From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 10 Nov 2005 11:00:08 +0000 (+0000)
Subject: PDM mapping
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=76389b07e78f92b6db0aeaf2f964d9dcb6671543;p=jalview.git

PDM mapping
---

diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
new file mode 100755
index 0000000..e9f8dce
--- /dev/null
+++ b/src/MCview/PDBCanvas.java
@@ -0,0 +1,686 @@
+/*
+* 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.*;
+
+import javax.swing.*;
+
+
+public class PDBCanvas extends JPanel 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.gui.SequenceRenderer sr;
+    jalview.gui.FeatureRenderer  fr;
+
+    public PDBCanvas()
+    {
+
+    }
+
+  public void setPDBFile(PDBfile pdb, Sequence sequence,
+                     jalview.gui.SequenceRenderer sr,
+                     jalview.gui.FeatureRenderer fr)
+   {
+
+
+        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++) {
+            // 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();
+            as.printAlignment();
+
+
+            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;
+            }
+
+            System.out.println("PDB start/end "  + pdbstart + " " + pdbend);
+            System.out.println("SEQ 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(getWidth(), getHeight());
+
+        //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();
+
+        scale = findScale();
+
+        System.out.println("Scale factor = " + scale);
+
+        updateSeqColours();
+        ToolTipManager.sharedInstance().registerComponent(this);
+        ToolTipManager.sharedInstance().setInitialDelay(0);
+        ToolTipManager.sharedInstance().setDismissDelay(10000);
+
+    }
+
+    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];
+                    }
+                }
+            }
+        }
+
+        System.out.println("xmax " + max[0] + " min " + min[0]);
+        System.out.println("ymax " + max[1] + " min " + min[1]);
+        System.out.println("zmax " + max[2] + " min " + min[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 (getWidth() != 0) {
+            width = getWidth();
+            height = getHeight();
+        } 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 paintComponent(Graphics g) {
+
+      if(pdb==null)
+      {
+        g.setColor(Color.black);
+        g.setFont(new Font("Verdana", Font.BOLD, 14));
+        g.drawString("Retrieving PDB data....", 20, getHeight()/2);
+
+        return;
+      }
+
+
+        //Only create the image at the beginning -
+        //this saves much memory usage
+        if ((img == null) || (prefsize.width != getWidth()) ||
+                (prefsize.height != getHeight())) {
+            prefsize.width = getWidth();
+            prefsize.height = getHeight();
+
+            scale = findScale();
+            img = createImage(prefsize.width, prefsize.height);
+            ig = img.getGraphics();
+            Graphics2D ig2 = (Graphics2D) ig;
+
+            ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                                 RenderingHints.VALUE_ANTIALIAS_ON);
+
+
+            redrawneeded = true;
+        }
+
+
+        if (redrawneeded)
+        {
+          drawAll(ig, prefsize.width, prefsize.height);
+          redrawneeded = false;
+        }
+
+        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)
+      {
+        for (int ii = 0; ii < pdb.chains.size(); ii++)
+        {
+          ( (PDBChain) pdb.chains.elementAt(ii)).colourBySequence(sr, fr);
+        }
+      }
+
+      redrawneeded=true;
+      repaint();
+
+    }
+
+    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) +
+                (getWidth() / 2));
+            ystart = (int) (((tmpBond.start[1] - centre[1]) * scale) +
+                (getHeight() / 2));
+
+            xend = (int) (((tmpBond.end[0] - centre[0]) * scale) +
+                (getWidth() / 2));
+            yend = (int) (((tmpBond.end[1] - centre[1]) * scale) +
+                (getHeight() / 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 keyPressed(KeyEvent evt) {
+      int key = evt.getKeyChar();
+      System.out.println(key);
+      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 (fatom != null) {
+            this.setToolTipText(fatom.resNumber+" "+ fatom.resName);
+        } else {
+            this.setToolTipText("");
