X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=f34045795285b3a1953fef129e4d9fac2190455b;hb=3a2a5c2d6ae1e0aeeced5d11d6f9ffd5fafaa147;hp=4a091b20f30b19e3ab34601f23250975daf88d36;hpb=31b00a6d85b8a1b4032f11f448911938004a5f6b;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 4a091b2..f340457 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -33,6 +33,7 @@ import jalview.structure.*;
 import jalview.datamodel.PDBEntry;
 import jalview.io.*;
 import jalview.schemes.*;
+import jalview.ws.ebi.EBIFetchClient;
 
 import org.jmol.api.*;
 import org.jmol.adapter.smarter.SmarterJmolAdapter;
@@ -413,6 +414,7 @@ public synchronized void addSequence(SequenceI [] seq)
 
   public void seqColour_actionPerformed(ActionEvent actionEvent)
   {
+    lastCommand = null;
     colourBySequence = seqColour.isSelected();
     colourBySequence(ap.alignFrame.alignPanel);
   }
@@ -588,17 +590,13 @@ public synchronized void addSequence(SequenceI [] seq)
       resetLastRes.append(":" + chain);
     }
 
-    eval.append(";color gold;wireframe 100");
+    eval.append(";wireframe 100;"+eval.toString()+".CA;");
 
-    Color col = new Color(viewer.getAtomArgb(atomIndex));
+    resetLastRes.append(";wireframe 0;"+resetLastRes.toString()+".CA;spacefill 0;");
 
-    resetLastRes.append(";color["
-                        + col.getRed() + ","
-                        + col.getGreen() + ","
-                        + col.getBlue() + "];wireframe 0");
+    eval.append("spacefill 200;select none");
 
     viewer.evalStringQuiet(eval.toString());
-
   }
 
   public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
@@ -651,31 +649,33 @@ public synchronized void addSequence(SequenceI [] seq)
     StringBuffer command = new StringBuffer();
 
     int lastPos = -1;
-    for (int s = 0; s < sequence.length; s++)
+    for (int sp,s = 0; s < sequence.length; s++)
     {
       for (int m = 0; m < mapping.length; m++)
       {
-        System.out.println(mapping[m].getSequence().getName()+" "+sequence[s].getName()+" "
-        +((mapping[m].getSequence() == sequence[s])
-          +" "+(ap.av.alignment.findIndex(sequence[s]))));
-
-                           if (mapping[m].getSequence() == sequence[s]
-            && ap.av.alignment.findIndex(sequence[s])>-1)
+        if (mapping[m].getSequence() == sequence[s]
+            && (sp=ap.av.alignment.findIndex(sequence[s]))>-1)
         {
-          for (int r = 0; r < sequence[s].getLength(); r++)
+          SequenceI asp = ap.av.alignment.getSequenceAt(sp);
+          for (int r = 0; r < asp.getLength(); r++)
           {
+            // No mapping to gaps in sequence.
+            if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
+            {
+              continue;
+            }
             int pos = mapping[m].getPDBResNum(
-                sequence[s].findPosition(r));
+                    asp.findPosition(r));
 
             if (pos < 1 || pos==lastPos)
               continue;
 
             lastPos = pos;
 
-            Color col = sr.getResidueBoxColour(sequence[s], r);
+            Color col = sr.getResidueBoxColour(asp, r);
 
             if (showFeatures)
-              col = fr.findFeatureColour(col, sequence[s], r);
+              col = fr.findFeatureColour(col, asp, r);
 
             if (command.toString().endsWith(":" + mapping[m].getChain()+
                                             ";color["
@@ -851,7 +851,8 @@ public synchronized void addSequence(SequenceI [] seq)
     if (chainId != null)
       picked+=(":"+chainId.substring(1, chainId.length()));
 
-    picked+=".C";
+    picked+=".CA";
+
 
     if (!atomsPicked.contains(picked))
     {