X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=ed64215a28533e23ed7fc9528be005e7cd898d0c;hb=5f090b7d1cb8836903474f8f4d5e475be142d30c;hp=f2678581dd195b8dc7049e47bf0379a23024ecc7;hpb=aced09c4feeaf3406269442c14e54abeeb4cad81;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index f267858..ed64215 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -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();
   }
@@ -1805,7 +1834,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
 
     // !newAlignment
-    addHistoryItem(new EditCommand(MessageManager.getString("label.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(MessageManager.getString("label.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);
@@ -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;