From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 16 Nov 2005 16:41:08 +0000 (+0000)
Subject: No more myAtom, Highlight from alignment
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c6aaf0ef217426a5e23be7db9cbc6a8369115850;p=jalview.git

No more myAtom, Highlight from alignment
---

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index 1ee0828..1df39fa 100755
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -34,17 +34,6 @@ import java.util.*;
 
 public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotionListener
 {
-  public AppletPDBCanvas()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
 
   MCMatrix idmat = new MCMatrix(3, 3);
     MCMatrix objmat = new MCMatrix(3, 3);
@@ -80,10 +69,11 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
     jalview.appletgui.SequenceRenderer sr;
     jalview.appletgui.FeatureRenderer  fr;
     jalview.appletgui.SeqCanvas seqcanvas;
-    Sequence sequence;
+    public Sequence sequence;
     final StringBuffer mappingDetails = new StringBuffer();
     String appletToolTip = null;
     int toolx, tooly;
+    PDBChain mainchain;
 
     public AppletPDBCanvas(jalview.appletgui.SeqCanvas seqcanvas, Sequence seq)
     {
@@ -92,7 +82,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
       sr = seqcanvas.getSequenceRenderer();
       fr = seqcanvas.getFeatureRenderer();
 
-      seqcanvas.setPDBViewer(this);
+      seqcanvas.setPDBCanvas(this);
       addKeyListener(new KeyAdapter()
       {
 
@@ -101,9 +91,34 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
           doKeyPressed(evt);
         }
       });
-
     }
 
+    Bond highlightBond1, highlightBond2;
+    public void highlightRes(int ii)
+   {
+     highlightBond1 = null;
+     highlightBond2 = null;
+
+     int index = ii - mainchain.seqstart - mainchain.offset+1;
+     if(index <0 )
+       return;
+
+     if(index<=mainchain.bonds.size())
+     {
+       if(index>0)
+       {
+         highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);
+       }
+
+       if(index!=mainchain.bonds.size())
+         highlightBond2 = (Bond) mainchain.bonds.elementAt(index);
+     }
+
+     redrawneeded = true;
+     repaint();
+  }
+
+
   public void setPDBFile(PDBfile pdb)
    {
         this.sr = sr;
@@ -155,12 +170,14 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
             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;
+        mainchain = (PDBChain) pdb.chains.elementAt(maxchain);
+
+        mainchain.pdbstart = pdbstart;
+        mainchain.pdbend = pdbend;
+        mainchain.seqstart = seqstart;
+        mainchain.seqend = seqend;
+        mainchain.isVisible = true;
+        mainchain.sequence = sequence;
 
         this.pdb = pdb;
         this.prefsize = new Dimension(getSize().width, getSize().height);
@@ -373,14 +390,20 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
         //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();
+         try{     prefsize.width = getSize().width;
+           prefsize.height = getSize().height;
 
-            redrawneeded = true;
+           scale = findScale();
+           img = createImage(prefsize.width, prefsize.height);
+           ig = img.getGraphics();
+
+           redrawneeded = true;
+         }catch(Exception ex)
+         {
+           ex.printStackTrace();
+           System.out.println(getSize());
+         }
         }
 
 
@@ -430,16 +453,21 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
       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);
+          if(jalview.util.Comparison.isGap((sequence.getCharAt(index))))
+           {
+             index--;
+           }
+
+           tmp.startCol = sr.findSequenceColour(sequence, index);
 
         //  tmp.startCol = fr.findFeatureColour(tmp.startCol, sequence, index);
 
@@ -455,8 +483,13 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
           int pos = chain.seqstart +
               (tmp.at2.resNumber - chain.pdbstart - chain.offset);
           int index = sequence.findIndex(pos);
+          if (jalview.util.Comparison.isGap( (sequence.getCharAt(index))))
+          {
+            index--;
+          }
+
 
