add partial button fix to annotation and statistics output

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

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 95bbf28..1f3d5a9 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -87,6 +87,8 @@ public class AnnotationRenderer
 
   private boolean av_ignoreGapsConsensus;
 
+  private boolean av_ignoreBelowBackground;
+
   /**
    * attributes set from AwtRenderPanelI
    */
@@ -335,6 +337,7 @@ public class AnnotationRenderer
     complementConsensus = av.getComplementConsensusHash();
     hStrucConsensus = av.getRnaStructureConsensusHash();
     av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
+    av_ignoreBelowBackground = av.isIgnoreBelowBackground();
   }
 
 
@@ -357,7 +360,8 @@ public class AnnotationRenderer
     if (aa.label.startsWith("Information"))
     {
       return AAFrequency.getHMMProfileFor(aa, column,
-              true); // TODO detect setting
+              av_ignoreBelowBackground); // TODO check if this follows standard
+                                         // pipeline
     }
     if (aa.autoCalculated
             && (aa.label.startsWith("Consensus") || aa.label