X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAppletPDBCanvas.java;h=543d6802240037f8e121a081a19c059524b9ae86;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=a61ecb2a63b25b9ed1ac2a8b61e43bb7ffa6be2e;hpb=269257481bdc261d6f99cb43dac33c10c3b4e9e1;p=jalview.git

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index a61ecb2..543d680 100755
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package MCview;
 
@@ -31,60 +30,102 @@ import jalview.datamodel.*;
 import jalview.appletgui.*;
 import jalview.structure.*;
 
-public class AppletPDBCanvas
-    extends Panel implements MouseListener, MouseMotionListener, StructureListener
+public class AppletPDBCanvas extends Panel implements MouseListener,
+        MouseMotionListener, StructureListener
 {
 
   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;
+
   PDBEntry pdbentry;
+
   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);
-  public SequenceI [] sequence;
+
+  public SequenceI[] sequence;
+
   final StringBuffer mappingDetails = new StringBuffer();
+
   String appletToolTip = null;
+
   int toolx, tooly;
+
   PDBChain mainchain;
+
   Vector highlightRes;
+
   boolean pdbAction = false;
+
   Bond highlightBond1, highlightBond2;
+
   boolean errorLoading = false;
+
   boolean seqColoursReady = false;
+
   FeatureRenderer fr;
+
   AlignmentPanel ap;
+
   StructureSelectionManager ssm;
 
-  public AppletPDBCanvas(PDBEntry pdbentry,
-                         SequenceI[] seq,
-                         AlignmentPanel ap,
-                         String protocol)
+  public AppletPDBCanvas(PDBEntry pdbentry, SequenceI[] seq,
+          String[] chains, AlignmentPanel ap, String protocol)
 
   {
     this.ap = ap;
@@ -93,14 +134,14 @@ public class AppletPDBCanvas
 
     ssm = StructureSelectionManager.getStructureSelectionManager();
 
-    try{
-      pdb = ssm.setMapping(seq, pdbentry.getFile(), protocol);
+    try
+    {
+      pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
 
-      if(protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
-       pdbentry.setFile("INLINE"+pdb.id);
-      //if (fr!=null)
-      //  fr.featuresAdded();
-    }catch(Exception ex)
+      if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+        pdbentry.setFile("INLINE" + pdb.id);
+
+    } catch (Exception ex)
     {
       ex.printStackTrace();
       return;
@@ -110,9 +151,7 @@ public class AppletPDBCanvas
 
     ssm.addStructureViewerListener(this);
 
-    colourBySequence(ap.getSequenceRenderer(),
-                     ap.av.getShowSequenceFeatures() ?
-                     fr : null);
+    colourBySequence();
 
     int max = -10;
     int maxchain = -1;
@@ -120,27 +159,26 @@ public class AppletPDBCanvas
     int pdbend = 0;
     int seqstart = 0;
     int seqend = 0;
-    AlignSeq maxAlignseq = null;
 
-    //JUST DEAL WITH ONE SEQUENCE FOR NOW
+    // JUST DEAL WITH ONE SEQUENCE FOR NOW
     SequenceI sequence = seq[0];
 
     for (int i = 0; i < pdb.chains.size(); i++)
     {
 
-      mappingDetails.append("\n\nPDB Sequence is :\nSequence = " +
-                            ( (PDBChain) pdb.chains.elementAt(i)).sequence.
-                            getSequenceAsString());
-      mappingDetails.append("\nNo of residues = " +
-                            ( (PDBChain) pdb.chains.elementAt(i)).residues.size() +
-                            "\n\n");
+      mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
+              + ((PDBChain) pdb.chains.elementAt(i)).sequence
+                      .getSequenceAsString());
+      mappingDetails.append("\nNo of residues = "
+              + ((PDBChain) pdb.chains.elementAt(i)).residues.size()
+              + "\n\n");
 
