X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJSONFile.java;h=20148b49cb96aab17b922bf062b183965ecf4b0d;hb=e75847be3733978d2cd51d7121778e782ad0abf3;hp=ad4407333cdc5205bc23044ba927112cebe12639;hpb=4a5137b64f7ec23db2a09290bfcd392984a52150;p=jalview.git

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index ad44073..20148b4 100644
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -46,8 +46,11 @@ 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.ColourSchemeProperty;
-import jalview.schemes.UserColourScheme;
+import jalview.schemes.JalviewColourScheme;
+import jalview.schemes.ResidueColourScheme;
+import jalview.util.ColorUtils;
 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
 
 import java.awt.Color;
@@ -215,10 +218,13 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
       {
         // These color schemes require annotation, disable them if annotations
         // are not exported
-        if (globalColourScheme.equalsIgnoreCase("RNA Helices")
-                || globalColourScheme.equalsIgnoreCase("T-COFFEE SCORES"))
+        if (globalColourScheme
+                .equalsIgnoreCase(JalviewColourScheme.RNAHelices.toString())
+                || globalColourScheme
+                        .equalsIgnoreCase(JalviewColourScheme.TCoffee
+                                .toString()))
         {
-          jsonAlignmentPojo.setGlobalColorScheme("None");
+          jsonAlignmentPojo.setGlobalColorScheme(ResidueColourScheme.NONE);
         }
       }
 
@@ -236,7 +242,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
           SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
           seqGrpPojo.setGroupName(seqGrp.getName());
           seqGrpPojo.setColourScheme(ColourSchemeProperty
-                  .getColourName(seqGrp.cs));
+                  .getColourName(seqGrp.getColourScheme()));
           seqGrpPojo.setColourText(seqGrp.getColourText());
           seqGrpPojo.setDescription(seqGrp.getDescription());
           seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
@@ -324,6 +330,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
       return sequenceFeaturesPojo;
     }
 
+    FeatureColourFinder finder = new FeatureColourFinder(fr);
+
     for (SequenceI seq : sqs)
     {
       SequenceI dataSetSequence = seq.getDatasetSequence();
@@ -346,7 +354,7 @@ 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()));
@@ -524,8 +532,8 @@ 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);
@@ -563,7 +571,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
             annotations[count] = new Annotation(displayChar, desc, ss, val);
             if (annot.get("colour") != null)
             {
-              Color color = UserColourScheme.getColourFromString(annot.get(
+              Color color = ColorUtils.parseColourString(annot.get(
                       "colour").toString());
               annotations[count].colour = color;
             }
@@ -737,6 +745,10 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
   @Override
   public void configureForView(AlignmentViewPanel avpanel)
   {
+    if (avpanel == null)
+    {
+      return;
+    }
     super.configureForView(avpanel);
     AlignViewportI viewport = avpanel.getAlignViewport();
     AlignmentI alignment = viewport.getAlignment();