1 package jalview.io.gff;
3 import static org.testng.AssertJUnit.assertEquals;
4 import static org.testng.AssertJUnit.assertSame;
5 import static org.testng.AssertJUnit.assertTrue;
6 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
8 import jalview.datamodel.AlignedCodonFrame;
9 import jalview.datamodel.Alignment;
10 import jalview.datamodel.AlignmentI;
11 import jalview.datamodel.Sequence;
12 import jalview.datamodel.SequenceDummy;
13 import jalview.datamodel.SequenceI;
15 import java.io.IOException;
16 import java.util.ArrayList;
17 import java.util.List;
20 import org.testng.annotations.Test;
22 public class InterProScanHelperTest
26 * Test processing one InterProScan GFF line
30 @Test(groups = "Functional")
31 public void testProcessProteinMatch() throws IOException
33 InterProScanHelper testee = new InterProScanHelper();
34 List<SequenceI> newseqs = new ArrayList<SequenceI>();
35 String[] gff = "Submitted\tPfam\tprotein_match\t5\t30\t0\t+\t.\tName=PF12838;Target=Submitted 5 30;signature_desc=4Fe-4S dicluster domain;ID=match$17_5_30"
37 SequenceI seq = new Sequence("Prot1", "PQRASTGKEEDVMIWCHQN");
38 seq.createDatasetSequence();
39 AlignmentI align = new Alignment(new SequenceI[] {});
40 Map<String, List<String>> set = Gff3Helper.parseNameValuePairs(gff[8]);
43 * this should create a mapping from Prot1/5-30 to virtual sequence
44 * match$17_5_30 (added to newseqs) positions 1-26
46 testee.processProteinMatch(set, seq, gff, align, newseqs, false);
47 assertEquals(1, newseqs.size());
48 assertTrue(newseqs.get(0) instanceof SequenceDummy);
49 assertEquals("match$17_5_30", newseqs.get(0).getName());
50 assertEquals(1, align.getCodonFrames().size());
51 AlignedCodonFrame mapping = align.getCodonFrames().iterator().next();
54 * 'dnaseqs' (map from) is here [Prot1]
55 * 'aaseqs' (map to) is here [match$17_5_30]
57 // TODO use more suitable naming in AlignedCodonFrame
58 assertEquals(1, mapping.getAaSeqs().length);
59 assertSame(seq.getDatasetSequence(), mapping.getdnaSeqs()[0]);
60 assertEquals(1, mapping.getdnaSeqs().length);
61 assertSame(newseqs.get(0), mapping.getAaSeqs()[0]);
62 assertEquals(1, mapping.getdnaToProt().length);
63 assertEquals(1, mapping.getdnaToProt()[0].getFromRanges().size());
64 assertArrayEquals(new int[] { 5, 30 }, mapping.getdnaToProt()[0]
65 .getFromRanges().get(0));
66 assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());
67 assertArrayEquals(new int[] { 1, 26 }, mapping.getdnaToProt()[0]
68 .getToRanges().get(0));