JAL-2591 Hidden columns regions can be output to string + test

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

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index dcf0f5d..c293cd4 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -47,6 +47,7 @@ import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
 import jalview.json.binding.biojson.v1.SequenceGrpPojo;
 import jalview.json.binding.biojson.v1.SequencePojo;
 import jalview.renderer.seqfeatures.FeatureColourFinder;
+import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.JalviewColourScheme;
 import jalview.schemes.ResidueColourScheme;
 import jalview.util.ColorUtils;
@@ -83,8 +84,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
   private FeatureRenderer fr;
 
-  private List<int[]> hiddenColumnsList;
-
   private HiddenColumns hiddenColumns;
 
   private List<String> hiddenSeqRefs;
@@ -240,8 +239,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         {
           SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
           seqGrpPojo.setGroupName(seqGrp.getName());
-          seqGrpPojo.setColourScheme(seqGrp.getColourScheme()
-                  .getSchemeName());
+          seqGrpPojo.setColourScheme(ColourSchemeProperty
+                  .getColourName(seqGrp.getColourScheme()));
           seqGrpPojo.setColourText(seqGrp.getColourText());
           seqGrpPojo.setDescription(seqGrp.getDescription());
           seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
@@ -280,18 +279,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     // hidden column business
     if (getViewport().hasHiddenColumns())
     {
-      List<int[]> hiddenCols = getViewport().getAlignment()
-              .getHiddenColumns()
-              .getListOfCols();
-      StringBuilder hiddenColsBuilder = new StringBuilder();
-      for (int[] range : hiddenCols)
-      {
-        hiddenColsBuilder.append(";").append(range[0]).append("-")
-                .append(range[1]);
-      }
-
-      hiddenColsBuilder.deleteCharAt(0);
-      hiddenSections[0] = hiddenColsBuilder.toString();
+      hiddenSections[0] = getViewport().getAlignment().getHiddenColumns()
+              .regionsToString(";", "-");
     }
 
     // hidden rows/seqs business
@@ -324,7 +313,7 @@ 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;
@@ -375,7 +364,7 @@ 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;
@@ -472,8 +461,8 @@ 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();)
       {
@@ -516,7 +505,7 @@ 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();
@@ -650,7 +639,7 @@ 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())
     {
@@ -667,12 +656,12 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
     if (hiddenCols != null && !hiddenCols.isEmpty())
     {
-      HiddenColumns hidden = new HiddenColumns();
+      hiddenColumns = new HiddenColumns();
       String[] rangeStrings = hiddenCols.split(";");
       for (String rangeString : rangeStrings)
       {
         String[] range = rangeString.split("-");
-        hidden.hideColumns(Integer.valueOf(range[0]),
+        hiddenColumns.hideColumns(Integer.valueOf(range[0]),
                 Integer.valueOf(range[1]));
       }
     }
@@ -768,7 +757,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         }
       }
     }
-    globalColourScheme = viewport.getGlobalColourScheme().getSchemeName();
+    globalColourScheme = ColourSchemeProperty.getColourName(viewport
+            .getGlobalColourScheme());
     setDisplayedFeatures(viewport.getFeaturesDisplayed());
     showSeqFeatures = viewport.isShowSequenceFeatures();