From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 23 Jun 2016 13:09:44 +0000 (+0100)
Subject: JAL-2110 JAL-1551 formatting
X-Git-Tag: Release_2_10_0~140^2~5^2~42
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f2e52ac07216e1fa3a5d1975e6afd6bc03d6a946;p=jalview.git

JAL-2110 JAL-1551 formatting
---

diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java
index c2d7ca6..0c3e4d5 100644
--- a/test/jalview/analysis/CrossRefTest.java
+++ b/test/jalview/analysis/CrossRefTest.java
@@ -396,7 +396,7 @@ public class CrossRefTest
     dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "P00314"));
     final SequenceI pep1 = new Sequence("Q9ZTS2", "MYQLIRSSW");
     final SequenceI pep2 = new Sequence("P00314", "MRKLLAASG");
-  
+
     /*
      * argument false suppresses adding DAS sources
      * todo: define an interface type SequenceFetcherI and mock that
@@ -473,7 +473,7 @@ public class CrossRefTest
      */
     final SequenceI pep1 = new Sequence("UNIPROT|P15056", "MAAL");
     final SequenceI pep2 = new Sequence("UNIPROT|H7C5K3", "QALF");
-  
+
     /*
      * argument false suppresses adding DAS sources
      * todo: define an interface type SequenceFetcherI and mock that
@@ -485,7 +485,7 @@ public class CrossRefTest
       {
         return true;
       }
-  
+
       @Override
       public SequenceI[] getSequences(List<DBRefEntry> refs, boolean dna)
       {
@@ -493,7 +493,7 @@ public class CrossRefTest
       }
     };
     SequenceFetcherFactory.setSequenceFetcher(mockFetcher);
-  
+
     /*
      * find UNIPROT xrefs for gene and transcripts
      * verify that
@@ -503,8 +503,7 @@ public class CrossRefTest
      */
     SequenceI[] seqs = new SequenceI[] { gene, braf001, braf002 };
     AlignmentI al = new Alignment(seqs);
-    Alignment xrefs = new CrossRef(seqs, al)
-.findXrefSequences("UNIPROT",
+    Alignment xrefs = new CrossRef(seqs, al).findXrefSequences("UNIPROT",
             true);
     assertEquals(2, xrefs.getHeight());
     assertSame(pep1, xrefs.getSequenceAt(0));
@@ -550,14 +549,14 @@ public class CrossRefTest
     p0ce20.addDBRef(new DBRefEntry("EMBL", "0", "J03321"));
     p0ce20.addDBRef(new DBRefEntry("EMBL", "0", "X06707"));
     p0ce20.addDBRef(new DBRefEntry("EMBL", "0", "X07547"));
-  
+
     /*
      * EMBL sequences to be 'fetched', complete with dbrefs and mappings
      * to their protein products (CDS location  and translations  are provided
      * in  EMBL XML); these should be matched to, and replaced with,
      * the corresponding uniprot sequences after fetching
      */
-    
+
     /*
      * J03321 with mappings to P0CE19 and P0CE20
      */
@@ -565,7 +564,8 @@ public class CrossRefTest
     DBRefEntry dbref1 = new DBRefEntry("UNIPROT", "0", "P0CE19");
     MapList mapList = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 },
             3, 1);
-    Mapping map = new Mapping(new Sequence("UNIPROT|P0CE19", "KPFG"), mapList);
+    Mapping map = new Mapping(new Sequence("UNIPROT|P0CE19", "KPFG"),
+            mapList);
     // add a dbref to the mapped to sequence - should get copied to p0ce19
     map.getTo().addDBRef(new DBRefEntry("PIR", "0", "S01875"));
     dbref1.setMap(map);
@@ -575,7 +575,7 @@ public class CrossRefTest
     dbref2.setMap(new Mapping(new Sequence("UNIPROT|P0CE20", "PFGK"),
             new MapList(mapList)));
     j03321.addDBRef(dbref2);
-    
+
     /*
      * X06707 with mappings to P0CE19 and P0CE20
      */
@@ -590,7 +590,7 @@ public class CrossRefTest
             1);
     dbref4.setMap(new Mapping(new Sequence("UNIPROT|P0CE20", "PFGK"), map3));
     x06707.addDBRef(dbref4);
-    
+
     /*
      * M19487 with mapping to P0CE19 and Q46432
      */
@@ -616,7 +616,7 @@ public class CrossRefTest
     dbref8.setMap(new Mapping(new Sequence("UNIPROT|B0BCM4", "KPFG"),
             new MapList(map2)));
     x07547.addDBRef(dbref8);
-  
+
     /*
      * mock sequence fetcher to 'return' the EMBL sequences
      * TODO: Mockito would allow .thenReturn().thenReturn() here, 
@@ -626,27 +626,34 @@ public class CrossRefTest
      */
     SequenceFetcher mockFetcher = new SequenceFetcher(false)
     {
-      int call  = 0;
+      int call = 0;
+
       @Override
       public boolean isFetchable(String source)
       {
         return true;
       }
+
       @Override
       public SequenceI[] getSequences(List<DBRefEntry> refs, boolean dna)
       {
         call++;
-        if (call == 1) {
-          assertEquals("Expected 3 embl seqs in first fetch", 3, refs.size());
-        return new SequenceI[] { j03321, x06707, m19487 };
-        } else {
-          assertEquals("Expected 1 embl seq in second fetch", 1, refs.size());
-                return new SequenceI[] { x07547 };
+        if (call == 1)
+        {
+          assertEquals("Expected 3 embl seqs in first fetch", 3,
+                  refs.size());
+          return new SequenceI[] { j03321, x06707, m19487 };
+        }
+        else
+        {
+          assertEquals("Expected 1 embl seq in second fetch", 1,
+                  refs.size());
+          return new SequenceI[] { x07547 };
         }
       }
     };
     SequenceFetcherFactory.setSequenceFetcher(mockFetcher);
-  
+
     /*
      * find EMBL xrefs for Uniprot seqs and verify that
      * - the EMBL xref'd sequences are retrieved without duplicates