-          tmp.endCol = sr.findSequenceColour( sequence, index);
+            tmp.endCol = sr.findSequenceColour(sequence, index);
       //    tmp.endCol = fr.findFeatureColour(tmp.endCol, sequence, index);
         }
         else
@@ -479,7 +512,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
 
             for (int i = 0; i < tmp.size(); i++)
             {
-              bonds.addElement(tmp.elementAt(i));
+                bonds.addElement(tmp.elementAt(i));
             }
           }
         }
@@ -491,6 +524,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
         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) +
@@ -504,7 +538,8 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
             xmid = (xend + xstart) / 2;
             ymid = (yend + ystart) / 2;
 
-            if (depthcue && !bymolecule) {
+            if (depthcue && !bymolecule)
+            {
                 if (tmpBond.start[2] < (centre[2] - (maxwidth / 6))) {
                     g.setColor(tmpBond.startCol.darker().darker());
                     drawLine(g, xstart, ystart, xmid, ymid);
@@ -543,6 +578,19 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
             } else {
                 drawLine(g, xstart, ystart, xend, yend);
             }
+
+            if(highlightBond1!=null && highlightBond1==tmpBond)
+            {
+              g.setColor(Color.white);
+              drawLine(g, xmid, ymid, xend, yend);
+            }
+
+            if(highlightBond2!=null && highlightBond2==tmpBond)
+            {
+              g.setColor(Color.white);
+              drawLine(g, xstart, ystart, xmid, ymid);
+            }
+
         }
     }
 
@@ -588,7 +636,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
     }
 
     public void mousePressed(MouseEvent e) {
-        myAtom fatom = findAtom(e.getX(), e.getY());
+        Atom fatom = findAtom(e.getX(), e.getY());
         if(fatom!=null)
         {
           fatom.isSelected = !fatom.isSelected;
@@ -604,17 +652,23 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
 
     public void mouseMoved(MouseEvent e) {
 
-        myAtom fatom = findAtom(e.getX(), e.getY());
+        Atom fatom = findAtom(e.getX(), e.getY());
 
+        PDBChain chain = null;
         if(foundchain!=-1)
         {
-          PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain);
-          int pos = chain.seqstart +
-              (fatom.resNumber - chain.pdbstart - chain.offset)+1;
+          chain = (PDBChain) pdb.chains.elementAt(foundchain);
+          if(chain == mainchain)
+          {
+            int pos = chain.seqstart +
+                (fatom.resNumber - chain.pdbstart - chain.offset) + 1;
 
-          int index = seqcanvas.getViewport().getAlignment().findIndex(sequence);
+            int index = seqcanvas.getViewport().getAlignment().findIndex(
+                sequence);
 
-          seqcanvas.highlightSearchResults(new int[]{index, pos, pos});
+            seqcanvas.highlightSearchResults(new int[]
+                                             {index, pos, pos});
+          }
         }
         else
           seqcanvas.highlightSearchResults(null);
@@ -622,7 +676,8 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
         if (fatom != null) {
             toolx = e.getX();
             tooly = e.getY();
-            appletToolTip = fatom.resNumber+" "+ fatom.resName;
+
+            appletToolTip = chain.id+":"+ fatom.resNumber+" "+ fatom.resName;
             redrawneeded = true;
             repaint();
         } else {
@@ -747,8 +802,8 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
     }
 
     int foundchain = -1;
-    public myAtom findAtom(int x, int y) {
-        myAtom fatom = null;
+    public Atom findAtom(int x, int y) {
+        Atom fatom = null;
 
         foundchain = -1;
 
@@ -792,8 +847,15 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
       paint(g);
     }
 
-  private void jbInit()
-      throws Exception
-  {
-  }
+    public void setAllchainsVisible(boolean b)
+    {
+      for (int ii = 0; ii < pdb.chains.size(); ii++)
+      {
+        PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
+        chain.isVisible = b;
+      }
+      mainchain.isVisible = true;
+      findCentre();
+    }
+
 }
diff --git a/src/MCview/AppletPDBViewer.java b/src/MCview/AppletPDBViewer.java
index 77bbd8c..1ed4d10 100755
--- a/src/MCview/AppletPDBViewer.java
+++ b/src/MCview/AppletPDBViewer.java
@@ -125,21 +125,30 @@ public class AppletPDBViewer extends Frame
             molecule_actionPerformed();
           }
         });
-        jMenuBar1.add(fileMenu);
+    allchains.setLabel("All Chains Visible");
+    allchains.addItemListener(new ItemListener()
+    {
+      public void itemStateChanged(ItemEvent itemEvent)
+      {
+        allchains_itemStateChanged(itemEvent);
+      }
+    });
+    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(hydro);
+    coloursMenu.add(charge);
+    coloursMenu.add(molecule);
+    coloursMenu.addSeparator();
         coloursMenu.add(wire);
         coloursMenu.add(depth);
         coloursMenu.add(zbuffer);
-        coloursMenu.add(molecule);
-
-      }
+    coloursMenu.add(allchains);
+    allchains.setState(true);
+  }
 
