X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=7fd746127eacd37f5c314def3b16c276386a7a18;hb=e7ed63f1ea56432246a6ed1553f0fe56d26f56ea;hp=36270209228a21332ad2f9e0d6c2c669fc95dda5;hpb=cd6569ba3b502e53e9aac0ce07858c36a4bf6ae3;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 3627020..7fd7461 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -75,57 +75,82 @@ 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()
   {
-    Annotation [] annotations = new Annotation[alignment.getWidth()];
-
     Conservation cons = new jalview.analysis.Conservation("All",
         jalview.schemes.ResidueProperties.propHash, 3,
         alignment.getSequences(), 0,
-        alignment.getWidth());
+        alignment.getWidth()-1);
     cons.calculate();
-    cons.verdict(false, 100);
+    cons.verdict(false, ConsPercGaps);
     cons.findQuality();
+    int alWidth = alignment.getWidth();
+    Annotation [] annotations = new Annotation[alWidth];
+    Annotation [] qannotations = new Annotation[alWidth];
     String sequence = cons.getConsSequence().getSequence();
     float minR,minG,minB, maxR,maxG,maxB;
     minR = 0.3f;
-    minG = 0f;
+    minG = 0.0f;
     minB = 0f;
-    maxR = 1.0f-minR; maxG=0.9f-minG; maxB=0f-minB; // scalable range for colouring
-    float min = cons.qualityRange[0].floatValue();
-    float max = cons.qualityRange[1].floatValue();
+    maxR = 1.0f-minR; maxG=0.9f-minG; maxB=0f-minB; // scalable range for colouring both Conservation and Quality
+    float min = 0f;
+    float max = 11f;
+    float qmin = cons.qualityRange[0].floatValue();
+    float qmax = cons.qualityRange[1].floatValue();
 
-    for (int i = 0; i < alignment.getWidth(); i++)
+    for (int i = 0; i < alWidth; i++)
     {
       float value = 0;
       try
-      {
-        //value = Integer.parseInt(sequence.charAt(i) + "");
-        value = ((Double) cons.quality.get(i)).floatValue();
-      }
+        {
+          value = Integer.parseInt(sequence.charAt(i) + "");
+        }
       catch (Exception ex)
-      {
-        if (sequence.charAt(i) == '*') value = 10;
-      }
+        {
+          if (sequence.charAt(i) == '*') value = 11;
+          if (sequence.charAt(i) == '+') value = 10;
+        }
       float vprop = value-min;
       vprop/=max;
       annotations[i] = new Annotation(sequence.charAt(i) + "",
-                                      "Conservation graph", ' ', value, new Color(minR+maxR*vprop, minB+maxB*vprop, minB+maxB*vprop));
+                                      "Conservation graph", ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));
+      // Quality calc
+      value = ((Double) cons.quality.get(i)).floatValue();
+      vprop = value - qmin;
+      vprop/=qmax;
+      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("Quality",
-                                             "Quality of total alignment",
+      conservation = new AlignmentAnnotation("Conservation",
+                                             "Conservation of total alignment less than "+ConsPercGaps+"% gaps",
                                              annotations,
-                                             cons.qualityRange[0].floatValue(),
-                                             cons.qualityRange[1].floatValue(), 1);
+                                             0f, // cons.qualityRange[0].floatValue(),
+                                             11f, // cons.qualityRange[1].floatValue()
+                                             1);
       alignment.addAnnotation(conservation);
+      quality = new AlignmentAnnotation("Quality",
+                                        "Alignment Quality based on Blosum62 scores",
+                                        qannotations,
+                                        cons.qualityRange[0].floatValue(),
+                                        cons.qualityRange[1].floatValue(),
+                                        1);
+      alignment.addAnnotation(quality);
     }
-    else
+    else {
       conservation.annotations = annotations;
+      quality.annotations = qannotations;
+    }
+
 
   }
 
@@ -133,11 +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++)
+    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());
 
@@ -166,32 +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; i < consensusV.size(); i++)
-      {
-        hash = (Hashtable) consensusV.elementAt(i);
-        sb.append(hash.get("maxResidue").toString().charAt(0));
-      }
-      visibleConsensus = sb.toString();
-    }
-
-
-    return consensusV;
-  }
-
 
   public SequenceGroup getSelectionGroup()
   {
@@ -256,7 +269,7 @@ public class AlignViewport
   public void setEndRes(int res) {
     if (res > alignment.getWidth()-1) {
       System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
-       res = alignment.getWidth() -1;
+       res = alignment.getWidth()-1;
     }
     if (res < 0) {
       res = 0;