From c7e8d3a34d2bac0206a942b393e9b6d4d52c55a2 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 21 Jan 2016 14:56:27 +0000
Subject: [PATCH] JAL-1705 tidy and todo comment, no functional change

---
 test/jalview/ws/seqfetcher/DbRefFetcherTest.java |   19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
index ddd8b33..5265a72 100644
--- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
+++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
@@ -33,6 +33,8 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.util.DBRefUtils;
 import jalview.ws.SequenceFetcher;
+import jalview.ws.dbsources.Pdb;
+import jalview.ws.dbsources.Uniprot;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -67,7 +69,7 @@ public class DbRefFetcherTest
 
   /**
    * Tests that standard protein database sources include Uniprot (as the first)
-   * and also PDB. (Additional sources are dependent on available of DAS
+   * and also PDB. (Additional sources are dependent on availability of DAS
    * services.)
    */
   @Test(groups = { "Functional" })
@@ -75,30 +77,31 @@ public class DbRefFetcherTest
   {
     String[] defdb = DBRefSource.PROTEINDBS;
     List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
+    SequenceFetcher sfetcher = new SequenceFetcher();
+    boolean pdbFound = false;
+
     for (String ddb : defdb)
     {
-      SequenceFetcher sfetcher = new SequenceFetcher();
       List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
 
       if (srcesfordb != null)
       {
+        // TODO is this right? get duplicate entries
         srces.addAll(srcesfordb);
       }
     }
 
     int i = 0;
     int uniprotPos = -1;
-    int pdbPos = -1;
-    // append the selected sequence sources to the default dbs
     for (DbSourceProxy s : srces)
     {
-      if (s instanceof jalview.ws.dbsources.Uniprot)
+      if (s instanceof Uniprot && uniprotPos == -1)
       {
         uniprotPos = i;
       }
-      if (s instanceof jalview.ws.dbsources.Pdb)
+      if (s instanceof Pdb)
       {
-        pdbPos = i;
+        pdbFound = true;
       }
       i++;
     }
@@ -107,7 +110,7 @@ public class DbRefFetcherTest
             + srces.size() + " sources (source was at position "
             + uniprotPos + ")", uniprotPos == 0);
     assertTrue("Failed to find PDB source amongst " + srces.size()
-            + " sources", pdbPos >= 0);
+            + " sources", pdbFound);
   }
 
   /**
-- 
1.7.10.2