/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 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.analysis.AlignSeq;

import jalview.datamodel.*;

// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug
import java.awt.*;
import java.awt.event.*;

import java.io.*;

import java.util.*;



public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotionListener
{

    MCMatrix idmat = new MCMatrix(3, 3);
    MCMatrix objmat = new MCMatrix(3, 3);
    boolean redrawneeded = true;
    int omx = 0;
    int mx = 0;
    int omy = 0;
    int my = 0;
    public PDBfile pdb;
    int bsize;
    Image img;
    Graphics ig;
    Dimension prefsize;
    float[] centre = new float[3];
    float[] width = new float[3];
    float maxwidth;
    float scale;
    String inStr;
    String inType;
    boolean bysequence = true;
    boolean depthcue = true;
    boolean wire = false;
    boolean bymolecule = false;
    boolean zbuffer = true;
    boolean dragging;
    int xstart;
    int xend;
    int ystart;
    int yend;
    int xmid;
    int ymid;
    Font font = new Font("Helvetica", Font.PLAIN, 10);
    jalview.appletgui.SeqCanvas seqcanvas;
    public Sequence sequence;
    final StringBuffer mappingDetails = new StringBuffer();
    String appletToolTip = null;
    int toolx, tooly;
    PDBChain mainchain;
    Vector highlightRes;
    boolean pdbAction = false;
    Bond highlightBond1, highlightBond2;
    boolean errorLoading = false;

    public AppletPDBCanvas(jalview.appletgui.SeqCanvas seqcanvas, Sequence seq)
    {
      this.seqcanvas = seqcanvas;
      this.sequence = seq;

      seqcanvas.setPDBCanvas(this);
      addKeyListener(new KeyAdapter()
      {

        public void keyPressed(KeyEvent evt)
        {
          doKeyPressed(evt);
        }
      });
    }


  public void setPDBFile(PDBfile pdb)
   {
        int max = -10;
        int maxchain = -1;
        int pdbstart = 0;
        int pdbend = 0;
        int seqstart = 0;
        int seqend = 0;
        AlignSeq maxAlignseq = null;;

        for (int i = 0; i < pdb.chains.size(); i++)
        {

          mappingDetails.append("\n\nPDB Sequence is :\nSequence = " + ((PDBChain) pdb.chains.elementAt(i)).sequence.getSequence());
          mappingDetails.append("\nNo of residues = " + ((PDBChain) pdb.chains.elementAt(i)).residues.size()+"\n\n");

            // Now lets compare the sequences to get
            // the start and end points.
            // Align the sequence to the pdb
            AlignSeq as = new AlignSeq(sequence,
                    ((PDBChain) pdb.chains.elementAt(i)).sequence, "pep");
            as.calcScoreMatrix();
            as.traceAlignment();
            PrintStream  ps = new PrintStream(System.out)
           {
              public void print(String x) {
                   mappingDetails.append(x);
               }
               public void println()
               {
                 mappingDetails.append("\n");
               }
            };

            as.printAlignment(ps);

            if (as.maxscore > max) {
                max = as.maxscore;
                maxchain = i;

                pdbstart = as.seq2start;
                pdbend = as.seq2end;
                seqstart = as.seq1start + sequence.getStart()-1;
                seqend = as.seq1end + sequence.getEnd()-1;
                maxAlignseq = as;
            }

            mappingDetails.append("\nPDB start/end "  + pdbstart + " " + pdbend);
            mappingDetails.append("\nSEQ start/end "+ seqstart + " " + seqend);
        }

        mainchain = (PDBChain) pdb.chains.elementAt(maxchain);

        mainchain.pdbstart = pdbstart;
        mainchain.pdbend = pdbend;
        mainchain.seqstart = seqstart;
        mainchain.seqend = seqend;
        mainchain.isVisible = true;
        mainchain.makeExactMapping(maxAlignseq, sequence);

        this.pdb = pdb;
        this.prefsize = new Dimension(getSize().width, getSize().height);

