From 90925a374cc14797c3e353f30af938a2eec025a8 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 14 Apr 2005 09:14:19 +0000
Subject: [PATCH] added quality calculation from Jalview118, and scale
 dependent colouring of conservation and quality histograms.
 Obvious for loop optimizations have also been applied.

---
 src/jalview/gui/AlignViewport.java |   73 ++++++++++++++++++++++++------------
 1 file changed, 48 insertions(+), 25 deletions(-)

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 3627020..5535dbb 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -77,55 +77,78 @@ public class AlignViewport
 
   AlignmentAnnotation consensus;
   AlignmentAnnotation conservation;
+  AlignmentAnnotation quality;
+
   public void updateConservation()
   {
-    Annotation [] annotations = new Annotation[alignment.getWidth()];
-
+    int percGaps = 100; // JBPNote : This should be a scalable property!
     Conservation cons = new jalview.analysis.Conservation("All",
-        jalview.schemes.ResidueProperties.propHash, 3,
+        jalview.schemes.ResidueProperties.propHash, 1,
         alignment.getSequences(), 0,
         alignment.getWidth());
     cons.calculate();
-    cons.verdict(false, 100);
+    cons.verdict(false, percGaps);
     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(sequence.charAt(i) + "",
+                                      new 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 "+percGaps+"% 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;
+    }
+
 
   }
 
@@ -135,7 +158,7 @@ public class AlignViewport
 
     Vector cons = alignment.getAAFrequency();
     Hashtable hash = null;
-    for (int i = 0; i < alignment.getWidth(); i++)
+    for (int i = 0, alWidth=alignment.getWidth(); i<alWidth; i++)
     {
         hash = (Hashtable) cons.elementAt(i);
         float value = Float.parseFloat(hash.get("maxCount").toString());
@@ -180,7 +203,7 @@ public class AlignViewport
       consensusV = alignment.getAAFrequency();
       StringBuffer sb = new StringBuffer();
       Hashtable hash = null;
-      for (int i = 0; i < consensusV.size(); i++)
+      for (int i = 0, sz=consensusV.size(); i < sz; i++)
       {
         hash = (Hashtable) consensusV.elementAt(i);
         sb.append(hash.get("maxResidue").toString().charAt(0));
@@ -256,7 +279,7 @@ 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;
-- 
1.7.10.2