import static org.junit.Assert.assertSame;
import static org.junit.Assert.assertTrue;
+import java.util.Arrays;
import java.util.List;
import org.junit.Before;
public class SequenceTest
{
- Sequence seq;
+ SequenceI seq;
@Before
public void setUp()
seq = new Sequence("FER1", "AKPNGVL");
}
@Test
+ public void testInsertGapsAndGapmaps()
+ {
+ SequenceI aseq = seq.deriveSequence();
+ aseq.insertCharAt(2, 3, '-');
+ aseq.insertCharAt(6, 3, '-');
+ assertEquals("Gap insertions not correct", "AK---P---NGVL",
+ aseq.getSequenceAsString());
+ List<int[]> gapInt = aseq.getInsertions();
+ assertEquals("Gap interval 1 start wrong", 2, gapInt.get(0)[0]);
+ assertEquals("Gap interval 1 end wrong", 4, gapInt.get(0)[1]);
+ assertEquals("Gap interval 2 start wrong", 6, gapInt.get(1)[0]);
+ assertEquals("Gap interval 2 end wrong", 8, gapInt.get(1)[1]);
+ }
+
+ @Test
public void testGetAnnotation()
{
// initial state returns null not an empty array
@Test
public void testAddAlignmentAnnotation()
{
- assertNull(seq.annotation);
+ assertNull(seq.getAnnotation());
final AlignmentAnnotation annotation = new AlignmentAnnotation("a",
"b", 2d);
assertNull(annotation.sequenceRef);
assertSame(annotation2, anns[1]);
}
+
+ @Test
+ public void testGetStartGetEnd()
+ {
+ SequenceI seq = new Sequence("test", "ABCDEF");
+ assertEquals(1, seq.getStart());
+ assertEquals(6, seq.getEnd());
+
+ seq = new Sequence("test", "--AB-C-DEF--");
+ assertEquals(1, seq.getStart());
+ assertEquals(6, seq.getEnd());
+
+ seq = new Sequence("test", "----");
+ assertEquals(1, seq.getStart());
+ assertEquals(0, seq.getEnd()); // ??
+ }
+
+ /**
+ * Tests for the method that returns an alignment column position (base 1) for
+ * a given sequence position (base 1).
+ */
+ @Test
+ public void testFindIndex()
+ {
+ SequenceI seq = new Sequence("test", "ABCDEF");
+ assertEquals(0, seq.findIndex(0));
+ assertEquals(1, seq.findIndex(1));
+ assertEquals(5, seq.findIndex(5));
+ assertEquals(6, seq.findIndex(6));
+ assertEquals(6, seq.findIndex(9));
+
+ seq = new Sequence("test", "-A--B-C-D-E-F--");
+ assertEquals(2, seq.findIndex(1));
+ assertEquals(5, seq.findIndex(2));
+ assertEquals(7, seq.findIndex(3));
+
+ // before start returns 0
+ assertEquals(0, seq.findIndex(0));
+ assertEquals(0, seq.findIndex(-1));
+
+ // beyond end returns last residue column
+ assertEquals(13, seq.findIndex(99));
+
+ }
+
+ /**
+ * Tests for the method that returns a dataset sequence position (base 1) for
+ * an aligned column position (base 0).
+ */
+ @Test
+ public void testFindPosition()
+ {
+ SequenceI seq = new Sequence("test", "ABCDEF");
+ assertEquals(1, seq.findPosition(0));
+ assertEquals(6, seq.findPosition(5));
+ // assertEquals(-1, seq.findPosition(6)); // fails
+
+ seq = new Sequence("test", "AB-C-D--");
+ assertEquals(1, seq.findPosition(0));
+ assertEquals(2, seq.findPosition(1));
+ // gap position 'finds' residue to the right (not the left as per javadoc)
+ assertEquals(3, seq.findPosition(2));
+ assertEquals(3, seq.findPosition(3));
+ assertEquals(4, seq.findPosition(4));
+ assertEquals(4, seq.findPosition(5));
+ // returns 1 more than sequence length if off the end ?!?