       MenuBar jMenuBar1 = new MenuBar();
       Menu fileMenu = new Menu();
@@ -156,8 +165,9 @@ public class AppletPDBViewer extends Frame
       MenuItem seqButton = new MenuItem();
 
       CheckboxMenuItem molecule = new CheckboxMenuItem();
+     CheckboxMenuItem allchains = new CheckboxMenuItem();
 
-       public void charge_actionPerformed()
+  public void charge_actionPerformed()
       {
         clearButtonGroup();
         pdbcanvas.pdb.setChargeColours();
@@ -231,4 +241,9 @@ public class AppletPDBViewer extends Frame
         jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 500, 600);
         cap.setText(pdbcanvas.mappingDetails.toString());
       }
-    }
+
+      public void allchains_itemStateChanged(ItemEvent itemEvent)
+      {
+        pdbcanvas.setAllchainsVisible(allchains.getState());
+      }
+}
diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index b1d8805..f0806a8 100755
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -69,8 +69,9 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
     jalview.gui.SequenceRenderer sr;
     jalview.gui.FeatureRenderer  fr;
     jalview.gui.SeqCanvas seqcanvas;
-    Sequence sequence;
+    public Sequence sequence;
     final StringBuffer mappingDetails = new StringBuffer();
+    PDBChain mainchain;
 
     public PDBCanvas(jalview.gui.SeqCanvas seqcanvas, Sequence seq)
     {
@@ -79,7 +80,7 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
       sr = seqcanvas.getSequenceRenderer();
       fr = seqcanvas.getFeatureRenderer();
 
-      seqcanvas.setPDBViewer(this);
+      seqcanvas.setPDBCanvas(this);
     }
 
   public void setPDBFile(PDBfile pdb)
@@ -133,12 +134,14 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
             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;
+        mainchain = (PDBChain) pdb.chains.elementAt(maxchain);
+
+        mainchain.pdbstart = pdbstart;
+        mainchain.pdbend = pdbend;
+        mainchain.seqstart = seqstart;
+        mainchain.seqend = seqend;
+        mainchain.isVisible = true;
+        mainchain.sequence = sequence;
 
         this.pdb = pdb;
         this.prefsize = new Dimension(getWidth(), getHeight());
@@ -495,8 +498,9 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
             Zsort.Zsort(bonds);
         }
 
+        Bond tmpBond=null;
         for (int i = 0; i < bonds.size(); i++) {
-            Bond tmpBond = (Bond) bonds.elementAt(i);
+            tmpBond = (Bond) bonds.elementAt(i);
 
             xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) +
                 (getWidth() / 2));
@@ -550,7 +554,22 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
             } else {
                 drawLine(g, xstart, ystart, xend, yend);
             }
+
+            if(highlightBond1!=null && highlightBond1==tmpBond)
+            {
+              g.setColor(tmpBond.endCol.brighter().brighter().brighter());
+              drawLine(g, xmid, ymid, xend, yend);
+            }
+
+            if(highlightBond2!=null && highlightBond2==tmpBond)
+            {
+              g.setColor(tmpBond.startCol.brighter().brighter().brighter());
+              drawLine(g, xstart, ystart, xmid, ymid);
+            }
+
         }
+
+
     }
 
     public void drawLine(Graphics g, int x1, int y1, int x2, int y2) {
@@ -595,7 +614,7 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
     }
 
     public void mousePressed(MouseEvent e) {
-        myAtom fatom = findAtom(e.getX(), e.getY());
+        Atom fatom = findAtom(e.getX(), e.getY());
         if(fatom!=null)
         {
           fatom.isSelected = !fatom.isSelected;
@@ -611,24 +630,32 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
 
     public void mouseMoved(MouseEvent e) {
 
-        myAtom fatom = findAtom(e.getX(), e.getY());
+        Atom fatom = findAtom(e.getX(), e.getY());
 
