X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJMol.java;h=da94e4cf420b3e63416666a8bb769536e59132b8;hb=eafcdaa3f6786f1f00a0c5d551f5ec7401b118fb;hp=14acb143f38bd13de38137e6e61dd3a08bd5c6af;hpb=8c24d666aa965338168416f8ca3be864569a1c24;p=jalview.git

diff --git a/src/jalview/gui/AppJMol.java b/src/jalview/gui/AppJMol.java
index 14acb14..da94e4c 100644
--- a/src/jalview/gui/AppJMol.java
+++ b/src/jalview/gui/AppJMol.java
@@ -195,6 +195,8 @@ public synchronized void addSequence(SequenceI [] seq)
     jmolpopup = JmolPopup.newJmolPopup(viewer);
 
     viewer.evalStringQuiet(command);
+
+    colourBySequence = true;
   }
 
 
@@ -604,12 +606,13 @@ public synchronized void addSequence(SequenceI [] seq)
     SequenceRenderer sr = ap.seqPanel.seqCanvas.getSequenceRenderer();
 
     boolean showFeatures = false;
+
     if (ap.av.showSequenceFeatures)
     {
       showFeatures = true;
       if (fr == null)
       {
-        fr = new jalview.gui.FeatureRenderer(ap.av);
+        fr = new jalview.gui.FeatureRenderer(ap);
       }
 
       fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
@@ -622,7 +625,8 @@ public synchronized void addSequence(SequenceI [] seq)
     {
       for (int m = 0; m < mapping.length; m++)
       {
-        if (mapping[m].getSequence() == sequence[s])
+        if (mapping[m].getSequence() == sequence[s]
+            && ap.av.alignment.findIndex(sequence[s])>-1)
         {
           for (int r = 0; r < sequence[s].getLength(); r++)
           {