X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FrotCanvas.java;h=be14db8039303460f26f2bcd62b093fd83a56009;hb=a28c9340eeadfdaa551a21b9dea1d0f1530126e3;hp=9b822f3043b58b179372d4a8cb20bbdbccad54e6;hpb=1dbe649695c2c5d4475dcf61e51ed24cddf16594;p=jalview.git

diff --git a/src/MCview/rotCanvas.java b/src/MCview/rotCanvas.java
index 9b822f3..be14db8 100755
--- a/src/MCview/rotCanvas.java
+++ b/src/MCview/rotCanvas.java
@@ -1,705 +1,730 @@
+/*
+* 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 java.awt.*;
-import java.awt.event.*;
-import java.util.*;
-import java.io.*;
-import javax.swing.*;
 import jalview.analysis.AlignSeq;
-import jalview.datamodel.*;
-
-public class rotCanvas extends JPanel implements KeyListener,
-                                                 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];
+import jalview.datamodel.*;
 
-  float maxwidth;
-  float scale;
+// JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug
+import java.awt.*;
+import java.awt.event.*;
 
-  String inStr;
-  String inType;
+import java.io.*;
 
-  boolean depthcue   = true;
-  boolean wire       = false;
-  boolean bymolecule = false;
-  boolean zbuffer    = true;
+import java.util.*;
 
-  boolean dragging;
+import javax.swing.*;
 
-  int xstart;
-  int xend;
-  int ystart;
-  int yend;
-  int xmid;
-  int ymid;
 
-  Font font = new Font("Helvetica",Font.PLAIN,10);
+public class rotCanvas extends JPanel implements KeyListener, 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 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);
+
+    public rotCanvas(PDBfile pdb, Sequence sequence,
+        jalview.gui.AlignViewport av) throws IOException {
+        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.
+            java.util.StringTokenizer str = new java.util.StringTokenizer(sequence.getSequence(),
+                    ".");
+            String newString = "";
+
+            while (str.hasMoreTokens()) {
+                newString += str.nextToken();
+            }
 
-  public rotCanvas(PDBfile pdb, Sequence sequence, jalview.gui.AlignViewport av) throws IOException {
+            // 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 - 1;
+                seqend = as.seq1end - 1;
+            }
 
-    int max = -10;
-    int maxchain = -1;
-    int pdbstart=0, pdbend=0,  seqstart =0,  seqend=0;
+            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;
+        ((PDBChain) pdb.chains.elementAt(maxchain)).colourBySequence(av,
+            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);
+                }
+            }
+        }
 
-    for (int i=0; i < pdb.chains.size(); i++) {
-      // Now lets compare the sequences to get
-      // the start and end points.
+        addMouseMotionListener(this);
+        addMouseListener(this);
+        addKeyListener(this);
 
-    java.util.StringTokenizer str = new java.util.StringTokenizer(sequence.getSequence(), ".");
-    String newString = "";
+        addPDBfile();
+        ToolTipManager.sharedInstance().registerComponent(this);
+        ToolTipManager.sharedInstance().setInitialDelay(0);
+        ToolTipManager.sharedInstance().setDismissDelay(10000);
 
-    while (str.hasMoreTokens()) {
-        newString += str.nextToken();
-    }
-      // 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  - 1 ;
-        seqend = as.seq1end  -1;
-      }
-
-      System.out.println("PDB start/end " + pdbstart + " " + pdbend);
-      System.out.println("SEQ start/end " + seqstart + " " + seqend);
     }
 
+    public void addPDBfile() {
+        findCentre();
+        findWidth();
 
-    ( (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;
-     ( (PDBChain)pdb.chains.elementAt(maxchain)).colourBySequence(av, sequence);
+        scale = findScale();
 
+        System.out.println("Scale factor = " + scale);
+    }
 
+    public void deleteBonds() {
+        scale = 0;
+        maxwidth = 0;
 
-    this.pdb      = pdb;
-    this.prefsize = new Dimension( getWidth(), getHeight());
+        width[0] = 0;
+        width[1] = 0;
+        width[2] = 0;
 
