merge from develop

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 68d7397..bdcf8a4 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -795,7 +795,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       public void internalFrameClosed(
               javax.swing.event.InternalFrameEvent evt)
       {
-        System.out.println("deregistering discoverer listener");
+        // System.out.println("deregistering discoverer listener");
         Desktop.instance.removeJalviewPropertyChangeListener("services",
                 thisListener);
         closeMenuItem_actionPerformed(true);
@@ -1030,7 +1030,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void addFromText_actionPerformed(ActionEvent e)
   {
-    Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
+    Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
+            .getAlignPanel());
   }
 
   @Override
@@ -1251,7 +1252,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   }
 
-  public static AlignmentExportData getAlignmentForExport(String exportFomat,
+  public static AlignmentExportData getAlignmentForExport(String exportFormat,
           AlignViewportI viewport)
   {
     AlignmentI alignmentToExport = null;
@@ -1268,7 +1269,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
     AlignExportSettings settings = new AlignExportSettings(hasHiddenSeqs,
-            viewport.hasHiddenColumns(), exportFomat);
+            viewport.hasHiddenColumns(), exportFormat);
     settings.isExportAnnotations();
 
     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
@@ -1291,7 +1292,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return ed;
   }
 
-  private static int[] getStartEnd(int[] aligmentStartEnd,
+  public static int[] getStartEnd(int[] aligmentStartEnd,
           List<int[]> hiddenCols)
   {
     int startPos = aligmentStartEnd[0];
@@ -1303,7 +1304,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     for (int[] hiddenCol : hiddenCols)
     {
       // System.out.println("comparing : " + hiddenCol[0] + "-" + hiddenCol[1]);
-
       lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
       higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
     }
@@ -1498,6 +1498,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       if (closeAllTabs)
       {
+        /*
+         * this will raise an INTERNAL_FRAME_CLOSED event and this method will
+         * be called recursively, with the frame now in 'closed' state
+         */
         this.setClosed(true);
       }
     } catch (Exception ex)
@@ -2750,12 +2754,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     /*
-     * Views share the same edits, undo and redo stacks, mappings.
+     * Views share the same edits undo and redo stacks
      */
     newap.av.setHistoryList(viewport.getHistoryList());
     newap.av.setRedoList(viewport.getRedoList());
-    newap.av.getAlignment().setCodonFrames(
-            viewport.getAlignment().getCodonFrames());
+
+    /*
+     * Views share the same mappings; need to deregister any new mappings
+     * created by copyAlignPanel, and register the new reference to the shared
+     * mappings
+     */
+    newap.av.replaceMappings(viewport.getAlignment());
 
     newap.av.viewName = getNewViewName(viewTitle);
 
@@ -4526,8 +4535,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
         try
         {
-          System.err.println("Building ws menu again "
-                  + Thread.currentThread());
+          // System.err.println("Building ws menu again "
+          // + Thread.currentThread());
           // TODO: add support for context dependent disabling of services based
           // on
           // alignment and current selection
@@ -4879,7 +4888,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 al.getCodonFrames().addAll(cf);
                 final StructureSelectionManager ssm = StructureSelectionManager
                         .getStructureSelectionManager(Desktop.instance);
-                ssm.addMappings(cf);
+                ssm.registerMappings(cf);
               }
               else
               {
@@ -4969,10 +4978,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               "Exception during translation. Please report this !", ex);
       final String msg = MessageManager
               .getString("label.error_when_translating_sequences_submit_bug_report");
-      final String title = MessageManager
+      final String errorTitle = MessageManager
               .getString("label.implementation_error")
               + MessageManager.getString("translation_failed");
-      JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
+      JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
               JOptionPane.ERROR_MESSAGE);
       return;
     }
@@ -4980,9 +4989,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       final String msg = MessageManager
               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
-      final String title = MessageManager
+      final String errorTitle = MessageManager
               .getString("label.translation_failed");
-      JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
+      JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
               JOptionPane.WARNING_MESSAGE);
     }
     else
@@ -4996,8 +5005,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
       {
         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
-        viewport.openSplitFrame(af, new Alignment(seqs),
-                al.getCodonFrames());
+        viewport.openSplitFrame(af, new Alignment(seqs));
       }
       else
       {
@@ -6089,7 +6097,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       sf.setComplementVisible(this, show);
     }
   }
-
 }
 
 class PrintThread extends Thread