JAL-795 JAL-674 tweaked logic to avoid black annotation shading and hard-wire seconda...

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 3bca94b..713e55d 100755 (executable)
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -23,6 +23,7 @@ package jalview.schemes;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.Annotation;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
@@ -47,12 +48,18 @@ public class AnnotationColourGradient extends FollowerColourScheme
 
   GraphLine annotationThreshold;
 
-  float r1, g1, b1, rr, gg, bb, dr, dg, db;
+  float r1, g1, b1, rr, gg, bb;
 
   private boolean predefinedColours = false;
 
   private boolean seqAssociated = false;
 
+  /**
+   * false if the scheme was constructed without a minColour and maxColour used
+   * to decide if existing colours should be taken from annotation elements when
+   * they exist
+   */
+  private boolean noGradient = false;
   IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
 
   @Override
@@ -70,12 +77,9 @@ public class AnnotationColourGradient extends FollowerColourScheme
     acg.rr = rr;
     acg.gg = gg;
     acg.bb = bb;
-    acg.dr = dr;
-    acg.dg = dg;
-    acg.db = db;
     acg.predefinedColours = predefinedColours;
     acg.seqAssociated = seqAssociated;
-
+    acg.noGradient = noGradient;
     return acg;
   }
 
@@ -102,6 +106,15 @@ public class AnnotationColourGradient extends FollowerColourScheme
     {
       annotationThreshold = annotation.threshold;
     }
+    // clear values so we don't get weird black bands...
+    r1 = 254;
+    g1 = 254;
+    b1 = 254;
+    rr = 0;
+    gg = 0;
+    bb = 0;
+
+    noGradient = true;
   }
 
   /**
@@ -126,6 +139,8 @@ public class AnnotationColourGradient extends FollowerColourScheme
     rr = maxColour.getRed() - r1;
     gg = maxColour.getGreen() - g1;
     bb = maxColour.getBlue() - b1;
+
+    noGradient = false;
   }
 
   @Override
@@ -232,74 +247,101 @@ public class AnnotationColourGradient extends FollowerColourScheme
               && annotation.annotations[j] != null
               && !jalview.util.Comparison.isGap(c))
       {
+        Annotation aj = annotation.annotations[j];
+        // 'use original colours' => colourScheme != null
+        // -> look up colour to be used
+        // predefined colours => preconfigured shading
+        // -> only use original colours reference if thresholding enabled &
+        // minmax exists
+        // annotation.hasIcons => null or black colours replaced with glyph
+        // colours
+        // -> reuse original colours if present
+        // -> if thresholding enabled then return colour on non-whitespace glyph
 
