added quality calculation from Jalview118, and scale dependent

colouring of conservation and quality histograms.
Obvious for loop optimizations have also been applied.

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 3627020..5535dbb 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -77,55 +77,78 @@ public class AlignViewport
 \r
   AlignmentAnnotation consensus;\r
   AlignmentAnnotation conservation;\r
+  AlignmentAnnotation quality;\r
+\r
   public void updateConservation()\r
   {\r
-    Annotation [] annotations = new Annotation[alignment.getWidth()];\r
-\r
+    int percGaps = 100; // JBPNote : This should be a scalable property!\r
     Conservation cons = new jalview.analysis.Conservation("All",\r
-        jalview.schemes.ResidueProperties.propHash, 3,\r
+        jalview.schemes.ResidueProperties.propHash, 1,\r
         alignment.getSequences(), 0,\r
         alignment.getWidth());\r
     cons.calculate();\r
-    cons.verdict(false, 100);\r
+    cons.verdict(false, percGaps);\r
     cons.findQuality();\r
+    int alWidth = alignment.getWidth();\r
+    Annotation [] annotations = new Annotation[alWidth];\r
+    Annotation [] qannotations = new Annotation[alWidth];\r
     String sequence = cons.getConsSequence().getSequence();\r
     float minR,minG,minB, maxR,maxG,maxB;\r
     minR = 0.3f;\r
-    minG = 0f;\r
+    minG = 0.0f;\r
     minB = 0f;\r
-    maxR = 1.0f-minR; maxG=0.9f-minG; maxB=0f-minB; // scalable range for colouring\r
-    float min = cons.qualityRange[0].floatValue();\r
-    float max = cons.qualityRange[1].floatValue();\r
+    maxR = 1.0f-minR; maxG=0.9f-minG; maxB=0f-minB; // scalable range for colouring both Conservation and Quality\r
+    float min = 0f;\r
+    float max = 11f;\r
+    float qmin = cons.qualityRange[0].floatValue();\r
+    float qmax = cons.qualityRange[1].floatValue();\r
 \r
-    for (int i = 0; i < alignment.getWidth(); i++)\r
+    for (int i = 0; i < alWidth; i++)\r
     {\r
       float value = 0;\r
       try\r
-      {\r
-        //value = Integer.parseInt(sequence.charAt(i) + "");\r
-        value = ((Double) cons.quality.get(i)).floatValue();\r
-      }\r
+        {\r
+          value = Integer.parseInt(sequence.charAt(i) + "");\r
+        }\r
       catch (Exception ex)\r
-      {\r
-        if (sequence.charAt(i) == '*') value = 10;\r
-      }\r
+        {\r
+          if (sequence.charAt(i) == '*') value = 11;\r
+          if (sequence.charAt(i) == '+') value = 10;\r
+        }\r
       float vprop = value-min;\r
       vprop/=max;\r
       annotations[i] = new Annotation(sequence.charAt(i) + "",\r
-                                      "Conservation graph", ' ', value, new Color(minR+maxR*vprop, minB+maxB*vprop, minB+maxB*vprop));\r
+                                      "Conservation graph", ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));\r
+      // Quality calc\r
+      value = ((Double) cons.quality.get(i)).floatValue();\r
+      vprop = value - qmin;\r
+      vprop/=qmax;\r
+      qannotations[i] = new Annotation(sequence.charAt(i) + "",\r
+                                      new String().valueOf(value), ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));\r
     }\r
 \r
     if(conservation==null)\r
     {\r
-      conservation = new AlignmentAnnotation("Quality",\r
-                                             "Quality of total alignment",\r
+      conservation = new AlignmentAnnotation("Conservation",\r
+                                             "Conservation of total alignment less than "+percGaps+"% gaps",\r
                                              annotations,\r
-                                             cons.qualityRange[0].floatValue(),\r
-                                             cons.qualityRange[1].floatValue(), 1);\r
+                                             0f, // cons.qualityRange[0].floatValue(),\r
+                                             11f, // cons.qualityRange[1].floatValue()\r
+                                             1);\r
       alignment.addAnnotation(conservation);\r
+      quality = new AlignmentAnnotation("Quality",\r
+                                        "Alignment Quality based on Blosum62 scores",\r
+                                        qannotations,\r
+                                        cons.qualityRange[0].floatValue(),\r
+                                        cons.qualityRange[1].floatValue(),\r
+                                        1);\r
+      alignment.addAnnotation(quality);\r
     }\r
-    else\r
+    else {\r
       conservation.annotations = annotations;\r
+      quality.annotations = qannotations;\r
+    }\r
+\r
 \r
   }\r
 \r
@@ -135,7 +158,7 @@ public class AlignViewport
 \r
     Vector cons = alignment.getAAFrequency();\r
     Hashtable hash = null;\r
-    for (int i = 0; i < alignment.getWidth(); i++)\r
+    for (int i = 0, alWidth=alignment.getWidth(); i<alWidth; i++)\r
     {\r
         hash = (Hashtable) cons.elementAt(i);\r
         float value = Float.parseFloat(hash.get("maxCount").toString());\r
@@ -180,7 +203,7 @@ public class AlignViewport
       consensusV = alignment.getAAFrequency();\r
       StringBuffer sb = new StringBuffer();\r
       Hashtable hash = null;\r
-      for (int i = 0; i < consensusV.size(); i++)\r
+      for (int i = 0, sz=consensusV.size(); i < sz; i++)\r
       {\r
         hash = (Hashtable) consensusV.elementAt(i);\r
         sb.append(hash.get("maxResidue").toString().charAt(0));\r
@@ -256,7 +279,7 @@ public class AlignViewport
   public void setEndRes(int res) {\r
     if (res > alignment.getWidth()-1) {\r
       System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));\r
-       res = alignment.getWidth() -1;\r
+       res = alignment.getWidth()-1;\r
     }\r
     if (res < 0) {\r
       res = 0;\r