jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
}
}
- org.json.JSONObject generatedJSon = new org.json.JSONObject(jsonAlignmentPojo);
- jsonOutput = generatedJSon.toString();
+
+ jsonOutput = JSONUtils.stringify(jsonAlignmentPojo);
return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
"xEnd");
} catch (Exception e)
if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
{
String[] seqRefs = hiddenSeqs.split(";");
- for (int i = seqRefs.length; --i >= 0;)
+ for (int i = 0, n = seqRefs.length; i < n; i++)
{
hiddenSeqRefs.add(seqRefs[i]);
}
{
hiddenColumns = new HiddenColumns();
String[] rangeStrings = hiddenCols.split(";");
- for (int i = rangeStrings.length; --i >= 0;)
+ for (int i = 0, n = rangeStrings.length; i < n; i++)
{
String[] range = rangeStrings[i].split("-");
hiddenColumns.hideColumns(Integer.valueOf(range[0]),