Merge remote-tracking branch

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

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index dcf0f5d..816346a 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());
@@ -282,7 +281,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     {
       List<int[]> hiddenCols = getViewport().getAlignment()
               .getHiddenColumns()
-              .getListOfCols();
+              .getHiddenRegions();
       StringBuilder hiddenColsBuilder = new StringBuilder();
       for (int[] range : hiddenCols)
       {
@@ -667,12 +666,12 @@ 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 +767,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         }
       }
     }
-    globalColourScheme = viewport.getGlobalColourScheme().getSchemeName();
+    globalColourScheme = ColourSchemeProperty.getColourName(viewport
+            .getGlobalColourScheme());
     setDisplayedFeatures(viewport.getFeaturesDisplayed());
     showSeqFeatures = viewport.isShowSequenceFeatures();