X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=f34045795285b3a1953fef129e4d9fac2190455b;hb=3a2a5c2d6ae1e0aeeced5d11d6f9ffd5fafaa147;hp=7269e1da4cf112c01b7554e05b0ab9ee9d074203;hpb=0eda2ac2f334f55f6e5f137789453a9f4dfe4d73;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 7269e1d..f340457 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -649,27 +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++)
       {
         if (mapping[m].getSequence() == sequence[s]
-            && ap.av.alignment.findIndex(sequence[s])>-1)
+            && (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["