JAL-1620 version bump and release notes

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index cc1703c..4473877 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -21,13 +21,13 @@
 package jalview.appletgui;
 
 import jalview.analysis.AlignmentSorter;
-import jalview.analysis.Conservation;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.SequenceStructureBinding;
 import jalview.bin.JalviewLite;
 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
 import jalview.commands.OrderCommand;
 import jalview.commands.RemoveGapColCommand;
 import jalview.commands.RemoveGapsCommand;
@@ -56,7 +56,6 @@ import jalview.schemes.PIDColourScheme;
 import jalview.schemes.PurinePyrimidineColourScheme;
 import jalview.schemes.RNAHelicesColourChooser;
 import jalview.schemes.RNAInteractionColourScheme;
-import jalview.schemes.ResidueProperties;
 import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.schemes.TaylorColourScheme;
@@ -324,7 +323,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
                     .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
                     .getKeyCode() <= KeyEvent.VK_NUMPAD9))
             && Character.isDigit(evt.getKeyChar()))
+    {
       alignPanel.seqPanel.numberPressed(evt.getKeyChar());
+    }
 
     switch (evt.getKeyCode())
     {
@@ -385,16 +386,24 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     case KeyEvent.VK_LEFT:
       if (evt.isAltDown() || !viewport.cursorMode)
+      {
         slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
+      }
       else
+      {
         alignPanel.seqPanel.moveCursor(-1, 0);
+      }
       break;
 
     case KeyEvent.VK_RIGHT:
       if (evt.isAltDown() || !viewport.cursorMode)
+      {
         slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
+      }
       else
+      {
         alignPanel.seqPanel.moveCursor(1, 0);
+      }
       break;
 
     case KeyEvent.VK_SPACE:
@@ -1257,7 +1266,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     else
     {
       if (features == null)
+      {
         features = "";
+      }
     }
 
     return features;
@@ -1573,7 +1584,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
     {
       if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
+      {
         invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
+      }
     }
 
     SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
@@ -1581,30 +1594,44 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
             .size()]);
     for (int i = 0; i < invertGroup.size(); i++)
+    {
       seqs2[i] = invertGroup.elementAt(i);
+    }
 
     SlideSequencesCommand ssc;
     if (right)
+    {
       ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
               size, viewport.getGapCharacter());
+    }
     else
+    {
       ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
               size, viewport.getGapCharacter());
+    }
 
     int groupAdjustment = 0;
     if (ssc.getGapsInsertedBegin() && right)
     {
       if (viewport.cursorMode)
+      {
         alignPanel.seqPanel.moveCursor(size, 0);
+      }
       else
+      {
         groupAdjustment = size;
+      }
     }
     else if (!ssc.getGapsInsertedBegin() && !right)
     {
       if (viewport.cursorMode)
+      {
         alignPanel.seqPanel.moveCursor(-size, 0);
+      }
       else
+      {
         groupAdjustment = -size;
+      }
     }
 
     if (groupAdjustment != 0)
@@ -1625,7 +1652,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
 
     if (!appendHistoryItem)
+    {
       addHistoryItem(ssc);
+    }
 
     repaint();
   }
@@ -1763,14 +1792,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
       if (newAlignment)
       {
-        String newtitle = new String("Copied sequences");
-        if (getTitle().startsWith("Copied sequences"))
+        String newtitle = MessageManager.getString("label.copied_sequences");
+        if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
         {
           newtitle = getTitle();
         }
         else
         {
-          newtitle = newtitle.concat("- from " + getTitle());
+          newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
         }
         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
                 viewport.applet, newtitle, false);
@@ -1805,7 +1834,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
 
     // !newAlignment
-    addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
+    addHistoryItem(new EditCommand(
+            MessageManager.getString("label.add_sequences"), Action.PASTE,
             seqs, 0, viewport.getAlignment().getWidth(),
             viewport.getAlignment()));
 
@@ -1855,8 +1885,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     /*
      * //ADD HISTORY ITEM
      */
-    addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
-            sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+    addHistoryItem(new EditCommand(
+            MessageManager.getString("label.cut_sequences"), Action.CUT,
+            cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
             viewport.getAlignment()));
 
     viewport.setSelectionGroup(null);
@@ -2780,10 +2811,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
           MessageManager.getString("label.load_features_annotations"));
 
   MenuItem outputFeatures = new MenuItem(
-          MessageManager.getString("label.export_features"));
+          MessageManager.getString("label.export_features").concat("..."));
 
   MenuItem outputAnnotations = new MenuItem(
-          MessageManager.getString("label.export_annotations"));
+          MessageManager.getString("label.export_annotations").concat("..."));
 
   MenuItem closeMenuItem = new MenuItem(
           MessageManager.getString("action.close"));
@@ -3043,7 +3074,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
     sortGroupMenuItem.addActionListener(this);
     removeRedundancyMenuItem.setLabel(MessageManager
-            .getString("action.remove_redundancy"));
+            .getString("action.remove_redundancy").concat("..."));
     removeRedundancyMenuItem.addActionListener(this);
     pairwiseAlignmentMenuItem.setLabel(MessageManager
             .getString("action.pairwise_alignment"));
@@ -3656,6 +3687,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         }
         pdbentry.getProperty().put("protocol", protocol);
         toaddpdb.addPDBId(pdbentry);
+        alignPanel.getStructureSelectionManager()
+                .registerPDBEntry(pdbentry);
       }
     }
     return true;