X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;fp=src%2Fjalview%2Fgui%2FAppJmol.java;h=7b4af5612d4b76056fe7aab4fe940759629e7e3a;hb=e06ef51ba3dd8cdae7632d71db162ff416b88256;hp=29f02d6c68bd16bacdd1fa9c24462c0ad6782ce7;hpb=0e07457ca16b632091d64ec76934b6bf772b180c;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 29f02d6..7b4af56 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -175,10 +175,13 @@ public class AppJmol extends StructureViewerBase
   {
     progressBar = ap.alignFrame;
 
-    openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
+    openNewJmol(ap, alignAddedStructures, new PDBEntry[] { pdbentry },
+            new SequenceI[][]
+            { seq });
   }
 
-  private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,
+  private void openNewJmol(AlignmentPanel ap, boolean alignAdded,
+          PDBEntry[] pdbentrys,
           SequenceI[][] seqs)
   {
     progressBar = ap.alignFrame;
@@ -187,8 +190,8 @@ public class AppJmol extends StructureViewerBase
     addAlignmentPanel(ap);
     useAlignmentPanelForColourbyseq(ap);
 
-    alignAddedStructures = true;
-      useAlignmentPanelForSuperposition(ap);
+    alignAddedStructures = alignAdded;
+    useAlignmentPanelForSuperposition(ap);
 
     jmb.setColourBySequence(true);
     setSize(400, 400); // probably should be a configurable/dynamic default here
@@ -210,16 +213,19 @@ public class AppJmol extends StructureViewerBase
   }
 
   /**
-   * create a new Jmol containing several structures superimposed using the
-   * given alignPanel.
+   * create a new Jmol containing several structures optionally superimposed
+   * using the given alignPanel.
    * 
    * @param ap
+   * @param alignAdded
+   *          - true to superimpose
    * @param pe
    * @param seqs
    */
-  public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs)
+  public AppJmol(AlignmentPanel ap, boolean alignAdded, PDBEntry[] pe,
+          SequenceI[][] seqs)
   {
-    openNewJmol(ap, pe, seqs);
+    openNewJmol(ap, alignAdded, pe, seqs);
   }
 
 
@@ -397,7 +403,7 @@ public class AppJmol extends StructureViewerBase
       jmb.updateColours(ap);
     }
     // do superposition if asked to
-    if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
+    if (alignAddedStructures)
     {
       alignAddedStructures();
     }
@@ -431,7 +437,7 @@ public class AppJmol extends StructureViewerBase
         }
       }
     });
-    alignAddedStructures = false;
+
   }
 
   /**