From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 16 Jun 2016 12:50:55 +0000 (+0100)
Subject: JAL-2110 todo - select mappings involving sequences in alignment
X-Git-Tag: Release_2_10_0~140^2~5^2~49^2~10
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a7bda2e291fc5d01b6e3e43ba6215b78067beb5d;p=jalview.git

JAL-2110 todo - select mappings involving sequences in alignment
---

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index f14539b..ed1c92e 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1357,6 +1357,10 @@ public class Alignment implements AlignmentI
   @Override
   public List<AlignedCodonFrame> getCodonFrames()
   {
+    // TODO: Fix this method to fix failing AlignedCodonFrame tests
+    // this behaviour is currently incorrect. method should return codon frames
+    // for just the alignment,
+    // selected from dataset
     return dataset != null ? dataset.getCodonFrames() : codonFrameList;
   }