+        }
+    }
+
+    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) +
+                (getWidth() / 2));
+            int ystart = (int) (((b.start[1] - centre[1]) * scale) +
+                (getHeight() / 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) +
+                (getWidth() / 2));
+            int ystart = (int) (((b.end[1] - centre[1]) * scale) +
+                (getHeight() / 2));
+
+            g.setColor(Color.red);
+            g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
+        }
+    }
+
+    public myAtom findAtom(int x, int y) {
+        myAtom fatom = null;
+
+        int 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) +
+                        (getWidth() / 2));
+
+                    if (Math.abs(truex - x) <= 2) {
+                        int truey = (int) (((tmpBond.start[1] - centre[1]) * scale) +
+                            (getHeight() / 2));
+
+                        if (Math.abs(truey - y) <= 2)
+                        {
+                            fatom = tmpBond.at1;
+                            foundchain = ii;
+                        }
+                    }
+                }
+            }
+
+            if (fatom != null) //)&& chain.ds != null)
+             {
+                chain = (PDBChain) pdb.chains.elementAt(foundchain);
+
+                // SMJS TODO
+                // int tmp = chain.ds.seqstart + fatom.resNumber - chain.offset;
+                // int pos = chain.ds.findIndex(tmp);
+                // System.out.println("Found seq " + chain.ds.name + " "  + tmp + " " + pos);
+            }
+        }
+
+        return fatom;
+    }
+
+    public void update(Graphics g) {
+        paint(g);
+    }
+}
diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
new file mode 100755
index 0000000..2610b40
--- /dev/null
+++ b/src/MCview/PDBViewer.java
@@ -0,0 +1,400 @@
+package MCview;
+
+import javax.swing.*;
+import java.awt.event.*;
+import jalview.datamodel.*;
+import jalview.gui.*;
+import jalview.io.EBIFetchClient;
+import java.awt.event.ActionListener;
+import java.awt.event.ActionEvent;
+import java.io.FileOutputStream;
+import org.jibble.epsgraphics.EpsGraphics2D;
+import javax.imageio.ImageIO;
+import java.awt.image.BufferedImage;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+
+public class PDBViewer extends JInternalFrame implements Runnable
+{
+  PDBEntry pdb;
+  Sequence sequence;
+  SeqCanvas seqcanvas;
+  PDBCanvas pdbcanvas;
+
+
+  public PDBViewer(PDBEntry entry,
+                   Sequence seq,
+                   SeqCanvas seqcanvas)
+  {
+    pdb = entry;
+    sequence = seq;
+    this.seqcanvas = seqcanvas;
+
+
+    try
+    {
+      jbInit();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+
+    pdbcanvas = new PDBCanvas();
+    setContentPane(pdbcanvas);
+    Desktop.addInternalFrame(this,
+                         sequence.getName() + ":" + pdb.getId()
+                         + " Method: " + pdb.getProperty().get("method")
+                         + " Chain:" + pdb.getProperty().get("chains"),
+                         400, 400);
+
+     Thread worker = new Thread(this);
+     worker.start();
+  }
+
+  public void run()
+  {
+    try
+    {
+      EBIFetchClient ebi = new EBIFetchClient();
+      String[] result = ebi.fetchData("pdb:" + pdb.getId(), null,
+                                      null);
+
+      PDBfile pdbfile = new PDBfile(result);
+
+      pdbcanvas.setPDBFile(pdbfile,
+                        sequence,
+                        seqcanvas.getSequenceRenderer(),
+                        seqcanvas.getFeatureRenderer());
+
+      seqcanvas.setPDBViewer(pdbcanvas);
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  private void jbInit()
+      throws Exception
+  {
+    this.addKeyListener(new KeyAdapter()
+        {
+            public void keyPressed(KeyEvent evt)
+            {
+              System.out.println("key press");
+              pdbcanvas.keyPressed(evt);
+            }
+        });
+
+    this.setJMenuBar(jMenuBar1);
+    fileMenu.setText("File");
+    coloursMenu.setText("Colours");
+    saveMenu.setActionCommand("Save Image");
+    saveMenu.setText("Save As");
+    png.setText("PNG");
+    png.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        png_actionPerformed(e);
+      }
+    });
+    eps.setText("EPS");
