X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJSONFile.java;h=e0f28bbff64d2080454634af8fab4e20b669a7e1;hb=07179fa211fc224a57afbb79f6e8239f36fbf6f0;hp=390c771174105d3a53b07d6cf9964bf8d6fbcd57;hpb=26b115b0a77d521da92a06572d9b7819c2d0d49a;p=jalview.git

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 390c771..e0f28bb 100644
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -218,8 +218,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
           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)
@@ -601,7 +601,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     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]);
       }
@@ -615,7 +615,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     {
       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]),