JAL-3187 handle no mapping / complement features without NPE

[jalview.git] / src / jalview / viewmodel / seqfeatures / FeatureRendererModel.java

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 7faf7ea..f090190 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -25,6 +25,7 @@ import jalview.api.FeatureColourI;
 import jalview.api.FeaturesDisplayedI;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.MappedFeatures;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResults;
@@ -1155,18 +1156,27 @@ public abstract class FeatureRendererModel
   }
 
   /**
-   * Answers a (possibly empty) list of features in this alignment at a position
-   * (or range) which is mappable from the given sequence residue position in a
-   * mapped alignment.
+   * Answers a bean containing a mapping, and a list of features in this
+   * alignment at a position (or range) which is mappable from the given
+   * sequence residue position in a mapped alignment. Features are returned in
+   * render order of feature type (on top last), with order within feature type
+   * undefined. If no features or mapping are found, answers null.
    * 
    * @param sequence
    * @param pos
    * @return
    */
-  public List<SequenceFeature> findComplementFeaturesAtResidue(SequenceI sequence, int pos)
+  public MappedFeatures findComplementFeaturesAtResidue(SequenceI sequence,
+          int pos)
   {
     SequenceI ds = sequence.getDatasetSequence();
-    List<SequenceFeature> result = new ArrayList<>();
+    if (ds == null)
+    {
+      ds = sequence;
+    }
+    final char residue = ds.getCharAt(pos - ds.getStart());
+
+    List<SequenceFeature> found = new ArrayList<>();
     List<AlignedCodonFrame> mappings = this.av.getAlignment()
             .getCodonFrame(sequence);
 
@@ -1174,9 +1184,12 @@ public abstract class FeatureRendererModel
      * todo: direct lookup of CDS for peptide and vice-versa; for now,
      * have to search through an unordered list of mappings for a candidate
      */
+    Mapping mapping = null;
+    SequenceI mapFrom = null;
+
     for (AlignedCodonFrame acf : mappings)
     {
-      Mapping mapping = acf.getMappingForSequence(sequence, true);
+      mapping = acf.getMappingForSequence(sequence, true);
       if (mapping == null || mapping.getMap().getFromRatio() == mapping
               .getMap().getToRatio())
       {
@@ -1188,19 +1201,52 @@ public abstract class FeatureRendererModel
       {
         int fromRes = match.getStart();
         int toRes = match.getEnd();
+        mapFrom = match.getSequence();
         List<SequenceFeature> fs = findFeaturesAtResidue(
                 match.getSequence(), fromRes, toRes);
         for (SequenceFeature sf : fs)
         {
-          if (!result.contains(sf))
+          if (!found.contains(sf))
+          {
+            found.add(sf);
+          }
+        }
+      }
+
+      /*
+       * just take the first mapped features we find
+       */
+      if (!found.isEmpty())
+      {
+        break;
+      }
+    }
+    if (found.isEmpty())
+    {
+      return null;
+    }
+
+    /*
+     * sort by renderorder, inefficiently
+     */
+    List<SequenceFeature> result = new ArrayList<>();
+    for (String type : renderOrder)
+    {
+      for (SequenceFeature sf : found)
+      {
+        if (type.equals(sf.getType()))
+        {
+          result.add(sf);
+          if (result.size() == found.size())
           {
-            result.add(sf);
+            return new MappedFeatures(mapping, mapFrom, pos, residue,
+                    result);
           }
         }
       }
     }
     
-    return result;
+    return new MappedFeatures(mapping, mapFrom, pos, residue, result);
   }
 
 }