+    eps.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        eps_actionPerformed(e);
+      }
+    });
+    mapping.setText("View Mapping");
+    wire.setText("Wireframe");
+    wire.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        wire_actionPerformed(e);
+      }
+    });
+    depth.setSelected(true);
+    depth.setText("Depthcue");
+    depth.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        depth_actionPerformed(e);
+      }
+    });
+    zbuffer.setSelected(true);
+    zbuffer.setText("Z Buffering");
+    zbuffer.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        zbuffer_actionPerformed(e);
+      }
+    });
+    charge.setText("Charge & Cysteine");
+    charge.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        charge_actionPerformed(e);
+      }
+    });
+    hydro.setText("Hydrophobicity");
+    hydro.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        hydro_actionPerformed(e);
+      }
+    });
+    chain.setText("By Chain");
+    chain.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        chain_actionPerformed(e);
+      }
+    });
+    seqButton.setSelected(true);
+    seqButton.setText("By Sequence");
+    seqButton.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        seqButton_actionPerformed(e);
+      }
+    });
+    molecule.setText("By Molecule");
+    molecule.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        molecule_actionPerformed(e);
+      }
+    });
+    jMenuBar1.add(fileMenu);
+    jMenuBar1.add(coloursMenu);
+    fileMenu.add(saveMenu);
+    fileMenu.add(mapping);
+    saveMenu.add(png);
+    saveMenu.add(eps);
+    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);
+    ButtonGroup bg = new ButtonGroup();
+    bg.add(seqButton);
+    bg.add(chain);
+    bg.add(hydro);
+    bg.add(charge);
+  }
+
+  JMenuBar jMenuBar1 = new JMenuBar();
+  JMenu fileMenu = new JMenu();
+  JMenu coloursMenu = new JMenu();
+  JMenu saveMenu = new JMenu();
+  JMenuItem png = new JMenuItem();
+  JMenuItem eps = new JMenuItem();
+  JMenuItem mapping = new JMenuItem();
+  JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
+  JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
+  JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
+  JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
+  JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
+  JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
+  JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
+  JCheckBoxMenuItem molecule = new JCheckBoxMenuItem();
+
+  public void png_actionPerformed(ActionEvent e)
+  {
+    int width =  pdbcanvas.getWidth();
+    int height = pdbcanvas.getHeight();
+
+    try
+    {
+        jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
+                    "LAST_DIRECTORY"), new String[] { "png" },
+                new String[] { "Portable network graphics" },
+                "Portable network graphics");
+
+        chooser.setFileView(new jalview.io.JalviewFileView());
+        chooser.setDialogTitle("Create PNG Image of Molecule");
+        chooser.setToolTipText("Save");
+
+        int value = chooser.showSaveDialog(this);
+
+        if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+        {
+            return;
+        }
+
+        jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+            chooser.getSelectedFile().getParent());
+
+        FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+
+        BufferedImage bi = new BufferedImage(width, height,
+                BufferedImage.TYPE_INT_RGB);
+        Graphics png = bi.getGraphics();
+        Graphics2D ig2 = (Graphics2D) png;
+        ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                                 RenderingHints.VALUE_ANTIALIAS_ON);
+
+
+        pdbcanvas.drawAll(png, width, height);
+
+        ImageIO.write(bi, "png", out);
+        out.close();
+    }
+    catch (Exception ex)
+    {
+        ex.printStackTrace();
+    }
+  }
+
+  public void eps_actionPerformed(ActionEvent e)
+  {
+    boolean accurateText = true;
+
+    String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
+        "Prompt each time");
+
+  // If we need to prompt, and if the GUI is visible then
+  // Prompt for EPS rendering style
+    if (renderStyle.equalsIgnoreCase("Prompt each time")
+        && !