-    //Initialize the matrices to identity
+        centre[0] = 0;
+        centre[1] = 0;
+        centre[2] = 0;
 
-    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);
+        for (int i = 0; i < pdb.chains.size(); i++) {
+            ((PDBChain) pdb.chains.elementAt(i)).bonds = null;
         }
-      }
     }
 
-    addMouseMotionListener(this);
-    addMouseListener(this);
-    addKeyListener(this);
-
-    addPDBfile();
-    ToolTipManager.sharedInstance().registerComponent(this);
+    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;
 
-  public void addPDBfile() {
-    findCentre();
-    findWidth();
+        min[0] = (float) 1e30;
+        min[1] = (float) 1e30;
+        min[2] = (float) 1e30;
 
-    scale = findScale();
+        for (int ii = 0; ii < pdb.chains.size(); ii++) {
+            if (((PDBChain) pdb.chains.elementAt(ii)).isVisible) {
+                Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
-    System.out.println("Scale factor = " + scale);
-  }
+                for (int i = 0; i < bonds.size(); i++) {
+                    Bond tmp = (Bond) bonds.elementAt(i);
 
-  public void deleteBonds() {
-    scale     = 0;
-    maxwidth  = 0;
+                    if (tmp.start[0] >= max[0]) {
+                        max[0] = tmp.start[0];
+                    }
 
-    width[0] = 0;
-    width[1] = 0;
-    width[2] = 0;
+                    if (tmp.start[1] >= max[1]) {
+                        max[1] = tmp.start[1];
+                    }
 
-    centre[0] = 0;
-    centre[1] = 0;
-    centre[2] = 0;
+                    if (tmp.start[2] >= max[2]) {
+                        max[2] = tmp.start[2];
+                    }
 
-    for (int i=0; i < pdb.chains.size(); i++) {
-      ((PDBChain)pdb.chains.elementAt(i)).bonds = null;
-    }
-  }
+                    if (tmp.start[0] <= min[0]) {
+                        min[0] = tmp.start[0];
+                    }
 
-  public void findWidth() {
-    float max[] = new float[3];
-    float min[] = new float[3];
+                    if (tmp.start[1] <= min[1]) {
+                        min[1] = tmp.start[1];
+                    }
 
-    max[0] = (float)-1e30;
-    max[1] = (float)-1e30;
-    max[2] = (float)-1e30;
+                    if (tmp.start[2] <= min[2]) {
+                        min[2] = tmp.start[2];
+                    }
 
-    min[0] = (float)1e30;
-    min[1] = (float)1e30;
-    min[2] = (float)1e30;
+                    if (tmp.end[0] >= max[0]) {
+                        max[0] = tmp.end[0];
+                    }
 
-    for (int ii=0; ii < pdb.chains.size(); ii++) {
-      if (((PDBChain)pdb.chains.elementAt(ii)).isVisible) {
+                    if (tmp.end[1] >= max[1]) {
+                        max[1] = tmp.end[1];
+                    }
 
-        Vector bonds = ((PDBChain)pdb.chains.elementAt(ii)).bonds;
+                    if (tmp.end[2] >= max[2]) {
+                        max[2] = tmp.end[2];
+                    }
 
-        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];
-        }
-      }
-    }
+                    if (tmp.end[0] <= min[0]) {
+                        min[0] = tmp.end[0];
+                    }
 
-    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]);
+                    if (tmp.end[1] <= min[1]) {
+                        min[1] = tmp.end[1];
+                    }
 
-    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 (tmp.end[2] <= min[2]) {
+                        min[2] = tmp.end[2];
+                    }
+                }
+            }
+        }
 
-    if (width[1] > width[0])
-      maxwidth = width[1];
-    if (width[2] > width[1])
-      maxwidth = width[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]);
 
-    System.out.println("Maxwidth = " + maxwidth);
-  }
+        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]);
 
-  public float findScale() {
-    int dim, width, height;
+        maxwidth = width[0];
 
-    if ( getWidth() != 0) {
-      width  = getWidth();
-      height = getHeight();
+        if (width[1] > width[0]) {
+            maxwidth = width[1];
+        }
 
