X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=e975884e6fcaaf6fab9116c90827e6398310c7af;hb=2a7662654294c090754af3eab70f1b65fcf36a14;hp=f619d071cfc9128647e96aae4b18f353e74d450c;hpb=50eb1f492f5c64b56594ee49be8183fab8a2f73b;p=jalview.git

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index f619d07..e975884 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,24 +1,27 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.schemes;
 
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.SequenceCollectionI;
@@ -51,13 +54,16 @@ public class AnnotationColourGradient extends FollowerColourScheme
   private boolean seqAssociated = false;
 
   IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
+
   @Override
   public ColourSchemeI applyTo(AnnotatedCollectionI sg,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
-    AnnotationColourGradient acg = new AnnotationColourGradient(annotation, colourScheme, aboveAnnotationThreshold);
+    AnnotationColourGradient acg = new AnnotationColourGradient(annotation,
+            colourScheme, aboveAnnotationThreshold);
     acg.thresholdIsMinMax = thresholdIsMinMax;
-    acg.annotationThreshold = (annotationThreshold==null) ? null : new GraphLine(annotationThreshold);
+    acg.annotationThreshold = (annotationThreshold == null) ? null
+            : new GraphLine(annotationThreshold);
     acg.r1 = r1;
     acg.g1 = g1;
     acg.b1 = b1;
@@ -69,9 +75,10 @@ public class AnnotationColourGradient extends FollowerColourScheme
     acg.db = db;
     acg.predefinedColours = predefinedColours;
     acg.seqAssociated = seqAssociated;
-    
+
     return acg;
   }
+
   /**
    * Creates a new AnnotationColourGradient object.
    */
@@ -125,7 +132,6 @@ public class AnnotationColourGradient extends FollowerColourScheme
   public void alignmentChanged(AnnotatedCollectionI alignment,
           Map<SequenceI, SequenceCollectionI> hiddenReps)
   {
-    // TODO Auto-generated method stub
     super.alignmentChanged(alignment, hiddenReps);
 
     if (seqAssociated && annotation.getCalcId() != null)
@@ -138,7 +144,10 @@ public class AnnotationColourGradient extends FollowerColourScheme
       {
         seqannot = new IdentityHashMap<SequenceI, AlignmentAnnotation>();
       }
-      for (AlignmentAnnotation alan : alignment.findAnnotation(annotation
+      // resolve the context containing all the annotation for the sequence
+      AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
+              : alignment.getContext();
+      for (AlignmentAnnotation alan : alcontext.findAnnotation(annotation
               .getCalcId()))
       {
         if (alan.sequenceRef != null
@@ -218,19 +227,26 @@ public class AnnotationColourGradient extends FollowerColourScheme
     }
     if ((threshold == 0) || aboveThreshold(c, j))
     {
-      if (annotation.annotations!=null && j < annotation.annotations.length
+      if (annotation.annotations != null
+              && j < annotation.annotations.length
               && annotation.annotations[j] != null
               && !jalview.util.Comparison.isGap(c))
       {
 
-        if (predefinedColours)
+        if (annotation.annotations[j].colour != null)
         {
-          if (annotation.annotations[j].colour != null)
+          if (predefinedColours || annotation.hasIcons)
+          {
             return annotation.annotations[j].colour;
-          else
+          }
+        }
+        else
+        {
+          if (predefinedColours)
+          {
             return currentColour;
+          }
         }
-
         if (aboveAnnotationThreshold == NO_THRESHOLD
                 || (annotationThreshold != null
                         && aboveAnnotationThreshold == ABOVE_THRESHOLD && annotation.annotations[j].value >= annotationThreshold.value)
@@ -264,7 +280,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
           {
             currentColour = colourScheme.findColour(c, j, seq);
           }
-          else 
+          else
           {
             dr = rr * range + r1;
             dg = gg * range + g1;