JAL-2388 Working hidden regions hide/show in desktop

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

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index bdd2dcb..8dbede6 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -32,7 +32,7 @@ import jalview.bin.BuildDetails;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
@@ -46,6 +46,7 @@ import jalview.json.binding.biojson.v1.ColourSchemeMapper;
 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.JalviewColourScheme;
 import jalview.schemes.ResidueColourScheme;
 import jalview.util.ColorUtils;
@@ -82,9 +83,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
   private FeatureRenderer fr;
 
-  private List<int[]> hiddenColumns;
-
-  private ColumnSelection columnSelection;
+  private HiddenColumns hiddenColumns;
 
   private List<String> hiddenSeqRefs;
 
@@ -239,7 +238,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         {
           SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
           seqGrpPojo.setGroupName(seqGrp.getName());
-          seqGrpPojo.setColourScheme(seqGrp.cs.getSchemeName());
+          seqGrpPojo.setColourScheme(seqGrp.getColourScheme()
+                  .getSchemeName());
           seqGrpPojo.setColourText(seqGrp.getColourText());
           seqGrpPojo.setDescription(seqGrp.getDescription());
           seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
@@ -278,8 +278,9 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     // hidden column business
     if (getViewport().hasHiddenColumns())
     {
-      List<int[]> hiddenCols = getViewport().getColumnSelection()
-              .getHiddenColumns();
+      List<int[]> hiddenCols = getViewport().getAlignment()
+              .getHiddenColumns()
+              .getHiddenRegions();
       StringBuilder hiddenColsBuilder = new StringBuilder();
       for (int[] range : hiddenCols)
       {
@@ -327,6 +328,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
       return sequenceFeaturesPojo;
     }
 
+    FeatureColourFinder finder = new FeatureColourFinder(fr);
+
     for (SequenceI seq : sqs)
     {
       SequenceI dataSetSequence = seq.getDatasetSequence();
@@ -349,7 +352,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
                   String.valueOf(seq.hashCode()));
 
           String featureColour = (fr == null) ? null : jalview.util.Format
-                  .getHexString(fr.findFeatureColour(Color.white, seq,
+                  .getHexString(finder.findFeatureColour(Color.white, seq,
                           seq.findIndex(sf.getBegin())));
           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
@@ -527,8 +530,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         }
         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
                 displayBoxes, displayText, colourText, startRes, endRes);
-        seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
-                seqGrp);
+        seqGrp.setColourScheme(ColourSchemeMapper.getJalviewColourScheme(
+                colourScheme, seqGrp));
         seqGrp.setShowNonconserved(showNonconserved);
         seqGrp.setDescription(description);
         this.seqGroups.add(seqGrp);
@@ -662,12 +665,12 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     String hiddenCols = (String) jvSettingsJson.get("hiddenCols");
     if (hiddenCols != null && !hiddenCols.isEmpty())
     {
-      columnSelection = new ColumnSelection();
+      hiddenColumns = new HiddenColumns();
       String[] rangeStrings = hiddenCols.split(";");
       for (String rangeString : rangeStrings)
       {
         String[] range = rangeString.split("-");
-        columnSelection.hideColumns(Integer.valueOf(range[0]),
+        hiddenColumns.hideColumns(Integer.valueOf(range[0]),
                 Integer.valueOf(range[1]));
       }
     }
@@ -785,20 +788,15 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     return annotations;
   }
 
-  public List<int[]> getHiddenColumns()
-  {
-    return hiddenColumns;
-  }
-
   @Override
-  public ColumnSelection getColumnSelection()
+  public HiddenColumns getHiddenColumns()
   {
-    return columnSelection;
+    return hiddenColumns;
   }
 
-  public void setColumnSelection(ColumnSelection columnSelection)
+  public void setHiddenColumns(HiddenColumns hidden)
   {
-    this.columnSelection = columnSelection;
+    this.hiddenColumns = hidden;
   }
 
   @Override