        //Initialize the matrices to identity
        for (int i = 0; i < 3; i++) {
            for (int j = 0; j < 3; j++) {
                if (i != j) {
                    idmat.addElement(i, j, 0);
                    objmat.addElement(i, j, 0);
                } else {
                    idmat.addElement(i, j, 1);
                    objmat.addElement(i, j, 1);
                }
            }
        }

        addMouseMotionListener(this);
        addMouseListener(this);


        findCentre();
        findWidth();

        setupBonds();

        scale = findScale();
    }


    Vector visiblebonds;
    void setupBonds()
    {
      // Sort the bonds by z coord
      visiblebonds = new Vector();

      for (int ii = 0; ii < pdb.chains.size(); ii++)
      {
        if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)
        {
          Vector tmp = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;

          for (int i = 0; i < tmp.size(); i++)
          {
            visiblebonds.addElement(tmp.elementAt(i));
          }
        }
      }
      updateSeqColours();
      redrawneeded = true;
      repaint();
    }


    public void findWidth() {
        float[] max = new float[3];
        float[] min = new float[3];

        max[0] = (float) -1e30;
        max[1] = (float) -1e30;
        max[2] = (float) -1e30;

        min[0] = (float) 1e30;
        min[1] = (float) 1e30;
        min[2] = (float) 1e30;

        for (int ii = 0; ii < pdb.chains.size(); ii++) {
            if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) {
                Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;

                for (int i = 0; i < bonds.size(); i++) {
                    Bond tmp = (Bond) bonds.elementAt(i);

                    if (tmp.start[0] >= max[0]) {
                        max[0] = tmp.start[0];
                    }

                    if (tmp.start[1] >= max[1]) {
                        max[1] = tmp.start[1];
                    }

                    if (tmp.start[2] >= max[2]) {
                        max[2] = tmp.start[2];
                    }

                    if (tmp.start[0] <= min[0]) {
                        min[0] = tmp.start[0];
                    }

                    if (tmp.start[1] <= min[1]) {
                        min[1] = tmp.start[1];
                    }

                    if (tmp.start[2] <= min[2]) {
                        min[2] = tmp.start[2];
                    }

                    if (tmp.end[0] >= max[0]) {
                        max[0] = tmp.end[0];
                    }

                    if (tmp.end[1] >= max[1]) {
                        max[1] = tmp.end[1];
                    }

                    if (tmp.end[2] >= max[2]) {
                        max[2] = tmp.end[2];
                    }

                    if (tmp.end[0] <= min[0]) {
                        min[0] = tmp.end[0];
                    }

                    if (tmp.end[1] <= min[1]) {
                        min[1] = tmp.end[1];
                    }

                    if (tmp.end[2] <= min[2]) {
                        min[2] = tmp.end[2];
                    }
                }
            }
        }

        width[0] = (float) Math.abs(max[0] - min[0]);
        width[1] = (float) Math.abs(max[1] - min[1]);
        width[2] = (float) Math.abs(max[2] - min[2]);

        maxwidth = width[0];

        if (width[1] > width[0]) {
            maxwidth = width[1];
        }

        if (width[2] > width[1]) {
            maxwidth = width[2];
        }

       // System.out.println("Maxwidth = " + maxwidth);
    }

    public float findScale() {
        int dim;
        int width;
        int height;

        if (getSize().width != 0) {
            width = getSize().width;
            height = getSize().height;
        } else {
            width = prefsize.width;
            height = prefsize.height;
        }

        if (width < height) {
            dim = width;
        } else {
            dim = height;
        }

        return (float) (dim / (1.5d * maxwidth));
    }

    public void findCentre() {
        float xtot = 0;
        float ytot = 0;
        float ztot = 0;

        int bsize = 0;

