X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=50043e69678c977458d79eead84a6b73e1cef4c5;hb=9b64dc0dc8e072d3dd8269518687364424e30202;hp=03a394461bf1cd14a312b0c16491a0d13f021fc6;hpb=d1c135b99c34e0eea52b464df91fbbd3a3c19446;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 03a3944..50043e6 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -30,10 +30,12 @@ import jalview.analysis.ParseProperties;
 import jalview.analysis.SequenceIdMatcher;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
+import jalview.api.AlignmentViewPanel;
 import jalview.api.analysis.ScoreModelI;
 import jalview.bin.Cache;
 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;
@@ -114,6 +116,7 @@ import java.beans.PropertyChangeEvent;
 import java.io.File;
 import java.net.URL;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.List;
@@ -1410,7 +1413,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (viewport.historyList.size() > 0)
     {
       undoMenuItem.setEnabled(true);
-      CommandI command = (CommandI) viewport.historyList.peek();
+      CommandI command = viewport.historyList.peek();
       undoMenuItem.setText(MessageManager.formatMessage(
               "label.undo_command", new String[]
               { command.getDescription() }));
@@ -1425,7 +1428,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       redoMenuItem.setEnabled(true);
 
-      CommandI command = (CommandI) viewport.redoList.peek();
+      CommandI command = viewport.redoList.peek();
       redoMenuItem.setText(MessageManager.formatMessage(
               "label.redo_command", new String[]
               { command.getDescription() }));
@@ -1489,7 +1492,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       return;
     }
-    CommandI command = (CommandI) viewport.historyList.pop();
+    CommandI command = viewport.historyList.pop();
     viewport.redoList.push(command);
     command.undoCommand(getViewAlignments());
 
@@ -1528,7 +1531,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return;
     }
 
-    CommandI command = (CommandI) viewport.redoList.pop();
+    CommandI command = viewport.redoList.pop();
     viewport.historyList.push(command);
     command.doCommand(getViewAlignments());
 
@@ -1990,7 +1993,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         // /////
         // ADD HISTORY ITEM
         //
-        addHistoryItem(new EditCommand(MessageManager.getString("label.add_sequences"), EditCommand.PASTE,
+        addHistoryItem(new EditCommand(
+                MessageManager.getString("label.add_sequences"),
+                Action.PASTE,
                 sequences, 0, alignment.getWidth(), alignment));
       }
       // Add any annotations attached to sequences
@@ -2261,8 +2266,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     /*
      * //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);
@@ -4180,16 +4186,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
        */
       msa = viewport.getAlignmentView(true);
     }
+    else if (viewport.getSelectionGroup() != null
+            && viewport.getSelectionGroup().getSize() == 1)
+    {
+      int option = JOptionPane.showConfirmDialog(this,
+              MessageManager.getString("warn.oneseq_msainput_selection"),
+              MessageManager.getString("label.invalid_selection"),
+              JOptionPane.OK_CANCEL_OPTION);
+      if (option == JOptionPane.OK_OPTION)
+      {
+        msa = viewport.getAlignmentView(false);
+      }
+    }
     else
     {
-      /*
-       * Vector seqs = viewport.getAlignment().getSequences();
-       * 
-       * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()];
-       * 
-       * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI)
-       * seqs.elementAt(i); } }
-       */
       msa = viewport.getAlignmentView(false);
     }
     return msa;
@@ -5812,6 +5822,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
     alignPanel.paintAlignment(true);
   }
+
+  /**
+   * 
+   * @return alignment panels in this alignemnt frame
+   */
+  public List<AlignmentViewPanel> getAlignPanels()
+  {
+    return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+  }
 }
 
 class PrintThread extends Thread