From 1719c61073682fdfe66a63408bab498b6ca4234c Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 13 Feb 2018 13:47:37 +0000
Subject: [PATCH] JAL-2781 refactor StructureSelectionManager.siftsClient to
 local variable in computeMapping

---
 src/jalview/structure/StructureSelectionManager.java |   16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 434d4ff..0e43841 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -74,8 +74,6 @@ public class StructureSelectionManager
 
   private boolean addTempFacAnnot = false;
 
-  private SiftsClient siftsClient = null;
-
   /*
    * Set of any registered mappings between (dataset) sequences.
    */
@@ -414,7 +412,10 @@ public class StructureSelectionManager
       ex.printStackTrace();
       return null;
     }
-
+    /*
+     * sifts client - non null if SIFTS mappings are to be used 
+     */
+    SiftsClient siftsClient = null;
     try
     {
       if (isMapUsingSIFTs)
@@ -527,7 +528,7 @@ public class StructureSelectionManager
           try
           {
             siftsMapping = getStructureMapping(seq, pdbFile, targetChainId,
-                    pdb, maxChain, sqmpping, maxAlignseq);
+                    pdb, maxChain, sqmpping, maxAlignseq, siftsClient);
             seqToStrucMapping.add(siftsMapping);
             maxChain.makeExactMapping(siftsMapping, seq);
             maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this
@@ -559,7 +560,8 @@ public class StructureSelectionManager
             try
             {
               siftsMapping = getStructureMapping(seq,
-                      pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq);
+                      pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq,
+                      siftsClient);
               foundSiftsMappings.add(siftsMapping);
               chain.makeExactMapping(siftsMapping, seq);
               chain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this
@@ -668,13 +670,15 @@ public class StructureSelectionManager
    * @param maxChain
    * @param sqmpping
    * @param maxAlignseq
+   * @param siftsClient
+   *          client for retrieval of SIFTS mappings for this structure
    * @return
    * @throws SiftsException
    */
   private StructureMapping getStructureMapping(SequenceI seq,
           String pdbFile, String targetChainId, StructureFile pdb,
           PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
-          AlignSeq maxAlignseq) throws SiftsException
+          AlignSeq maxAlignseq, SiftsClient siftsClient) throws SiftsException
   {
     StructureMapping curChainMapping = siftsClient
             .getSiftsStructureMapping(seq, pdbFile, targetChainId);
-- 
1.7.10.2