JAL-2557 removal of Sequence.sequenceFeatures

[jalview.git] / src / jalview / analysis / AlignmentUtils.java

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 66be623..69ac947 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -2134,7 +2134,7 @@ public class AlignmentUtils
         int newBegin = Math.min(mappedTo[0], mappedTo[1]);
         int newEnd = Math.max(mappedTo[0], mappedTo[1]);
         SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd,
-                sf.getFeatureGroup());
+                sf.getFeatureGroup(), sf.getScore());
         copyTo.addSequenceFeature(copy);
         count++;
       }
@@ -2439,10 +2439,9 @@ public class AlignmentUtils
       String trans3Char = StringUtils
               .toSentenceCase(ResidueProperties.aa2Triplet.get(trans));
       String desc = "p." + residue3Char + peptidePos + trans3Char;
-      // set score to 0f so 'graduated colour' option is offered! JAL-2060
       SequenceFeature sf = new SequenceFeature(
               SequenceOntologyI.SEQUENCE_VARIANT, desc, peptidePos,
-              peptidePos, 0f, var.getSource());
+              peptidePos, var.getSource());
       StringBuilder attributes = new StringBuilder(32);
       String id = (String) var.variant.getValue(ID);
       if (id != null)