From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 7 Aug 2019 09:25:09 +0000 (+0100)
Subject: JAL-3187 (fudge) look in both alignments for stored mappings
X-Git-Tag: Release_2_11_1_0~27
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2Ffeature%2FJAL-3187linkedFeatures;p=jalview.git

JAL-3187 (fudge) look in both alignments for stored mappings
---

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index f9c9782..aba5601 100644
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -1177,6 +1177,16 @@ public abstract class FeatureRendererModel
             .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
      */