JAL-1713 refactorings to allow save/restore Overview to/from project

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 910ab63..5fe7c59 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1782,10 +1782,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection or the sequence under cursor in keyboard mode 
    * 
    * @param up
-   *          DOCUMENT ME!
+   *          or down (if !up)
    */
   public void moveSelectedSequences(boolean up)
   {
@@ -1793,8 +1793,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (sg == null)
     {
-      return;
+      if (viewport.cursorMode) 
+      {
+        sg = new SequenceGroup();
+        sg.addSequence(viewport.getAlignment()
+                .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY),false);
+      } else {
+        return;
+      }
+    }
+    
+    if (sg.getSize() < 1)
+    {
+        return;
     }
+    
+    // TODO: JAL-3733 - add an event to the undo buffer for this !
+    
     viewport.getAlignment().moveSelectedSequencesByOne(sg,
             viewport.getHiddenRepSequences(), up);
     alignPanel.paintAlignment(true, false);
@@ -2749,15 +2764,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Opens a Finder dialog
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
-    new Finder();
+    new Finder(alignPanel);
   }
 
   /**
@@ -3354,10 +3368,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * DOCUMENT ME!
+   * Opens an Overview panel for the alignment, unless one is open already
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   @Override
   public void overviewMenuItem_actionPerformed(ActionEvent e)
@@ -3367,8 +3380,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return;
     }
 
+    boolean showHiddenRegions = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
+                false);
+    openOverviewPanel(showHiddenRegions);
+  }
+
+  public OverviewPanel openOverviewPanel(boolean showHidden)
+  {
     JInternalFrame frame = new JInternalFrame();
-    final OverviewPanel overview = new OverviewPanel(alignPanel);
+    final OverviewPanel overview = new OverviewPanel(alignPanel, showHidden);
     frame.setContentPane(overview);
     Desktop.addInternalFrame(frame, MessageManager
             .formatMessage("label.overview_params", new Object[]
@@ -3393,6 +3413,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     alignPanel.setOverviewPanel(overview);
+    
+    return overview;
   }
 
   @Override