        //Find centre coordinate
        for (int ii = 0; ii < pdb.chains.size(); ii++) {
            if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) {
                Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;

                bsize += bonds.size();

                for (int i = 0; i < bonds.size(); i++) {
                    xtot = xtot + ((Bond) bonds.elementAt(i)).start[0] +
                        ((Bond) bonds.elementAt(i)).end[0];

                    ytot = ytot + ((Bond) bonds.elementAt(i)).start[1] +
                        ((Bond) bonds.elementAt(i)).end[1];

                    ztot = ztot + ((Bond) bonds.elementAt(i)).start[2] +
                        ((Bond) bonds.elementAt(i)).end[2];
                }
            }
        }

        centre[0] = xtot / (2 * (float) bsize);
        centre[1] = ytot / (2 * (float) bsize);
        centre[2] = ztot / (2 * (float) bsize);
    }

    public void paint(Graphics g)
    {

      if(errorLoading)
      {
        g.setColor(Color.white);
        g.fillRect(0,0,getSize().width, getSize().height);
        g.setColor(Color.black);
        g.setFont(new Font("Verdana", Font.BOLD, 14));
        g.drawString("Error loading PDB data!!", 50, getSize().height/2);
        return;
      }
      else if(visiblebonds==null)
      {
        g.setColor(Color.black);
        g.setFont(new Font("Verdana", Font.BOLD, 14));
        g.drawString("Fetching PDB data...", 50, getSize().height/2);
        return;
      }



        //Only create the image at the beginning -
        //this saves much memory usage
        if ((img == null) || (prefsize.width != getSize().width) ||
                (prefsize.height != getSize().height)) {

         try{     prefsize.width = getSize().width;
           prefsize.height = getSize().height;

           scale = findScale();
           img = createImage(prefsize.width, prefsize.height);
           ig = img.getGraphics();

           redrawneeded = true;
         }catch(Exception ex)
         {
           ex.printStackTrace();
         }
        }


        if (redrawneeded)
        {
          drawAll(ig, prefsize.width, prefsize.height);
          redrawneeded = false;
        }
        if(appletToolTip!=null)
        {
          ig.setColor(Color.red);
          ig.drawString(appletToolTip, toolx, tooly);
        }

        g.drawImage(img, 0, 0, this);

        pdbAction = false;
    }

    public void drawAll(Graphics g, int width, int height)
    {
      ig.setColor(Color.black);
      ig.fillRect(0, 0, width, height);
      drawScene(ig);
      drawLabels(ig);
    }


    public void updateSeqColours()
    {
      if (pdbAction)
      {
        return;
      }

      if(bysequence && pdb!=null)
      {
        for (int ii = 0; ii < pdb.chains.size(); ii++)
        {
          colourBySequence((PDBChain) pdb.chains.elementAt(ii));
        }
      }

      redrawneeded=true;
      repaint();
    }


    int findTrueIndex(int pos)
    {
      // returns the alignment position for a residue
      int j = sequence.getStart();
      int i = 0;

      while ( (i < sequence.getLength()) && (j <= sequence.getEnd()) && (j <= pos+1))
      {
        if (!jalview.util.Comparison.isGap(sequence.getCharAt(i)))
        {
          j++;
        }

        i++;
      }

      if(i>1)
         i--;

      if ( (j == sequence.getEnd()) && (j < pos))
      {
        return sequence.getEnd() + 1;
      }
      else
      {
        return i;
      }
    }


    // This method has been taken out of PDBChain to allow
    // Applet and Application specific sequence renderers to be used
    void colourBySequence(PDBChain chain)
    {
      for (int i = 0; i < chain.bonds.size(); i++)
      {
        Bond tmp = (Bond) chain.bonds.elementAt(i);
        tmp.startCol = Color.lightGray;
        tmp.endCol = Color.lightGray;
        if(chain!=mainchain)
          continue;

        if ( (tmp.at1.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&
            (tmp.at1.resNumber <= ( (chain.offset + chain.pdbend) - 1)))
        {

          int index = findTrueIndex(tmp.at1.alignmentMapping);
                //sequence.findIndex(tmp.at1.alignmentMapping);
            if (index != -1)
            {
              tmp.startCol = seqcanvas.getSequenceRenderer().
                  getResidueBoxColour( sequence, index);

