JAL-1641 added type to BioJSON sequence object and modified seqsHash to sequenceRefs...

[jalview.git] / src / jalview / io / JSONFile.java

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index b8e2454..89518e5 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -234,7 +234,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
           seqGrpPojo.setShowNonconserved(seqGrp.getShowNonconserved());
           for (SequenceI seq : seqGrp.getSequences())
           {
-            seqGrpPojo.getSeqsHash().add(String.valueOf(seq.hashCode()));
+            seqGrpPojo.getSequenceRefs()
+                    .add(String.valueOf(seq.hashCode()));
           }
           jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
         }
@@ -454,12 +455,12 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         int startRes = Integer
                 .valueOf(seqGrpObj.get("startRes").toString());
         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
-        JSONArray seqsHashArray = (JSONArray) seqGrpObj.get("seqsHash");
+        JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
 
         ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
-        if (seqsHashArray.size() > 0)
+        if (sequenceRefs.size() > 0)
         {
-          Iterator<String> seqHashIter = seqsHashArray.iterator();
+          Iterator<String> seqHashIter = sequenceRefs.iterator();
           while (seqHashIter.hasNext())
           {
             String seqHash = seqHashIter.next();