       // Now lets compare the sequences to get
       // the start and end points.
       // Align the sequence to the pdb
-      AlignSeq as = new AlignSeq(sequence,
-                                 ( (PDBChain) pdb.chains.elementAt(i)).sequence,
-                                 "pep");
+      // TODO: DNa/Pep switch
+      AlignSeq as = new AlignSeq(sequence, ((PDBChain) pdb.chains
+              .elementAt(i)).sequence, ((PDBChain) pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA : AlignSeq.PEP);
       as.calcScoreMatrix();
       as.traceAlignment();
       PrintStream ps = new PrintStream(System.out)
@@ -167,7 +205,6 @@ public class AppletPDBCanvas
         pdbend = as.seq2end;
         seqstart = as.seq1start + sequence.getStart() - 1;
         seqend = as.seq1end + sequence.getEnd() - 1;
-        maxAlignseq = as;
       }
 
       mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend);
@@ -181,12 +218,12 @@ public class AppletPDBCanvas
     mainchain.seqstart = seqstart;
     mainchain.seqend = seqend;
     mainchain.isVisible = true;
-  //  mainchain.makeExactMapping(maxAlignseq, sequence);
-  //  mainchain.transferRESNUMFeatures(sequence, null);
+    // mainchain.makeExactMapping(maxAlignseq, sequence);
+    // mainchain.transferRESNUMFeatures(sequence, null);
     this.pdb = pdb;
     this.prefsize = new Dimension(getSize().width, getSize().height);
 
-    //Initialize the matrices to identity
+    // Initialize the matrices to identity
     for (int i = 0; i < 3; i++)
     {
       for (int j = 0; j < 3; j++)
@@ -224,6 +261,7 @@ public class AppletPDBCanvas
   }
 
   Vector visiblebonds;
+
   void setupBonds()
   {
     seqColoursReady = false;
@@ -232,9 +270,9 @@ public class AppletPDBCanvas
 
     for (int ii = 0; ii < pdb.chains.size(); ii++)
     {
-      if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)
+      if (((PDBChain) pdb.chains.elementAt(ii)).isVisible)
       {
-        Vector tmp = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+        Vector tmp = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
         for (int i = 0; i < tmp.size(); i++)
         {
@@ -243,9 +281,7 @@ public class AppletPDBCanvas
       }
     }
     seqColoursReady = true;
-    colourBySequence(ap.getSequenceRenderer(),
-                               ap.av.getShowSequenceFeatures() ?
-                               fr : null);
+    colourBySequence();
     redrawneeded = true;
     repaint();
   }
@@ -255,9 +291,9 @@ public class AppletPDBCanvas
     float[] max = new float[3];
     float[] min = new float[3];
 
-    max[0] = (float) - 1e30;
-    max[1] = (float) - 1e30;
-    max[2] = (float) - 1e30;
+    max[0] = (float) -1e30;
+    max[1] = (float) -1e30;
+    max[2] = (float) -1e30;
 
     min[0] = (float) 1e30;
     min[1] = (float) 1e30;
@@ -265,9 +301,9 @@ public class AppletPDBCanvas
 
     for (int ii = 0; ii < pdb.chains.size(); ii++)
     {
-      if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)
+      if (((PDBChain) pdb.chains.elementAt(ii)).isVisible)
       {
-        Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+        Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
         for (int i = 0; i < bonds.size(); i++)
         {
@@ -392,25 +428,25 @@ public class AppletPDBCanvas
 
     int bsize = 0;
 
-    //Find centre coordinate
+    // Find centre coordinate
     for (int ii = 0; ii < pdb.chains.size(); ii++)
     {
-      if ( ( (PDBChain) pdb.chains.elementAt(ii)).isVisible)
+      if (((PDBChain) pdb.chains.elementAt(ii)).isVisible)
       {
-        Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+        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];
+          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];
         }
       }
     }
@@ -441,10 +477,10 @@ public class AppletPDBCanvas
       return;
     }
 