+        PDBChain chain = null;
         if(foundchain!=-1)
         {
-          PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain);
-          int pos = chain.seqstart +
-              (fatom.resNumber - chain.pdbstart - chain.offset)+1;
+          chain = (PDBChain) pdb.chains.elementAt(foundchain);
+          if(chain == mainchain)
+          {
+            int pos = chain.seqstart +
+                (fatom.resNumber - chain.pdbstart - chain.offset) + 1;
 
-          int index = seqcanvas.getViewport().getAlignment().findIndex(sequence);
+            int index = seqcanvas.getViewport().getAlignment().findIndex(
+                sequence);
 
-          seqcanvas.highlightSearchResults(new int[]{index, pos, pos});
+            seqcanvas.highlightSearchResults(new int[]
+                                             {index, pos, pos});
+          }
         }
         else
           seqcanvas.highlightSearchResults(null);
 
-        if (fatom != null) {
-            this.setToolTipText(fatom.resNumber+" "+ fatom.resName);
-        } else {
+        if (fatom != null)
+        {
+            this.setToolTipText(chain.id+":"+ fatom.resNumber+" "+ fatom.resName);
+        } else
+        {
             this.setToolTipText("");
         }
     }
@@ -748,24 +775,30 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
     }
 
     int foundchain = -1;
-    public myAtom findAtom(int x, int y) {
-        myAtom fatom = null;
+    public Atom findAtom(int x, int y) {
+        Atom fatom = null;
 
         foundchain = -1;
 
-        for (int ii = 0; ii < pdb.chains.size(); ii++) {
+        for (int ii = 0; ii < pdb.chains.size(); ii++)
+        {
             PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
+            int truex;
+            Bond tmpBond=null;
 
-            if (chain.isVisible) {
+            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);
+                for (int i = 0; i < bonds.size(); i++)
+                {
+                    tmpBond = (Bond) bonds.elementAt(i);
 
-                    int truex = (int) (((tmpBond.start[0] - centre[0]) * scale) +
+                    truex = (int) (((tmpBond.start[0] - centre[0]) * scale) +
                         (getWidth() / 2));
 
-                    if (Math.abs(truex - x) <= 2) {
+                    if (Math.abs(truex - x) <= 2)
+                    {
                         int truey = (int) (((tmpBond.start[1] - centre[1]) * scale) +
                             (getHeight() / 2));
 
@@ -777,6 +810,25 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
                         }
                     }
                 }
+
+                // Still here? Maybe its the last bond
+
+                truex = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) +
+                               (getWidth() / 2));
+
+                if (Math.abs(truex - x) <= 2)
+                {
+                  int truey = (int) ( ( (tmpBond.end[1] - centre[1]) * scale) +
+                                     (getHeight() / 2));
+
+                  if (Math.abs(truey - y) <= 2)
+                  {
+                    fatom = tmpBond.at2;
+                    foundchain = ii;
+                    break;
+                  }
+                }
+
             }
 
             if (fatom != null) //)&& chain.ds != null)
@@ -787,4 +839,40 @@ public class PDBCanvas extends JPanel implements MouseListener, MouseMotionListe
 