-    } else {
-      width  = prefsize.width;
-      height = prefsize.height;
-    }
+        if (width[2] > width[1]) {
+            maxwidth = width[2];
+        }
 
-    if (width < height) {
-      dim = width;
-    } else {
-      dim = height;
+        System.out.println("Maxwidth = " + maxwidth);
     }
 
-    return (float)(dim/(1.5d*maxwidth));
-  }
-
+    public float findScale() {
+        int dim;
+        int width;
+        int height;
 
+        if (getWidth() != 0) {
+            width = getWidth();
+            height = getHeight();
+        } else {
+            width = prefsize.width;
+            height = prefsize.height;
+        }
 
-  public void findCentre() {
-    float xtot = 0;
-    float ytot = 0;
-    float ztot = 0;
+        if (width < height) {
+            dim = width;
+        } else {
+            dim = height;
+        }
 
-    int bsize  = 0;
-    //Find centre coordinate
+        return (float) (dim / (1.5d * maxwidth));
+    }
 
-    for (int ii = 0; ii < pdb.chains.size() ; ii++) {
-      if (((PDBChain)pdb.chains.elementAt(ii)).isVisible) {
+    public void findCentre() {
+        float xtot = 0;
+        float ytot = 0;
+        float ztot = 0;
 
-        Vector bonds = ((PDBChain)pdb.chains.elementAt(ii)).bonds;
+        int bsize = 0;
 
-        bsize += bonds.size();
+        //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;
 
-        for (int i = 0; i < bonds.size(); i++) {
+                bsize += bonds.size();
 
-          xtot = xtot + ((Bond)bonds.elementAt(i)).start[0] +
-                 ((Bond)bonds.elementAt(i)).end[0];
+                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];
+                    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];
+                    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);
     }
 
-    centre[0] = xtot / (2 * (float)bsize);
-    centre[1] = ytot / (2 * (float)bsize);
-    centre[2] = ztot / (2 * (float)bsize);
-  }
+    public void paint(Graphics g) {
+        //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();
 
-  public void paint(Graphics g) {
-    //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();
 
-      scale = findScale();
-      img   = createImage(prefsize.width,prefsize.height);
-      ig    = img.getGraphics();
+            redrawneeded = true;
+        }
 
-      redrawneeded = true;
-    }
+        if (redrawneeded == true) {
+            drawBackground(ig, Color.black);
+            drawScene(ig);
+            redrawneeded = false;
+        } else {
+            ig = img.getGraphics();
+        }
 
-    if (redrawneeded == true) {
-      drawBackground(ig,Color.black);
-      drawScene(ig);
-      redrawneeded = false;
-    } else {
-      ig = img.getGraphics();
+        g.drawImage(img, 0, 0, this);
     }
 
-    g.drawImage(img,0,0,this);
-  }
+    public void drawBackground(Graphics g, Color col) {
+        g.setColor(col);
+        g.fillRect(0, 0, prefsize.width, prefsize.height);
+    }
 
-  public void drawBackground(Graphics g, Color col) {
-    g.setColor(col);
-    g.fillRect(0,0,prefsize.width,prefsize.height);
-  }
+    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;
 
-  public void drawScene(Graphics g) {
-    // Sort the bonds by z coord
+                for (int i = 0; i < tmp.size(); i++) {
+                    bonds.addElement(tmp.elementAt(i));
+                }
+            }
+        }
 
-    Vector bonds = new Vector();
+        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);
+            }
+        }
+    }
 
-    for (int ii = 0; ii < pdb.chains.size() ; ii++) {
-      if (((PDBChain)pdb.chains.elementAt(ii)).isVisible) {
+    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);
+        }
+    }
 
-        Vector tmp = ((PDBChain)pdb.chains.elementAt(ii)).bonds;
+    public Dimension minimumsize() {
+        return prefsize;
+    }
 
-        for (int i=0; i < tmp.size(); i++) {
-          bonds.addElement(tmp.elementAt(i));
-        }
-      }
+    public Dimension preferredsize() {
+        return prefsize;
     }
 
