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JAL-1953 update canonical db test for PFAM canonical name - also note could do the...
[jalview.git] / test / jalview / util / DBRefUtilsTest.java
diff --git a/test/jalview/util/DBRefUtilsTest.java b/test/jalview/util/DBRefUtilsTest.java
index 963ca7c..3984920 100644 (file)
--- a/test/jalview/util/DBRefUtilsTest.java
+++ b/test/jalview/util/DBRefUtilsTest.java
@@ -21,7 +21,6 @@
 package jalview.util;
 
 import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
@@ -64,7 +63,9 @@ public class DBRefUtilsTest
     DBRefEntry ref2 = new DBRefEntry("UNIPROT", "1.2", "A12346");
     // Source is converted to upper-case by this constructor!
     DBRefEntry ref3 = new DBRefEntry("Uniprot", "1.2", "A12347");
-    List<DBRefEntry> dbrefs = Arrays.asList(new DBRefEntry[] { ref1, ref2, ref3 });
+    List<DBRefEntry> dbrefs = Arrays
+            .asList(new DBRefEntry[]
+            { ref1, ref2, ref3 });
     String[] sources = new String[] { "EMBL", "UNIPROT" };
 
     List<DBRefEntry> selected = DBRefUtils.selectRefs(dbrefs, sources);
@@ -109,49 +110,20 @@ public class DBRefUtilsTest
     assertEquals("PDB", DBRefUtils.getCanonicalName("Pdb"));
     assertEquals("UNIPROT",
             DBRefUtils.getCanonicalName("uniprotkb/swiss-prot"));
-    assertEquals("UNIPROT", DBRefUtils.getCanonicalName("uniprotkb/trembl"));
+    assertEquals("UNIPROT",
+            DBRefUtils.getCanonicalName("uniprotkb/trembl"));
     assertEquals("UNIPROT",
             DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-PROT"));
-    assertEquals("UNIPROT", DBRefUtils.getCanonicalName("UNIPROTKB/TREMBL"));
+    assertEquals("UNIPROT",
+            DBRefUtils.getCanonicalName("UNIPROTKB/TREMBL"));
     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"));
-
-  }
+    assertEquals("pfam", DBRefUtils.getCanonicalName("PFAM")); // since JAL-1953 Pfam is also a canonical database name 
 
-  @Test(groups = { "Functional" })
-  public void testIsDasCoordinateSystem()
-  {
-    assertFalse(DBRefUtils.isDasCoordinateSystem(null, null));
-    assertFalse(DBRefUtils.isDasCoordinateSystem("pdbresnum", null));
-    assertFalse(DBRefUtils.isDasCoordinateSystem(null, new DBRefEntry(
-            "PDB", "v1", "a1")));
-
-    assertTrue(DBRefUtils.isDasCoordinateSystem("pdbresnum",
-            new DBRefEntry("PDB", "v1", "a1")));
-    assertTrue(DBRefUtils.isDasCoordinateSystem("PDBRESNUM",
-            new DBRefEntry("PDB", "v1", "a1")));
-    // "pdb" is converted to upper-case in DBRefEntry constructor
-    assertTrue(DBRefUtils.isDasCoordinateSystem("pdbresnum",
-            new DBRefEntry("pdb", "v1", "a1")));
-    assertFalse(DBRefUtils.isDasCoordinateSystem("pdb", new DBRefEntry(
-            "pdb", "v1", "a1")));
-
-    assertTrue(DBRefUtils.isDasCoordinateSystem("UNIPROT", new DBRefEntry(
-            "Uniprot", "v1", "a1")));
-    assertTrue(DBRefUtils.isDasCoordinateSystem("Uniprot", new DBRefEntry(
-            "UNIPROT", "v1", "a1")));
-    assertFalse(DBRefUtils.isDasCoordinateSystem("UNIPROTKB",
-            new DBRefEntry("pdb", "v1", "a1")));
-
-    assertTrue(DBRefUtils.isDasCoordinateSystem("EMBL", new DBRefEntry(
-            "EMBL", "v1", "a1")));
-    assertTrue(DBRefUtils.isDasCoordinateSystem("embl", new DBRefEntry(
-            "embl", "v1", "a1")));
   }
 
   /**
@@ -169,6 +141,11 @@ public class DBRefUtilsTest
     assertEquals("1.2", ref.getVersion());
     assertEquals("a7890", ref.getAccessionId());
     assertTrue(seq.getAllPDBEntries().isEmpty());
+    SequenceI seq2 = new Sequence("Seq2", "ABCD");
+    // Check that whitespace doesn't confuse parseToDbRef
+    DBRefEntry ref2 = DBRefUtils.parseToDbRef(seq2, "EMBL", "1.2",
+            " a7890");
+    assertEquals(ref, ref2);
   }
 
