From d3fb461d66f67625686387cb75f6e9589510a577 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 23 Apr 2007 15:13:00 +0000
Subject: [PATCH] functions that operate on references to sequences in
 alignment rather than copies.

---
 src/jalview/gui/AlignFrame.java |   26 ++++++++++++++++----------
 1 file changed, 16 insertions(+), 10 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 61e2af4..c60355c 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1310,7 +1310,7 @@ public class AlignFrame
       return;
     }
     //  TODO: preserve the ordering of displayed alignment annotation in any internal paste (particularly sequence associated annotation)
-    SequenceI [] seqs = viewport.getSelectionAsNewSequence();
+    SequenceI [] seqs = viewport.getSelectionAsNewSequence();  
     String[] omitHidden = null;
 
     if (viewport.hasHiddenColumns)
@@ -1477,7 +1477,7 @@ public class AlignFrame
 
      if (newAlignment)
      {
-
+       
        if (Desktop.jalviewClipboard != null)
        {
          // dataset is inherited
@@ -1503,10 +1503,10 @@ public class AlignFrame
         // an existing alignment
         Vector newDs = (importDs) ? new Vector() : null; // used to create
                                                           // minimum dataset set
-
+        
         for (int i = 0; i < sequences.length; i++)
         {
-          if (importDs)
+          if (importDs) 
           {
             newDs.addElement(null);
           }
@@ -1516,7 +1516,7 @@ public class AlignFrame
           {
             if (!newDs.contains(ds))
             {
-              newDs.setElementAt(ds, i);
+              newDs.setElementAt(ds, i); 
               ds = new Sequence(ds);
               // update with new dataset sequence
               sequences[i].setDatasetSequence(ds);
@@ -1581,7 +1581,7 @@ public class AlignFrame
            alignment.setAnnotationIndex(sequences[i].getAnnotation()[a], a);
          }
 
-
+         
        }
      }
      if (!newAlignment) {
@@ -1610,7 +1610,7 @@ public class AlignFrame
        //>>>This is a fix for the moment, until a better solution is found!!<<<
        af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(
            alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
-
+       
        // TODO: maintain provenance of an alignment, rather than just make the title a concatenation of operations.
        if (!externalPaste) {
          if (title.startsWith("Copied sequences"))
@@ -3336,21 +3336,27 @@ public class AlignFrame
   }
 
 
+  /**
+   * empty the web service menu and add any ad-hoc functions
+   * not dynamically discovered.
+   *
+   */
   private void resetWebServiceMenu()
   {
     webService.removeAll();
     // Temporary hack - DBRef Fetcher always top level ws entry.
     JMenuItem rfetch = new JMenuItem("Fetch DB References");
+    rfetch.setToolTipText("Retrieve and parse uniprot records for the alignment or the currently selected sequences");
     webService.add(rfetch);
     rfetch.addActionListener(new ActionListener() {
 
       public void actionPerformed(ActionEvent e)
       {
         new jalview.io.DBRefFetcher(
-                alignPanel.av.alignment.getSequencesArray(),
+                alignPanel.av.getSequenceSelection(),
                 alignPanel.alignFrame).fetchDBRefs(false);
       }
-
+      
     });
   }
 
@@ -3380,7 +3386,7 @@ public void showTranslation_actionPerformed(ActionEvent e)
   ///////////////////////////////
   // Collect Data to be translated/transferred
 
-  SequenceI [] selection = viewport.getSelectionAsNewSequence();
+  SequenceI [] selection = viewport.getSequenceSelection();
   String [] seqstring = viewport.getViewAsString(true);
   AlignmentI al  = null;
   try {
-- 
1.7.10.2