JAL-2591 simplifying hidden columns usage

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

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 816346a..a48ee33 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -279,11 +279,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     // hidden column business
     if (getViewport().hasHiddenColumns())
     {
-      List<int[]> hiddenCols = getViewport().getAlignment()
-              .getHiddenColumns()
-              .getHiddenRegions();
       StringBuilder hiddenColsBuilder = new StringBuilder();
-      for (int[] range : hiddenCols)
+      for (int[] range : getViewport().getAlignment().getHiddenColumns())
       {
         hiddenColsBuilder.append(";").append(range[0]).append("-")
                 .append(range[1]);
@@ -323,7 +320,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
           SequenceI[] sqs, FeatureRenderer fr)
   {
     displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
-    List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
+    List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<>();
     if (sqs == null)
     {
       return sequenceFeaturesPojo;
@@ -374,7 +371,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
           Vector<AlignmentAnnotation> annotations)
   {
-    List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
+    List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<>();
     if (annotations == null)
     {
       return jsonAnnotations;
@@ -471,8 +468,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         parseHiddenCols(jvSettingsJsonObj);
       }
 
-      hiddenSequences = new ArrayList<SequenceI>();
-      seqMap = new Hashtable<String, Sequence>();
+      hiddenSequences = new ArrayList<>();
+      seqMap = new Hashtable<>();
       for (Iterator<JSONObject> sequenceIter = seqJsonArray.iterator(); sequenceIter
               .hasNext();)
       {
@@ -515,7 +512,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
         JSONArray sequenceRefs = (JSONArray) seqGrpObj.get("sequenceRefs");
 
-        ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
+        ArrayList<SequenceI> grpSeqs = new ArrayList<>();
         if (sequenceRefs.size() > 0)
         {
           Iterator<String> seqHashIter = sequenceRefs.iterator();
@@ -649,7 +646,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
   public void parseHiddenSeqRefsAsList(JSONObject jvSettingsJson)
   {
-    hiddenSeqRefs = new ArrayList<String>();
+    hiddenSeqRefs = new ArrayList<>();
     String hiddenSeqs = (String) jvSettingsJson.get("hiddenSeqs");
     if (hiddenSeqs != null && !hiddenSeqs.isEmpty())
     {