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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 83ee1c3..afb1f0c 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -82,8 +82,11 @@ public class AlignFrame extends GAlignFrame
 
       if (currentFileFormat.equals("Jalview"))
       {
-        String shortName = title.replace('/', '_');
-        title = title.replace('\\', '_');
+        String shortName = title;
+        if(shortName.indexOf(java.io.File.separatorChar)>-1)
+              shortName = shortName.substring(
+                    shortName.lastIndexOf(java.io.File.separatorChar)+1);
+
         String choice = chooser.getSelectedFile().getPath();
         Jalview2XML.SaveState(this, choice, shortName);
         // USE Jalview2XML to save this file
@@ -250,12 +253,12 @@ 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)
@@ -1090,6 +1093,7 @@ public class AlignFrame extends GAlignFrame
     }
 
    addTreeMenuItem(tp, title);
+   viewport.setCurrentTree(tp.getTree());
 
    Desktop.addInternalFrame(tp, title, 600, 500);
   }
@@ -1187,10 +1191,46 @@ public class AlignFrame extends GAlignFrame
 
         }
         if (msa!=null) {
+          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)
 {
     SequenceI seq=null;
@@ -1273,7 +1313,7 @@ public class AlignFrame extends GAlignFrame
 
       }
       if (msa!=null) {
-        MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS",title, msa, true, true);
+        MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS",title, msa, false, true);
       }
   }
     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {