JAL-2281 Unit test updates

[jalview.git] / test / jalview / util / DBRefUtilsTest.java

diff --git a/test/jalview/util/DBRefUtilsTest.java b/test/jalview/util/DBRefUtilsTest.java
index 96935ce..0431cf6 100644 (file)
--- a/test/jalview/util/DBRefUtilsTest.java
+++ b/test/jalview/util/DBRefUtilsTest.java
@@ -74,7 +74,7 @@ public class DBRefUtilsTest
     assertSame(ref2, selected[0]);
     assertSame(ref3, selected[1]);
 
-    sources = new String[] { "Uniprot", "EMBLCDS" };
+    sources = new String[] { "EMBLCDS" };
     selected = DBRefUtils.selectRefs(dbrefs, sources);
     assertNull(selected);
   }
@@ -99,6 +99,11 @@ public class DBRefUtilsTest
     assertEquals("UNIPROTKB/SWISS-CHEESE",
             DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-CHEESE"));
     assertEquals("ENSEMBL", DBRefUtils.getCanonicalName("Ensembl"));
+
+    // these are not 'known' to Jalview
+    assertEquals("PFAM", DBRefUtils.getCanonicalName("PFAM"));
+    assertEquals("pfam", DBRefUtils.getCanonicalName("pfam"));
+
   }
 
   @Test(groups = { "Functional" })
@@ -158,6 +163,9 @@ 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 +202,7 @@ 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 +235,7 @@ 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 +248,7 @@ 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 +258,8 @@ 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 +275,7 @@ 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 +286,9 @@ 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));