X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJSONFile.java;h=27ebe5a538f5936e9ff58922b1e22dc8e9726ae5;hb=70af62ad365829d2fc430db10336cf13c4d4ce1a;hp=36980f8d7616facc6103e358bc8d308b98136966;hpb=f3392c352962c6827674ada5948500725e4eed1e;p=jalview.git

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 36980f8..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;
@@ -71,10 +72,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
   private String application = "Jalview";
 
-  public static final String FILE_EXT = "json";
-
-  public static final String FILE_DESC = "JSON";
-
   private String globalColourScheme;
 
   private boolean showSeqFeatures;
@@ -105,9 +102,10 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     super(source);
   }
 
-  public JSONFile(String inFile, String type) throws IOException
+  public JSONFile(String inFile, DataSourceType sourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, sourceType);
   }
 
   @Override
@@ -118,7 +116,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
   }
 
   @Override
-  public String print()
+  public String print(SequenceI[] sqs, boolean jvsuffix)
   {
     String jsonOutput = null;
     try
@@ -171,7 +169,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
       }
 
       int count = 0;
-      for (SequenceI seq : seqs)
+      for (SequenceI seq : sqs)
       {
         StringBuilder name = new StringBuilder();
         name.append(seq.getName()).append("/").append(seq.getStart())
@@ -218,17 +216,20 @@ 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);
         }
       }
 
       if (exportSettings.isExportFeatures())
       {
         jsonAlignmentPojo
-                .setSeqFeatures(sequenceFeatureToJsonPojo(seqs, fr));
+                .setSeqFeatures(sequenceFeatureToJsonPojo(sqs, fr));
       }
 
       if (exportSettings.isExportGroups() && seqGroups != null
@@ -238,8 +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());
@@ -318,11 +319,16 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
   }
 
   public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
-          List<SequenceI> seqs, FeatureRenderer fr)
+          SequenceI[] sqs, FeatureRenderer fr)
   {
     displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
-    for (SequenceI seq : seqs)
+    if (sqs == null)
+    {
+      return sequenceFeaturesPojo;
+    }
+
+    for (SequenceI seq : sqs)
     {
       SequenceI dataSetSequence = seq.getDatasetSequence();
       SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
@@ -522,8 +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);
@@ -561,7 +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;
             }
@@ -735,6 +741,10 @@ 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();
@@ -744,15 +754,17 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     fr = avpanel.cloneFeatureRenderer();
 
     // Add non auto calculated annotation to AlignFile
-    for (AlignmentAnnotation annot : annots)
+    if (annots != null)
     {
-      if (annot != null && !annot.autoCalculated)
+      for (AlignmentAnnotation annot : annots)
       {
-        annotations.add(annot);
+        if (annot != null && !annot.autoCalculated)
+        {
+          annotations.add(annot);
+        }
       }
     }
-    globalColourScheme = ColourSchemeProperty.getColourName(viewport
-            .getGlobalColourScheme());
+    globalColourScheme = viewport.getGlobalColourScheme().getSchemeName();
     setDisplayedFeatures(viewport.getFeaturesDisplayed());
     showSeqFeatures = viewport.isShowSequenceFeatures();