatom.chain);
                chains.addElement(tmpchain);
                tmpchain.atoms.addElement(tmpatom);
              }
          }
          index ++;
        }

       makeResidueList();
       makeCaBondList();

       if(id==null)
       {
         id = inFile.getName();
       }
       for (int i = 0; i < chains.size(); i++)
       {
         SequenceI seq = ( (PDBChain) chains.elementAt(i)).
             sequence;
         seq.setName(id + "|" + seq.getName());
         Sequence dataset = new Sequence(seq.
             getName(),
             seq.getSequence().toString(), seq.getStart(), seq.getEnd());

         PDBEntry entry = new PDBEntry();
         entry.setId(id);
         if(inFile!=null)
           entry.setFile(inFile.getAbsolutePath());

         seq.setDatasetSequence(dataset);
         dataset.addPDBId(entry);

         getSeqs().addElement(seq);
       }
    }

    public void makeResidueList() {
        for (int i = 0; i < chains.size(); i++) {
            ((PDBChain) chains.elementAt(i)).makeResidueList();
        }
    }

    public void makeCaBondList() {
        for (int i = 0; i < chains.size(); i++) {
            ((PDBChain) chains.elementAt(i)).makeCaBondList();
        }
    }

    public PDBChain findChain(String id) {
        for (int i = 0; i < chains.size(); i++) {
            if (((PDBChain) chains.elementAt(i)).id.equals(id)) {
                return (PDBChain) chains.elementAt(i);
            }
        }

        return null;
    }

    public void setChargeColours() {
        for (int i = 0; i < chains.size(); i++) {
            ((PDBChain) chains.elementAt(i)).setChargeColours();
        }
    }

    public void setColours(jalview.schemes.ColourSchemeI cs) {
        for (int i = 0; i < chains.size(); i++) {
            ((PDBChain) chains.elementAt(i)).setChainColours(cs);
        }
    }

    public void setChainColours()
    {
       for (int i = 0; i < chains.size(); i++)
       {
            ((PDBChain) chains.elementAt(i)).setChainColours(
                     Color.getHSBColor(1.0f / (float)i, .4f, 1.0f)
                );
        }
    }
}