From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 14 Nov 2005 18:21:17 +0000 (+0000)
Subject: Applet PDB viewer
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=28c093f681b769feb7b69bd4cbe309d580ef6179;p=jalview.git

Applet PDB viewer
---

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
new file mode 100755
index 0000000..478dd45
--- /dev/null
+++ b/src/MCview/AppletPDBCanvas.java
@@ -0,0 +1,782 @@
+/*
+* 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.SequenceRenderer sr;
+    jalview.appletgui.FeatureRenderer  fr;
+    jalview.appletgui.SeqCanvas seqcanvas;
+    Sequence sequence;
+    final StringBuffer mappingDetails = new StringBuffer();
+    String appletToolTip = null;
+    int toolx, tooly;
+
+    public AppletPDBCanvas(jalview.appletgui.SeqCanvas seqcanvas, Sequence seq)
+    {
+      this.seqcanvas = seqcanvas;
+      this.sequence = seq;
+      sr = seqcanvas.getSequenceRenderer();
+      fr = seqcanvas.getFeatureRenderer();
+
+      seqcanvas.setPDBViewer(this);
+      addKeyListener(new KeyAdapter()
+      {
+
+        public void keyPressed(KeyEvent evt)
+        {
+          doKeyPressed(evt);
+        }
+      });
+
+    }
+
+  public void setPDBFile(PDBfile pdb)
+   {
+        this.sr = sr;
+        this.fr = fr;
+        int max = -10;
+        int maxchain = -1;
+        int pdbstart = 0;
+        int pdbend = 0;
+        int seqstart = 0;
+        int seqend = 0;
+
+        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;
+            }
+
+            mappingDetails.append("\nPDB start/end "  + pdbstart + " " + pdbend);
+            mappingDetails.append("\nSEQ start/end "+ seqstart + " " + seqend);
+        }
+
+        ((PDBChain) pdb.chains.elementAt(maxchain)).pdbstart = pdbstart;
+        ((PDBChain) pdb.chains.elementAt(maxchain)).pdbend = pdbend;
+        ((PDBChain) pdb.chains.elementAt(maxchain)).seqstart = seqstart;
+        ((PDBChain) pdb.chains.elementAt(maxchain)).seqend = seqend;
+        ((PDBChain) pdb.chains.elementAt(maxchain)).isVisible = true;
+        ((PDBChain) pdb.chains.elementAt(maxchain)).sequence = 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);
+
+      /*
+       SequenceGroup sg = new SequenceGroup("PDB",
+                                            null, true,true,false,
+                                            sequence.findIndex(seqstart-1),
+                                            sequence.findIndex(seqend-1));
+       sg.addSequence(sequence, false);
+       sg.setOutlineColour(Color.black);
+       seqcanvas.getViewport().getAlignment().addGroup(sg);
+       */
+
+        findCentre();
+        findWidth();
+
+        scale = findScale();
+
+        updateSeqColours();
+    }
+
+    public void deleteBonds() {
+        scale = 0;
+        maxwidth = 0;
+
+        width[0] = 0;
+        width[1] = 0;
+        width[2] = 0;
+
+        centre[0] = 0;
+        centre[1] = 0;
+        centre[2] = 0;
+
+        for (int i = 0; i < pdb.chains.size(); i++) {
+            ((PDBChain) pdb.chains.elementAt(i)).bonds = null;
+        }
+    }
+
+    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(pdb==null)
+      {
+        g.setColor(Color.black);
+        g.setFont(new Font("Verdana", Font.BOLD, 14));
+        g.drawString("Error Parsing Pasted 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)) {
+            prefsize.width = getSize().width;
+            prefsize.height = getSize().height;
+
+            scale = findScale();
+            img = createImage(prefsize.width, prefsize.height);
+            ig = img.getGraphics();
+
+            redrawneeded = true;
+        }
+
+
+        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);
+
+
+    }
+
+    public void drawAll(Graphics g, int width, int height)
+    {
+      g.setColor(Color.black);
+      g.fillRect(0, 0, width, height);
+      drawScene(g);
+      drawLabels(g);
+    }
+
+
+    public void updateSeqColours()
+    {
+      if(bysequence && pdb!=null)
+      {
+        for (int ii = 0; ii < pdb.chains.size(); ii++)
+        {
+          colourBySequence((PDBChain) pdb.chains.elementAt(ii));
+        }
+      }
+
+      redrawneeded=true;
+      repaint();
+    }
+
+    // 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);
+
+        if ( (tmp.at1.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&
+            (tmp.at1.resNumber <= ( (chain.offset + chain.pdbend) - 1)))
+        {
+          int pos = chain.seqstart +
+              (tmp.at1.resNumber - chain.pdbstart - chain.offset);
+
+          int index = sequence.findIndex(pos);
+
+          tmp.startCol = sr.findSequenceColour(sequence, index);
+
+        //  tmp.startCol = fr.findFeatureColour(tmp.startCol, sequence, index);
+
+        }
+        else
+        {
+          tmp.startCol = Color.gray;
+        }
+
+        if ( (tmp.at2.resNumber >= ( (chain.offset + chain.pdbstart) - 1)) &&
