Merge branch 'develop' into bug/JAL-1841rnaSecStr

[jalview.git] / test / jalview / datamodel / SequenceTest.java

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 03c4a96..71719dd 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -29,6 +29,7 @@ import static org.testng.AssertJUnit.assertTrue;
 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
 import jalview.datamodel.PDBEntry.Type;
+import jalview.util.MapList;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -64,6 +65,30 @@ public class SequenceTest
     assertEquals("Gap interval 2 end wrong", 8, gapInt.get(1)[1]);
   }
 
+  @Test(groups = ("Functional"))
+  public void testIsProtein()
+  {
+    // test Protein
+    assertTrue(new Sequence("prot","ASDFASDFASDF").isProtein());
+    // test DNA
+    assertFalse(new Sequence("prot","ACGTACGTACGT").isProtein());
+    // test RNA
+    SequenceI sq = new Sequence("prot","ACGUACGUACGU");
+    assertFalse(sq.isProtein());
+    // change sequence, should trigger an update of cached result
+    sq.setSequence("ASDFASDFADSF");
+    assertTrue(sq.isProtein());
+    /*
+     * in situ change of sequence doesn't change hashcode :-O
+     * (sequence should not expose internal implementation)
+     */
+    for (int i = 0; i < sq.getSequence().length; i++)
+    {
+      sq.getSequence()[i] = "acgtu".charAt(i % 5);
+    }
+    assertTrue(sq.isProtein()); // but it isn't
+  }
+
   @Test(groups = { "Functional" })
   public void testGetAnnotation()
   {
@@ -387,6 +412,20 @@ public class SequenceTest
   }
 
   /**
+   * test createDatasetSequence behaves to doc
+   */
+  @Test(groups = { "Functional" })
+  public void testCreateDatasetSequence()
+  {
+    SequenceI sq = new Sequence("my","ASDASD");
+    assertNull(sq.getDatasetSequence());
+    SequenceI rds = sq.createDatasetSequence();
+    assertNotNull(rds);
+    assertNull(rds.getDatasetSequence());
+    assertEquals(sq.getDatasetSequence(), rds);
+  }
+
+  /**
    * Test for deriveSequence applied to a sequence with a dataset
    */
   @Test(groups = { "Functional" })
@@ -616,4 +655,85 @@ public class SequenceTest
     assertEquals(' ', sq.getCharAt(5));
     assertEquals(' ', sq.getCharAt(-1));
   }
+
+  /**
+   * Tests for adding (or updating) dbrefs
+   * 
+   * @see DBRefEntry#updateFrom(DBRefEntry)
+   */
+  @Test(groups = { "Functional" })
+  public void testAddDBRef()
+  {
+    SequenceI sq = new Sequence("", "abcde");
+    assertNull(sq.getDBRefs());
+    DBRefEntry dbref = new DBRefEntry("Uniprot", "1", "P00340");
+    sq.addDBRef(dbref);
+    assertEquals(1, sq.getDBRefs().length);
+    assertSame(dbref, sq.getDBRefs()[0]);
+
+    /*
+     * change of version - new entry
+     */
+    DBRefEntry dbref2 = new DBRefEntry("Uniprot", "2", "P00340");
+    sq.addDBRef(dbref2);
+    assertEquals(2, sq.getDBRefs().length);
+    assertSame(dbref, sq.getDBRefs()[0]);
+    assertSame(dbref2, sq.getDBRefs()[1]);
+
+    /*
+     * matches existing entry - not added
+     */
+    sq.addDBRef(new DBRefEntry("UNIPROT", "1", "p00340"));
+    assertEquals(2, sq.getDBRefs().length);
+
+    /*
+     * different source = new entry
+     */
+    DBRefEntry dbref3 = new DBRefEntry("UniRef", "1", "p00340");
+    sq.addDBRef(dbref3);
+    assertEquals(3, sq.getDBRefs().length);
+    assertSame(dbref3, sq.getDBRefs()[2]);
+
+    /*
+     * different ref = new entry
+     */
+    DBRefEntry dbref4 = new DBRefEntry("UniRef", "1", "p00341");
+    sq.addDBRef(dbref4);
+    assertEquals(4, sq.getDBRefs().length);
+    assertSame(dbref4, sq.getDBRefs()[3]);
+
+    /*
+     * matching ref with a mapping - map updated
+     */
+    DBRefEntry dbref5 = new DBRefEntry("UniRef", "1", "p00341");
+    Mapping map = new Mapping(new MapList(new int[] { 1, 3 }, new int[] {
+        1, 1 }, 3, 1));
+    dbref5.setMap(map);
+    sq.addDBRef(dbref5);
+    assertEquals(4, sq.getDBRefs().length);
+    assertSame(dbref4, sq.getDBRefs()[3]);
+    assertSame(map, dbref4.getMap());
+
+    /*
+     * 'real' version replaces "0" version
+     */
+    dbref2.setVersion("0");
+    DBRefEntry dbref6 = new DBRefEntry(dbref2.getSource(), "3",
+            dbref2.getAccessionId());
+    sq.addDBRef(dbref6);
+    assertEquals(4, sq.getDBRefs().length);
+    assertSame(dbref2, sq.getDBRefs()[1]);
+    assertEquals("3", dbref2.getVersion());
+
+    /*
+     * 'real' version replaces "source:0" version
+     */
+    dbref3.setVersion("Uniprot:0");
+    DBRefEntry dbref7 = new DBRefEntry(dbref3.getSource(), "3",
+            dbref3.getAccessionId());
+    sq.addDBRef(dbref7);
+    assertEquals(4, sq.getDBRefs().length);
+    assertSame(dbref3, sq.getDBRefs()[2]);
+    assertEquals("3", dbref2.getVersion());
+  }
 }