JAL-2629 add option to set HMM Logo letter height to info content

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

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 6099a85..70d534c 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -75,7 +75,7 @@ public class AnnotationRenderer
           av_normaliseProfile = false;
 
   boolean av_renderInformationHistogram = true, av_renderHMMProfile = true,
-          av_normaliseHMMProfile = false;
+          av_normaliseHMMProfile = false, av_infoHeight = false;
 
   ResidueShaderI profcolour = null;
 
@@ -353,6 +353,7 @@ public class AnnotationRenderer
     hStrucConsensus = av.getRnaStructureConsensusHash();
     av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
     av_ignoreBelowBackground = av.isIgnoreBelowBackground();
+    av_infoHeight = av.isInfoLetterHeight();
   }
 
 
@@ -376,7 +377,7 @@ public class AnnotationRenderer
     {
       HiddenMarkovModel hmm = aa.sequenceRef.getHMM();
       return AAFrequency.extractHMMProfile(hmm, column,
-              av_ignoreBelowBackground); // TODO check if this follows standard
+              av_ignoreBelowBackground, av_infoHeight); // TODO check if this follows standard
                                          // pipeline
     }
     if (aa.autoCalculated