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

[jalview.git] / src / jalview / gui / StructureViewerBase.java

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;
   }