X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Futil%2FDBRefUtilsTest.java;h=1c68a71b38ede1bee4d872c0813dec31078c7f28;hb=cc9198fe331720d914817739531b47a9f3016148;hp=5e0683e106fa5f5c58c8df781c3d1f8bbe3d14a7;hpb=318e3baf6738dea7b20640bc3e46814bd566811c;p=jalview.git

diff --git a/test/jalview/util/DBRefUtilsTest.java b/test/jalview/util/DBRefUtilsTest.java
index 5e0683e..1c68a71 100644
--- a/test/jalview/util/DBRefUtilsTest.java
+++ b/test/jalview/util/DBRefUtilsTest.java
@@ -74,9 +74,16 @@ 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);
+
+    sources = new String[] { "embl", "uniprot" };
+    selected = DBRefUtils.selectRefs(dbrefs, sources);
+    assertEquals(3, selected.length);
+    assertSame(ref1, selected[0]);
+    assertSame(ref2, selected[1]);
+    assertSame(ref3, selected[2]);
   }
 
   /**
@@ -99,6 +106,11 @@ 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" })
@@ -197,8 +209,7 @@ 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));
@@ -231,8 +242,7 @@ 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));
@@ -245,7 +255,7 @@ 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
@@ -255,9 +265,8 @@ 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));
@@ -273,7 +282,7 @@ 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
@@ -284,10 +293,9 @@ 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));