From 87a707afdbbe1675330f7e82faaf9443af89cefe Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 8 Oct 2020 15:06:57 +0100
Subject: [PATCH] JAL-3763 refactored getCoveringMapping for virtual feature
 discovery

---
 src/jalview/datamodel/AlignedCodonFrame.java       |   90 ++++++++++++++------
 .../seqfeatures/FeatureRendererModel.java          |   14 +--
 2 files changed, 72 insertions(+), 32 deletions(-)

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 96c9792..0927dda 100644
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -206,6 +206,40 @@ public class AlignedCodonFrame
       }
       return length;
     }
+
+    /**
+     * Adds any regions mapped to or from position {@code pos} in sequence
+     * {@code seq} to the given search results
+     * 
+     * @param seq
+     * @param pos
+     * @param sr
+     */
+    public void markMappedRegion(SequenceI seq, int pos, SearchResultsI sr)
+    {
+      int[] codon = null;
+      SequenceI mappedSeq = null;
+      SequenceI ds = seq.getDatasetSequence();
+      
+      if (this.fromSeq == seq || this.fromSeq == ds)
+      {
+        codon = this.mapping.map.locateInTo(pos, pos);
+        mappedSeq = this.mapping.to;
+      }
+      else if (this.mapping.to == seq || this.mapping.to == ds)
+      {
+        codon = this.mapping.map.locateInFrom(pos, pos);
+        mappedSeq = this.fromSeq;
+      }
+
+      if (codon != null)
+      {
+        for (int i = 0; i < codon.length; i += 2)
+        {
+          sr.addResult(mappedSeq, codon[i], codon[i + 1]);
+        }
+      }
+    }
   }
 
   private List<SequenceToSequenceMapping> mappings;
@@ -406,34 +440,10 @@ public class AlignedCodonFrame
   public void markMappedRegion(SequenceI seq, int index,
           SearchResultsI results)
   {
-    int[] codon;
     SequenceI ds = seq.getDatasetSequence();
     for (SequenceToSequenceMapping ssm : mappings)
     {
-      if (ssm.fromSeq == seq || ssm.fromSeq == ds)
-      {
-        codon = ssm.mapping.map.locateInTo(index, index);
-        if (codon != null)
-        {
-          for (int i = 0; i < codon.length; i += 2)
-          {
-            results.addResult(ssm.mapping.to, codon[i], codon[i + 1]);
-          }
-        }
-      }
-      else if (ssm.mapping.to == seq || ssm.mapping.to == ds)
-      {
-        {
-          codon = ssm.mapping.map.locateInFrom(index, index);
-          if (codon != null)
-          {
-            for (int i = 0; i < codon.length; i += 2)
-            {
-              results.addResult(ssm.fromSeq, codon[i], codon[i + 1]);
-            }
-          }
-        }
-      }
+      ssm.markMappedRegion(ds, index, results);
     }
   }
 
@@ -933,4 +943,34 @@ public class AlignedCodonFrame
     }
     return null;
   }
+
+  /**
+   * Returns the first mapping found which is between the given sequence and
+   * another, is a triplet mapping (3:1 or 1:3), and covers the full extent of
+   * both sequences involved.
+   * 
+   * @param seq
+   * @return
+   */
+  public SequenceToSequenceMapping getCoveringCodonMapping(SequenceI seq)
+  {
+    for (SequenceToSequenceMapping mapping : mappings)
+    {
+      if (mapping.getMapping().getMap().isTripletMap()
+              && mapping.covers(seq))
+      {
+        if (mapping.fromSeq == seq
+                && mapping.covers(mapping.getMapping().getTo()))
+        {
+          return mapping;
+        }
+        else if (mapping.getMapping().getTo() == seq
+                && mapping.covers(mapping.fromSeq))
+        {
+          return mapping;
+        }
+      }
+    }
+    return null;
+  }
 }
diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index b348766..8f513c9 100644
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -38,9 +38,9 @@ import jalview.api.AlignViewportI;
 import jalview.api.FeatureColourI;
 import jalview.api.FeaturesDisplayedI;
 import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.MappedFeatures;
-import jalview.datamodel.Mapping;
 import jalview.datamodel.SearchResultMatchI;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
@@ -1196,18 +1196,18 @@ 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;
+    SequenceToSequenceMapping mapping = null;
     SequenceI mapFrom = null;
 
     for (AlignedCodonFrame acf : mappings)
     {
-      mapping = acf.getMappingForSequence(sequence);
-      if (mapping == null || !mapping.getMap().isTripletMap())
+      mapping = acf.getCoveringCodonMapping(ds);
+      if (mapping == null)
       {
-        continue; // we are only looking for 3:1 or 1:3 mappings
+        continue;
       }
       SearchResultsI sr = new SearchResults();
-      acf.markMappedRegion(ds, pos, sr);
+      mapping.markMappedRegion(ds, pos, sr);
       for (SearchResultMatchI match : sr.getResults())
       {
         int fromRes = match.getStart();
@@ -1260,7 +1260,7 @@ public abstract class FeatureRendererModel
       }
     }
     
-    return new MappedFeatures(mapping, mapFrom, pos, residue, result);
+    return new MappedFeatures(mapping.getMapping(), mapFrom, pos, residue, result);
   }
 
   @Override
-- 
1.7.10.2