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AlignSeqTest | 33 | 24 | 5 |
1 | /* | |
2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
4 | * | |
5 | * This file is part of Jalview. | |
6 | * | |
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. | |
11 | * | |
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. | |
16 | * | |
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. | |
20 | */ | |
21 | package jalview.analysis; | |
22 | ||
23 | import static org.testng.Assert.assertEquals; | |
24 | import static org.testng.Assert.assertNull; | |
25 | import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals; | |
26 | ||
27 | import jalview.datamodel.Sequence; | |
28 | import jalview.gui.JvOptionPane; | |
29 | ||
30 | import org.testng.annotations.BeforeClass; | |
31 | import org.testng.annotations.Test; | |
32 | ||
33 | public class AlignSeqTest | |
34 | { | |
35 | ||
36 | 1 | @BeforeClass(alwaysRun = true) |
37 | public void setUpJvOptionPane() | |
38 | { | |
39 | 1 | JvOptionPane.setInteractiveMode(false); |
40 | 1 | JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
41 | } | |
42 | ||
43 | 1 | @Test(groups = { "Functional" }) |
44 | public void testExtractGaps() | |
45 | { | |
46 | 1 | assertNull(AlignSeq.extractGaps(null, null)); |
47 | 1 | assertNull(AlignSeq.extractGaps(null, "ACG")); |
48 | 1 | assertNull(AlignSeq.extractGaps("-. ", null)); |
49 | ||
50 | 1 | assertEquals(AlignSeq.extractGaps("", " AC-G.T"), " AC-G.T"); |
51 | 1 | assertEquals(AlignSeq.extractGaps(" ", " AC-G.T"), "AC-G.T"); |
52 | 1 | assertEquals(AlignSeq.extractGaps(" -", " AC-G.T"), "ACG.T"); |
53 | 1 | assertEquals(AlignSeq.extractGaps(" -.", " AC-G.T ."), "ACGT"); |
54 | 1 | assertEquals(AlignSeq.extractGaps("-", " AC-G.T"), " ACG.T"); |
55 | 1 | assertEquals(AlignSeq.extractGaps("-. ", " -. .-"), ""); |
56 | } | |
57 | ||
58 | 1 | @Test(groups = { "Functional" }) |
59 | public void testIndexEncode_nucleotide() | |
60 | { | |
61 | 1 | AlignSeq as = new AlignSeq(new Sequence("s1", "TTAG"), |
62 | new Sequence("s2", "ACGT"), AlignSeq.DNA); | |
63 | 1 | int[] expected = new int[] { 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6, |
64 | 7, 7, 8, 8, 9, 9, -1, -1, 10, -1 }; | |
65 | 1 | String s = "aAcCgGtTuUiIxXrRyYnN .-?"; |
66 | 1 | assertArrayEquals(expected, as.indexEncode(s)); |
67 | } | |
68 | ||
69 | 1 | @Test(groups = { "Functional" }) |
70 | public void testIndexEncode_peptide() | |
71 | { | |
72 | 1 | AlignSeq as = new AlignSeq(new Sequence("s1", "PFY"), |
73 | new Sequence("s2", "RQW"), AlignSeq.PEP); | |
74 | 1 | int[] expected = new int[] { 0, 0, 1, 1, 2, 2, 21, 21, 22, 22, -1, 23, |
75 | -1, -1, -1 }; | |
76 | 1 | String s = "aArRnNzZxX *.-?"; |
77 | 1 | assertArrayEquals(expected, as.indexEncode(s)); |
78 | } | |
79 | ||
80 | 1 | @Test(groups = { "Functional" }) |
81 | public void testGlobalAlignment() | |
82 | { | |
83 | 1 | String seq1 = "CAGCTAGCG", seq2 = "CCATACGA"; |
84 | 1 | Sequence sq1 = new Sequence("s1", seq1), sq2 = new Sequence("s2", seq2); |
85 | // AlignSeq doesn't report the unaligned regions at either end of sequences | |
86 | // String alseq1="-CAGCTAGCG-",alseq2="CCA--TA-CGA"; | |
87 | // so we check we have the aligned segment correct only | |
88 | 1 | String alseq1 = "CAGCTAGCG", alseq2 = "CA--TA-CG"; |
89 | 1 | AlignSeq as = AlignSeq.doGlobalNWAlignment(sq1, sq2, AlignSeq.DNA); |
90 | 1 | assertEquals(as.getAStr1() + "\n" + as.getAStr2(), |
91 | alseq1 + "\n" + alseq2); | |
92 | } | |
93 | } |