          //    tmp.startCol = seqcanvas.getFeatureRenderer().
         //         findFeatureColour(tmp.startCol, sequence, index);
            }
        }

        int index =  findTrueIndex(tmp.at2.alignmentMapping);
            //sequence.findIndex( tmp.at2.alignmentMapping );
        if (index != -1)
        {
          tmp.endCol = seqcanvas.getSequenceRenderer().
              getResidueBoxColour( sequence, index);
        //  tmp.endCol = seqcanvas.getFeatureRenderer().
        //      findFeatureColour(tmp.endCol, sequence, index);
        }
      }
    }


    public void drawScene(Graphics g)
    {

        if (zbuffer) {
            Zsort.Zsort(visiblebonds);
        }


        Bond tmpBond=null;
        for (int i = 0; i < visiblebonds.size(); i++)
        {
            tmpBond = (Bond) visiblebonds.elementAt(i);


            xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) +
                (getSize().width / 2));
            ystart = (int) (((tmpBond.start[1] - centre[1]) * scale) +
                (getSize().height / 2));

            xend = (int) (((tmpBond.end[0] - centre[0]) * scale) +
                (getSize().width / 2));
            yend = (int) (((tmpBond.end[1] - centre[1]) * scale) +
                (getSize().height / 2));

            xmid = (xend + xstart) / 2;
            ymid = (yend + ystart) / 2;

            if (depthcue && !bymolecule)
            {
                if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {
                    g.setColor(tmpBond.startCol.darker().darker());
                    drawLine(g, xstart, ystart, xmid, ymid);

                    g.setColor(tmpBond.endCol.darker().darker());
                    drawLine(g, xmid, ymid, xend, yend);
                } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) {
                    g.setColor(tmpBond.startCol.darker());
                    drawLine(g, xstart, ystart, xmid, ymid);

                    g.setColor(tmpBond.endCol.darker());
                    drawLine(g, xmid, ymid, xend, yend);
                } else {
                    g.setColor(tmpBond.startCol);
                    drawLine(g, xstart, ystart, xmid, ymid);

                    g.setColor(tmpBond.endCol);
                    drawLine(g, xmid, ymid, xend, yend);
                }

            } else if (depthcue && bymolecule) {
                if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {
                    g.setColor(Color.green.darker().darker());
                    drawLine(g, xstart, ystart, xend, yend);
                } else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6))) {
                    g.setColor(Color.green.darker());
                    drawLine(g, xstart, ystart, xend, yend);
                } else {
                    g.setColor(Color.green);
                    drawLine(g, xstart, ystart, xend, yend);
                }
            } else if (!depthcue && !bymolecule) {
                g.setColor(tmpBond.startCol);
                drawLine(g, xstart, ystart, xmid, ymid);
                g.setColor(tmpBond.endCol);
                drawLine(g, xmid, ymid, xend, yend);
            } else {
                drawLine(g, xstart, ystart, xend, yend);
            }

            if(highlightBond1!=null && highlightBond1==tmpBond)
            {
              g.setColor(Color.white);
              drawLine(g, xmid, ymid, xend, yend);
            }

            if(highlightBond2!=null && highlightBond2==tmpBond)
            {
              g.setColor(Color.white);
              drawLine(g, xstart, ystart, xmid, ymid);
            }

        }
    }

    public void drawLine(Graphics g, int x1, int y1, int x2, int y2) {
        if (!wire) {
            if (((float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5) {
                g.drawLine(x1, y1, x2, y2);
                g.drawLine(x1 + 1, y1 + 1, x2 + 1, y2 + 1);
                g.drawLine(x1, y1 - 1, x2, y2 - 1);
            } else {
                g.setColor(g.getColor().brighter());
                g.drawLine(x1, y1, x2, y2);
                g.drawLine(x1 + 1, y1, x2 + 1, y2);
                g.drawLine(x1 - 1, y1, x2 - 1, y2);
            }
        } else {
            g.drawLine(x1, y1, x2, y2);
        }
    }

    public Dimension minimumsize() {
        return prefsize;
    }

    public Dimension preferredsize() {
        return prefsize;
    }

    public void doKeyPressed(KeyEvent evt)
    {
      if (evt.getKeyCode() == KeyEvent.VK_UP)
      {
        scale = (float) (scale * 1.1);
        redrawneeded = true;
        repaint();
      }
      else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
      {
        scale = (float) (scale * 0.9);
        redrawneeded = true;
        repaint();
      }
    }