-    if (zbuffer) {
-      Zsort.Zsort(bonds);
+    public void keyTyped(KeyEvent evt) {
     }
 
-    for (int i = 0; i < bonds.size(); i++) {
-      Bond tmpBond = (Bond)bonds.elementAt(i);
+    public void keyReleased(KeyEvent evt) {
+    }
 
-      xstart = (int)((tmpBond.start[0] - centre[0])*scale + getWidth()/2);
-      ystart = (int)((tmpBond.start[1] - centre[1])*scale + getHeight()/2);
+    public void keyPressed(KeyEvent evt) {
+        int key = evt.getKeyChar();
+
+        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();
+        } else if (key == 'w') {
+            wire = !wire;
+            System.out.println("wireframe " + wire);
+            redrawneeded = true;
+            repaint();
+        } else if (key == 'd') {
+            depthcue = !depthcue;
+            System.out.println("Depth cueing is " + depthcue);
+            redrawneeded = true;
+            repaint();
+        } else if (key == 'm') {
+            bymolecule = !bymolecule;
+            System.out.println("Bymolecule is " + bymolecule);
+            redrawneeded = true;
+            repaint();
+        } else if (key == 'z') {
+            zbuffer = !zbuffer;
+            System.out.println("Z buffering is " + zbuffer);
+            redrawneeded = true;
+            repaint();
+        } else if (key == 'c') {
+            bymolecule = false;
+            pdb.setChainColours();
+            System.out.println("Colouring by chain");
+            redrawneeded = true;
+            repaint();
+        } else if (key == 'h') {
+            bymolecule = false;
+            pdb.setHydrophobicityColours();
+            System.out.println("Colouring by hydrophobicity");
+            redrawneeded = true;
+            repaint();
+        } else if (key == 'q') {
+            bymolecule = false;
+            pdb.setChargeColours();
+            System.out.println("Colouring charges and cysteines");
+            redrawneeded = true;
+            repaint();
+        }
 
-      xend = (int)((tmpBond.end[0] - centre[0])*scale + getWidth()/2);
-      yend = (int)((tmpBond.end[1] - centre[1])*scale + getHeight()/2);
+        return;
+    }
 
-      xmid = (xend+xstart)/2;
-      ymid = (yend+ystart)/2;
+    public void mousePressed(MouseEvent e) {
+        mx = e.getX();
+        my = e.getY();
+        omx = mx;
+        omy = my;
+        dragging = false;
+    }
 
+    public void mouseMoved(MouseEvent e) {
+        myAtom fatom = null;
 
-      if (depthcue && !bymolecule) {
+        for (int ii = 0; ii < pdb.chains.size(); ii++) {
+            PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
 
-        if (tmpBond.start[2] < (centre[2] - maxwidth/6))  {
-          g.setColor(tmpBond.startCol.darker().darker());
-          drawLine(g,xstart,ystart,xmid,ymid);
+            if (chain.isVisible) {
+                Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
-          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);
+                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));
 
-          g.setColor(tmpBond.endCol.darker());
-          drawLine(g,xmid,ymid,xend,yend);
-        } else {
-          g.setColor(tmpBond.startCol);
-          drawLine(g,xstart,ystart,xmid,ymid);
+                    if (Math.abs(truex - e.getX()) <= 2) {
+                        int truey = (int) (((tmpBond.start[1] - centre[1]) * scale) +
+                            (getHeight() / 2));
 
-          g.setColor(tmpBond.endCol);
-          drawLine(g,xmid,ymid,xend,yend);
+                        if (Math.abs(truey - e.getY()) <= 2) {
+                            fatom = tmpBond.at1;
+                        }
+                    }
+                }
+            }
         }
-      } 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);
 
+        if (fatom != null) {
+            this.setToolTipText(fatom.resName);
         } else {
-          g.setColor(Color.green);
-          drawLine(g,xstart,ystart,xend,yend);
-
+            this.setToolTipText(null);
         }
-      } 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);
+    public void mouseClicked(MouseEvent e) {
+    }
 
