X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FJSONFile.java;h=27ebe5a538f5936e9ff58922b1e22dc8e9726ae5;hb=902a15eeb7361608e4b0b8b421a5435d21b1ee63;hp=7a12076fe0e5b1c104a65afc21c93795ee1e2d24;hpb=8b27085fa7fc5f2877e078421284c2636b85b8c6;p=jalview.git

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 7a12076..27ebe5a 100644
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -46,8 +46,9 @@ 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.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 +216,13 @@ 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);
         }
       }
 
@@ -235,8 +239,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         {
           SequenceGrpPojo seqGrpPojo = new SequenceGrpPojo();
           seqGrpPojo.setGroupName(seqGrp.getName());
-          seqGrpPojo.setColourScheme(ColourSchemeProperty
-                  .getColourName(seqGrp.cs));
+          seqGrpPojo.setColourScheme(seqGrp.getColourScheme()
+                  .getSchemeName());
           seqGrpPojo.setColourText(seqGrp.getColourText());
           seqGrpPojo.setDescription(seqGrp.getDescription());
           seqGrpPojo.setDisplayBoxes(seqGrp.getDisplayBoxes());
@@ -524,8 +528,8 @@ 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 +567,7 @@ 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;
             }
@@ -760,8 +764,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         }
       }
     }
-    globalColourScheme = ColourSchemeProperty.getColourName(viewport
-            .getGlobalColourScheme());
+    globalColourScheme = viewport.getGlobalColourScheme().getSchemeName();
     setDisplayedFeatures(viewport.getFeaturesDisplayed());
     showSeqFeatures = viewport.isShowSequenceFeatures();