JAL-3853 JAL-1870 patch tests for annotation colour gradient without transparency...

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

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 220d3ab..8526684 100755 (executable)
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -20,6 +20,7 @@
  */
 package jalview.schemes;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AnnotatedCollectionI;
@@ -36,6 +37,16 @@ import java.util.Map;
 
 public class AnnotationColourGradient extends FollowerColourScheme
 {
+  /**
+   * map positional scores to transparency rather than colour
+   */
+  boolean positionToTransparency = false;
+
+  /**
+   * compute shade based on annotation row score
+   */
+  boolean perLineScore = false;
+
   public static final int NO_THRESHOLD = -1;
 
   public static final int BELOW_THRESHOLD = 0;
@@ -76,8 +87,8 @@ public class AnnotationColourGradient extends FollowerColourScheme
   private IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
 
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI sg,
-          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI sg)
   {
     AnnotationColourGradient acg = new AnnotationColourGradient(annotation,
             getColourScheme(), aboveAnnotationThreshold);
@@ -93,6 +104,8 @@ public class AnnotationColourGradient extends FollowerColourScheme
     acg.predefinedColours = predefinedColours;
     acg.seqAssociated = seqAssociated;
     acg.noGradient = noGradient;
+    acg.positionToTransparency = positionToTransparency;
+    acg.perLineScore = perLineScore;
     return acg;
   }
 
@@ -185,19 +198,22 @@ public class AnnotationColourGradient extends FollowerColourScheme
       }
       else
       {
-        seqannot = new IdentityHashMap<SequenceI, AlignmentAnnotation>();
+        seqannot = new IdentityHashMap<>();
       }
       // resolve the context containing all the annotation for the sequence
-      AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
+      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()))
       {
         if (alan.sequenceRef != null
-                && (alan.label != null && annotation != null && alan.label
-                        .equals(annotation.label)))
+                && (alan.label != null && annotation != null
+                        && alan.label.equals(annotation.label)))
         {
+          ancount++;
           if (!rna && alan.isRNA())
           {
             rna = true;
@@ -212,8 +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 = plmax!=plmin;
+        aamax=plmax;
+      }
+      else
+      {
+        perLineScore = false;
+      }
       if (rna)
       {
         ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
@@ -221,7 +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()
   {
@@ -252,8 +298,8 @@ public class AnnotationColourGradient extends FollowerColourScheme
 
   public Color getMaxColour()
   {
-    return new Color(redMin + redRange, greenMin + greenRange, blueMin
-            + blueRange);
+    return new Color(redMin + redRange, greenMin + greenRange,
+            blueMin + blueRange);
   }
 
   /**
@@ -287,8 +333,9 @@ public class AnnotationColourGradient extends FollowerColourScheme
     /*
      * locate the annotation we are configured to colour by
      */
-    AlignmentAnnotation ann = (seqAssociated && seqannot != null ? seqannot
-            .get(seq) : this.annotation);
+    AlignmentAnnotation ann = (seqAssociated && seqannot != null
+            ? seqannot.get(seq)
+            : this.annotation);
 
     /*
      * if gap or no annotation at position, no colour (White)
@@ -316,8 +363,10 @@ public class AnnotationColourGradient extends FollowerColourScheme
      */
     if (annotationThreshold != null)
     {
-      if ((aboveAnnotationThreshold == ABOVE_THRESHOLD && aj.value < annotationThreshold.value)
-              || (aboveAnnotationThreshold == BELOW_THRESHOLD && aj.value > annotationThreshold.value))
+      if ((aboveAnnotationThreshold == ABOVE_THRESHOLD
+              && aj.value <= annotationThreshold.value)
+              || (aboveAnnotationThreshold == BELOW_THRESHOLD
+                      && aj.value >= annotationThreshold.value))
       {
         return Color.white;
       }
@@ -354,8 +403,10 @@ public class AnnotationColourGradient extends FollowerColourScheme
           }
           else
           {
-            result = ann.annotations[j].secondaryStructure == 'H' ? AnnotationRenderer.HELIX_COLOUR
-                    : ann.annotations[j].secondaryStructure == 'E' ? AnnotationRenderer.SHEET_COLOUR
+            result = ann.annotations[j].secondaryStructure == 'H'
+                    ? AnnotationRenderer.HELIX_COLOUR
+                    : ann.annotations[j].secondaryStructure == 'E'
+                            ? AnnotationRenderer.SHEET_COLOUR
                             : AnnotationRenderer.STEM_COLOUR;
           }
         }
@@ -408,14 +459,17 @@ public class AnnotationColourGradient extends FollowerColourScheme
             && aboveAnnotationThreshold == ABOVE_THRESHOLD
             && value >= ann.threshold.value)
     {
-      range = (value - ann.threshold.value)
+      range = ann.graphMax == ann.threshold.value ? 1f
+              : (value - ann.threshold.value)
               / (ann.graphMax - ann.threshold.value);
     }
     else if (thresholdIsMinMax && ann.threshold != null
             && aboveAnnotationThreshold == BELOW_THRESHOLD
             && value <= ann.threshold.value)
     {
-      range = (value - ann.graphMin) / (ann.threshold.value - ann.graphMin);
+      range = ann.graphMin == ann.threshold.value ? 0f
+              : (value - ann.graphMin)
+                      / (ann.threshold.value - ann.graphMin);
     }
     else
     {
@@ -429,11 +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()
@@ -469,7 +537,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
   @Override
   public String getSchemeName()
   {
-    return "Annotation";
+    return ANNOTATION_COLOUR;
   }
 
   @Override
@@ -477,4 +545,14 @@ public class AnnotationColourGradient extends FollowerColourScheme
   {
     return false;
   }
+
+  public boolean isPositionToTransparency()
+  {
+    return positionToTransparency;
+  }
+
+  public void setPositionToTransparency(boolean positionToTransparency)
+  {
+    this.positionToTransparency = positionToTransparency;
+  }
 }