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

[jalview.git] / src / jalview / workers / InformationThread.java

diff --git a/src/jalview/workers/InformationThread.java b/src/jalview/workers/InformationThread.java
index 2c92879..2abfc69 100644 (file)
--- a/src/jalview/workers/InformationThread.java
+++ b/src/jalview/workers/InformationThread.java
@@ -15,6 +15,9 @@ import java.util.List;
 
 public class InformationThread extends AlignCalcWorker
 {
+  
+  Float max = 0f;
+  
   /**
    * Constructor for information thread.
    * 
@@ -125,11 +128,13 @@ public class InformationThread extends AlignCalcWorker
       int width = alignment.getWidth();
     List<SequenceI> hmmSeqs = alignment.getHMMConsensusSequences(false);
     int index = 0;
+
     for (SequenceI seq : hmmSeqs)
     {
       HiddenMarkovModel hmm = seq.getHMM();
       ProfilesI hinformation = AAFrequency.calculateHMMProfiles(hmm, width,
-              0, width, true, alignViewport.isIgnoreBelowBackground());
+              0, width, true, alignViewport.isIgnoreBelowBackground(),
+              alignViewport.isInfoLetterHeight());
       alignViewport.setSequenceInformationHash(hinformation, index);
       // setColourSchemeInformation(hinformation);
       index++;
@@ -219,12 +224,10 @@ public class InformationThread extends AlignCalcWorker
   protected void deriveInformation(
           AlignmentAnnotation informationAnnotation, ProfilesI hinformation)
     {
-
       long nseq = getSequences().length;
-    AAFrequency.completeInformation(informationAnnotation, hinformation,
-            hinformation.getStartColumn(), hinformation.getEndColumn() + 1,
-            alignViewport.isIgnoreBelowBackground(),
-              alignViewport.isShowHMMSequenceLogo(), nseq);
+    max = AAFrequency.completeInformation(informationAnnotation,
+            hinformation, hinformation.getStartColumn(),
+            hinformation.getEndColumn() + 1, nseq, max);
     }