-    //Only create the image at the beginning -
-    //this saves much memory usage
-    if ( (img == null) || (prefsize.width != getSize().width) ||
-        (prefsize.height != getSize().height))
+    // Only create the image at the beginning -
+    // this saves much memory usage
+    if ((img == null) || (prefsize.width != getSize().width)
+            || (prefsize.height != getSize().height))
     {
 
       try
@@ -457,8 +493,7 @@ public class AppletPDBCanvas
         ig = img.getGraphics();
 
         redrawneeded = true;
-      }
-      catch (Exception ex)
+      } catch (Exception ex)
       {
         ex.printStackTrace();
       }
@@ -496,23 +531,23 @@ public class AppletPDBCanvas
     repaint();
   }
 
-
-
   // This method has been taken out of PDBChain to allow
   // Applet and Application specific sequence renderers to be used
-  void colourBySequence(SequenceRenderer sr, FeatureRenderer seqcanvasfr)
+  void colourBySequence()
   {
+    SequenceRenderer sr = new SequenceRenderer(ap.av);
+
     StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
 
     boolean showFeatures = false;
-    if (seqcanvasfr!=null)
+    if (ap.av.getShowSequenceFeatures())
     {
       if (fr == null)
       {
         fr = new jalview.appletgui.FeatureRenderer(ap.av);
       }
 
-      fr.transferSettings(seqcanvasfr);
+      fr.transferSettings(ap.getFeatureRenderer());
 
       showFeatures = true;
     }
@@ -540,7 +575,7 @@ public class AppletPDBCanvas
             {
               if (mapping[m].getSequence() == sequence[s])
               {
-                int pos = mapping[m].getSeqPos(tmp.at1.resNumber)-1;
+                int pos = mapping[m].getSeqPos(tmp.at1.resNumber) - 1;
                 if (pos > 0)
                 {
                   pos = sequence[s].findIndex(pos);
@@ -548,11 +583,10 @@ public class AppletPDBCanvas
                   if (showFeatures)
                   {
                     tmp.startCol = fr.findFeatureColour(tmp.startCol,
-                                                        sequence[s],
-                                                        pos);
+                            sequence[s], pos);
                   }
                 }
-                pos = mapping[m].getSeqPos(tmp.at2.resNumber)-1;
+                pos = mapping[m].getSeqPos(tmp.at2.resNumber) - 1;
                 if (pos > 0)
                 {
                   pos = sequence[s].findIndex(pos);
@@ -560,8 +594,7 @@ public class AppletPDBCanvas
                   if (showFeatures)
                   {
                     tmp.endCol = fr.findFeatureColour(tmp.endCol,
-                                                        sequence[s],
-                                                        pos);
+                            sequence[s], pos);
                   }
                 }
 
@@ -574,6 +607,7 @@ public class AppletPDBCanvas
   }
 
   Zsort zsort;
+
   public void drawScene(Graphics g)
   {
     if (zbuffer)
@@ -591,15 +625,11 @@ public class AppletPDBCanvas
     {
       tmpBond = (Bond) visiblebonds.elementAt(i);
 
-      xstart = (int) ( ( (tmpBond.start[0] - centre[0]) * scale) +
-                      (getSize().width / 2));
-      ystart = (int) ( ( (tmpBond.start[1] - centre[1]) * scale) +
-                      (getSize().height / 2));
+      xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getSize().width / 2));
+      ystart = (int) (((centre[1] - tmpBond.start[1]) * scale) + (getSize().height / 2));
 
-      xend = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) +
-                    (getSize().width / 2));
-      yend = (int) ( ( (tmpBond.end[1] - centre[1]) * scale) +
-                    (getSize().height / 2));
+      xend = (int) (((tmpBond.end[0] - centre[0]) * scale) + (getSize().width / 2));
+      yend = (int) (((centre[1] - tmpBond.end[1]) * scale) + (getSize().height / 2));
 
       xmid = (xend + xstart) / 2;
       ymid = (yend + ystart) / 2;
@@ -681,7 +711,7 @@ public class AppletPDBCanvas
   {
     if (!wire)
     {
-      if ( ( (float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5)
+      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);
@@ -797,13 +827,14 @@ public class AppletPDBCanvas
       toolx = e.getX();
       tooly = e.getY();
 
