JAL-1233 TODO concerning the way we propagate annotation colourschemes to new groups.

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

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index f492d9c..09152d6 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -240,7 +240,7 @@ public class AnnotationRenderer
       }
       // TODO extend annotation row to enable dynamic and static profile data to
       // be stored
-      if (aa.groupRef == null && aa.sequenceRef == null && av_renderProfile)
+      if (aa.groupRef == null && aa.sequenceRef == null)
       {
         return AAFrequency.extractProfile(hconsensus[column],
                 av_ignoreGapsConsensus);
@@ -262,7 +262,7 @@ public class AnnotationRenderer
         // to
         // be stored
         if (aa.groupRef == null && aa.sequenceRef == null
-                && av_renderProfile && hStrucConsensus != null
+                && hStrucConsensus != null
                 && hStrucConsensus.length > column)
         {
           return StructureFrequency.extractProfile(hStrucConsensus[column],
@@ -318,7 +318,7 @@ public class AnnotationRenderer
     boolean centreColLabels, centreColLabelsDef = av
             .getCentreColumnLabels();
     boolean scaleColLabel = false;
-    AlignmentAnnotation consensusAnnot=av.getAlignmentConsensusAnnotation();
+    AlignmentAnnotation consensusAnnot=av.getAlignmentConsensusAnnotation(),structConsensusAnnot=av.getAlignmentStrucConsensusAnnotation();
     boolean renderHistogram = true, renderProfile = true, normaliseProfile = false;
 
     BitSet graphGroupDrawn = new BitSet();
@@ -333,6 +333,26 @@ public class AnnotationRenderer
     for (int i = 0; i < aa.length; i++)
     {
       AlignmentAnnotation row = aa[i];
+      {
+        // check if this is a consensus annotation row and set the display settings appropriately
+        // TODO: generalise this to have render styles for consensus/profile
+        // data
+        if (row.groupRef != null && row == row.groupRef.getConsensus())
+        {
+          renderHistogram = row.groupRef.isShowConsensusHistogram();
+          renderProfile = row.groupRef.isShowSequenceLogo();
+          normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
+        }
+        else if (row == consensusAnnot || row == structConsensusAnnot)
+        {
+          renderHistogram = av_renderHistogram;
+          renderProfile = av_renderProfile;
+          normaliseProfile = av_normaliseProfile;
+        } else {
+          renderHistogram = true;
+          // don't need to set render/normaliseProfile since they are not currently used in any other annotation track renderer
+        }
+      }
       Annotation[] row_annotations = row.annotations;
       if (!row.visible)
       {