Merge remote-tracking branch 'origin/develop' into bug/JAL-2282

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

diff --git a/test/jalview/util/DBRefUtilsTest.java b/test/jalview/util/DBRefUtilsTest.java
index 371bb91..468bc3e 100644 (file)
--- a/test/jalview/util/DBRefUtilsTest.java
+++ b/test/jalview/util/DBRefUtilsTest.java
@@ -33,6 +33,8 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
+import java.util.List;
+
 import org.testng.annotations.Test;
 
 public class DBRefUtilsTest
@@ -72,9 +74,23 @@ public class DBRefUtilsTest
     assertSame(ref2, selected[0]);
     assertSame(ref3, selected[1]);
 
-    sources = new String[] { "Uniprot", "EMBLCDS" };
+    // case insensitive
+    sources = new String[] { "Uniprot" };
+    selected = DBRefUtils.selectRefs(dbrefs, sources);
+    assertEquals(2, selected.length);
+    assertSame(ref2, selected[0]);
+    assertSame(ref3, selected[1]);
+
+    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]);
   }
 
   /**
@@ -97,6 +113,11 @@ 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" })
@@ -144,7 +165,7 @@ public class DBRefUtilsTest
     assertEquals("EMBL", ref.getSource());
     assertEquals("1.2", ref.getVersion());
     assertEquals("a7890", ref.getAccessionId());
-    assertNull(seq.getAllPDBEntries());
+    assertTrue(seq.getAllPDBEntries().isEmpty());
   }
 
   /**
@@ -156,6 +177,9 @@ 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]);
@@ -191,12 +215,12 @@ public class DBRefUtilsTest
     ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
         1 }, 1, 1)));
 
-    DBRefEntry[] matches = DBRefUtils.searchRefs(new DBRefEntry[] { ref1,
-        ref2, ref3, ref4, ref5 }, target);
-    assertEquals(3, matches.length);
-    assertSame(ref1, matches[0]);
-    assertSame(ref2, matches[1]);
-    assertSame(ref5, matches[2]);
+    List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
+        ref1, ref2, ref3, ref4, ref5 }, target);
+    assertEquals(3, matches.size());
+    assertSame(ref1, matches.get(0));
+    assertSame(ref2, matches.get(1));
+    assertSame(ref5, matches.get(2));
   }
 
   /**
@@ -224,11 +248,11 @@ public class DBRefUtilsTest
             new int[] { 1, 1 }, 2, 2));
     ref3.setMap(map3);
 
-    DBRefEntry[] matches = DBRefUtils.searchRefs(new DBRefEntry[] { ref1,
-        ref2, ref3 }, target);
-    assertEquals(2, matches.length);
-    assertSame(ref1, matches[0]);
-    assertSame(ref2, matches[1]);
+    List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
+        ref1, ref2, ref3 }, target);
+    assertEquals(2, matches.size());
+    assertSame(ref1, matches.get(0));
+    assertSame(ref2, matches.get(1));
   }
 
   /**
@@ -238,7 +262,7 @@ 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
@@ -248,12 +272,41 @@ 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[] matches = DBRefUtils.searchRefs(new DBRefEntry[] { ref1,
-        ref2, ref3, ref4, ref5 }, "A1234");
-    assertEquals(3, matches.length);
-    assertSame(ref1, matches[0]);
-    assertSame(ref2, matches[1]);
-    assertSame(ref5, matches[2]);
+
+    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));
+    assertSame(ref2, matches.get(1));
+    assertSame(ref5, matches.get(2));
+  }
+
+  /**
+   * Test the method that searches for matches references - case when we are
+   * matching a reference with null (any) accession id
+   */
+  @Test(groups = { "Functional" })
+  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
+    // constructor does not upper-case accession id
+    DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "A1236"); // matches
+    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(new DBRefEntry[] {
+        ref1, ref2, ref3, ref4, ref5 }, target);
+    assertEquals(4, matches.size());
+    assertSame(ref1, matches.get(0));
+    assertSame(ref2, matches.get(1));
+    assertSame(ref3, matches.get(2));
+    assertSame(ref5, matches.get(3));
   }
 }