X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=86ab5367d197acffa2338e1395e6827bf79d9980;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=bd4a393b5b1b3682f857f3b272b7b344a026cd31;hpb=0c5e8f8ba81b913c63b60d7670d66aca661ea4f5;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index bd4a393..86ab536 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -147,9 +147,7 @@ public class AppJmol extends StructureViewerBase
     PDBEntry[] pdbentrys = new PDBEntry[files.length];
     for (int i = 0; i < pdbentrys.length; i++)
     {
-      PDBEntry pdbentry = new PDBEntry();
-      pdbentry.setFile(files[i]);
-      pdbentry.setId(ids[i]);
+      PDBEntry pdbentry = new PDBEntry(files[i], ids[i]);
       pdbentrys[i] = pdbentry;
     }
     // / TODO: check if protocol is needed to be set, and if chains are
@@ -169,7 +167,7 @@ public class AppJmol extends StructureViewerBase
       seqColour.setSelected(false);
       viewerColour.setSelected(true);
     }
-    if (usetoColour)
+    else if (usetoColour)
     {
       useAlignmentPanelForColourbyseq(ap);
       jmb.setColourBySequence(true);
@@ -940,7 +938,7 @@ public class AppJmol extends StructureViewerBase
       // Set the colour using the current view for the associated alignframe
       for (AlignmentPanel ap : _colourwith)
       {
-        jmb.colourBySequence(ap.av.showSequenceFeatures, ap);
+        jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
       }
     }
   }