X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBCanvas.java;h=a5c0e701021787fd749bad5b6127ef495cc2ff93;hb=98db6c30a9d5539276236a7885bf22a161aa9df9;hp=bd90b1921b49359f24099274dcb62c6d24b4c685;hpb=c088a5ef1796d60ee32304c8a010224b852ae3bd;p=jalview.git

diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index bd90b19..a5c0e70 100755
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -77,7 +77,6 @@ public class PDBCanvas
   {
     this.seqcanvas = seqcanvas;
     this.sequence = seq;
-    seqcanvas.setPDBCanvas(this);
   }
 
   public void setPDBFile(PDBfile pdb)
@@ -146,7 +145,7 @@ public class PDBCanvas
     mainchain.seqend = seqend;
     mainchain.isVisible = true;
     mainchain.makeExactMapping(maxAlignseq, sequence);
-    mainchain.transferRESNUMFeatures(sequence.getDatasetSequence(), null);
+    mainchain.transferRESNUMFeatures(sequence, null);
     seqcanvas.getFeatureRenderer().featuresAdded();
     this.pdb = pdb;
     this.prefsize = new Dimension(getWidth(), getHeight());
@@ -513,12 +512,15 @@ public class PDBCanvas
   {
     // System.out.println("colour by seq");
     boolean showFeatures = false;
-    if (seqcanvas.getViewport().getShowSequenceFeatures())
+
+ //NO LONGER USED SINCE APPJMOL
+// if (seqcanvas.getViewport().getShowSequenceFeatures())
     {
       showFeatures = true;
       if (fr == null)
       {
-        fr = new jalview.gui.FeatureRenderer(seqcanvas.getViewport());
+    //NO LONGER USED SINCE APPJMOL
+//    fr = new jalview.gui.FeatureRenderer(seqcanvas.getViewport());
       }
 
       fr.transferSettings(seqcanvas.getFeatureRenderer());
@@ -539,7 +541,7 @@ public class PDBCanvas
       {
         int index = findTrueIndex(tmp.at1.alignmentMapping);
         //sequence.findIndex(tmp.at1.alignmentMapping);
-        if (index > 0)
+        if (index != -1)
         {
           tmp.startCol = seqcanvas.getSequenceRenderer().
               getResidueBoxColour(sequence, index);
@@ -562,7 +564,7 @@ public class PDBCanvas
 
         int index = findTrueIndex(tmp.at2.alignmentMapping);
         //sequence.findIndex( tmp.at2.alignmentMapping );
-        if (index > 0)
+        if (index != -1)
         {
           tmp.endCol = seqcanvas.getSequenceRenderer().
               getResidueBoxColour(sequence, index);