+ assertEquals(5, seq.findPosition(6));
+ assertEquals(5, seq.findPosition(7));
+
+ seq = new Sequence("test", "--AB-C-DEF--");
+ assertEquals(1, seq.findPosition(0));
+ assertEquals(1, seq.findPosition(1));
+ assertEquals(1, seq.findPosition(2));
+ assertEquals(2, seq.findPosition(3));
+ assertEquals(3, seq.findPosition(4));
+ assertEquals(3, seq.findPosition(5));
+ assertEquals(4, seq.findPosition(6));
+ assertEquals(4, seq.findPosition(7));
+ assertEquals(5, seq.findPosition(8));
+ assertEquals(6, seq.findPosition(9));
+ assertEquals(7, seq.findPosition(10));
+ assertEquals(7, seq.findPosition(11));
+ }
+
+ @Test
+ public void testDeleteChars()
+ {
+ SequenceI seq = new Sequence("test", "ABCDEF");
+ assertEquals(1, seq.getStart());
+ assertEquals(6, seq.getEnd());
+ seq.deleteChars(2, 3);
+ assertEquals("ABDEF", seq.getSequenceAsString());
+ assertEquals(1, seq.getStart());
+ assertEquals(5, seq.getEnd());
+
+ seq = new Sequence("test", "ABCDEF");
+ seq.deleteChars(0, 2);
+ assertEquals("CDEF", seq.getSequenceAsString());
+ assertEquals(3, seq.getStart());
+ assertEquals(6, seq.getEnd());
+ }
+
+ @Test
+ public void testInsertCharAt()
+ {
+ // non-static methods:
+ SequenceI seq = new Sequence("test", "ABCDEF");
+ seq.insertCharAt(0, 'z');
+ assertEquals("zABCDEF", seq.getSequenceAsString());
+ seq.insertCharAt(2, 2, 'x');
+ assertEquals("zAxxBCDEF", seq.getSequenceAsString());
+
+ // for static method see StringUtilsTest
+ }
+
+ /**
+ * Test the method that returns an array of aligned sequence positions where
+ * the array index is the data sequence position (both base 0).
+ */
+ @Test
+ public void testGapMap()
+ {
+ SequenceI seq = new Sequence("test", "-A--B-CD-E--F-");
+ seq.createDatasetSequence();
+ assertEquals("[1, 4, 6, 7, 9, 12]", Arrays.toString(seq.gapMap()));
+ }
+
+ /**
+ * Test the method that gets sequence features, either from the sequence or
+ * its dataset.
+ */
+ @Test
+ public void testGetSequenceFeatures()
+ {
+ SequenceI seq = new Sequence("test", "GATCAT");
+ seq.createDatasetSequence();
+
+ assertNull(seq.getSequenceFeatures());
+
+ /*
+ * SequenceFeature on sequence
+ */
+ SequenceFeature sf = new SequenceFeature();
+ seq.addSequenceFeature(sf);
+ SequenceFeature[] sfs = seq.getSequenceFeatures();
+ assertEquals(1, sfs.length);
+ assertSame(sf, sfs[0]);
+
+ /*
+ * SequenceFeature on sequence and dataset sequence; returns that on
+ * sequence
+ */
+ SequenceFeature sf2 = new SequenceFeature();
+ seq.getDatasetSequence().addSequenceFeature(sf2);
+ sfs = seq.getSequenceFeatures();
+ assertEquals(1, sfs.length);
+ assertSame(sf, sfs[0]);
+
+ /*
+ * SequenceFeature on dataset sequence only
+ */
+ seq.setSequenceFeatures(null);
+ sfs = seq.getSequenceFeatures();
+ assertEquals(1, sfs.length);
+ assertSame(sf2, sfs[0]);
+
+ /*
+ * Corrupt case - no SequenceFeature, dataset's dataset is the original
+ * sequence. Test shows no infinite loop results.
+ */
+ seq.getDatasetSequence().setSequenceFeatures(null);
+ seq.getDatasetSequence().setDatasetSequence(seq); // loop!
+ assertNull(seq.getSequenceFeatures());
+ }
}
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