X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJSONFile.java;h=3cda444958fc76a6716128ffa3f8b0ed102ecad6;hb=4bd4726a6cd30825c18525c2a0851e207d687423;hp=103892562101abb68712ee2d1ed70921e62f28e1;hpb=b95ec6f233e933437c48fc221b68810ddeb08d0c;p=jalview.git

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 1038925..3cda444 100644
--- 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;
@@ -709,6 +710,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     }
   }
 
+  @Override
   public String getGlobalColourScheme()
   {
     return globalColourScheme;
@@ -730,6 +732,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     this.displayedFeatures = displayedFeatures;
   }
 
+  @Override
   public void configureForView(AlignmentViewPanel avpanel)
   {
     super.configureForView(avpanel);
@@ -741,11 +744,14 @@ 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
@@ -755,6 +761,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
   }
 
+  @Override
   public boolean isShowSeqFeatures()
   {
     return showSeqFeatures;
@@ -775,6 +782,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     return hiddenColumns;
   }
 
+  @Override
   public ColumnSelection getColumnSelection()
   {
     return columnSelection;
@@ -785,6 +793,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     this.columnSelection = columnSelection;
   }
 
+  @Override
   public SequenceI[] getHiddenSequences()
   {
     if (hiddenSequences == null || hiddenSequences.isEmpty())
@@ -864,4 +873,19 @@ 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();
+  }
 }