X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=53562cb7d5df91598c7d26b8c186a6c7a1670f42;hb=4f8907121d304b0f9b499578578c3381b815db9d;hp=67b049a4f25f8f2773ea06e8f4c4e7d96325da63;hpb=ce66c3a512ba0d21dca3f389afc50b4a39ea5e1f;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 67b049a..53562cb 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -445,42 +445,109 @@ public class SeqPanel
   {
     if (endEdit == startEdit)
     {
-      ap.alignFrame.historyList.pop();
-      ap.alignFrame.updateEditMenuBar();
+        ap.alignFrame.historyList.pop();
+        ap.alignFrame.updateEditMenuBar();
     }
 
     av.updateConservation();
     av.updateConsensus();
 
-    // Y O Y CLUSTALX
-    ColourSchemeI cs = av.getGlobalColourScheme();
-    if (cs instanceof ConservationColourScheme)
+
+    //Does the edit affect any groups?
+    //////////////////////////////
+    Vector groupsToUpdate = new Vector();
+    SequenceGroup sg = av.getSelectionGroup();
+
+    int s, g, gSize = av.alignment.getGroups().size();
+    if (sg != null)
     {
-      ConservationColourScheme ccs = (ConservationColourScheme) cs;
-      if (ccs.cs instanceof ClustalxColourScheme)
+      groupsToUpdate.addElement(av.getSelectionGroup());
+      int sSize = sg.getSize();
+      for (s = 0; s < sSize; s++)
       {
-        jalview.analysis.Conservation c = new jalview.analysis.Conservation
-            ("All",
-             ResidueProperties.propHash, 3,
-             av.alignment.getSequences(), 0,
-             av.alignment.getWidth() - 1);
-        c.calculate();
-        c.verdict(false, av.ConsPercGaps);
+        SequenceI seq = sg.getSequenceAt(s);
 
-        ClustalxColourScheme cxs = (ClustalxColourScheme) ccs.cs;
-        cxs.resetClustalX(av.alignment.getSequences(), av.alignment.getWidth());
-        ccs = new ConservationColourScheme(c, cxs);
-        av.setGlobalColourScheme(ccs);
+        for (g = 0; g < gSize; g++)
+        {
+          SequenceGroup sg2 = (SequenceGroup) av.alignment.getGroups().
+              elementAt(
+                  g);
+          if (sg2.sequences.contains(seq))
+          {
+            if (!groupsToUpdate.contains(sg2))
+              groupsToUpdate.addElement(sg2);
+            continue;
+          }
+        }
       }
     }
+    else
+    {
+      SequenceI seq = av.alignment.getSequenceAt(startseq);
+      for (g = 0; g < gSize; g++)
+      {
+        SequenceGroup sg2 = (SequenceGroup) av.alignment.getGroups().elementAt(
+            g);
+        if (sg2.sequences.contains(seq))
+        {
+          if (!groupsToUpdate.contains(sg2))
+            groupsToUpdate.addElement(sg2);
+          continue;
+        }
+      }
+    }
+
+    gSize = groupsToUpdate.size();
+    for (g = 0; g < gSize; g++)
+    {
+      ( (SequenceGroup) groupsToUpdate.elementAt(g)).recalcConservation();
+    }
+    ////End of updating groups
+      //////////////////////////////////////////
+
+
+    // Y O Y CLUSTALX
+    ColourSchemeI cs = av.getGlobalColourScheme();
 
-    if (cs instanceof ClustalxColourScheme)
+    if (av.getSelectionGroup() != null)
     {
-      ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),
-                                                 av.alignment.getWidth());
-      av.setGlobalColourScheme(cs);
+        av.getSelectionGroup().recalcConservation();
     }
 
+    if(cs!=null)
+    {
+      if (cs.conservationApplied())
+      {
+        jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
+                                          ResidueProperties.propHash, 3,
+                                          av.alignment.getSequences(),
+                                          0, av.alignment.getWidth() - 1);
+        c.calculate();
+        c.verdict(false, av.ConsPercGaps);
+
+        if (cs instanceof ClustalxColourScheme)
+        {
+          ClustalxColourScheme cxs = (ClustalxColourScheme) cs;
+          cxs.resetClustalX(av.alignment.getSequences(),
+                            av.alignment.getWidth());
+          cs.setConservation(c);
+          av.setGlobalColourScheme(cs);
+        }
+        else
+        {
+          cs.setConservation(c);
+          av.setGlobalColourScheme(cs);
+        }
+
+      }
+
+      if (cs instanceof ClustalxColourScheme)
+      {
+        ( (ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),
+                                                   av.alignment.getWidth());
+        av.setGlobalColourScheme(cs);
+      }
+        }
   }
 
 //////////////////////////////////////////
@@ -566,7 +633,7 @@ public class SeqPanel
     else if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
              InputEvent.BUTTON3_MASK)
     {
-      APopupMenu popup = new APopupMenu(ap, null);
+      APopupMenu popup = new APopupMenu(ap, null, null);
       this.add(popup);
       popup.show(this, evt.getX(), evt.getY());
     }
@@ -604,19 +671,19 @@ public class SeqPanel
       return;
     }
 
-    if (stretchGroup.cs instanceof ConservationColourScheme)
-    {
-      ConservationColourScheme ccs = (ConservationColourScheme) stretchGroup.cs;
-      stretchGroup.cs = ccs;
-      SliderPanel.setConservationSlider(ap, stretchGroup.cs,
-                                        stretchGroup.getName());
-    }
-    else
+    if(stretchGroup.cs!=null)
     {
+      if (stretchGroup.cs.conservationApplied())
+      {
+        SliderPanel.setConservationSlider(ap, stretchGroup.cs,
+                                          stretchGroup.getName());
+      }
+      else
+      {
         SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
                                        stretchGroup.getName());
+      }
     }
-
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
@@ -698,7 +765,6 @@ public class SeqPanel
       if (stretchGroup.sequences.contains(nextSeq))
       {
         stretchGroup.deleteSequence(seq, false);
-        stretchGroup.deleteSequence(nextSeq, false);
       }
       else
       {