Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

[jalview.git] / src / jalview / schemes / AnnotationColourGradient.java

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 75a07b9..a84ea52 100755 (executable)
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -37,6 +37,16 @@ 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;
@@ -94,6 +104,8 @@ public class AnnotationColourGradient extends FollowerColourScheme
     acg.predefinedColours = predefinedColours;
     acg.seqAssociated = seqAssociated;
     acg.noGradient = noGradient;
+    acg.positionToTransparency = positionToTransparency;
+    acg.perLineScore = perLineScore;
     return acg;
   }
 
@@ -192,14 +204,16 @@ public class AnnotationColourGradient extends FollowerColourScheme
       AnnotatedCollectionI alcontext = alignment instanceof AlignmentI
               ? alignment
               : alignment.getContext();
-      boolean f = true, rna = false;
-      for (AlignmentAnnotation alan : alcontext
-              .findAnnotation(annotation.getCalcId()))
+      boolean f = true, sf = true, rna = false;
+      long plcount = 0, ancount = 0;
+      for (AlignmentAnnotation alan : alcontext.findAnnotation(annotation
+              .getCalcId()))
       {
         if (alan.sequenceRef != null
                 && (alan.label != null && annotation != null
                         && alan.label.equals(annotation.label)))
         {
+          ancount++;
           if (!rna && alan.isRNA())
           {
             rna = true;
@@ -214,8 +228,30 @@ 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;
+      }
+      else
+      {
+        perLineScore = false;
+      }
       if (rna)
       {
         ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
@@ -223,7 +259,15 @@ 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 AlignmentAnnotation getAnnotation()
   {
@@ -439,11 +483,25 @@ public class AnnotationColourGradient extends FollowerColourScheme
       }
     }
 
-    int dr = (int) (redRange * range + redMin);
-    int dg = (int) (greenRange * range + greenMin);
-    int db = (int) (blueRange * range + blueMin);
-
-    return new Color(dr, dg, db);
+    // midtr sets the ceiling for bleaching out the shading
+    int trans = 0, midtr = 239;
+    if (perLineScore)
+    {
+      trans = (int) ((1f - range) * midtr);
+      range = (float) ((ann.score - plmin) / (plmax - aamin));
+    }
+    int dr = (int) (redRange * range + redMin),
+            dg = (int) (greenRange * range + greenMin),
+            db = (int) (blueRange * range + blueMin);
+    if (ann.score == ann.score && positionToTransparency)
+    {
+      return new Color(Math.min(dr + trans, midtr), Math.min(dg
+              + trans, midtr), Math.min(db + trans, midtr));
+    }
+    else
+    {
+      return new Color(dr, dg, db);
+    }
   }
 
   public boolean isPredefinedColours()