    public void mousePressed(MouseEvent e) {
      pdbAction = true;
      Atom fatom = findAtom(e.getX(), e.getY());
      if(fatom!=null)
      {
        fatom.isSelected = !fatom.isSelected;

        redrawneeded = true;
        repaint();
        if (foundchain != -1)
        {
          PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain);
          if (chain == mainchain)
          {
            if (fatom.alignmentMapping != -1)
            {
              if (highlightRes == null)
                highlightRes = new Vector();

              if (highlightRes.contains(fatom.alignmentMapping+"" + ""))
                highlightRes.removeElement(fatom.alignmentMapping + "");
              else
                highlightRes.addElement(fatom.alignmentMapping + "");
            }
          }
        }

        }
        mx = e.getX();
        my = e.getY();
        omx = mx;
        omy = my;
        dragging = false;
    }

    public void mouseMoved(MouseEvent e) {
      pdbAction = true;
      if(highlightBond1!=null)
      {
        highlightBond1.at2.isSelected = false;
        highlightBond2.at1.isSelected = false;
        highlightBond1 = null;
        highlightBond2 = null;
      }

        Atom fatom = findAtom(e.getX(), e.getY());

        PDBChain chain = null;
        if(foundchain!=-1)
        {
          chain = (PDBChain) pdb.chains.elementAt(foundchain);
          if(chain == mainchain)
          {
            highlightSeqcanvas( fatom.alignmentMapping );
          }
        }

        if (fatom != null) {
            toolx = e.getX();
            tooly = e.getY();

            appletToolTip = chain.id+":"+ fatom.resNumber+" "+ fatom.resName;
            redrawneeded = true;
            repaint();
        } else {
            highlightSeqcanvas( -1);
            appletToolTip = null;
            redrawneeded = true;
            repaint();
        }
    }


    void highlightSeqcanvas(int pos)
    {
      int index = seqcanvas.getViewport().getAlignment().findIndex(sequence);

      int size = pos==-1?0:3;

      if(highlightRes!=null)
        size += highlightRes.size()*3;

      int [] array = new int[size];
      int i=0;
      if(highlightRes!=null)
      {
        for (i = 0; i < highlightRes.size(); i++)
        {
          int a = Integer.parseInt(highlightRes.elementAt(
              i).toString())+1;
          array[i * 3] = index;
          array[ (i * 3) + 1] = a;
          array[ (i * 3) + 2] = a;
        }
      }

      if(pos!=-1)
      {
        array[i * 3] = index;
        array[i * 3 + 1] = pos+1;
        array[i * 3 + 2] = pos+1;
      }

      seqcanvas.highlightSearchResults(array);
    }


    public void mouseClicked(MouseEvent e) {
    }

    public void mouseEntered(MouseEvent e) {
    }

    public void mouseExited(MouseEvent e) {
    }

    public void mouseDragged(MouseEvent evt) {
        int x = evt.getX();
        int y = evt.getY();
        mx = x;
        my = y;

        MCMatrix objmat = new MCMatrix(3, 3);
        objmat.setIdentity();

        if ((evt.getModifiers() & Event.META_MASK) != 0) {
            objmat.rotatez((float) ((mx - omx)));
        } else {
            objmat.rotatex((float) ((my - omy)));
            objmat.rotatey((float) ((omx - mx)));
        }

        //Alter the bonds
        for (int ii = 0; ii < pdb.chains.size(); ii++) {
            Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;

            for (int i = 0; i < bonds.size(); i++) {
                Bond tmpBond = (Bond) bonds.elementAt(i);

                //Translate the bond so the centre is 0,0,0
                tmpBond.translate(-centre[0], -centre[1], -centre[2]);

                //Now apply the rotation matrix
                tmpBond.start = objmat.vectorMultiply(tmpBond.start);
                tmpBond.end = objmat.vectorMultiply(tmpBond.end);

