Merge branch 'develop' into features/JAL-518_justify_seqs_in_region

[jalview.git] / src / jalview / jbgui / GAlignFrame.java

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 8ae97b0..9b9a44a 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -220,6 +220,7 @@ public class GAlignFrame extends JInternalFrame
   {
     try
     {
+      setFrameIcon(null);
 
       // for Web-page embedding using id=align-frame-div
       setName("jalview-alignment");
@@ -245,7 +246,7 @@ public class GAlignFrame extends JInternalFrame
       }
     } catch (Exception e)
     {
-      System.err.println(e.toString());
+      jalview.bin.Console.errPrintln(e.toString());
     }
 
     if (Platform.allowMnemonics()) // was "not mac and not JS"
@@ -263,6 +264,7 @@ public class GAlignFrame extends JInternalFrame
 
   private void jbInit() throws Exception
   {
+    setFrameIcon(null);
     initColourMenu();
 
     JMenuItem saveAs = new JMenuItem(
@@ -439,7 +441,9 @@ public class GAlignFrame extends JInternalFrame
     addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
 
     JMenuItem justifyLeftMenuItem = new JMenuItem(
-            MessageManager.getString("action.left_justify_alignment"));
+            MessageManager.getString("action.left_justify"));
+    justifyLeftMenuItem.setToolTipText(
+            MessageManager.getString("tooltip.left_justify"));
     justifyLeftMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -449,7 +453,10 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     JMenuItem justifyRightMenuItem = new JMenuItem(
-            MessageManager.getString("action.right_justify_alignment"));
+            MessageManager.getString("action.right_justify"));
+    justifyRightMenuItem.setToolTipText(
+            MessageManager.getString("action.left_justify"));
+
     justifyRightMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -1080,7 +1087,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        createPNG(null);
+        createPNG_actionPerformed(e);
       }
     });
     createPNG.setActionCommand(
@@ -1112,7 +1119,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        createEPS(null);
+        createEPS_actionPerformed(e);
       }
     });
 
@@ -1122,7 +1129,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        createSVG(null);
+        createSVG_actionPerformed(e);
       }
     });
 
@@ -1838,11 +1845,11 @@ public class GAlignFrame extends JInternalFrame
     editMenu.add(removeAllGapsMenuItem);
     editMenu.add(removeRedundancyMenuItem);
     editMenu.addSeparator();
-    // dont add these yet in the CVS build - they cannot be undone!
-    // Excluded from Jalview 2.5 release - undo needs to be implemented.
-    // editMenu.add(justifyLeftMenuItem);
-    // editMenu.add(justifyRightMenuItem);
-    // editMenu.addSeparator();
+
+    editMenu.add(justifyLeftMenuItem);
+    editMenu.add(justifyRightMenuItem);
+
+    editMenu.addSeparator();
     editMenu.add(padGapsMenuitem);
 
     showMenu.add(showAllColumns);
@@ -1974,6 +1981,24 @@ public class GAlignFrame extends JInternalFrame
     // selectMenu.add(listenToViewSelections);
   }
 
+  protected void createPNG_actionPerformed(ActionEvent object)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void createEPS_actionPerformed(ActionEvent object)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void createSVG_actionPerformed(ActionEvent object)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
   protected void copyHighlightedColumns_actionPerformed(
           ActionEvent actionEvent)
   {
@@ -2157,7 +2182,7 @@ public class GAlignFrame extends JInternalFrame
    * @param forAlignment
    *          update non-sequence-related annotations
    */
-  protected void setAnnotationsVisibility(boolean visible,
+  public void setAnnotationsVisibility(boolean visible,
           boolean forSequences, boolean forAlignment)
   {
 
@@ -2467,10 +2492,6 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  public void createPNG(java.io.File f)
-  {
-  }
-
   protected void font_actionPerformed(ActionEvent e)
   {
   }
@@ -2484,15 +2505,6 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  public void createEPS(java.io.File f)
-  {
-  }
-
-  public void createSVG(java.io.File f)
-  {
-
-  }
-
   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
   {