1 package jalview.datamodel;
3 import static org.junit.Assert.assertEquals;
4 import static org.junit.Assert.assertFalse;
5 import static org.junit.Assert.assertTrue;
6 import jalview.gui.AlignFrame;
7 import jalview.gui.AlignmentPanel;
8 import jalview.io.AppletFormatAdapter;
10 import java.io.IOException;
11 import java.util.Iterator;
13 import org.junit.Before;
14 import org.junit.Test;
17 * Unit tests for Alignment datamodel.
22 public class AlignmentTest
25 private static final String TEST_DATA =
27 "#=GS D.melanogaster.1 AC AY119185.1/838-902\n" +
28 "#=GS D.melanogaster.2 AC AC092237.1/57223-57161\n" +
29 "#=GS D.melanogaster.3 AC AY060611.1/560-627\n" +
30 "D.melanogaster.1 G.AGCC.CU...AUGAUCGA\n" +
31 "#=GR D.melanogaster.1 SS ................((((\n" +
32 "D.melanogaster.2 C.AUUCAACU.UAUGAGGAU\n" +
33 "#=GR D.melanogaster.2 SS ................((((\n" +
34 "D.melanogaster.3 G.UGGCGCU..UAUGACGCA\n" +
35 "#=GR D.melanogaster.3 SS (.(((...(....(((((((\n";
42 * Read in Stockholm format test data including secondary structure
46 public void setUp() throws IOException
48 al = new jalview.io.FormatAdapter().readFile(TEST_DATA,
49 AppletFormatAdapter.PASTE, "STH");
50 AlignFrame af = new AlignFrame(al, 700, 500);
51 new AlignmentPanel(af, af.getViewport());
55 * Test method that returns annotations that match on calcId.
58 public void testFindAnnotation_byCalcId()
60 Iterable<AlignmentAnnotation> anns = al
61 .findAnnotation("D.melanogaster.3");
62 Iterator<AlignmentAnnotation> iter = anns.iterator();
63 assertTrue(iter.hasNext());
64 AlignmentAnnotation ann = iter.next();
65 assertEquals("D.melanogaster.3", ann.sequenceRef.getName());
66 assertFalse(iter.hasNext());