From 9a00b2b8ea44b66453ced7b961fea8003670e5a3 Mon Sep 17 00:00:00 2001
From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Fri, 29 Jan 2016 16:24:29 +0000
Subject: [PATCH] JAL-1979 refactor out duplicated similar block of code in
 StructureSelectionManger to a single method

---
 .../structure/StructureSelectionManager.java       |   91 ++++++++++----------
 1 file changed, 47 insertions(+), 44 deletions(-)

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index b3b5708..6bc8f84 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -73,6 +73,8 @@ public class StructureSelectionManager
 
   private IProgressIndicator progressIndicator;
 
+  private SiftsClient siftsClient = null;
+
   private long progressSessionId;
 
   /*
@@ -380,7 +382,6 @@ public class StructureSelectionManager
     }
     PDBfile pdb = null;
     boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
-    SiftsClient siftsClient = null;
     try
     {
       pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
@@ -487,69 +488,73 @@ public class StructureSelectionManager
         pdbFile = "INLINE" + pdb.id;
       }
 
-      ArrayList<StructureMapping> seqToStrucMapping = null;
+      ArrayList<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
       if (isMapUsingSIFTs)
       {
         setProgressBar(null);
         setProgressBar("Obtaining mapping with SIFTS");
-        try
+        jalview.datamodel.Mapping sqmpping = maxAlignseq
+                .getMappingFromS1(false);
+        if (targetChainId != null && !targetChainId.trim().isEmpty())
         {
-          jalview.datamodel.Mapping sqmpping = maxAlignseq
-                  .getMappingFromS1(false);
-          seqToStrucMapping = new ArrayList<StructureMapping>();
-          if (targetChainId != null && !targetChainId.trim().isEmpty())
-          {
-            StructureMapping curChainMapping = siftsClient
-                    .getSiftsStructureMapping(seq, pdbFile, targetChainId);
-            seqToStrucMapping.add(curChainMapping);
-            maxChainId = targetChainId;
-            PDBChain chain = pdb.findChain(targetChainId);
-            if (chain != null)
-            {
-              chain.transferResidueAnnotation(curChainMapping, sqmpping);
-            }
-          }
-          else
+          StructureMapping mapping = getStructureMapping(seq, pdbFile,
+                  targetChainId, pdb, maxChain, sqmpping, maxAlignseq);
+          seqToStrucMapping.add(mapping);
+        }
+        else
+        {
+          for (PDBChain chain : pdb.chains)
           {
-            for (PDBChain chain : pdb.chains)
-            {
-              StructureMapping curChainMapping = siftsClient
-                      .getSiftsStructureMapping(seq, pdbFile, chain.id);
-              seqToStrucMapping.add(curChainMapping);
-              maxChainId = chain.id;
-              chain.transferResidueAnnotation(curChainMapping, sqmpping);
-            }
+            StructureMapping mapping = getStructureMapping(seq, pdbFile,
+                    chain.id, pdb, chain, sqmpping, maxAlignseq);
+            seqToStrucMapping.add(mapping);
           }
-        } catch (SiftsException e)
-        {
-          System.err.println(e.getMessage());
-          System.err
-                  .println(">>> Now switching mapping with NW alignment...");
-          setProgressBar(null);
-          setProgressBar(">>> Now switching mapping with NW alignment...");
-          seqToStrucMapping = getNWMappings(seq, pdbFile, maxChainId,
-                  maxChain, pdb, maxAlignseq);
         }
       }
       else
       {
         setProgressBar(null);
         setProgressBar("Obtaining mapping with NW alignment");
-        seqToStrucMapping = getNWMappings(seq, pdbFile,
-                maxChainId, maxChain, pdb,
-                maxAlignseq);
+        seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
+                maxChain, pdb, maxAlignseq));
       }
 
       if (forStructureView)
       {
-        // mappings.add(seqToStrucMapping);
         mappings.addAll(seqToStrucMapping);
       }
     }
     return pdb;
   }
 
-  private ArrayList<StructureMapping> getNWMappings(SequenceI seq,
+  private StructureMapping getStructureMapping(SequenceI seq,
+          String pdbFile, String targetChainId, PDBfile pdb,
+          PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
+          AlignSeq maxAlignseq)
+  {
+    String maxChainId = targetChainId;
+    try
+    {
+      StructureMapping curChainMapping = siftsClient
+              .getSiftsStructureMapping(seq, pdbFile, targetChainId);
+      PDBChain chain = pdb.findChain(targetChainId);
+      if (chain != null)
+      {
+        chain.transferResidueAnnotation(curChainMapping, sqmpping);
+      }
+      return curChainMapping;
+    } catch (SiftsException e)
+    {
+      System.err.println(e.getMessage());
+      System.err.println(">>> Now switching mapping with NW alignment...");
+      setProgressBar(null);
+      setProgressBar(">>> Now switching mapping with NW alignment...");
+      return getNWMappings(seq, pdbFile, maxChainId, maxChain, pdb,
+              maxAlignseq);
+    }
+  }
+
+  private StructureMapping getNWMappings(SequenceI seq,
           String pdbFile,
           String maxChainId, PDBChain maxChain, PDBfile pdb,
           AlignSeq maxAlignseq)
@@ -624,9 +629,7 @@ public class StructureSelectionManager
     StructureMapping nwMapping = new StructureMapping(seq, pdbFile,
             pdb.id, maxChainId, mapping, mappingDetails.toString());
     maxChain.transferResidueAnnotation(nwMapping, sqmpping);
-    ArrayList<StructureMapping> mappings = new ArrayList<StructureMapping>();
-    mappings.add(nwMapping);
-    return mappings;
+    return nwMapping;
   }
 
   public void removeStructureViewerListener(Object svl, String[] pdbfiles)
-- 
1.7.10.2