X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FDBRefUtilsTest.java;h=d1c24d189231add9d327539066398267ff972909;hb=528c0f1815bc67b54618ad5b16c2162946974caf;hp=96935cea0a87cc58f8a85f8777fb3b8713e9e5c0;hpb=65675b2d016736f8ca4dfb2493863c4d53cec591;p=jalview.git

diff --git a/test/jalview/util/DBRefUtilsTest.java b/test/jalview/util/DBRefUtilsTest.java
index 96935ce..d1c24d1 100644
--- a/test/jalview/util/DBRefUtilsTest.java
+++ b/test/jalview/util/DBRefUtilsTest.java
@@ -158,6 +158,9 @@ public class DBRefUtilsTest
     SequenceI seq = new Sequence("Seq1", "ABCD");
     DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "pdb", "1.2",
             "1WRI A; 7-80;");
+    // TODO: correct PDBEntry and PDB DBRef accessions need to be generated for
+    // PDB ref in Stockholm
+
     DBRefEntry[] refs = seq.getDBRefs();
     assertEquals(1, refs.length);
     assertSame(ref, refs[0]);
@@ -194,8 +197,7 @@ public class DBRefUtilsTest
         1 }, 1, 1)));
 
     List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
-        ref1,
-        ref2, ref3, ref4, ref5 }, target);
+        ref1, ref2, ref3, ref4, ref5 }, target);
     assertEquals(3, matches.size());
     assertSame(ref1, matches.get(0));
     assertSame(ref2, matches.get(1));
@@ -228,8 +230,7 @@ public class DBRefUtilsTest
     ref3.setMap(map3);
 
     List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
-        ref1,
-        ref2, ref3 }, target);
+        ref1, ref2, ref3 }, target);
     assertEquals(2, matches.size());
     assertSame(ref1, matches.get(0));
     assertSame(ref2, matches.get(1));
@@ -242,7 +243,7 @@ public class DBRefUtilsTest
   @Test(groups = { "Functional" })
   public void testSearchRefs_accessionid()
   {
-  
+
     DBRefEntry ref1 = new DBRefEntry("Uniprot", "1", "A1234"); // matches
     DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
     // constructor does not upper-case accession id
@@ -252,9 +253,8 @@ public class DBRefUtilsTest
     DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
     ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
         1 }, 1, 1)));
-  
-    DBRefEntry[] dbrefs = new DBRefEntry[] { ref1,
-        ref2, ref3, ref4, ref5 };
+
+    DBRefEntry[] dbrefs = new DBRefEntry[] { ref1, ref2, ref3, ref4, ref5 };
     List<DBRefEntry> matches = DBRefUtils.searchRefs(dbrefs, "A1234");
     assertEquals(3, matches.size());
     assertSame(ref1, matches.get(0));
@@ -270,7 +270,7 @@ public class DBRefUtilsTest
   public void testSearchRefs_wildcardAccessionid()
   {
     DBRefEntry target = new DBRefEntry("EMBL", "2", null);
-  
+
     DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
     // constructor changes embl to EMBL
     DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1235"); // matches
@@ -281,10 +281,9 @@ public class DBRefUtilsTest
     DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1237");
     ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
         1 }, 1, 1)));
-  
+
     List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
-        ref1,
-        ref2, ref3, ref4, ref5 }, target);
+        ref1, ref2, ref3, ref4, ref5 }, target);
     assertEquals(4, matches.size());
     assertSame(ref1, matches.get(0));
     assertSame(ref2, matches.get(1));