JAL-1896 revised implementation to construct a ColourSchemeI instance after creating...

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

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 717ab8b..8725556 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -28,7 +28,6 @@ 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;
@@ -45,7 +44,6 @@ 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.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
 
@@ -64,8 +62,6 @@ import org.json.simple.parser.JSONParser;
 
 public class JSONFile extends AlignFile implements ComplexAlignFile
 {
-  private ColourSchemeI colourScheme;
-
   private static String version = new BuildDetails().getVersion();
 
   private String webstartUrl = "http://www.jalview.org/services/launchApp";
@@ -76,7 +72,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
   public static final String FILE_DESC = "JSON";
 
-  private String globalColorScheme;
+  private String globalColourScheme;
 
   private boolean showSeqFeatures;
 
@@ -184,7 +180,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         jsonSeqPojo.setSeq(seq.getSequenceAsString());
         jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
       }
-      jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
+      jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
       jsonAlignmentPojo.getAppSettings().put("application", application);
       jsonAlignmentPojo.getAppSettings().put("version", version);
       jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
@@ -389,7 +385,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
   @SuppressWarnings("unchecked")
   public JSONFile parse(Reader jsonAlignmentString)
   {
-    String jsColourScheme = null;
     try
     {
       JSONParser jsonParser = new JSONParser();
@@ -407,7 +402,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
       if (jvSettingsJsonObj != null)
       {
-        jsColourScheme = (String) jvSettingsJsonObj
+        globalColourScheme = (String) jvSettingsJsonObj
                 .get("globalColorScheme");
         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
                 "showSeqFeatures").toString());
@@ -437,12 +432,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         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
@@ -529,7 +519,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
                 .toString(), annotations);
         this.annotations.add(alignAnnot);
       }
-
     } catch (Exception e)
     {
       e.printStackTrace();
@@ -609,24 +598,14 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     }
   }
 
-  public String getGlobalColorScheme()
-  {
-    return globalColorScheme;
-  }
-
-  public void setGlobalColorScheme(String globalColorScheme)
-  {
-    this.globalColorScheme = globalColorScheme;
-  }
-
-  public ColourSchemeI getColourScheme()
+  public String getGlobalColourScheme()
   {
-    return colourScheme;
+    return globalColourScheme;
   }
 
-  public void setColourScheme(ColourSchemeI colourScheme)
+  public void setGlobalColorScheme(String globalColourScheme)
   {
-    this.colourScheme = colourScheme;
+    this.globalColourScheme = globalColourScheme;
   }
 
   @Override
@@ -662,7 +641,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         annotations.add(annot);
       }
     }
-    globalColorScheme = ColourSchemeProperty.getColourName(viewport
+    globalColourScheme = ColourSchemeProperty.getColourName(viewport
             .getGlobalColourScheme());
     setDisplayedFeatures(viewport.getFeaturesDisplayed());
     showSeqFeatures = viewport.isShowSequenceFeatures();