From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 8 May 2017 16:45:01 +0000 (+0100)
Subject: JAL-2505 set type,desc,begin,end,group,score in SequenceFeature
X-Git-Tag: Release_2_10_3b1~293
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e28854ac11c339662d931324c32d89aca3313ed9;p=jalview.git

JAL-2505 set type,desc,begin,end,group,score in SequenceFeature
constructor
---

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 20148b4..0d6e02f 100644
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -692,12 +692,17 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         Long end = (Long) jsonFeature.get("xEnd");
         String type = (String) jsonFeature.get("type");
         String featureGrp = (String) jsonFeature.get("featureGroup");
-        String descripiton = (String) jsonFeature.get("description");
+        String description = (String) jsonFeature.get("description");
         String seqRef = (String) jsonFeature.get("sequenceRef");
         Float score = Float.valueOf(jsonFeature.get("score").toString());
 
         Sequence seq = seqMap.get(seqRef);
-        SequenceFeature sequenceFeature = new SequenceFeature();
+        int featureBegin = seq.findPosition(begin.intValue());
+        int featureEnd = seq.findPosition(end.intValue()) - 1;
+
+        SequenceFeature sequenceFeature = new SequenceFeature(type,
+                description, featureBegin, featureEnd, score, featureGrp);
+
         JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
         if (linksJsonArray != null && linksJsonArray.size() > 0)
         {
@@ -708,12 +713,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
             sequenceFeature.addLink(link);
           }
         }
-        sequenceFeature.setFeatureGroup(featureGrp);
-        sequenceFeature.setScore(score);
-        sequenceFeature.setDescription(descripiton);
-        sequenceFeature.setType(type);
-        sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
-        sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
+
         seq.addSequenceFeature(sequenceFeature);
         displayedFeatures.setVisible(type);
       }