package MCview;

import jalview.datamodel.*;
import java.io.*;
import java.net.*;
import java.util.*;


public class PDBfile extends jalview.io.FileParse {

  public Vector chains = new Vector();

  Vector lineArray = new Vector();

  public PDBfile(String [] lines)
  {
    for(int i=0; i<lines.length; i++)
      lineArray.addElement(lines[i]);

    noLines = lineArray.size();
    parse();
  }

  public PDBfile(String inFile, String inType) throws IOException {

    super(inFile,inType);

    String line;
    this.lineArray = new Vector();
    BufferedReader dataIn;

    if (inType.equals("File"))
      dataIn =  new BufferedReader(new FileReader( inFile ));

    else
    {
      URL url = new URL(inFile);
      this.fileSize = 0;
      dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
    }

    while ((line = dataIn.readLine()) != null) {
      lineArray.addElement(line);
    }
    noLines = lineArray.size();

    parse();

}


  public void parse() {

    for (int i = 0; i < lineArray.size(); i++) {
      StringTokenizer str = new StringTokenizer(lineArray.elementAt(i).toString());
      if (str.hasMoreTokens()) {
        String inStr = str.nextToken();

        if (inStr.indexOf("ATOM") != -1) {
          try {
            myAtom tmpatom = new myAtom(str);
            if (findChain(tmpatom.chain) != null) {
           //   System.out.println("Adding to chain " + tmpatom.chain);
              findChain(tmpatom.chain).atoms.addElement(tmpatom);
            } else {
            //  System.out.println("Making chain " + tmpatom.chain);
              PDBChain tmpchain = new PDBChain(tmpatom.chain);
              chains.addElement(tmpchain);
              tmpchain.atoms.addElement(tmpatom);
            }
          } catch(NumberFormatException e) {
            System.err.println("Caught" +  e);
            System.err.println("Record not added to PDB model:"+lineArray.elementAt(i).toString());
          }
        }
      }
    }
    makeResidueList();
    makeCaBondList();
    //    for (int i=0; i < chains.size() ; i++) {
    //  String pog = ((PDBChain)chains.elementAt(i)).print();
    //  System.out.println(pog);
    // }
  }

  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++) {
      // System.out.println("ID = " + id + " " +((PDBChain)chains.elementAt(i)).id);
      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 setHydrophobicityColours() {
    for (int i=0; i < chains.size(); i++) {
      ((PDBChain)chains.elementAt(i)).setHydrophobicityColours();
    }
  }

  public void colourBySequence(Sequence seq) {
//SMJS TODO
//    int max = seq.maxchain;
//    if (seq.maxchain != -1) {
//      ((PDBChain)chains.elementAt(max)).colourBySequence(seq);
//    }
  }

  public void setChainColours() {
    for (int i=0; i < chains.size(); i++) {
      ((PDBChain)chains.elementAt(i)).setChainColours();
    }
  }
  public static void main(String[] args) {
    try {
      PDBfile pdb = new PDBfile("enkp1.pdb","File");
    } catch(IOException e) {
      System.out.println(e);
      e.printStackTrace();
      System.exit(0);
    }
  }
}