JAL-1896 bugfix to enabled Jalview restore clustal, RNA Helices and T-Coffee colour...

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

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 0c0f395..717ab8b 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -28,6 +28,7 @@ import jalview.api.ComplexAlignFile;
 import jalview.api.FeatureRenderer;
 import jalview.api.FeaturesDisplayedI;
 import jalview.bin.BuildDetails;
+import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
@@ -40,7 +41,7 @@ import jalview.datamodel.SequenceI;
 import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo;
 import jalview.json.binding.biojson.v1.AlignmentPojo;
 import jalview.json.binding.biojson.v1.AnnotationPojo;
-import jalview.json.binding.biojson.v1.JalviewBioJsColorSchemeMapper;
+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;
@@ -388,6 +389,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
   @SuppressWarnings("unchecked")
   public JSONFile parse(Reader jsonAlignmentString)
   {
+    String jsColourScheme = null;
     try
     {
       JSONParser jsonParser = new JSONParser();
@@ -405,11 +407,10 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
       if (jvSettingsJsonObj != null)
       {
-        String jsColourScheme = (String) jvSettingsJsonObj
+        jsColourScheme = (String) jvSettingsJsonObj
                 .get("globalColorScheme");
         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
                 "showSeqFeatures").toString());
-        setColourScheme(getJalviewColorScheme(jsColourScheme));
         setShowSeqFeatures(showFeatures);
         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
         parseHiddenCols(jvSettingsJsonObj);
@@ -435,6 +436,13 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         seqs.add(seq);
         seqMap.put(seqUniqueId, seq);
       }
+
+      if (jsColourScheme != null)
+      {
+        setColourScheme(ColourSchemeMapper.getJalviewColourScheme(
+                jsColourScheme,
+                new Alignment(seqs.toArray(new SequenceI[0]))));
+      }
       parseFeatures(jsonSeqArray);
 
       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
@@ -472,10 +480,11 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
             }
           }
         }
-        ColourSchemeI grpColourScheme = getJalviewColorScheme(colourScheme);
-        SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName,
-                grpColourScheme, displayBoxes, displayText, colourText,
+        SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
+                displayBoxes, displayText, colourText,
                 startRes, endRes);
+        seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
+                seqGrp);
         seqGrp.setShowNonconserved(showNonconserved);
         seqGrp.setDescription(description);
         this.seqGroups.add(seqGrp);
@@ -600,24 +609,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     }
   }
 
-  public static ColourSchemeI getJalviewColorScheme(
-          String bioJsColourSchemeName)
-  {
-    ColourSchemeI jalviewColor = null;
-    for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
-            .values())
-    {
-      if (cs.getBioJsName().equalsIgnoreCase(bioJsColourSchemeName)
-              || cs.getJalviewName()
-                      .equalsIgnoreCase(bioJsColourSchemeName))
-      {
-        jalviewColor = cs.getJvColourScheme();
-        break;
-      }
-    }
-    return jalviewColor;
-  }
-
   public String getGlobalColorScheme()
   {
     return globalColorScheme;