(JAL-978) refactored JABAWS2 service handle class to own package

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

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index e8b2e72..d063c5b 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -163,7 +163,8 @@ public class AnnotationRenderer
     {
       if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
       {
-        if (aa.groupRef != null && aa.groupRef.consensusData != null
+        // TODO implement group structure consensus
+        /* if (aa.groupRef != null && aa.groupRef.consensusData != null
                 && aa.groupRef.isShowSequenceLogo())
         {
           //TODO check what happens for group selections
@@ -171,11 +172,12 @@ public class AnnotationRenderer
                   aa.groupRef.consensusData[column], aa.groupRef
                           .getIgnoreGapsConsensus());
         }
+        */
         // TODO extend annotation row to enable dynamic and static profile data
         // to
         // be stored
         if (aa.groupRef == null && aa.sequenceRef == null
-                && av_renderProfile)
+                && av_renderProfile && hStrucConsensus!=null && hStrucConsensus.length>column)
         {
           return StructureFrequency.extractProfile(hStrucConsensus[column],
                   av_ignoreGapsConsensus);
@@ -201,6 +203,7 @@ public class AnnotationRenderer
     // NOTES:
     // AnnotationPanel needs to implement: ImageObserver, access to AlignViewport
     updateFromAwtRenderPanel(annotPanel, av);
+    fm = g.getFontMetrics();  
     AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
   
     int x = 0, y = 0;