-        if (annotation.annotations[j].colour != null)
-        {
-          if (predefinedColours || annotation.hasIcons)
-          {
-            return annotation.annotations[j].colour;
-          }
-        }
-        else
-        {
-          if (predefinedColours)
-          {
-            return (annotation.annotations[j].secondaryStructure == 'H' ? jalview.renderer.AnnotationRenderer.HELIX_COLOUR
-                    : annotation.annotations[j].secondaryStructure == 'E' ? jalview.renderer.AnnotationRenderer.SHEET_COLOUR
-                            : annotation.annotations[j].secondaryStructure != ' ' ? jalview.renderer.AnnotationRenderer.STEM_COLOUR
-                                    : currentColour);
-          }
-        }
         if (aboveAnnotationThreshold == NO_THRESHOLD
-                || (annotationThreshold != null
-                        && aboveAnnotationThreshold == ABOVE_THRESHOLD && annotation.annotations[j].value >= annotationThreshold.value)
-                || (annotationThreshold != null
-                        && aboveAnnotationThreshold == BELOW_THRESHOLD && annotation.annotations[j].value <= annotationThreshold.value))
+                || (annotationThreshold != null && (aboveAnnotationThreshold == ABOVE_THRESHOLD ? aj.value >= annotationThreshold.value
+                        : aj.value <= annotationThreshold.value)))
         {
-
-          float range = 1f;
-          if (thresholdIsMinMax
-                  && annotation.threshold != null
-                  && aboveAnnotationThreshold == ABOVE_THRESHOLD
-                  && annotation.annotations[j].value >= annotation.threshold.value)
-          {
-            range = (annotation.annotations[j].value - annotation.threshold.value)
-                    / (annotation.graphMax - annotation.threshold.value);
-          }
-          else if (thresholdIsMinMax && annotation.threshold != null
-                  && aboveAnnotationThreshold == BELOW_THRESHOLD
-                  && annotation.annotations[j].value >= annotation.graphMin)
+          if (predefinedColours && aj.colour != null)
           {
-            range = (annotation.annotations[j].value - annotation.graphMin)
-                    / (annotation.threshold.value - annotation.graphMin);
+            currentColour = aj.colour;
           }
-          else
+          else if (annotation.hasIcons
+                  && annotation.graph == AlignmentAnnotation.NO_GRAPH)
           {
-            range = (annotation.annotations[j].value - annotation.graphMin)
-                    / (annotation.graphMax - annotation.graphMin);
+            if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.'
+                    && aj.secondaryStructure != '-')
+            {
+              if (colourScheme != null)
+              {
+                currentColour = colourScheme.findColour(c, j, seq);
+              }
+              else
+              {
+              currentColour = annotation.annotations[j].secondaryStructure == 'H' ? jalview.renderer.AnnotationRenderer.HELIX_COLOUR
+                      : annotation.annotations[j].secondaryStructure == 'E' ? jalview.renderer.AnnotationRenderer.SHEET_COLOUR
+                              : jalview.renderer.AnnotationRenderer.STEM_COLOUR;
+              }
+            }
+            else
+            {
+              //
+              return Color.white;
+            }
           }
-
-          if (colourScheme != null)
+          else if (noGradient)
           {
-            currentColour = colourScheme.findColour(c, j, seq);
+            if (colourScheme != null)
+            {
+              currentColour = colourScheme.findColour(c, j, seq);
+            }
+            else
+            {
+              if (aj.colour != null)
+              {
+                currentColour = aj.colour;
+              }
+            }
           }
           else
           {
-            dr = rr * range + r1;
-            dg = gg * range + g1;
-            db = bb * range + b1;
+            // calculate a shade
+            float range = 1f;
+            if (thresholdIsMinMax
+                    && annotation.threshold != null
+                    && aboveAnnotationThreshold == ABOVE_THRESHOLD
+                    && annotation.annotations[j].value >= annotation.threshold.value)
+            {
+              range = (annotation.annotations[j].value - annotation.threshold.value)
+                      / (annotation.graphMax - annotation.threshold.value);
+            }
+            else if (thresholdIsMinMax
+                    && annotation.threshold != null
+                    && aboveAnnotationThreshold == BELOW_THRESHOLD
+                    && annotation.annotations[j].value >= annotation.graphMin)
+            {
+              range = (annotation.annotations[j].value - annotation.graphMin)
+                      / (annotation.threshold.value - annotation.graphMin);
+            }
+            else
+            {
+              range = (annotation.annotations[j].value - annotation.graphMin)
+                      / (annotation.graphMax - annotation.graphMin);
+            }
+
+            int dr = (int) (rr * range + r1), dg = (int) (gg * range + g1), db = (int) (bb
+                    * range + b1);
+
+            currentColour = new Color(dr, dg, db);
 
-            currentColour = new Color((int) dr, (int) dg, (int) db);
           }
         }
+        if (conservationColouring)
+        {
+          currentColour = applyConservation(currentColour, j);
+        }
       }
     }
-
-    if (conservationColouring)
-    {
-      currentColour = applyConservation(currentColour, j);
-    }
-
     return currentColour;
   }