+ new JSONFile().parse(alignmentJsonString);
+
+ // JSONParser jsonParser = new JSONParser();
+ // JSONObject alignmentJsonObj = (JSONObject) jsonParser
+ // .parse(alignmentJsonString);
+ // JSONArray seqJsonArray = (JSONArray) alignmentJsonObj.get("seqs");
+ // String bioJsColourScheme = (String) alignmentJsonObj
+ // .get("globalColorScheme");
+ // cs = getJalviewColorScheme(bioJsColourScheme);
+ //
+ // for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator();
+ // sequenceIter
+ // .hasNext();)
+ // {
+ // JSONObject sequence = sequenceIter.next();
+ // String sequcenceString = sequence.get("seq").toString();
+ // Sequence seq = new Sequence(sequence.get("name").toString(),
+ // sequcenceString, Integer.valueOf(sequence.get("start")
+ // .toString()), Integer.valueOf(sequence.get("end")
+ // .toString()));
+ //
+ // JSONArray jsonSeqArray = (JSONArray) sequence.get("features");
+ // SequenceFeature[] retrievedSeqFeatures = getJalviewSequenceFeatures(
+ // jsonSeqArray, seq);
+ // if (retrievedSeqFeatures != null)
+ // {
+ // seq.setSequenceFeatures(retrievedSeqFeatures);
+ // }
+ // seqs.add(seq);
+ //
+ // }