X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureViewerBase.java;h=840dbae06e19ca91634e08897cf89a11f78fb218;hb=d156987a513b1da92fd6fbf7678b4a8e7ffc8d08;hp=3b80ff0962c1b527aad56056275863aa1e7ee0e3;hpb=591a5a4f3a552b103be552f1e942fb0c3a65cfa6;p=jalview.git

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 3b80ff0..840dbae 100644
--- 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);
@@ -412,35 +410,23 @@ public abstract class StructureViewerBase extends GStructureViewer
     return Desktop.instance.getStructureViewers(alp, this.getClass());
   }
 
-
-  /**
-   * Check for any existing views involving this alignment and give user the
-   * option to add and align this molecule to one of them
-   * 
-   * @param pdbentry
-   * @param seq
-   * @param chains
-   * @param apanel
-   * @param pdbId
-   * @return true if user adds to a view, or cancels entirely, else false
-   */
   @Override
-  public boolean addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq,
+  public void addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq,
           String[] chains, final AlignmentViewPanel apanel, String pdbId)
   {
     /*
      * JAL-1742 exclude view with this structure already mapped (don't offer
-     * to align chain B to chain A of the same structure)
+     * to align chain B to chain A of the same structure); code may defend
+     * against this possibility before we reach here
      */
     if (hasPdbId(pdbId))
     {
-      return false;
+      return;
     }
-    AlignmentPanel ap = (AlignmentPanel) apanel; // Implementation error if this
+    AlignmentPanel alignPanel = (AlignmentPanel) apanel; // Implementation error if this
                                                  // cast fails
-    useAlignmentPanelForSuperposition(ap);
-    addStructure(pdbentry, seq, chains, true, ap.alignFrame);
-    return true;
+    useAlignmentPanelForSuperposition(alignPanel);
+    addStructure(pdbentry, seq, chains, alignPanel.alignFrame);
   }
 
   /**
@@ -504,33 +490,20 @@ public abstract class StructureViewerBase extends GStructureViewer
     }
   }
 
-  /**
-   * Check if the PDB file is already loaded, if so offer to add it to the
-   * existing viewer
-   * 
-   * @param seq
-   * @param chains
-   * @param apanel
-   * @param pdbId
-   * @return true if the user chooses to add to a viewer, or to cancel entirely
-   */
   @Override
   public boolean addAlreadyLoadedFile(SequenceI[] seq, String[] chains,
           final AlignmentViewPanel apanel, String pdbId)
   {
-    boolean finished = false;
     String alreadyMapped = apanel.getStructureSelectionManager()
             .alreadyMappedToFile(pdbId);
 
-    if (alreadyMapped != null)
+    if (alreadyMapped == null)
     {
-      /*
-       * the PDB file is already loaded
-       */
-      addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped);
-      finished = true;
+      return false;
     }
-    return finished;
+
+    addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped);
+    return true;
   }
 
   void setChainMenuItems(List<String> chainNames)
@@ -810,11 +783,11 @@ public abstract class StructureViewerBase extends GStructureViewer
       int[] alm = new int[_alignwith.size()];
       int a = 0;
 
-      for (AlignmentPanel ap : _alignwith)
+      for (AlignmentPanel alignPanel : _alignwith)
       {
-        als[a] = ap.av.getAlignment();
+        als[a] = alignPanel.av.getAlignment();
         alm[a] = -1;
-        alc[a++] = ap.av.getAlignment().getHiddenColumns();
+        alc[a++] = alignPanel.av.getAlignment().getHiddenColumns();
       }
       reply = getBinding().superposeStructures(als, alm, alc);
       if (reply != null)
@@ -826,9 +799,9 @@ public abstract class StructureViewerBase extends GStructureViewer
     } catch (Exception e)
     {
       StringBuffer sp = new StringBuffer();
-      for (AlignmentPanel ap : _alignwith)
+      for (AlignmentPanel alignPanel : _alignwith)
       {
-        sp.append("'" + ap.alignFrame.getTitle() + "' ");
+        sp.append("'" + alignPanel.alignFrame.getTitle() + "' ");
       }
       Cache.log.info("Couldn't align structures with the " + sp.toString()
               + "associated alignment panels.", e);
@@ -892,9 +865,9 @@ public abstract class StructureViewerBase extends GStructureViewer
         }
       }
       // Set the colour using the current view for the associated alignframe
-      for (AlignmentPanel ap : _colourwith)
+      for (AlignmentPanel alignPanel : _colourwith)
       {
-        binding.colourBySequence(ap);
+        binding.colourBySequence(alignPanel);
       }
       seqColoursApplied = true;
     }