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JAL-2505 set type,desc,begin,end,group,score in SequenceFeature
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Mon, 8 May 2017 16:45:01 +0000
(17:45 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Mon, 8 May 2017 16:45:01 +0000
(17:45 +0100)
constructor
src/jalview/io/JSONFile.java
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diff --git
a/src/jalview/io/JSONFile.java
b/src/jalview/io/JSONFile.java
index
20148b4
..
0d6e02f
100644
(file)
--- 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");
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);
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)
{
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.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);
}
seq.addSequenceFeature(sequenceFeature);
displayedFeatures.setVisible(type);
}