JAL-1925 update source version in license

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

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 1a4d7d7..5f1c886 100755 (executable)
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -60,6 +60,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
    * they exist
    */
   private boolean noGradient = false;
+
   IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
 
   @Override
@@ -115,6 +116,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
     bb = 0;
 
     noGradient = true;
+    checkLimits();
   }
 
   /**
@@ -141,6 +143,19 @@ public class AnnotationColourGradient extends FollowerColourScheme
     bb = maxColour.getBlue() - b1;
 
     noGradient = false;
+    checkLimits();
+  }
+
+  private void checkLimits()
+  {
+    aamax = annotation.graphMax;
+    aamin = annotation.graphMin;
+    if (annotation.isRNA())
+    {
+      // reset colour palette
+      ColourSchemeProperty.resetRnaHelicesShading();
+      ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
+    }
   }
 
   @Override
@@ -162,6 +177,7 @@ 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 +185,31 @@ 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)
+      {
+        ColourSchemeProperty.initRnaHelicesShading(1 + (int) aamax);
+      }
     }
   }
 
+  float aamin = 0f, aamax = 0f;
+
   public String getAnnotation()
   {
     return annotation.label;
@@ -234,8 +269,8 @@ public class AnnotationColourGradient extends FollowerColourScheme
   public Color findColour(char c, int j, SequenceI seq)
   {
     Color currentColour = Color.white;
-    AlignmentAnnotation annotation = (seqAssociated && seqannot!=null ? seqannot.get(seq)
-            : this.annotation);
+    AlignmentAnnotation annotation = (seqAssociated && seqannot != null ? seqannot
+            .get(seq) : this.annotation);
     if (annotation == null)
     {
       return currentColour;
@@ -262,7 +297,8 @@ public class AnnotationColourGradient extends FollowerColourScheme
                 || (annotationThreshold != null && (aboveAnnotationThreshold == ABOVE_THRESHOLD ? aj.value >= annotationThreshold.value
                         : aj.value <= annotationThreshold.value)))
         {
-          if (predefinedColours && aj.colour != null)
+          if (predefinedColours && aj.colour != null
+                  && !aj.colour.equals(Color.black))
           {
             currentColour = aj.colour;
           }
@@ -278,9 +314,16 @@ 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 = ColourSchemeProperty.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 +348,7 @@ 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 +360,46 @@ 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;