+        (System.getProperty("java.awt.headless") != null
+         && System.getProperty("java.awt.headless").equals("true")))
+    {
+      EPSOptions eps = new EPSOptions();
+      renderStyle = eps.getValue();
+
+      if (renderStyle==null || eps.cancelled)
+        return;
+
+
+    }
+
+    if (renderStyle.equalsIgnoreCase("text"))
+    {
+      accurateText = false;
+    }
+
+      int width = getWidth();
+      int height = getHeight();
+
+      try
+      {
+          jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
+                      "LAST_DIRECTORY"), new String[] { "eps" },
+                  new String[] { "Encapsulated Postscript" },
+                  "Encapsulated Postscript");
+          chooser.setFileView(new jalview.io.JalviewFileView());
+          chooser.setDialogTitle("Create EPS file from tree");
+          chooser.setToolTipText("Save");
+
+          int value = chooser.showSaveDialog(this);
+
+          if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+          {
+              return;
+          }
+
+          jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+                                        chooser.getSelectedFile().getParent());
+
+          FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+          EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
+                                               height);
+          Graphics2D ig2 = (Graphics2D) pg;
+          ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+                         RenderingHints.VALUE_ANTIALIAS_ON);
+
+
+          pg.setAccurateTextMode(accurateText);
+
+          pdbcanvas.drawAll(pg, width, height);
+
+          pg.flush();
+          pg.close();
+      }
+      catch (Exception ex)
+      {
+          ex.printStackTrace();
+        }
+
+  }
+
+  public void charge_actionPerformed(ActionEvent e)
+  {
+    pdbcanvas.pdb.setChargeColours();
+    pdbcanvas.redrawneeded=true;
+    pdbcanvas.repaint();
+  }
+
+  public void hydro_actionPerformed(ActionEvent e)
+  {
+    pdbcanvas.pdb.setHydrophobicityColours();
+    pdbcanvas.redrawneeded=true;
+    pdbcanvas.repaint();
+  }
+
+  public void chain_actionPerformed(ActionEvent e)
+  {
+    pdbcanvas.pdb.setChainColours();
+    pdbcanvas.redrawneeded=true;
+    pdbcanvas.repaint();
+  }
+
+  public void zbuffer_actionPerformed(ActionEvent e)
+  {
+    pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;
+    pdbcanvas.redrawneeded=true;
+    pdbcanvas.repaint();
+  }
+
+  public void molecule_actionPerformed(ActionEvent e)
+  {
+    pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;
+    pdbcanvas.redrawneeded=true;
+    pdbcanvas.repaint();
+  }
+
+  public void depth_actionPerformed(ActionEvent e)
+  {
+  pdbcanvas.depthcue = ! pdbcanvas.depthcue;
+  pdbcanvas.redrawneeded=true;
+    pdbcanvas.repaint();
+  }
+
+  public void wire_actionPerformed(ActionEvent e)
+  {
+    pdbcanvas.wire = ! pdbcanvas.wire;
+    pdbcanvas.redrawneeded=true;
+    pdbcanvas.repaint();
+  }
+
+  public void seqButton_actionPerformed(ActionEvent e)
+  {
+    pdbcanvas.bysequence = seqButton.isSelected();
+    pdbcanvas.updateSeqColours();
+  }
+
+  void clearButtonGroup()
+  {
+   charge.setSelected(false);
+   hydro.setSelected(false);
+   chain.setSelected(false);
+   seqButton.setSelected(false);
+  }
+}
diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
new file mode 100755
index 0000000..508e530
--- /dev/null
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -0,0 +1,38 @@
+package jalview.datamodel;
+
+import java.util.*;
+public class PDBEntry
+{
+  String type;
+  String id;
+ // //String method;
+  //String chains;
+  Hashtable properties;
+
+  public PDBEntry()
+  {  }
+
+  public void setType(String type)
+  { this.type = type; }
+
+  public String getType()
+  { return type; }
+
+  public void setId(String id)
+  { this.id = id; }
+
+  public String getId()
+  { return id; }
+
+  public void setProperty(Hashtable property)
+  {
+    this.properties = property;
+  }
+
+  public Hashtable getProperty()
+  {
+    return properties;
+  }
+
+
+}