X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureViewer.java;h=0c8354be1fb797b74a39aec11df69672b737e9d5;hb=712aae0966c10bcb460ec63b81f85ae95cd182e6;hp=b7767facf7580fd0e26a03ce02c54dfeb2d18dea;hpb=b927b6af7e5654e0df7e2dbaa337322f2b52940f;p=jalview.git

diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java
index b7767fa..0c8354b 100644
--- a/src/jalview/gui/StructureViewer.java
+++ b/src/jalview/gui/StructureViewer.java
@@ -49,6 +49,11 @@ public class StructureViewer
 
   StructureSelectionManager ssm;
 
+  /**
+   * decide if new structures are aligned to existing ones
+   */
+  private boolean superposeAdded = true;
+
   public enum ViewerType
   {
     JMOL, CHIMERA
@@ -127,6 +132,7 @@ public class StructureViewer
             new SequenceI[seqsForPdbs.size()][]);
     if (sview != null)
     {
+      sview.setAlignAddedStructures(superposeAdded);
       new Thread(new Runnable()
       {
         @Override
@@ -152,11 +158,12 @@ public class StructureViewer
 
     if (viewerType.equals(ViewerType.JMOL))
     {
-      sview = new AppJmol(ap, pdbsForFile, theSeqs);
+      sview = new AppJmol(ap, superposeAdded, pdbsForFile, theSeqs);
     }
     else if (viewerType.equals(ViewerType.CHIMERA))
     {
-      sview = new ChimeraViewFrame(pdbsForFile, theSeqs, ap);
+      sview = new ChimeraViewFrame(pdbsForFile, superposeAdded, theSeqs,
+              ap);
     }
     else
     {
@@ -279,11 +286,14 @@ public class StructureViewer
   {
     if (sview != null)
     {
-      if (!sview.addAlreadyLoadedFile(seqsForPdb, null, ap, pdb.getId()))
+      sview.setAlignAddedStructures(superposeAdded);
+      String pdbId = pdb.getId();
+      if (!sview.addAlreadyLoadedFile(seqsForPdb, null, ap, pdbId))
       {
-        sview.addToExistingViewer(pdb, seqsForPdb, null, ap, pdb.getId());
+        sview.addToExistingViewer(pdb, seqsForPdb, null, ap, pdbId);
       }
       sview.updateTitleAndMenus();
+      sview.raiseViewer();
       return sview;
     }
     ViewerType viewerType = getViewerType();
@@ -373,4 +383,9 @@ public class StructureViewer
     return sview != null && sview.isVisible();
   }
 
+  public void setSuperpose(boolean alignAddedStructures)
+  {
+    superposeAdded = alignAddedStructures;
+  }
+
 }