   /**
@@ -215,12 +192,14 @@ public class DBRefUtilsTest
     DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
     // ref5 matches although it has a mapping - ignored
     DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
-    ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
-        1 }, 1, 1)));
-
-    List<DBRefEntry> matches = DBRefUtils.searchRefs(
-               Arrays.asList(new DBRefEntry[] {
-        ref1, ref2, ref3, ref4, ref5 }), target, DBRefUtils.SEARCH_MODE_FULL);
+    ref5.setMap(
+            new Mapping(new MapList(new int[]
+            { 1, 1 }, new int[] { 1, 1 }, 1, 1)));
+
+    List<DBRefEntry> matches = DBRefUtils
+            .searchRefs(Arrays.asList(new DBRefEntry[]
+            { ref1, ref2, ref3, ref4, ref5 }), target,
+                    DBRefUtils.SEARCH_MODE_FULL);
     assertEquals(3, matches.size());
     assertSame(ref1, matches.get(0));
     assertSame(ref2, matches.get(1));
@@ -235,26 +214,29 @@ public class DBRefUtilsTest
   public void testSearchRefs_withMapping()
   {
     DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234");
-    final Mapping map1 = new Mapping(new MapList(new int[] { 1, 1 },
-            new int[] { 1, 1 }, 1, 1));
+    final Mapping map1 = new Mapping(
+            new MapList(new int[]
+            { 1, 1 }, new int[] { 1, 1 }, 1, 1));
     target.setMap(map1);
 
     // these all match target iff mappings match
     DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // no map: matches
     DBRefEntry ref2 = new DBRefEntry("EMBL", "1", "A1234"); // =map: matches
-    final Mapping map2 = new Mapping(new MapList(new int[] { 1, 1 },
-            new int[] { 1, 1 }, 1, 1));
+    final Mapping map2 = new Mapping(
+            new MapList(new int[]
+            { 1, 1 }, new int[] { 1, 1 }, 1, 1));
     ref2.setMap(map2);
 
     // different map: no match
     DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "A1234");
-    final Mapping map3 = new Mapping(new MapList(new int[] { 1, 1 },
-            new int[] { 1, 1 }, 2, 2));
+    final Mapping map3 = new Mapping(
+            new MapList(new int[]
+            { 1, 1 }, new int[] { 1, 1 }, 2, 2));
     ref3.setMap(map3);
 
-    List<DBRefEntry> matches = DBRefUtils.searchRefs(
-               Arrays.asList(new DBRefEntry[] {
-        ref1, ref2, ref3 }), target, DBRefUtils.SEARCH_MODE_FULL);
+    List<DBRefEntry> matches = DBRefUtils
+            .searchRefs(Arrays.asList(new DBRefEntry[]
+            { ref1, ref2, ref3 }), target, DBRefUtils.SEARCH_MODE_FULL);
     assertEquals(2, matches.size());
     assertSame(ref1, matches.get(0));
     assertSame(ref2, matches.get(1));
@@ -275,11 +257,13 @@ public class DBRefUtilsTest
     DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1235"); // no match
     // ref5 matches although it has a mapping - ignored
     DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
-    ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
-        1 }, 1, 1)));
+    ref5.setMap(
+            new Mapping(new MapList(new int[]
+            { 1, 1 }, new int[] { 1, 1 }, 1, 1)));
 
-    List<DBRefEntry> dbrefs = Arrays.asList(new DBRefEntry[] {
-                ref1, ref2, ref3, ref4, ref5 });
+    List<DBRefEntry> dbrefs = Arrays
+            .asList(new DBRefEntry[]
+            { ref1, ref2, ref3, ref4, ref5 });
     List<DBRefEntry> matches = DBRefUtils.searchRefs(dbrefs, "A1234");
     assertEquals(3, matches.size());
     assertSame(ref1, matches.get(0));
@@ -304,12 +288,14 @@ public class DBRefUtilsTest
     DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
     // ref5 matches although it has a mapping - ignored
     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(
-               Arrays.asList(new DBRefEntry[] {
-        ref1, ref2, ref3, ref4, ref5 }), target, DBRefUtils.SEARCH_MODE_FULL);
+    ref5.setMap(
+            new Mapping(new MapList(new int[]
+            { 1, 1 }, new int[] { 1, 1 }, 1, 1)));
+
+    List<DBRefEntry> matches = DBRefUtils
+            .searchRefs(Arrays.asList(new DBRefEntry[]
+            { ref1, ref2, ref3, ref4, ref5 }), target,
+                    DBRefUtils.SEARCH_MODE_FULL);
     assertEquals(4, matches.size());
     assertSame(ref1, matches.get(0));
     assertSame(ref2, matches.get(1));