+            (tmp.at2.resNumber <= ( (chain.pdbend + chain.offset) - 1)))
+        {
+          int pos = chain.seqstart +
+              (tmp.at2.resNumber - chain.pdbstart - chain.offset);
+          int index = sequence.findIndex(pos);
+
+          tmp.endCol = sr.findSequenceColour( sequence, index);
+      //    tmp.endCol = fr.findFeatureColour(tmp.endCol, sequence, index);
+        }
+        else
+        {
+          tmp.endCol = Color.gray;
+        }
+      }
+    }
+
+
+    public void drawScene(Graphics g) {
+        // Sort the bonds by z coord
+        Vector bonds = 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++)
+            {
+              bonds.addElement(tmp.elementAt(i));
+            }
+          }
+        }
+
+        if (zbuffer) {
+            Zsort.Zsort(bonds);
+        }
+
+        for (int i = 0; i < bonds.size(); i++) {
+            Bond tmpBond = (Bond) bonds.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);
+            }
+        }
+    }
+
+    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) {
+        myAtom fatom = findAtom(e.getX(), e.getY());
+        if(fatom!=null)
+        {
+          fatom.isSelected = !fatom.isSelected;
+          redrawneeded = true;
+          repaint();
+        }
+        mx = e.getX();
+        my = e.getY();
+        omx = mx;
+        omy = my;
+        dragging = false;
+    }
+
+    public void mouseMoved(MouseEvent e) {
+
+        myAtom fatom = findAtom(e.getX(), e.getY());
+
+        if(foundchain!=-1)
+        {
+          PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain);
+          int pos = chain.seqstart +
+              (fatom.resNumber - chain.pdbstart - chain.offset)+1;
+
+          int index = seqcanvas.getViewport().getAlignment().findIndex(sequence);
+
+          seqcanvas.highlightSearchResults(new int[]{index, pos, pos});
+        }
+        else
+          seqcanvas.highlightSearchResults(null);
+
+        if (fatom != null) {
+            toolx = e.getX();
+            tooly = e.getY();
+            appletToolTip = fatom.resNumber+" "+ fatom.resName;
+            redrawneeded = true;
+            repaint();
+        } else {
+            appletToolTip = null;
+            redrawneeded = true;
+            repaint();
+        }
+    }
+
+    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 myAtom findAtom(int x, int y) {
+        myAtom fatom = null;
+
+        foundchain = -1;
+
+        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);
+
+                    int 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;
+                        }
+                    }
+                }
+            }
+
+            if (fatom != null) //)&& chain.ds != null)
+             {
+                chain = (PDBChain) pdb.chains.elementAt(foundchain);
+            }
+        }
+
+        return fatom;
+    }
+
+    public void update(Graphics g)
+    {
+      paint(g);
+    }
+}
diff --git a/src/MCview/AppletPDBViewer.java b/src/MCview/AppletPDBViewer.java
new file mode 100755
index 0000000..e704f15
--- /dev/null
+++ b/src/MCview/AppletPDBViewer.java
@@ -0,0 +1,236 @@
+package MCview;
+
+import java.awt.*;
+
+import java.awt.event.*;
+import jalview.datamodel.*;
+import jalview.appletgui.*;
+import java.awt.event.ActionListener;
+import java.awt.event.ActionEvent;
+
+
+public class AppletPDBViewer extends Frame
+{
+      PDBEntry pdb;
+      Sequence sequence;
+      AppletPDBCanvas pdbcanvas;
+
+
+      public AppletPDBViewer(String pdbtext,
+                       Sequence seq,
+                       SeqCanvas seqcanvas)
+      {
+        sequence = seq;
+
+        try
+        {
+          jbInit();
+        }
+        catch (Exception ex)
+        {
+          ex.printStackTrace();
+        }
+
+        pdbcanvas = new AppletPDBCanvas(seqcanvas, seq);
+
+        add(pdbcanvas, BorderLayout.CENTER);
+
+        StringBuffer title = new StringBuffer(sequence.getName() + ":");
+
+        jalview.bin.JalviewLite.addFrame(this,title.toString(),400, 400);
+
+        try{
+        PDBfile pdbfile = new PDBfile(pdbtext, "Paste");
+        pdbcanvas.setPDBFile(pdbfile);
+        }catch(Exception ex){ex.printStackTrace();}
+      }
+
+
+      private void jbInit()
+          throws Exception
+      {
+        this.setMenuBar(jMenuBar1);
+        fileMenu.setLabel("File");
+        coloursMenu.setLabel("Colours");
+        mapping.setLabel("View Mapping");
+        mapping.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            mapping_actionPerformed();
+          }
+        });
+        wire.setLabel("Wireframe");
+        wire.addItemListener(new ItemListener()
+        {
+          public void itemStateChanged(ItemEvent e)
+          {
+            wire_actionPerformed();
+          }
+        });
+        depth.setState(true);
