X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=7fd746127eacd37f5c314def3b16c276386a7a18;hb=31a5f9724e7ba5c8f67a6db9a0c0f2356cd81b9d;hp=5535dbbaf3bbb5690e0dba43835e47134b7ebcfa;hpb=90925a374cc14797c3e353f30af938a2eec025a8;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 5535dbb..7fd7461 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -75,19 +75,21 @@ public class AlignViewport
    showSequenceFeatures = b;
  }
 
+  public Vector vconsensus;
   AlignmentAnnotation consensus;
   AlignmentAnnotation conservation;
   AlignmentAnnotation quality;
 
+  public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
+
   public void updateConservation()
   {
-    int percGaps = 100; // JBPNote : This should be a scalable property!
     Conservation cons = new jalview.analysis.Conservation("All",
-        jalview.schemes.ResidueProperties.propHash, 1,
+        jalview.schemes.ResidueProperties.propHash, 3,
         alignment.getSequences(), 0,
-        alignment.getWidth());
+        alignment.getWidth()-1);
     cons.calculate();
-    cons.verdict(false, percGaps);
+    cons.verdict(false, ConsPercGaps);
     cons.findQuality();
     int alWidth = alignment.getWidth();
     Annotation [] annotations = new Annotation[alWidth];
@@ -123,14 +125,14 @@ public class AlignViewport
       value = ((Double) cons.quality.get(i)).floatValue();
       vprop = value - qmin;
       vprop/=qmax;
-      qannotations[i] = new Annotation(sequence.charAt(i) + "",
-                                      new String().valueOf(value), ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));
+      qannotations[i] = new Annotation(" ",
+                                      String.valueOf(value), ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));
     }
 
     if(conservation==null)
     {
       conservation = new AlignmentAnnotation("Conservation",
-                                             "Conservation of total alignment less than "+percGaps+"% gaps",
+                                             "Conservation of total alignment less than "+ConsPercGaps+"% gaps",
                                              annotations,
                                              0f, // cons.qualityRange[0].floatValue(),
                                              11f, // cons.qualityRange[1].floatValue()
@@ -156,11 +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, alWidth=alignment.getWidth(); i<alWidth; i++)
+    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());
 
@@ -189,32 +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()
   {