package jalview.datamodel;
import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertTrue;
import jalview.util.MapList;
assertEquals("[C, T, T]", Arrays.toString(acf.getMappedCodon(
aseq1.getDatasetSequence(), 13)));
}
+
+ @Test(groups = { "Functional" })
+ public void testCouldReplaceSequence()
+ {
+ SequenceI seq1 = new Sequence("Seq1/10-21", "aaacccgggttt");
+ SequenceI seq2 = new Sequence("Seq2", "PG");
+ SequenceI seq1proxy = new SequenceDummy("Seq1");
+
+ // map to region within sequence is ok
+ assertTrue(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 12,
+ 17));
+ // map to region overlapping sequence is ok
+ assertTrue(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 5,
+ 10));
+ assertTrue(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 21,
+ 26));
+ // map to region before sequence is not ok
+ assertFalse(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 4,
+ 9));
+ // map to region after sequence is not ok
+ assertFalse(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 22,
+ 27));
+
+ /*
+ * test should fail if name doesn't match
+ */
+ seq1proxy.setName("Seq1a");
+ assertFalse(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 12,
+ 17));
+ seq1proxy.setName("Seq1");
+ seq1.setName("Seq1a");
+ assertFalse(AlignedCodonFrame.couldReplaceSequence(seq1proxy, seq1, 12,
+ 17));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testIsRealisableWith()
+ {
+ SequenceI seq1 = new Sequence("Seq1", "tttaaaCCCGGGtttaaa");
+ SequenceI seq2 = new Sequence("Seq2", "PG");
+ SequenceI seq1proxy = new SequenceDummy("Seq1");
+ seq1.createDatasetSequence();
+ seq2.createDatasetSequence();
+ MapList mapList = new MapList(new int[] { 7, 12 }, new int[] { 2, 3 },
+ 3, 1);
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ acf.addMap(seq1proxy, seq2, mapList);
+
+ /*
+ * Seq2 is mapped to SequenceDummy seq1proxy bases 4-9
+ * This is 'realisable' from real sequence Seq1
+ */
+ assertTrue(acf.isRealisableWith(seq1));
+
+ /*
+ * test should fail if name doesn't match
+ */
+ seq1proxy.setName("Seq1a");
+ assertFalse(acf.isRealisableWith(seq1));
+ seq1proxy.setName("Seq1");
+ seq1.setName("Seq1a");
+ assertFalse(acf.isRealisableWith(seq1));
+ seq1.setName("Seq1");
+
+ /*
+ * test should fail if no sequence overlap with mapping of bases 7-12
+ * use artificial start/end values to test this
+ */
+ seq1.setStart(1);
+ seq1.setEnd(6);
+ // seq1 precedes mapped region:
+ assertFalse(acf.isRealisableWith(seq1));
+ seq1.setEnd(7);
+ // seq1 includes first mapped base:
+ assertTrue(acf.isRealisableWith(seq1));
+ seq1.setStart(13);
+ seq1.setEnd(18);
+ // seq1 follows mapped region:
+ assertFalse(acf.isRealisableWith(seq1));
+ seq1.setStart(12);
+ // seq1 includes last mapped base:
+ assertTrue(acf.isRealisableWith(seq1));
+ }
}