         return fatom;
     }
+
+   Bond highlightBond1, highlightBond2;
+   public void highlightRes(int ii)
+  {
+    highlightBond1 = null;
+    highlightBond2 = null;
+
+    int index = ii - mainchain.seqstart - mainchain.offset+1;
+    if(index <0 )
+      return;
+
+    if(index<=mainchain.bonds.size())
+    {
+      if(index>0)
+      {
+        highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);
+      }
+
+      if(index!=mainchain.bonds.size())
+        highlightBond2 = (Bond) mainchain.bonds.elementAt(index);
+    }
+
+    redrawneeded = true;
+    repaint();
+  }
+
+    public void setAllchainsVisible(boolean b)
+    {
+      for (int ii = 0; ii < pdb.chains.size(); ii++)
+      {
+        PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
+        chain.isVisible = b;
+      }
+      mainchain.isVisible = true;
+      findCentre();
+    }
 }
diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 208ecd0..9c1d0e0 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -34,7 +34,7 @@ public class PDBChain {
     public Vector residues = new Vector();
     public int offset;
     public Sequence sequence;
-    public boolean isVisible = false;
+    public boolean isVisible = true;
     public int pdbstart = 0;
     public int pdbend = 0;
     public int seqstart = 0;
@@ -61,8 +61,8 @@ public class PDBChain {
         for (int i = 0; i < (residues.size() - 1); i++) {
             Residue tmpres = (Residue) residues.elementAt(i);
             Residue tmpres2 = (Residue) residues.elementAt(i + 1);
-            myAtom at1 = tmpres.findAtom("CA");
-            myAtom at2 = tmpres2.findAtom("CA");
+            Atom at1 = tmpres.findAtom("CA");
+            Atom at2 = tmpres2.findAtom("CA");
 
             if ((at1 != null) && (at2 != null)) {
                 if (at1.chain.equals(at2.chain)) {
@@ -72,7 +72,7 @@ public class PDBChain {
         }
     }
 
-    public void makeBond(myAtom at1, myAtom at2) {
+    public void makeBond(Atom at1, Atom at2) {
         float[] start = new float[3];
         float[] end = new float[3];
 
@@ -92,7 +92,7 @@ public class PDBChain {
         String seq = "";
 
         for (int i = 0; i < atoms.size(); i++) {
-            myAtom tmp = (myAtom) atoms.elementAt(i);
+            Atom tmp = (Atom) atoms.elementAt(i);
             //String resName = tmp.resName;
             int resNumber = tmp.resNumber;
             int res = resNumber;
@@ -103,18 +103,18 @@ public class PDBChain {
 
             Vector resAtoms = new Vector();
 
-            resAtoms.addElement((myAtom) atoms.elementAt(i));
+            resAtoms.addElement((Atom) atoms.elementAt(i));
             i++;
-            resNumber = ((myAtom) atoms.elementAt(i)).resNumber;
+            resNumber = ((Atom) atoms.elementAt(i)).resNumber;
 
             //Add atoms to a vector while the residue number
             //remains the same
             while ((resNumber == res) && (i < atoms.size())) {
-                resAtoms.addElement((myAtom) atoms.elementAt(i));
+                resAtoms.addElement((Atom) atoms.elementAt(i));
                 i++;
 
                 if (i < atoms.size()) {
-                    resNumber = ((myAtom) atoms.elementAt(i)).resNumber;
+                    resNumber = ((Atom) atoms.elementAt(i)).resNumber;
                 } else {
                     resNumber++;
                 }
@@ -128,7 +128,7 @@ public class PDBChain {
             count++;
 
             Residue tmpres = (Residue) residues.lastElement();
-            myAtom tmpat = (myAtom) tmpres.atoms.elementAt(0);
+            Atom tmpat = (Atom) tmpres.atoms.elementAt(0);
 
             // Keep totting up the sequence
             if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null) {
@@ -231,17 +231,13 @@ public class PDBChain {
 
 
 
