Merge branch 'develop' into features/JAL-2094_colourInterface

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

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 5cd09a1..94e498d 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -26,6 +26,7 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.ComplexAlignFile;
 import jalview.api.FeatureRenderer;
+import jalview.api.FeatureSettingsModelI;
 import jalview.api.FeaturesDisplayedI;
 import jalview.bin.BuildDetails;
 import jalview.datamodel.AlignmentAnnotation;
@@ -45,6 +46,7 @@ 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.Colour;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.UserColourScheme;
 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
@@ -343,7 +345,7 @@ 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(fr.findFeatureColour(Colour.white, seq,
                           seq.findIndex(sf.getBegin())));
           jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
           jsonFeature.setXend(seq.findIndex(sf.getEnd()));
@@ -572,8 +574,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
                 .get("label").toString(), alAnnot.get("description")
                 .toString(), annotations);
         alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
-                .valueOf(alAnnot.get("graphType")
-                        .toString());
+                .valueOf(alAnnot.get("graphType").toString());
 
         JSONObject diplaySettings = (JSONObject) alAnnot
                 .get("annotationSettings");
@@ -710,6 +711,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     }
   }
 
+  @Override
   public String getGlobalColourScheme()
   {
     return globalColourScheme;
@@ -731,8 +733,13 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     this.displayedFeatures = displayedFeatures;
   }
 
+  @Override
   public void configureForView(AlignmentViewPanel avpanel)
   {
+    if (avpanel == null)
+    {
+      return;
+    }
     super.configureForView(avpanel);
     AlignViewportI viewport = avpanel.getAlignViewport();
     AlignmentI alignment = viewport.getAlignment();
@@ -742,11 +749,14 @@ 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
@@ -756,6 +766,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
   }
 
+  @Override
   public boolean isShowSeqFeatures()
   {
     return showSeqFeatures;
@@ -776,6 +787,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     return hiddenColumns;
   }
 
+  @Override
   public ColumnSelection getColumnSelection()
   {
     return columnSelection;
@@ -786,6 +798,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     this.columnSelection = columnSelection;
   }
 
+  @Override
   public SequenceI[] getHiddenSequences()
   {
     if (hiddenSequences == null || hiddenSequences.isEmpty())
@@ -865,4 +878,19 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
       this.exportJalviewSettings = exportJalviewSettings;
     }
   }
+
+  /**
+   * Returns a descriptor for suitable feature display settings with
+   * <ul>
+   * <li>ResNums or insertions features visible</li>
+   * <li>insertions features coloured red</li>
+   * <li>ResNum features coloured by label</li>
+   * <li>Insertions displayed above (on top of) ResNums</li>
+   * </ul>
+   */
+  @Override
+  public FeatureSettingsModelI getFeatureColourScheme()
+  {
+    return new PDBFeatureSettings();
+  }
 }