JAL-1950 JAL-1958 bitscore is more effective for shading than e-value

diff --git a/src/jalview/ws/ebi/HmmerJSONProcessor.java b/src/jalview/ws/ebi/HmmerJSONProcessor.java
index 731df91..bb3e95a 100644 (file)
--- a/src/jalview/ws/ebi/HmmerJSONProcessor.java
+++ b/src/jalview/ws/ebi/HmmerJSONProcessor.java
@@ -157,6 +157,7 @@ public class HmmerJSONProcessor
           hitseq.addAlignmentAnnotation(eval);
           alipp.createSequenceMapping(hitseq, hitseq.getStart(), false);
           hitseq.addAlignmentAnnotation(alipp);
+          alipp.setScore(Double.valueOf("" + dhit.get("bitscore")));
           alipp.adjustForAlignment();
           resultAl.addAnnotation(pval);
           resultAl.addAnnotation(eval);