JAL-3741 http to https (and jar to jvp for exampleFile defaults!)

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

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 5d9c804..0e3cca7 100644 (file)
--- 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;
@@ -70,7 +71,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 {
   private static String version = new BuildDetails().getVersion();
 
-  private String webstartUrl = "http://www.jalview.org/services/launchApp";
+  private String webstartUrl = "https://www.jalview.org/services/launchApp";
 
   private String application = "Jalview";
 
@@ -227,8 +228,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
       if (exportSettings.isExportFeatures())
       {
-        jsonAlignmentPojo
-                .setSeqFeatures(sequenceFeatureToJsonPojo(sqs, fr));
+        jsonAlignmentPojo.setSeqFeatures(sequenceFeatureToJsonPojo(sqs));
       }
 
       if (exportSettings.isExportGroups() && seqGroups != null
@@ -308,8 +308,8 @@ 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<>();
@@ -320,42 +320,38 @@ 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;
@@ -687,12 +683,23 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         Long end = (Long) jsonFeature.get("xEnd");
         String type = (String) jsonFeature.get("type");
         String featureGrp = (String) jsonFeature.get("featureGroup");
-        String descripiton = (String) jsonFeature.get("description");
+        String description = (String) jsonFeature.get("description");
         String seqRef = (String) jsonFeature.get("sequenceRef");
         Float score = Float.valueOf(jsonFeature.get("score").toString());
 
         Sequence seq = seqMap.get(seqRef);
-        SequenceFeature sequenceFeature = new SequenceFeature();
+
+        /*
+         * 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);
+
         JSONArray linksJsonArray = (JSONArray) jsonFeature.get("links");
         if (linksJsonArray != null && linksJsonArray.size() > 0)
         {
@@ -703,12 +710,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
             sequenceFeature.addLink(link);
           }
         }
-        sequenceFeature.setFeatureGroup(featureGrp);
-        sequenceFeature.setScore(score);
-        sequenceFeature.setDescription(descripiton);
-        sequenceFeature.setType(type);
-        sequenceFeature.setBegin(seq.findPosition(begin.intValue()));
-        sequenceFeature.setEnd(seq.findPosition(end.intValue()) - 1);
+
         seq.addSequenceFeature(sequenceFeature);
         displayedFeatures.setVisible(type);
       }