JAL-3187 unit test for findComplementFeaturesAtResidue

[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 17f9362..9a8a086 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -23,7 +23,13 @@ package jalview.viewmodel.seqfeatures;
 import jalview.api.AlignViewportI;
 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;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.features.FeatureMatcherSetI;
@@ -320,12 +326,12 @@ public abstract class FeatureRendererModel
             visibleTypes);
 
     /*
-     * include features unless their feature group is not displayed, or
-     * they are hidden (have no colour) based on a filter or colour threshold
+     * include features unless they are hidden (have no colour), based on 
+     * feature group visibility, or a filter or colour threshold
      */
     for (SequenceFeature sf : features)
     {
-      if (!featureGroupNotShown(sf) && getColour(sf) != null)
+      if (getColour(sf) != null)
       {
         result.add(sf);
       }
@@ -983,7 +989,7 @@ public abstract class FeatureRendererModel
    * @param sequenceFeature
    * @return
    */
-  protected boolean featureGroupNotShown(final SequenceFeature sequenceFeature)
+  public boolean featureGroupNotShown(final SequenceFeature sequenceFeature)
   {
     return featureGroups != null
             && sequenceFeature.featureGroup != null
@@ -998,7 +1004,7 @@ public abstract class FeatureRendererModel
    */
   @Override
   public List<SequenceFeature> findFeaturesAtResidue(SequenceI sequence,
-          int resNo)
+          int fromResNo, int toResNo)
   {
     List<SequenceFeature> result = new ArrayList<>();
     if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null)
@@ -1011,12 +1017,11 @@ public abstract class FeatureRendererModel
      * displayed, and feature group is null or the empty string
      * or marked for display
      */
-    Set<String> visibleFeatures = getFeaturesDisplayed()
-            .getVisibleFeatures();
+    List<String> visibleFeatures = getDisplayedFeatureTypes();
     String[] visibleTypes = visibleFeatures
             .toArray(new String[visibleFeatures.size()]);
     List<SequenceFeature> features = sequence.getFeatures().findFeatures(
-            resNo, resNo, visibleTypes);
+            fromResNo, toResNo, visibleTypes);
   
     for (SequenceFeature sf : features)
     {
@@ -1157,6 +1162,99 @@ public abstract class FeatureRendererModel
   }
 
   @Override
+  public MappedFeatures findComplementFeaturesAtResidue(SequenceI sequence,
+          int pos)
+  {
+    SequenceI ds = sequence.getDatasetSequence();
+    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);
+
+    /*
+     * fudge: if no mapping found, check the complementary alignment
+     * todo: only store in one place? StructureSelectionManager?
+     */
+    if (mappings.isEmpty())
+    {
+      mappings = this.av.getCodingComplement().getAlignment()
+              .getCodonFrame(sequence);
+    }
+
+    /*
+     * 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 = acf.getMappingForSequence(sequence);
+      if (mapping == null || !mapping.getMap().isTripletMap())
+      {
+        continue; // we are only looking for 3:1 or 1:3 mappings
+      }
+      SearchResultsI sr = new SearchResults();
+      acf.markMappedRegion(ds, pos, sr);
+      for (SearchResultMatchI match : sr.getResults())
+      {
+        int fromRes = match.getStart();
+        int toRes = match.getEnd();
+        mapFrom = match.getSequence();
+        List<SequenceFeature> fs = findFeaturesAtResidue(
+                mapFrom, fromRes, toRes);
+        for (SequenceFeature sf : fs)
+        {
+          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())
+          {
+            return new MappedFeatures(mapping, mapFrom, pos, residue,
+                    result);
+          }
+        }
+      }
+    }
+    
+    return new MappedFeatures(mapping, mapFrom, pos, residue, result);
+  }
+
+  @Override
   public boolean isVisible(SequenceFeature feature)
   {
     if (feature == null)