From be707dc4d1ea70abc29cbe3fd4489be7bb692117 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 26 Apr 2007 11:51:26 +0000
Subject: [PATCH] Edit seqs

---
 src/jalview/gui/EditNameDialog.java |   11 +++++----
 src/jalview/gui/PopupMenu.java      |   45 +++++++++++++++++++++++++++++++++++
 2 files changed, 52 insertions(+), 4 deletions(-)

diff --git a/src/jalview/gui/EditNameDialog.java b/src/jalview/gui/EditNameDialog.java
index b6cc5a5..a3d2d47 100644
--- a/src/jalview/gui/EditNameDialog.java
+++ b/src/jalview/gui/EditNameDialog.java
@@ -63,10 +63,13 @@ public class EditNameDialog
     panel2.add(idlabel, BorderLayout.WEST);
     panel2.add(id, BorderLayout.CENTER);
     panel.add(panel2, BorderLayout.NORTH);
-    panel2 = new JPanel(new BorderLayout());
-    panel2.add(desclabel, BorderLayout.WEST);
-    panel2.add(description, BorderLayout.CENTER);
-    panel.add(panel2, BorderLayout.SOUTH);
+    if(desc!=null || label2!=null)
+    {
+      panel2 = new JPanel(new BorderLayout());
+      panel2.add(desclabel, BorderLayout.WEST);
+      panel2.add(description, BorderLayout.CENTER);
+      panel.add(panel2, BorderLayout.SOUTH);
+    }
 
     int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
         panel, title,
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index ef87c2f..1df8041 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -85,6 +85,7 @@ public class PopupMenu
   JMenu structureMenu = new JMenu();
   JMenu viewStructureMenu = new JMenu();
   JMenu colStructureMenu = new JMenu();
+  JMenuItem editSequence = new JMenuItem();
 
   /**
    * Creates a new PopupMenu object.
@@ -566,6 +567,14 @@ public class PopupMenu
     structureMenu.setText("Structure");
     viewStructureMenu.setText("View Structure");
     colStructureMenu.setText("Colour By Structure");
+    editSequence.setText("Edit Sequence...");
+    editSequence.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        editSequence_actionPerformed(actionEvent);
+      }
+    });
 
     add(groupMenu);
 
@@ -616,6 +625,7 @@ public class PopupMenu
     colourMenu.add(conservationMenuItem);
     editMenu.add(copy);
     editMenu.add(cut);
+    editMenu.add(editSequence);
     editMenu.add(upperCase);
     editMenu.add(lowerCase);
     editMenu.add(toggle);
@@ -1403,4 +1413,39 @@ public class PopupMenu
     sequence.addAlignmentAnnotation(an);
 
     }
+
+  public void editSequence_actionPerformed(ActionEvent actionEvent)
+  {
+      SequenceGroup sg = ap.av.getSelectionGroup();
+
+      if(sg!=null)
+      {
+        if (sequence == null)
+          sequence = (Sequence) sg.getSequenceAt(0);
+
+        EditNameDialog dialog = new EditNameDialog(
+            sequence.getSequenceAsString(
+                sg.getStartRes(),
+                sg.getEndRes() + 1),
+            null,
+            "Edit Sequence ",
+            null,
+            "Edit Sequence");
+
+        if (dialog.accept)
+        {
+          EditCommand editCommand = new EditCommand(
+              "Edit Sequences", EditCommand.REPLACE,
+              dialog.getName(),
+              sg.getSequencesAsArray(ap.av.hiddenRepSequences),
+              sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment
+              );
+
+          ap.alignFrame.addHistoryItem(editCommand);
+
+          ap.av.firePropertyChange("alignment", null,
+                                   ap.av.getAlignment().getSequences());
+        }
+      }
+  }
 }
-- 
1.7.10.2