JAL-1347 RNA Structure consensus follows the alignment viewport consensus rendering...

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

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 6ed2b9f..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],
@@ -318,6 +318,8 @@ public class AnnotationRenderer
     boolean centreColLabels, centreColLabelsDef = av
             .getCentreColumnLabels();
     boolean scaleColLabel = false;
+    AlignmentAnnotation consensusAnnot=av.getAlignmentConsensusAnnotation(),structConsensusAnnot=av.getAlignmentStrucConsensusAnnotation();
+    boolean renderHistogram = true, renderProfile = true, normaliseProfile = false;
 
     BitSet graphGroupDrawn = new BitSet();
     int charOffset = 0; // offset for a label
@@ -331,6 +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)
       {
@@ -674,7 +696,7 @@ public class AnnotationRenderer
         else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
         {
           drawBarGraph(g, row, row_annotations, startRes, endRes,
-                  row.graphMin, row.graphMax, y);
+                  row.graphMin, row.graphMax, y, renderHistogram,renderProfile,normaliseProfile);
         }
       }
     } else {
@@ -910,7 +932,7 @@ public class AnnotationRenderer
 
   public void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
           Annotation[] aa_annotations, int sRes, int eRes, float min,
-          float max, int y)
+          float max, int y, boolean renderHistogram,boolean renderProfile,boolean normaliseProfile)
   {
     if (sRes > aa_annotations.length)
     {
@@ -934,23 +956,6 @@ public class AnnotationRenderer
 
     int column;
     int aaMax = aa_annotations.length - 1;
-    boolean renderHistogram = true, renderProfile = true, normaliseProfile = false;
-    // if (aa.autoCalculated && aa.label.startsWith("Consensus"))
-    {
-      // TODO: generalise this to have render styles for consensus/profile data
-      if (_aa.groupRef != null)
-      {
-        renderHistogram = _aa.groupRef.isShowConsensusHistogram();
-        renderProfile = _aa.groupRef.isShowSequenceLogo();
-        normaliseProfile = _aa.groupRef.isNormaliseSequenceLogo();
-      }
-      else
-      {
-        renderHistogram = av_renderHistogram;
-        renderProfile = av_renderProfile;
-        normaliseProfile = av_normaliseProfile;
-      }
-    }
     while (x < eRes - sRes)
     {
       column = sRes + x;