X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJSONFile.java;h=14574d0e3263d1d1b9810e19e7b58fb93dc02ed3;hb=70a93ebbabd80e25c60a0e6444013ed4260b09a5;hp=8bbbcd156a40f147d921fc1d46d4c706c1568399;hpb=90029b4b40d8fcc9abed4567b11031e52cd74a2b;p=jalview.git

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 8bbbcd1..14574d0 100644
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -51,6 +51,7 @@ import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.JalviewColourScheme;
 import jalview.schemes.ResidueColourScheme;
 import jalview.util.ColorUtils;
+import jalview.util.Format;
 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
 
 import java.awt.Color;
@@ -228,8 +229,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
       if (exportSettings.isExportFeatures())
       {
-        jsonAlignmentPojo
-                .setSeqFeatures(sequenceFeatureToJsonPojo(sqs, fr));
+        jsonAlignmentPojo.setSeqFeatures(sequenceFeatureToJsonPojo(sqs));
       }
 
       if (exportSettings.isExportGroups() && seqGroups != null
@@ -319,8 +319,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     return hiddenSections;
   }
 
-  public List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
-          SequenceI[] sqs, FeatureRenderer fr)
+  protected List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
+          SequenceI[] sqs)
   {
     displayedFeatures = (fr == null) ? null : fr.getFeaturesDisplayed();
     List<SequenceFeaturesPojo> sequenceFeaturesPojo = new ArrayList<SequenceFeaturesPojo>();
@@ -331,41 +331,38 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
     FeatureColourFinder finder = new FeatureColourFinder(fr);
 
+    String[] visibleFeatureTypes = displayedFeatures == null ? null
+            : displayedFeatures.getVisibleFeatures().toArray(
+                    new String[displayedFeatures.getVisibleFeatureCount()]);
+
     for (SequenceI seq : sqs)
     {
-      SequenceI dataSetSequence = seq.getDatasetSequence();
-      SequenceFeature[] seqFeatures = (dataSetSequence == null) ? null
-              : seq.getDatasetSequence().getSequenceFeatures();
-
-      seqFeatures = (seqFeatures == null) ? seq.getSequenceFeatures()
-              : seqFeatures;
-      if (seqFeatures == null)
-      {
-        continue;
-      }
-
+      /*
+       * get all features currently visible (and any non-positional features)
+       */
+      List<SequenceFeature> seqFeatures = seq.getFeatures().getAllFeatures(
+              visibleFeatureTypes);
       for (SequenceFeature sf : seqFeatures)
       {
-        if (displayedFeatures != null
-                && displayedFeatures.isVisible(sf.getType()))
-        {
-          SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
-                  String.valueOf(seq.hashCode()));
-
-          String featureColour = (fr == null) ? null : jalview.util.Format
-                  .getHexString(finder.findFeatureColour(Color.white, seq,
-                          seq.findIndex(sf.getBegin())));
-          jsonFeature.setXstart(seq.findIndex(sf.getBegin()) - 1);
-          jsonFeature.setXend(seq.findIndex(sf.getEnd()));
-          jsonFeature.setType(sf.getType());
-          jsonFeature.setDescription(sf.getDescription());
-          jsonFeature.setLinks(sf.links);
-          jsonFeature.setOtherDetails(sf.otherDetails);
-          jsonFeature.setScore(sf.getScore());
-          jsonFeature.setFillColor(featureColour);
-          jsonFeature.setFeatureGroup(sf.getFeatureGroup());
-          sequenceFeaturesPojo.add(jsonFeature);
-        }
+        SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
+                String.valueOf(seq.hashCode()));
+
+        String featureColour = (fr == null) ? null : Format
+                .getHexString(finder.findFeatureColour(Color.white, seq,
+                        seq.findIndex(sf.getBegin())));
+        int xStart = sf.getBegin() == 0 ? 0
+                : seq.findIndex(sf.getBegin()) - 1;
+        int xEnd = sf.getEnd() == 0 ? 0 : seq.findIndex(sf.getEnd());
+        jsonFeature.setXstart(xStart);
+        jsonFeature.setXend(xEnd);
+        jsonFeature.setType(sf.getType());
+        jsonFeature.setDescription(sf.getDescription());
+        jsonFeature.setLinks(sf.links);
+        jsonFeature.setOtherDetails(sf.otherDetails);
+        jsonFeature.setScore(sf.getScore());
+        jsonFeature.setFillColor(featureColour);
+        jsonFeature.setFeatureGroup(sf.getFeatureGroup());
+        sequenceFeaturesPojo.add(jsonFeature);
       }
     }
     return sequenceFeaturesPojo;
@@ -696,8 +693,14 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         Float score = Float.valueOf(jsonFeature.get("score").toString());
 
         Sequence seq = seqMap.get(seqRef);
-        int featureBegin = seq.findPosition(begin.intValue());
-        int featureEnd = seq.findPosition(end.intValue()) - 1;
+
+        /*
+         * begin/end of 0 is for a non-positional feature
+         */
+        int featureBegin = begin.intValue() == 0 ? 0 : seq
+                .findPosition(begin.intValue());
+        int featureEnd = end.intValue() == 0 ? 0 : seq.findPosition(end
+                .intValue()) - 1;
 
         SequenceFeature sequenceFeature = new SequenceFeature(type,
                 description, featureBegin, featureEnd, score, featureGrp);