                //Now translate back again
                tmpBond.translate(centre[0], centre[1], centre[2]);
            }
        }

        objmat = null;

        omx = mx;
        omy = my;

        dragging = true;

        redrawneeded = true;

        repaint();
    }

    public void mouseReleased(MouseEvent evt) {
        dragging = false;
        return;
    }

    void drawLabels(Graphics g) {

        for (int ii = 0; ii < pdb.chains.size(); ii++)
        {
            PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);

            if (chain.isVisible)
            {
                Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;

                for (int i = 0; i < bonds.size(); i++)
                {
                    Bond tmpBond = (Bond) bonds.elementAt(i);

                    if (tmpBond.at1.isSelected)
                    {
                        labelAtom(g, tmpBond, 1);
                    }

                    if (tmpBond.at2.isSelected)
                    {

                        labelAtom(g, tmpBond, 2);
                    }
                }
            }
        }
    }

    public void labelAtom(Graphics g, Bond b, int n) {
        g.setFont(font);

        if (n == 1) {
            int xstart = (int) (((b.start[0] - centre[0]) * scale) +
                (getSize().width / 2));
            int ystart = (int) (((b.start[1] - centre[1]) * scale) +
                (getSize().height / 2));

            g.setColor(Color.red);
            g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
        }

        if (n == 2) {
            int xstart = (int) (((b.end[0] - centre[0]) * scale) +
                (getSize().width / 2));
            int ystart = (int) (((b.end[1] - centre[1]) * scale) +
                (getSize().height / 2));

            g.setColor(Color.red);
            g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
        }
    }

    int foundchain = -1;
    public Atom findAtom(int x, int y) {
        Atom fatom = null;

        foundchain = -1;

        for (int ii = 0; ii < pdb.chains.size(); ii++)
        {
            PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
            int truex;
            Bond tmpBond=null;

            if (chain.isVisible)
            {
                Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;

                for (int i = 0; i < bonds.size(); i++)
                {
                    tmpBond = (Bond) bonds.elementAt(i);

                    truex = (int) (((tmpBond.start[0] - centre[0]) * scale) +
                        (getSize().width / 2));

                    if (Math.abs(truex - x) <= 2)
                    {
                        int truey = (int) (((tmpBond.start[1] - centre[1]) * scale) +
                            (getSize().height / 2));

                        if (Math.abs(truey - y) <= 2)
                        {
                            fatom = tmpBond.at1;
                            foundchain = ii;
                            break;
                        }
                    }
                }

                // Still here? Maybe its the last bond

                truex = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) +
                               (getSize().width / 2));

                if (Math.abs(truex - x) <= 2)
                {
                  int truey = (int) ( ( (tmpBond.end[1] - centre[1]) * scale) +
                                     (getSize().height / 2));

                  if (Math.abs(truey - y) <= 2)
                  {
                    fatom = tmpBond.at2;
                    foundchain = ii;
                    break;
                  }
                }

            }

            if (fatom != null) //)&& chain.ds != null)
             {
                chain = (PDBChain) pdb.chains.elementAt(foundchain);
            }
        }

        return fatom;
    }

    public void update(Graphics g)
    {
      paint(g);
    }

    public void highlightRes(int ii)
   {

     if (highlightRes != null
         && highlightRes.contains((ii-1) + ""))
     {
       return;
     }

     int index = -1;
     Bond tmpBond;
     for(index=0; index<mainchain.bonds.size(); index++)
     {
       tmpBond = (Bond) mainchain.bonds.elementAt(index);
       if (tmpBond.at1.alignmentMapping == ii - 1)
       {
         if (highlightBond1 != null)
           highlightBond1.at2.isSelected = false;

         if (highlightBond2 != null)
           highlightBond2.at1.isSelected = false;

         highlightBond1 = null;
         highlightBond2 = null;

         if (index > 0)
         {
           highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);
           highlightBond1.at2.isSelected = true;
         }

         if (index != mainchain.bonds.size())
         {
           highlightBond2 = (Bond) mainchain.bonds.elementAt(index);
           highlightBond2.at1.isSelected = true;
         }

         break;
       }
     }

     redrawneeded = true;
     repaint();
   }


    public void setAllchainsVisible(boolean b)
    {
      for (int ii = 0; ii < pdb.chains.size(); ii++)
      {
        PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
        chain.isVisible = b;
      }
      mainchain.isVisible = true;
      findCentre();
      setupBonds();
    }

}