From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 7 Jul 2016 15:51:21 +0000 (+0100)
Subject: JAL-2110 field 'cf' moved to stack
X-Git-Tag: Release_2_10_0~140^2~5^2~12
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9975899291c5d1c4bed9139315e31382c2225d97;p=jalview.git

JAL-2110 field 'cf' moved to stack
---

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index df5ca10..288d60e 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -68,11 +68,6 @@ public class CrossRef
   List<SequenceI> rseqs;
 
   /**
-   * mappings constructed
-   */
-  AlignedCodonFrame cf;
-
-  /**
    * Constructor
    * 
    * @param seqs
@@ -213,7 +208,7 @@ public class CrossRef
   {
 
     rseqs = new ArrayList<SequenceI>();
-    cf = new AlignedCodonFrame();
+    AlignedCodonFrame cf = new AlignedCodonFrame();
     matcher = new SequenceIdMatcher(
             dataset.getSequences());
 
@@ -338,7 +333,7 @@ public class CrossRef
        */
       if (!sourceRefs.isEmpty())
       {
-        retrieveCrossRef(sourceRefs, seq, xrfs, fromDna);
+        retrieveCrossRef(sourceRefs, seq, xrfs, fromDna, cf);
       }
     }
 
@@ -355,7 +350,7 @@ public class CrossRef
   }
 
   private void retrieveCrossRef(List<DBRefEntry> sourceRefs, SequenceI seq,
-          DBRefEntry[] xrfs, boolean fromDna)
+          DBRefEntry[] xrfs, boolean fromDna, AlignedCodonFrame cf)
   {
     ASequenceFetcher sftch = SequenceFetcherFactory.getSequenceFetcher();
     SequenceI[] retrieved = null;