JAL-3741 http to https (and jar to jvp for exampleFile defaults!)

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

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 3f1b1a7..022148a 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -70,7 +70,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 {
   private static String version = new BuildDetails().getVersion();
 
-  private String webstartUrl = "http://www.jalview.org/services/launchApp";
+  private String webstartUrl = "https://www.jalview.org/services/launchApp";
 
   private String application = "Jalview";
 
@@ -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)
@@ -601,9 +601,9 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
     {
       String[] seqRefs = hiddenSeqs.split(";");
-      for (String seqRef : seqRefs)
+      for (int i = 0, n = seqRefs.length; i < n; i++)
       {
-        hiddenSeqRefs.add(seqRef);
+        hiddenSeqRefs.add(seqRefs[i]);
       }
     }
   }
@@ -615,9 +615,9 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     {
       hiddenColumns = new HiddenColumns();
       String[] rangeStrings = hiddenCols.split(";");
-      for (String rangeString : rangeStrings)
+      for (int i = 0, n = rangeStrings.length; i < n; i++)
       {
-        String[] range = rangeString.split("-");
+        String[] range = rangeStrings[i].split("-");
         hiddenColumns.hideColumns(Integer.valueOf(range[0]),
                 Integer.valueOf(range[1]));
       }
@@ -630,10 +630,9 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     if (jsonSeqFeatures != null)
     {
       displayedFeatures = new FeaturesDisplayed();
-      for (Iterator<Object> seqFeatureItr = jsonSeqFeatures
-              .iterator(); seqFeatureItr.hasNext();)
+      for (Object o : jsonSeqFeatures)
       {
-        Map<String, Object> jsonFeature = (Map<String, Object>) seqFeatureItr.next();
+       Map<String, Object> jsonFeature = (Map<String, Object>) o;
         Long begin = (Long) jsonFeature.get("xStart");
         Long end = (Long) jsonFeature.get("xEnd");
         String type = (String) jsonFeature.get("type");