Added clustalW 'realignment' (primitive)

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 343ca2b..4b2bdab 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -250,12 +250,12 @@ public class AlignFrame extends GAlignFrame
             viewport.alignment.deleteSequence(i);
         }
       }
-      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
       updateEditMenuBar();
 
       viewport.updateConsensus();
       viewport.updateConservation();
       alignPanel.repaint();
+      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
   }
 
   public void moveSelectedSequences(boolean up)
@@ -1190,6 +1190,42 @@ public class AlignFrame extends GAlignFrame
           jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS", title, msa, false, true);
         }
   }
+  public void ClustalRealign_actionPerformed(ActionEvent e)
+  {
+      // TODO:resolve which menu item was actually selected
+      // Now, check we have enough sequences
+        SequenceI[] msa=null;
+        if (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize()>1)
+        {
+          // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!
+          SequenceGroup seqs = viewport.getSelectionGroup();
+          int sz;
+          msa = new SequenceI[sz=seqs.getSize()];
+          for (int i = 0; i < sz; i++)
+          {
+            msa[i] = (SequenceI) seqs.getSequenceAt(i);
+          }
+
+          }
+        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);
+            }
+
+          }
+
+        }
+        if (msa!=null) {
+          jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS", title, msa, true, true);
+        }
+  }
+
 
   protected void jpred_actionPerformed(ActionEvent e)
 {