-    public void setChainColours() {
-        for (int i = 0; i < bonds.size(); i++) {
+    public void setChainColours(Color col)
+    {
+        for (int i = 0; i < bonds.size(); i++)
+        {
             Bond tmp = (Bond) bonds.elementAt(i);
-
-            try {
-                tmp.startCol = (Color) ResidueProperties.getChainColours().get(id);
-                tmp.endCol = (Color) ResidueProperties.getChainColours().get(id);
-            } catch (Exception e) {
-                tmp.startCol = Color.lightGray;
-                tmp.endCol = Color.lightGray;
-            }
+            tmp.startCol = col;
+            tmp.endCol = col;
         }
     }
 }
diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index 95d4b35..06b6f65 100755
--- a/src/MCview/PDBViewer.java
+++ b/src/MCview/PDBViewer.java
@@ -174,6 +174,15 @@ public class PDBViewer extends JInternalFrame implements Runnable
         molecule_actionPerformed(e);
       }
     });
+    allchains.setSelected(true);
+    allchains.setText("Show All Chains");
+    allchains.addItemListener(new ItemListener()
+    {
+      public void itemStateChanged(ItemEvent e)
+      {
+        allchains_itemStateChanged(e);
+      }
+    });
     jMenuBar1.add(fileMenu);
     jMenuBar1.add(coloursMenu);
     fileMenu.add(saveMenu);
@@ -189,6 +198,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
     coloursMenu.add(depth);
     coloursMenu.add(zbuffer);
     coloursMenu.add(molecule);
+    coloursMenu.add(allchains);
     ButtonGroup bg = new ButtonGroup();
     bg.add(seqButton);
     bg.add(chain);
@@ -211,6 +221,7 @@ public class PDBViewer extends JInternalFrame implements Runnable
   JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
   JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
   JCheckBoxMenuItem molecule = new JCheckBoxMenuItem();
+  JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
 
   /**
    * DOCUMENT ME!
@@ -329,4 +340,9 @@ public class PDBViewer extends JInternalFrame implements Runnable
     Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 500, 600);
     cap.setText(pdbcanvas.mappingDetails.toString());
   }
+
+  public void allchains_itemStateChanged(ItemEvent e)
+  {
+    pdbcanvas.setAllchainsVisible(allchains.getState());
+  }
 }
diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index f9d842f..d1e4d65 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -23,6 +23,7 @@ import java.io.*;
 import java.net.*;
 
 import java.util.*;
+import java.awt.Color;
 
 
 public class PDBfile extends jalview.io.FileParse {
@@ -77,7 +78,7 @@ public class PDBfile extends jalview.io.FileParse {
 
                 if (inStr.indexOf("ATOM") != -1) {
                     try {
-                        myAtom tmpatom = new myAtom(str);
+                        Atom tmpatom = new Atom(str);
 
                         if (findChain(tmpatom.chain) != null) {
                             //   System.out.println("Adding to chain " + tmpatom.chain);
@@ -114,7 +115,6 @@ public class PDBfile extends jalview.io.FileParse {
 
     public PDBChain findChain(String id) {
         for (int i = 0; i < chains.size(); i++) {
-            // System.out.println("ID = " + id + " " +((PDBChain)chains.elementAt(i)).id);
             if (((PDBChain) chains.elementAt(i)).id.equals(id)) {
                 return (PDBChain) chains.elementAt(i);
             }
@@ -135,17 +135,13 @@ public class PDBfile extends jalview.io.FileParse {
         }
     }
 
-    public void colourBySequence()//jalview.gui.SequenceRenderer sr,
-                                // jalview.gui.FeatureRenderer fr)
-                                {
-            for (int i = 0; i < chains.size(); i++) {
-              //((PDBChain)chains.elementAt(i)).colourBySequence(sr,fr);
-            }
-    }
-
-    public void setChainColours() {
-        for (int i = 0; i < chains.size(); i++) {
-            ((PDBChain) chains.elementAt(i)).setChainColours();
+    public void setChainColours()
+    {
+       for (int i = 0; i < chains.size(); i++)
+       {
+            ((PDBChain) chains.elementAt(i)).setChainColours(
+                     Color.getHSBColor(1.0f / (float)i, .4f, 1.0f)
+                );
         }
     }
 }
diff --git a/src/MCview/Residue.java b/src/MCview/Residue.java
index b01d982..efaf1f0 100755
--- a/src/MCview/Residue.java
+++ b/src/MCview/Residue.java
@@ -33,10 +33,10 @@ public class Residue {
         this.count = count;
     }
 
-    public myAtom findAtom(String name) {
+    public Atom findAtom(String name) {
         for (int i = 0; i < atoms.size(); i++) {
-            if (((myAtom) atoms.elementAt(i)).name.equals(name)) {
-                return (myAtom) atoms.elementAt(i);
+            if (((Atom) atoms.elementAt(i)).name.equals(name)) {
+                return (Atom) atoms.elementAt(i);
             }
         }