From bda5c08954f09de8129b4d8498c484d5f3a6b032 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 15 Apr 2005 14:58:13 +0000
Subject: [PATCH] public vconsensus available for PID and Blosum

---
 src/jalview/gui/AlignViewport.java |   45 ++++++++++++++----------------------
 1 file changed, 17 insertions(+), 28 deletions(-)

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index b661b87..7fd7461 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -75,6 +75,7 @@ public class AlignViewport
    showSequenceFeatures = b;
  }
 
+  public Vector vconsensus;
   AlignmentAnnotation consensus;
   AlignmentAnnotation conservation;
   AlignmentAnnotation quality;
@@ -157,11 +158,25 @@ public class AlignViewport
   {
     Annotation [] annotations = new Annotation[alignment.getWidth()];
 
-    Vector cons = alignment.getAAFrequency();
+    // this routine prevents vconsensus becoming a new object each time
+    // consenus is calculated. Important for speed of Blosum62
+    // and PID colouring of alignment
+    if(vconsensus == null)
+        vconsensus = alignment.getAAFrequency();
+    else
+    {
+        Vector temp = alignment.getAAFrequency();
+        vconsensus.clear();
+        Enumeration e = temp.elements();
+        while(e.hasMoreElements())
+        {
+          vconsensus.add(e.nextElement());
+        }
+    }
     Hashtable hash = null;
     for (int i = 0; i<alignment.getWidth(); i++)
     {
-        hash = (Hashtable) cons.elementAt(i);
+        hash = (Hashtable) vconsensus.elementAt(i);
         float value = Float.parseFloat(hash.get("maxCount").toString());
         value /= Float.parseFloat(hash.get("size").toString());
 
@@ -190,32 +205,6 @@ public class AlignViewport
 
   }
 
-  public String getVisibleConsensus()
-  {
-    return visibleConsensus;
-  }
-
-  String visibleConsensus;
-  Vector consensusV = new Vector();
-  public Vector getConsensus(boolean recalculate)
-  {
-    if(recalculate || consensusV.size()<1)
-    {
-      consensusV = alignment.getAAFrequency();
-      StringBuffer sb = new StringBuffer();
-      Hashtable hash = null;
-      for (int i = 0, sz=consensusV.size(); i < sz; i++)
-      {
-        hash = (Hashtable) consensusV.elementAt(i);
-        sb.append(hash.get("maxResidue").toString().charAt(0));
-      }
-      visibleConsensus = sb.toString();
-    }
-
-
-    return consensusV;
-  }
-
 
   public SequenceGroup getSelectionGroup()
   {
-- 
1.7.10.2