+        depth.setLabel("Depthcue");
+        depth.addItemListener(new ItemListener()
+        {
+          public void itemStateChanged(ItemEvent e)
+          {
+            depth_actionPerformed();
+          }
+        });
+        zbuffer.setState(true);
+        zbuffer.setLabel("Z Buffering");
+        zbuffer.addItemListener(new ItemListener()
+        {
+          public void itemStateChanged(ItemEvent e)
+          {
+            zbuffer_actionPerformed();
+          }
+        });
+        charge.setLabel("Charge & Cysteine");
+        charge.addItemListener(new ItemListener()
+        {
+          public void itemStateChanged(ItemEvent e)
+          {
+            charge_actionPerformed();
+          }
+        });
+        hydro.setLabel("Hydrophobicity");
+        hydro.addItemListener(new ItemListener()
+        {
+          public void itemStateChanged(ItemEvent e)
+          {
+            hydro_actionPerformed();
+          }
+        });
+        chain.setLabel("By Chain");
+        chain.addItemListener(new ItemListener()
+        {
+          public void itemStateChanged(ItemEvent e)
+          {
+            chain_actionPerformed();
+          }
+        });
+        seqButton.setState(true);
+        seqButton.setLabel("By Sequence");
+        seqButton.addItemListener(new ItemListener()
+        {
+          public void itemStateChanged(ItemEvent e)
+          {
+            seqButton_actionPerformed();
+          }
+        });
+        molecule.setLabel("By Molecule");
+        molecule.addItemListener(new ItemListener()
+        {
+          public void itemStateChanged(ItemEvent e)
+          {
+            molecule_actionPerformed();
+          }
+        });
+        jMenuBar1.add(fileMenu);
+        jMenuBar1.add(coloursMenu);
+        fileMenu.add(mapping);;
+
+        coloursMenu.add(seqButton);
+        coloursMenu.add(chain);
+        coloursMenu.add(hydro);
+        coloursMenu.add(charge);
+        coloursMenu.addSeparator();
+        coloursMenu.add(wire);
+        coloursMenu.add(depth);
+        coloursMenu.add(zbuffer);
+        coloursMenu.add(molecule);
+
+      }
+
+      MenuBar jMenuBar1 = new MenuBar();
+      Menu fileMenu = new Menu();
+      Menu coloursMenu = new Menu();
+      MenuItem mapping = new MenuItem();
+      CheckboxGroup bg = new CheckboxGroup();
+      CheckboxMenuItem wire = new CheckboxMenuItem();
+      CheckboxMenuItem depth = new CheckboxMenuItem();
+      CheckboxMenuItem zbuffer = new CheckboxMenuItem();
+      CheckboxMenuItem charge = new CheckboxMenuItem();
+
+
+      CheckboxMenuItem hydro = new CheckboxMenuItem();
+      CheckboxMenuItem chain = new CheckboxMenuItem();
+      CheckboxMenuItem seqButton = new CheckboxMenuItem();
+      CheckboxMenuItem molecule = new CheckboxMenuItem();
+
+       public void charge_actionPerformed()
+      {
+        clearButtonGroup();
+        pdbcanvas.pdb.setChargeColours();
+        pdbcanvas.redrawneeded=true;
+        pdbcanvas.repaint();
+      }
+
+      public void hydro_actionPerformed()
+      {
+        clearButtonGroup();
+        pdbcanvas.pdb.setHydrophobicityColours();
+        pdbcanvas.redrawneeded=true;
+        pdbcanvas.repaint();
+      }
+
+      public void chain_actionPerformed()
+      {
+        clearButtonGroup();
+        pdbcanvas.pdb.setChainColours();
+        pdbcanvas.redrawneeded=true;
+        pdbcanvas.repaint();
+      }
+
+      public void zbuffer_actionPerformed()
+      {
+        pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;
+        pdbcanvas.redrawneeded=true;
+        pdbcanvas.repaint();
+      }
+
+      public void molecule_actionPerformed()
+      {
+        pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;
+        pdbcanvas.redrawneeded=true;
+        pdbcanvas.repaint();
+      }
+
+      public void depth_actionPerformed()
+      {
+      pdbcanvas.depthcue = ! pdbcanvas.depthcue;
+      pdbcanvas.redrawneeded=true;
+        pdbcanvas.repaint();
+      }
+
+      public void wire_actionPerformed()
+      {
+        pdbcanvas.wire = ! pdbcanvas.wire;
+        pdbcanvas.redrawneeded=true;
+        pdbcanvas.repaint();
+      }
+
+      public void seqButton_actionPerformed()
+      {
+        clearButtonGroup();
+        pdbcanvas.bysequence = seqButton.getState();
+        pdbcanvas.updateSeqColours();
+      }
+
+      void clearButtonGroup()
+      {
+       pdbcanvas.bysequence = false;
+       pdbcanvas.bymolecule = false;
+      }
+
+      public void mapping_actionPerformed()
+      {
+        jalview.appletgui.CutAndPasteTransfer cap
+            = new jalview.appletgui.CutAndPasteTransfer(false, null);
+        Frame frame = new Frame();
+        frame.add(cap);
+        jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 500, 600);
+        cap.setText(pdbcanvas.mappingDetails.toString());
+      }
+    }