-      }
-    } else {
-      g.drawLine(x1,y1,x2,y2);
+    public void mouseEntered(MouseEvent e) {
     }
-  }
-
-  public Dimension minimumsize() {
-    return prefsize;
-  }
-  public Dimension preferredsize() {
-    return prefsize;
-  }
-
-  public void keyTyped(KeyEvent evt) { }
-  public void keyReleased(KeyEvent evt) { }
-  public void keyPressed(KeyEvent evt) {
-    int key = evt.getKeyChar();
-
-    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();
-
-    } else if (key == 'w') {
-
-      wire = !wire;
-      System.out.println("wireframe " + wire);
-      redrawneeded = true;
-      repaint();
-
-    } else if (key == 'd') {
-      depthcue = !depthcue;
-      System.out.println("Depth cueing is " + depthcue);
-      redrawneeded = true;
-      repaint();
-
-    } else if (key == 'm') {
-      bymolecule = !bymolecule;
-      System.out.println("Bymolecule is " + bymolecule);
-      redrawneeded = true;
-      repaint();
-
-    } else if (key == 'z') {
-      zbuffer = !zbuffer;
-      System.out.println("Z buffering is " + zbuffer);
-      redrawneeded = true;
-      repaint();
-
-    } else if (key == 'c') {
-      bymolecule = false;
-      pdb.setChainColours();
-      System.out.println("Colouring by chain");
-      redrawneeded = true;
-      repaint();
-
-    } else if (key == 'h') {
-      bymolecule = false;
-      pdb.setHydrophobicityColours();
-      System.out.println("Colouring by hydrophobicity");
-      redrawneeded = true;
-      repaint();
-
-    } else if (key == 'q') {
-      bymolecule = false;
-      pdb.setChargeColours();
-      System.out.println("Colouring charges and cysteines");
-      redrawneeded = true;
-      repaint();
 
+    public void mouseExited(MouseEvent e) {
     }
-    return;
-  }
 
-  public void mousePressed(MouseEvent e)
-  {
+    public void mouseDragged(MouseEvent evt) {
+        int x = evt.getX();
+        int y = evt.getY();
+        mx = x;
+        my = y;
 
-      mx = e.getX();
-      my = e.getY();
-      omx = mx;
-      omy = my;
-      dragging = false;
-}
+        MCMatrix objmat = new MCMatrix(3, 3);
+        objmat.setIdentity();
 
-  public void mouseMoved(MouseEvent e)
-  {
-    myAtom fatom = null;
-    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 - e.getX()) <= 2)
-          {
-            int truey = (int) ( (tmpBond.start[1] - centre[1]) * scale +
-                               getHeight() / 2);
-            if (Math.abs(truey - e.getY()) <= 2)
-              fatom = tmpBond.at1;
-          }
+        if ((evt.getModifiers() & Event.META_MASK) != 0) {
+            objmat.rotatez((float) ((mx - omx)));
+        } else {
+            objmat.rotatex((float) ((my - omy)));
+            objmat.rotatey((float) ((omx - mx)));
         }
-      }
-    }
-    if(fatom!=null)
-     {
-       this.setToolTipText(fatom.resName);
-     }
-     else
-        this.setToolTipText(null);
-  }
-
-  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++) {
+        //Alter the bonds
+        for (int ii = 0; ii < pdb.chains.size(); ii++) {
+            Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
-        Bond tmpBond = (Bond)bonds.elementAt(i);
+            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]);
+                //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 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;
+                //Now translate back again
+                tmpBond.translate(centre[0], centre[1], centre[2]);
+            }
+        }
 
-    omx    = mx;
-    omy    = my;
+        objmat = null;
 
-    redrawneeded = true;
+        omx = mx;
+        omy = my;
 
-    paint(this.getGraphics());
+        redrawneeded = true;
 
-    dragging = true;
-    return;
-  }
+        paint(this.getGraphics());
 
-  public void mouseReleased(MouseEvent evt) {
-    int x = evt.getX();
-    int y = evt.getY();
+        dragging = true;
 
-    if (!dragging) {
-      myAtom tmp = findAtom(x,y);
+        return;
     }
-    drawLabels();
-    return;
-  }
-
-  public void drawLabels() {
-    redrawneeded = true;
-    paint(this.getGraphics());
-
-    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);
+    public void mouseReleased(MouseEvent evt) {
+        //int x = evt.getX();
+        //int y = evt.getY();
 
