JAL-1847 JAL-2944 make superposition step a configurable property when opening/adding...

diff --git a/src/jalview/api/structures/JalviewStructureDisplayI.java b/src/jalview/api/structures/JalviewStructureDisplayI.java
index c58e3c1..a27cec6 100644 (file)
--- a/src/jalview/api/structures/JalviewStructureDisplayI.java
+++ b/src/jalview/api/structures/JalviewStructureDisplayI.java
@@ -85,4 +85,8 @@ public interface JalviewStructureDisplayI
    */
   void updateTitleAndMenus();
 
+  boolean isAlignAddedStructures();
+
+  void setAlignAddedStructures(boolean alignAdded);
+
 }

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 29f02d6..7b4af56 100644 (file)
--- 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;
+
   }
 
   /**

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index c595d9d..b4520c4 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -241,7 +241,6 @@ public class ChimeraViewFrame extends StructureViewerBase
 
     if (pdbentrys.length > 1)
     {
-      alignAddedStructures = true;
       useAlignmentPanelForSuperposition(ap);
     }
     jmb.setColourBySequence(true);
@@ -300,17 +299,19 @@ public class ChimeraViewFrame extends StructureViewerBase
   }
 
   /**
-   * create a new viewer containing several structures superimposed using the
-   * given alignPanel.
+   * create a new viewer containing several structures, optionally superimposed
+   * using the given alignPanel.
    * 
    * @param pe
    * @param seqs
    * @param ap
    */
-  public ChimeraViewFrame(PDBEntry[] pe, SequenceI[][] seqs,
+  public ChimeraViewFrame(PDBEntry[] pe, boolean alignAdded,
+          SequenceI[][] seqs,
           AlignmentPanel ap)
   {
     this();
+    setAlignAddedStructures(alignAdded);
     openNewChimera(ap, pe, seqs);
   }
 
@@ -595,7 +596,7 @@ public class ChimeraViewFrame extends StructureViewerBase
         jmb.updateColours(ap);
       }
       // do superposition if asked to
-      if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
+      if (alignAddedStructures)
       {
         new Thread(new Runnable()
         {
@@ -605,7 +606,6 @@ public class ChimeraViewFrame extends StructureViewerBase
             alignStructs_withAllAlignPanels();
           }
         }).start();
-        alignAddedStructures = false;
       }
       addingStructures = false;
     }

diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java
index b7767fa..19e0a22 100644 (file)
--- 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
     {
@@ -279,6 +286,7 @@ public class StructureViewer
   {
     if (sview != null)
     {
+      sview.setAlignAddedStructures(superposeAdded);
       if (!sview.addAlreadyLoadedFile(seqsForPdb, null, ap, pdb.getId()))
       {
         sview.addToExistingViewer(pdb, seqsForPdb, null, ap, pdb.getId());
@@ -373,4 +381,9 @@ public class StructureViewer
     return sview != null && sview.isVisible();
   }
 
+  public void setSuperpose(boolean alignAddedStructures)
+  {
+    superposeAdded = alignAddedStructures;
+  }
+
 }

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 3b80ff0..20f5c1f 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -130,6 +130,26 @@ public abstract class StructureViewerBase extends GStructureViewer
   }
 
   /**
+   * @return true if added structures should be aligned to existing one(s)
+   */
+  @Override
+  public boolean isAlignAddedStructures()
+  {
+    return alignAddedStructures;
+  }
+
+  /**
+   * 
+   * @param true
+   *          if added structures should be aligned to existing one(s)
+   */
+  @Override
+  public void setAlignAddedStructures(boolean alignAdded)
+  {
+    alignAddedStructures = alignAdded;
+  }
+
+  /**
    * 
    * @param ap2
    * @return true if this Jmol instance is linked with the given alignPanel
@@ -335,7 +355,7 @@ public abstract class StructureViewerBase extends GStructureViewer
    */
   protected void addStructure(final PDBEntry pdbentry,
           final SequenceI[] seqs, final String[] chains,
-          final boolean align, final IProgressIndicator alignFrame)
+          final IProgressIndicator alignFrame)
   {
     if (pdbentry.getFile() == null)
     {
@@ -359,7 +379,7 @@ public abstract class StructureViewerBase extends GStructureViewer
               }
             }
             // and call ourselves again.
-            addStructure(pdbentry, seqs, chains, align, alignFrame);
+            addStructure(pdbentry, seqs, chains, alignFrame);
           }
         }).start();
         return;
@@ -371,33 +391,11 @@ public abstract class StructureViewerBase extends GStructureViewer
             { seqs }, new String[][] { chains });
     addingStructures = true;
     _started = false;
-    alignAddedStructures = align;
     worker = new Thread(this);
     worker.start();
     return;
   }
 
-  /**
-   * Presents a dialog with the option to add an align a structure to an
-   * existing structure view
-   * 
-   * @param pdbId
-   * @param view
-   * @return YES, NO or CANCEL JvOptionPane code
-   */
-  protected int chooseAlignStructureToViewer(String pdbId,
-          StructureViewerBase view)
-  {
-    int option = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
-            MessageManager.formatMessage("label.add_pdbentry_to_view",
-                    new Object[]
-                    { pdbId, view.getTitle() }),
-            MessageManager
-                    .getString("label.align_to_existing_structure_view"),
-            JvOptionPane.YES_NO_CANCEL_OPTION);
-    return option;
-  }
-
   protected boolean hasPdbId(String pdbId)
   {
     return getBinding().hasPdbId(pdbId);
@@ -439,7 +437,7 @@ public abstract class StructureViewerBase extends GStructureViewer
     AlignmentPanel ap = (AlignmentPanel) apanel; // Implementation error if this
                                                  // cast fails
     useAlignmentPanelForSuperposition(ap);
-    addStructure(pdbentry, seq, chains, true, ap.alignFrame);
+    addStructure(pdbentry, seq, chains, ap.alignFrame);
     return true;
   }