From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 15 Apr 2005 14:56:12 +0000 (+0000)
Subject: conservation & consensus recalc if group changed
X-Git-Tag: Release_2_0~415
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=29b7ff78d36ab33ab298001107b232d9a10c2fe5;p=jalview.git

conservation & consensus recalc if group changed
---

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 0cf954b..7aae434 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -14,7 +14,6 @@ public class SequenceGroup
   boolean displayBoxes;
   boolean displayText;
   boolean colourText;
-  boolean aaFrequencyValid = false;
   public Vector sequences = new Vector();
   int width = -1;
   public ColourSchemeI cs;
@@ -79,7 +78,6 @@ public class SequenceGroup
     if(endRes>=col)
       endRes = col;
 
-
     return true;
   }
 
@@ -108,6 +106,24 @@ public class SequenceGroup
   {
     if(!sequences.contains(s))
       sequences.addElement(s);
+
+
+    if(cs!=null)
+      cs.setConsensus( AAFrequency.calculate(sequences, 0, getWidth()) );
+
+    if(cs instanceof ConservationColourScheme)
+      recalcConservation();
+  }
+
+  void recalcConservation()
+  {
+      Conservation c = new Conservation(groupName,
+                                        ResidueProperties.propHash, 3,
+                                        sequences, 0, getWidth());
+      c.calculate();
+      c.verdict(false, 25);
+      ConservationColourScheme ccs = (ConservationColourScheme)cs;
+      ccs.conserve = c;
   }
 
   public void addOrRemove(SequenceI s)
@@ -121,6 +137,12 @@ public class SequenceGroup
   public void deleteSequence(SequenceI s)
   {
     sequences.removeElement(s);
+
+    if(cs!=null)
+      cs.setConsensus( AAFrequency.calculate(sequences, 0, getWidth()) );
+
+    if(cs instanceof ConservationColourScheme)
+      recalcConservation();
   }
 
 
@@ -184,19 +206,8 @@ public class SequenceGroup
     return displayBoxes;
   }
 
-  public Vector getAAFrequency()
-  {
-    if (aaFrequency == null || aaFrequencyValid == false)
-    {
-      aaFrequency = AAFrequency.calculate(sequences, 0, getWidth());
-      aaFrequencyValid = true;
-    }
-    return aaFrequency;
-  }
-
   public int getWidth()
   {
-    System.out.println("it is called");
     // MC This needs to get reset when characters are inserted and deleted
     for (int i = 0; i < sequences.size(); i++)
     {