-      appletToolTip = chain.id + ":" + fatom.resNumber + " " + fatom.resName;
+      appletToolTip = chain.id + ":" + fatom.resNumber + " "
+              + fatom.resName;
       redrawneeded = true;
       repaint();
     }
     else
     {
-      mouseOverStructure(-1, chain!=null?chain.id:null);
+      mouseOverStructure(-1, chain != null ? chain.id : null);
       appletToolTip = null;
       redrawneeded = true;
       repaint();
@@ -832,33 +863,33 @@ public class AppletPDBCanvas
     MCMatrix objmat = new MCMatrix(3, 3);
     objmat.setIdentity();
 
-    if ( (evt.getModifiers() & Event.META_MASK) != 0)
+    if ((evt.getModifiers() & Event.META_MASK) != 0)
     {
-      objmat.rotatez( (float) ( (mx - omx)));
+      objmat.rotatez((float) ((mx - omx)));
     }
     else
     {
-      objmat.rotatex( (float) ( (my - omy)));
-      objmat.rotatey( (float) ( (omx - mx)));
+      objmat.rotatex((float) ((omy - my)));
+      objmat.rotatey((float) ((omx - mx)));
     }
 
-    //Alter the bonds
+    // Alter the bonds
     for (int ii = 0; ii < pdb.chains.size(); ii++)
     {
-      Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+      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]);
+        // Translate the bond so the centre is 0,0,0
+        tmpBond.translate(-centre[0], -centre[1], -centre[2]);
 
-        //Now apply the rotation matrix
+        // Now apply the rotation matrix
         tmpBond.start = objmat.vectorMultiply(tmpBond.start);
         tmpBond.end = objmat.vectorMultiply(tmpBond.end);
 
-        //Now translate back again
+        // Now translate back again
         tmpBond.translate(centre[0], centre[1], centre[2]);
       }
     }
@@ -890,7 +921,7 @@ public class AppletPDBCanvas
 
       if (chain.isVisible)
       {
-        Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+        Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
         for (int i = 0; i < bonds.size(); i++)
         {
@@ -917,10 +948,8 @@ public class AppletPDBCanvas
 
     if (n == 1)
     {
-      int xstart = (int) ( ( (b.start[0] - centre[0]) * scale) +
-                          (getSize().width / 2));
-      int ystart = (int) ( ( (b.start[1] - centre[1]) * scale) +
-                          (getSize().height / 2));
+      int xstart = (int) (((b.start[0] - centre[0]) * scale) + (getSize().width / 2));
+      int ystart = (int) (((centre[1] - b.start[1]) * scale) + (getSize().height / 2));
 
       g.setColor(Color.red);
       g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
@@ -928,10 +957,8 @@ public class AppletPDBCanvas
 
     if (n == 2)
     {
-      int xstart = (int) ( ( (b.end[0] - centre[0]) * scale) +
-                          (getSize().width / 2));
-      int ystart = (int) ( ( (b.end[1] - centre[1]) * scale) +
-                          (getSize().height / 2));
+      int xstart = (int) (((b.end[0] - centre[0]) * scale) + (getSize().width / 2));
+      int ystart = (int) (((centre[1] - b.end[1]) * scale) + (getSize().height / 2));
 
       g.setColor(Color.red);
       g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
@@ -939,6 +966,7 @@ public class AppletPDBCanvas
   }
 
   int foundchain = -1;
+
   public Atom findAtom(int x, int y)
   {
     Atom fatom = null;
@@ -953,19 +981,17 @@ public class AppletPDBCanvas
 
       if (chain.isVisible)
       {
-        Vector bonds = ( (PDBChain) pdb.chains.elementAt(ii)).bonds;
+        Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
 
         for (int i = 0; i < bonds.size(); i++)
         {
           tmpBond = (Bond) bonds.elementAt(i);
 