-          if (tmpBond.at1.isSelected) {
-            labelAtom(img.getGraphics(),tmpBond,1);
-          }
+        //if (!dragging) {
+          //  myAtom tmp = findAtom(x, y);
+        //}
 
-          if (tmpBond.at2.isSelected) {
-            labelAtom(img.getGraphics(),tmpBond,2);
-          }
+        drawLabels();
 
-        }
-      }
+        return;
     }
 
-    this.getGraphics().drawImage(img,0,0,this);
-
-    dragging = false;
+    public void drawLabels() {
+        redrawneeded = true;
+        paint(this.getGraphics());
 
-  }
+        for (int ii = 0; ii < pdb.chains.size(); ii++) {
+            PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
 
-  public void labelAtom(Graphics g,Bond b, int n) {
+            if (chain.isVisible) {
+                Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
-    g.setFont(font);
+                for (int i = 0; i < bonds.size(); i++) {
+                    Bond tmpBond = (Bond) bonds.elementAt(i);
 
-    if (n ==1) {
+                    if (tmpBond.at1.isSelected) {
+                        labelAtom(img.getGraphics(), tmpBond, 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) {
+                    if (tmpBond.at2.isSelected) {
+                        labelAtom(img.getGraphics(), tmpBond, 2);
+                    }
+                }
+            }
+        }
 
-      int xstart = (int)((b.end[0] - centre[0])*scale + getWidth()/2);
-      int ystart = (int)((b.end[1] - centre[1])*scale + getHeight()/2);
+        this.getGraphics().drawImage(img, 0, 0, this);
 
-      g.setColor(Color.red);
-      g.drawString(b.at2.resName + "-" + b.at2.resNumber,xstart,ystart);
+        dragging = false;
     }
-  }
 
+    public void labelAtom(Graphics g, Bond b, int n) {
+        g.setFont(font);
 
-  public myAtom findAtom(int x, int y) {
-    myAtom fatom = null;
+        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));
 
-    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);
+            g.setColor(Color.red);
+            g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
+        }
 
-          int truex = (int)((tmpBond.start[0] - centre[0])*scale + getWidth()/2);
+        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));
 
-          if (Math.abs(truex - x) <= 2) {
+            g.setColor(Color.red);
+            g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
+        }
+    }
 
-            int truey = (int)((tmpBond.start[1] - centre[1])*scale + getHeight()/2);
+    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) {
+                            System.out.println("Found match");
+                            System.out.println(x + " " + y);
+                            System.out.println(truex + " " + truey);
+                            System.out.println(tmpBond.start[0] + " " +
+                                tmpBond.start[1]);
+                            System.out.println("Atom 1 = " +
+                                tmpBond.at1.resName + " " +
+                                tmpBond.at1.resNumber + " " +
+                                tmpBond.at1.chain);
+                            fatom = tmpBond.at1;
+                            fatom.isSelected = !fatom.isSelected;
+                            foundchain = ii;
+                        }
+                    }
+                }
+            }
 
-            if (Math.abs(truey - y) <= 2) {
+            if (fatom != null) //)&& chain.ds != null)
+             {
+                chain = (PDBChain) pdb.chains.elementAt(foundchain);
 
-              System.out.println("Found match");
-              System.out.println(x + " " + y);
-              System.out.println(truex + " " + truey);
-              System.out.println(tmpBond.start[0] + " " + tmpBond.start[1]);
-              System.out.println("Atom 1 = " + tmpBond.at1.resName + " " +
-                                 tmpBond.at1.resNumber + " " + tmpBond.at1.chain);
-              fatom = tmpBond.at1;
-              fatom.isSelected = !fatom.isSelected;
-              foundchain = ii;
+                // 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);
             }
-          }
         }
-      }
-
-      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;
     }
-    return fatom;
-  }
-
-  public void update(Graphics g) {
-    paint(g);
-  }
 
+    public void update(Graphics g) {
+        paint(g);
+    }
 }