JAL-1593 allow per-sequence shading of RNA helix (stored in each annotation element...

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 713e55d..ef77e4d 100755 (executable)
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -53,7 +53,33 @@ public class AnnotationColourGradient extends FollowerColourScheme
   private boolean predefinedColours = false;
 
   private boolean seqAssociated = false;
-
+  Color rnaHelices[] = null;
+  private void initRnaHelicesShading(int n)
+  {
+    int j = 0;
+    if (rnaHelices==null) 
+    {
+      rnaHelices = new Color[n + 1];
+    }
+    else
+    if (rnaHelices != null && rnaHelices.length <= n)
+    {
+      Color[] t = new Color[n + 1];
+      System.arraycopy(rnaHelices, 0, t, 0, rnaHelices.length);
+      j = rnaHelices.length;
+      rnaHelices = t;
+    }
+    else
+    {
+      return;
+    }
+    // Generate random colors and store
+    for (; j <= n; j++)
+    {
+      rnaHelices[j] = jalview.util.ColorUtils
+              .generateRandomColor(Color.white);
+    }
+  }
   /**
    * false if the scheme was constructed without a minColour and maxColour used
    * to decide if existing colours should be taken from annotation elements when
@@ -141,6 +167,12 @@ public class AnnotationColourGradient extends FollowerColourScheme
     bb = maxColour.getBlue() - b1;
 
     noGradient = false;
+    aamax = annotation.graphMax;
+    aamin = annotation.graphMin;
+    if (annotation.isRNA())
+    {
+      initRnaHelicesShading(1 + (int) aamax);
+    }
   }
 
   @Override
@@ -162,6 +194,7 @@ 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;
       for (AlignmentAnnotation alan : alcontext.findAnnotation(annotation
               .getCalcId()))
       {
@@ -169,12 +202,30 @@ public class AnnotationColourGradient extends FollowerColourScheme
                 && (alan.label != null && annotation != null && alan.label
                         .equals(annotation.label)))
         {
+          if (!rna && alan.isRNA())
+          {
+            rna = true;
+          }
           seqannot.put(alan.sequenceRef, alan);
+          if (f || alan.graphMax > aamax)
+          {
+            aamax = alan.graphMax;
+          }
+          if (f || alan.graphMin < aamin)
+          {
+            aamin = alan.graphMin;
+          }
+          f = false;
         }
       }
+      if (rna)
+      {
+        initRnaHelicesShading(1 + (int) aamax);
+      }
     }
   }
 
+  float aamin = 0f, aamax = 0f;
   public String getAnnotation()
   {
     return annotation.label;
@@ -278,9 +329,16 @@ public class AnnotationColourGradient extends FollowerColourScheme
               }
               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;
+                if (annotation.isRNA())
+                {
+                  currentColour = rnaHelices[(int) aj.value];
+                }
+                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
@@ -305,35 +363,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
           }
           else
           {
-            // 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 = shadeCalculation(annotation, j);
           }
         }
         if (conservationColouring)
@@ -345,6 +375,45 @@ public class AnnotationColourGradient extends FollowerColourScheme
     return currentColour;
   }
 
+  private Color shadeCalculation(AlignmentAnnotation annotation, int j)
+  {
+
+    // 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
+    {
+      if (annotation.graphMax != annotation.graphMin)
+      {
+        range = (annotation.annotations[j].value - annotation.graphMin)
+                / (annotation.graphMax - annotation.graphMin);
+      }
+      else
+      {
+        range = 0f;
+      }
+    }
+
+    int dr = (int) (rr * range + r1), dg = (int) (gg * range + g1), db = (int) (bb
+            * range + b1);
+
+    return new Color(dr, dg, db);
+
+  }
   public boolean isPredefinedColours()
   {
     return predefinedColours;