-          truex = (int) ( ( (tmpBond.start[0] - centre[0]) * scale) +
-                         (getSize().width / 2));
+          truex = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getSize().width / 2));
 
           if (Math.abs(truex - x) <= 2)
           {
-            int truey = (int) ( ( (tmpBond.start[1] - centre[1]) * scale) +
-                               (getSize().height / 2));
+            int truey = (int) (((centre[1] - tmpBond.start[1]) * scale) + (getSize().height / 2));
 
             if (Math.abs(truey - y) <= 2)
             {
@@ -978,13 +1004,11 @@ public class AppletPDBCanvas
 
         // Still here? Maybe its the last bond
 
-        truex = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) +
-                       (getSize().width / 2));
+        truex = (int) (((tmpBond.end[0] - centre[0]) * scale) + (getSize().width / 2));
 
         if (Math.abs(truex - x) <= 2)
         {
-          int truey = (int) ( ( (tmpBond.end[1] - centre[1]) * scale) +
-                             (getSize().height / 2));
+          int truey = (int) (((tmpBond.end[1] - centre[1]) * scale) + (getSize().height / 2));
 
           if (Math.abs(truey - y) <= 2)
           {
@@ -996,7 +1020,7 @@ public class AppletPDBCanvas
 
       }
 
-      if (fatom != null) //)&& chain.ds != null)
+      if (fatom != null) // )&& chain.ds != null)
       {
         chain = (PDBChain) pdb.chains.elementAt(foundchain);
       }
@@ -1017,8 +1041,7 @@ public class AppletPDBCanvas
       return;
     }
 
-    if (highlightRes != null
-        && highlightRes.contains( (ii - 1) + ""))
+    if (highlightRes != null && highlightRes.contains((ii - 1) + ""))
     {
       return;
     }
@@ -1075,36 +1098,36 @@ public class AppletPDBCanvas
     setupBonds();
   }
 
-
-  //////////////////////////////////
-  ///StructureListener
-  public String getPdbFile()
+  // ////////////////////////////////
+  // /StructureListener
+  public String[] getPdbFile()
   {
-    return "???";
+    return new String[] { pdbentry.getFile() };
   }
 
-
   String lastMessage;
+
   public void mouseOverStructure(int pdbResNum, String chain)
   {
-      if (lastMessage == null || !lastMessage.equals(pdbResNum+chain))
-        ssm.mouseOverStructure(pdbResNum, chain, pdbentry.getFile());
+    if (lastMessage == null || !lastMessage.equals(pdbResNum + chain))
+      ssm.mouseOverStructure(pdbResNum, chain, pdbentry.getFile());
 
-      lastMessage = pdbResNum+chain;
+    lastMessage = pdbResNum + chain;
   }
 
   StringBuffer resetLastRes = new StringBuffer();
+
   StringBuffer eval = new StringBuffer();
 
-  public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbfile)
+  public void highlightAtom(int atomIndex, int pdbResNum, String chain,
+          String pdbfile)
   {
     if (!seqColoursReady)
     {
       return;
     }
 
-    if (highlightRes != null
-        && highlightRes.contains( (atomIndex - 1) + ""))
+    if (highlightRes != null && highlightRes.contains((atomIndex - 1) + ""))
     {
       return;
     }
@@ -1149,25 +1172,21 @@ public class AppletPDBCanvas
     repaint();
   }
 
-
-  public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
+  public Color getColour(int atomIndex, int pdbResNum, String chain,
+          String pdbfile)
   {
     return Color.white;
-   // if (!pdbfile.equals(pdbentry.getFile()))
-   //   return null;
+    // if (!pdbfile.equals(pdbentry.getFile()))
+    // return null;
 
-    //return new Color(viewer.getAtomArgb(atomIndex));
+    // return new Color(viewer.getAtomArgb(atomIndex));
   }
 
   public void updateColours(Object source)
   {
-    AlignmentPanel ap = (AlignmentPanel) source;
-    colourBySequence(ap.getSequenceRenderer(),
-                     ap.av.getShowSequenceFeatures() ?
-                     fr : null);
+    colourBySequence();
     redrawneeded = true;
     repaint();
   }
 
-
 }