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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
8f25e77
..
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
}
// 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);
{
return AAFrequency.extractProfile(hconsensus[column],
av_ignoreGapsConsensus);
@@
-262,7
+262,7
@@
public class AnnotationRenderer
// to
// be stored
if (aa.groupRef == null && aa.sequenceRef == null
// to
// be stored
if (aa.groupRef == null && aa.sequenceRef == null
- && av_renderProfile && hStrucConsensus != null
+ && hStrucConsensus != null
&& hStrucConsensus.length > column)
{
return StructureFrequency.extractProfile(hStrucConsensus[column],
&& hStrucConsensus.length > column)
{
return StructureFrequency.extractProfile(hStrucConsensus[column],
@@
-318,7
+318,7
@@
public class AnnotationRenderer
boolean centreColLabels, centreColLabelsDef = av
.getCentreColumnLabels();
boolean scaleColLabel = false;
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();
boolean renderHistogram = true, renderProfile = true, normaliseProfile = false;
BitSet graphGroupDrawn = new BitSet();
@@
-343,7
+343,7
@@
public class AnnotationRenderer
renderProfile = row.groupRef.isShowSequenceLogo();
normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
}
renderProfile = row.groupRef.isShowSequenceLogo();
normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
}
- else if (row == consensusAnnot)
+ else if (row == consensusAnnot || row == structConsensusAnnot)
{
renderHistogram = av_renderHistogram;
renderProfile = av_renderProfile;
{
renderHistogram = av_renderHistogram;
renderProfile = av_renderProfile;