From 02be3ae9f384eb3af819a79ed3a2f7e54fb17851 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 9 Nov 2015 14:39:53 +0000
Subject: [PATCH] JAL-1950 - JAL-1958 hardwired hack to explore shading whole
 sequence by the annotation row score, and modulating shade
 with positional score.

---
 src/jalview/schemes/AnnotationColourGradient.java |   64 +++++++++++++++++++--
 1 file changed, 58 insertions(+), 6 deletions(-)

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 89b8f07..8511d86 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -34,6 +34,16 @@ import java.util.Map;
 
 public class AnnotationColourGradient extends FollowerColourScheme
 {
+  /**
+   * map positional scores to transparency rather than colour
+   */
+  boolean positionToTransparency = true;
+
+  /**
+   * compute shade based on annotation row score
+   */
+  boolean perLineScore = true;
+
   public static final int NO_THRESHOLD = -1;
 
   public static final int BELOW_THRESHOLD = 0;
@@ -81,6 +91,8 @@ public class AnnotationColourGradient extends FollowerColourScheme
     acg.predefinedColours = predefinedColours;
     acg.seqAssociated = seqAssociated;
     acg.noGradient = noGradient;
+    acg.positionToTransparency = positionToTransparency;
+    acg.perLineScore = perLineScore;
     return acg;
   }
 
@@ -177,7 +189,8 @@ public class AnnotationColourGradient extends FollowerColourScheme
       // resolve the context containing all the annotation for the sequence
       AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
               : alignment.getContext();
-      boolean f = true, rna = false;
+      boolean f = true, sf = true, rna = false;
+      long plcount = 0, ancount = 0;
       for (AlignmentAnnotation alan : alcontext.findAnnotation(annotation
               .getCalcId()))
       {
@@ -185,6 +198,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
                 && (alan.label != null && annotation != null && alan.label
                         .equals(annotation.label)))
         {
+          ancount++;
           if (!rna && alan.isRNA())
           {
             rna = true;
@@ -199,8 +213,26 @@ public class AnnotationColourGradient extends FollowerColourScheme
             aamin = alan.graphMin;
           }
           f = false;
+          if (alan.score == alan.score)
+          {
+            if (sf || alan.score < plmin)
+            {
+              plmin = alan.score;
+            }
+            if (sf || alan.score > plmax)
+            {
+              plmax = alan.score;
+            }
+            sf = false;
+            plcount++;
+          }
         }
       }
+      if (plcount > 0 && plcount == ancount)
+      {
+        perLineScore = plcount == ancount;
+        aamax=plmax;
+      }
       if (rna)
       {
         ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
@@ -208,7 +240,15 @@ public class AnnotationColourGradient extends FollowerColourScheme
     }
   }
 
-  float aamin = 0f, aamax = 0f;
+  /**
+   * positional annotation max/min
+   */
+  double aamin = 0.0, aamax = 0.0;
+
+  /**
+   * per line score max/min
+   */
+  double plmin = Double.NaN, plmax = Double.NaN;
 
   public String getAnnotation()
   {
@@ -250,6 +290,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public Color findColour(char c)
   {
     return Color.red;
@@ -392,12 +433,23 @@ public class AnnotationColourGradient extends FollowerColourScheme
         range = 0f;
       }
     }
-
+    int trans = 0;
+    if (perLineScore)
+    {
+      trans = (int) ((1f - range) * 255.0);
+      range = (float) ((annotation.score - plmin) / (plmax - aamin));
+    }
     int dr = (int) (rr * range + r1), dg = (int) (gg * range + g1), db = (int) (bb
             * range + b1);
-
-    return new Color(dr, dg, db);
-
+    if (annotation.score == annotation.score && positionToTransparency)
+    {
+      return new Color(Integer.min(dr + trans, 255), Integer.min(
+              dg + trans, 255), Integer.min(db + trans, 255));
+    }
+    else
+    {
+      return new Color(dr, dg, db);
+    }
   }
 
   public boolean isPredefinedColours()
-- 
1.7.10.2