2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.io.gff;
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertSame;
25 import static org.testng.AssertJUnit.assertTrue;
26 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
28 import jalview.datamodel.AlignedCodonFrame;
29 import jalview.datamodel.Alignment;
30 import jalview.datamodel.AlignmentI;
31 import jalview.datamodel.Sequence;
32 import jalview.datamodel.SequenceDummy;
33 import jalview.datamodel.SequenceI;
34 import jalview.gui.JvOptionPane;
36 import java.io.IOException;
37 import java.util.ArrayList;
38 import java.util.List;
41 import org.testng.annotations.BeforeClass;
42 import org.testng.annotations.Test;
44 public class InterProScanHelperTest
47 @BeforeClass(alwaysRun = true)
48 public void setUpJvOptionPane()
50 JvOptionPane.setInteractiveMode(false);
51 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
55 * Test processing one InterProScan GFF line
59 @Test(groups = "Functional")
60 public void testProcessProteinMatch() throws IOException
62 InterProScanHelper testee = new InterProScanHelper();
63 List<SequenceI> newseqs = new ArrayList<SequenceI>();
64 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"
66 SequenceI seq = new Sequence("Prot1", "PQRASTGKEEDVMIWCHQN");
67 seq.createDatasetSequence();
68 AlignmentI align = new Alignment(new SequenceI[] {});
69 Map<String, List<String>> set = Gff3Helper.parseNameValuePairs(gff[8]);
72 * this should create a mapping from Prot1/5-30 to virtual sequence
73 * match$17_5_30 (added to newseqs) positions 1-26
75 testee.processProteinMatch(set, seq, gff, align, newseqs, false);
76 assertEquals(1, newseqs.size());
77 assertTrue(newseqs.get(0) instanceof SequenceDummy);
78 assertEquals("match$17_5_30", newseqs.get(0).getName());
79 assertEquals(1, align.getCodonFrames().size());
80 AlignedCodonFrame mapping = align.getCodonFrames().iterator().next();
83 * 'dnaseqs' (map from) is here [Prot1]
84 * 'aaseqs' (map to) is here [match$17_5_30]
86 // TODO use more suitable naming in AlignedCodonFrame
87 assertEquals(1, mapping.getAaSeqs().length);
88 assertSame(seq.getDatasetSequence(), mapping.getdnaSeqs()[0]);
89 assertEquals(1, mapping.getdnaSeqs().length);
90 assertSame(newseqs.get(0), mapping.getAaSeqs()[0]);
91 assertEquals(1, mapping.getdnaToProt().length);
92 assertEquals(1, mapping.getdnaToProt()[0].getFromRanges().size());
93 assertArrayEquals(new int[] { 5, 30 }, mapping.getdnaToProt()[0]
94 .getFromRanges().get(0));
95 assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());
96 assertArrayEquals(new int[] { 1, 26 }, mapping.getdnaToProt()[0]
97 .getToRanges().get(0));