Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
InterProScanHelperTest	46	32	2	0.00%	Show methods

Class InterProScanHelperTest

Class InterProScanHelperTest	Line # 46	Total Statements 32	Complexity 2	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4949	2.02	1.01	0.0 0.00%
testProcessProteinMatch() : void   testProcessProteinMatch() : void	6161	30.030	1.01	0.0 0.00%

 

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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.io.gff;
22
23		import static org.testng.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertNotNull;
25		import static org.testng.AssertJUnit.assertSame;
26		import static org.testng.AssertJUnit.assertTrue;
27		import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
28
29		import jalview.datamodel.AlignedCodonFrame;
30		import jalview.datamodel.Alignment;
31		import jalview.datamodel.AlignmentI;
32		import jalview.datamodel.Sequence;
33		import jalview.datamodel.SequenceDummy;
34		import jalview.datamodel.SequenceFeature;
35		import jalview.datamodel.SequenceI;
36		import jalview.gui.JvOptionPane;
37
38		import java.io.IOException;
39		import java.util.ArrayList;
40		import java.util.List;
41		import java.util.Map;
42
43		import org.testng.annotations.BeforeClass;
44		import org.testng.annotations.Test;
45
		0% Uncovered Elements: 34 (34) Complexity: 2 Complexity Density: 0.06
46		public class InterProScanHelperTest
47		{
48
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
49	0	@BeforeClass(alwaysRun = true)...
50		public void setUpJvOptionPane()
51		{
52	0	JvOptionPane.setInteractiveMode(false);
53	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
54		}
55
56		/**
57		* Test processing one InterProScan GFF line
58		*
59		* @throws IOException
60		*/
		0% Uncovered Elements: 30 (30) Complexity: 1 Complexity Density: 0.03 4-
61	0	@Test(groups = "Functional")...
62		public void testProcessProteinMatch() throws IOException
63		{
64	0	InterProScanHelper testee = new InterProScanHelper();
65	0	List<SequenceI> newseqs = new ArrayList<SequenceI>();
66	0	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"
67		.split("\\t");
68	0	SequenceI seq = new Sequence("Prot1", "PQRASTGKEEDVMIWCHQN");
69	0	seq.createDatasetSequence();
70	0	AlignmentI align = new Alignment(new SequenceI[] {});
71	0	Map<String, List<String>> set = Gff3Helper.parseNameValuePairs(gff[8]);
72
73		/*
74		* this should create a mapping from Prot1/5-30 to virtual sequence
75		* match$17_5_30 (added to newseqs) positions 1-26
76		*/
77	0	testee.processProteinMatch(set, seq, gff, align, newseqs, false);
78	0	assertEquals(1, newseqs.size());
79	0	assertTrue(newseqs.get(0) instanceof SequenceDummy);
80	0	assertEquals("match$17_5_30", newseqs.get(0).getName());
81
82	0	assertNotNull(newseqs.get(0).getSequenceFeatures());
83	0	assertEquals(1, newseqs.get(0).getSequenceFeatures().size());
84	0	SequenceFeature sf = newseqs.get(0).getSequenceFeatures().get(0);
85	0	assertEquals(1, sf.getBegin());
86	0	assertEquals(26, sf.getEnd());
87	0	assertEquals("Pfam", sf.getType());
88	0	assertEquals("4Fe-4S dicluster domain", sf.getDescription());
89	0	assertEquals("InterProScan", sf.getFeatureGroup());
90
91	0	assertEquals(1, align.getCodonFrames().size());
92	0	AlignedCodonFrame mapping = align.getCodonFrames().iterator().next();
93
94		/*
95		* 'dnaseqs' (map from) is here [Prot1]
96		* 'aaseqs' (map to) is here [match$17_5_30]
97		*/
98		// TODO use more suitable naming in AlignedCodonFrame
99	0	assertEquals(1, mapping.getAaSeqs().length);
100	0	assertSame(seq.getDatasetSequence(), mapping.getdnaSeqs()[0]);
101	0	assertEquals(1, mapping.getdnaSeqs().length);
102	0	assertSame(newseqs.get(0), mapping.getAaSeqs()[0]);
103	0	assertEquals(1, mapping.getdnaToProt().length);
104	0	assertEquals(1, mapping.getdnaToProt()[0].getFromRanges().size());
105	0	assertArrayEquals(new int[] { 5, 30 },
106		mapping.getdnaToProt()[0].getFromRanges().get(0));
107	0	assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());
108	0	assertArrayEquals(new int[] { 1, 26 },
109		mapping.getdnaToProt()[0].getToRanges().get(0));
110		}
111
112		}