JAL-4386 - Implementation of substitution matrix and test cases.

[jalview.git] / src / jalview / renderer / AnnotationRenderer.java

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 015db5c..a56f06c 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -38,6 +38,7 @@ import org.jfree.graphics2d.svg.SVGGraphics2D;
 import org.jibble.epsgraphics.EpsGraphics2D;
 
 import jalview.analysis.AAFrequency;
+import jalview.analysis.AlignmentUtils;
 import jalview.analysis.CodingUtils;
 import jalview.analysis.Rna;
 import jalview.analysis.StructureFrequency;
@@ -1617,6 +1618,9 @@ public class AnnotationRenderer
               colour = profcolour.findColour(codonTranslation.charAt(0),
                       column, null);
             }
+            if(_aa.label == "SecondaryStructureConsensus") {
+              colour = AlignmentUtils.getSecondaryStructureAnnotationColour(dc[0]);              
+            }
             else
             {