Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
GffHelperFactoryTest	32	30	2	0.00%	Show methods

Class GffHelperFactoryTest

Class GffHelperFactoryTest	Line # 32	Total Statements 30	Complexity 2	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	3535	2.02	1.01	0.0 0.00%
testGetHelper() : void   testGetHelper() : void	4242	28.028	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.assertNull;
24		import static org.testng.AssertJUnit.assertSame;
25		import static org.testng.AssertJUnit.assertTrue;
26
27		import jalview.gui.JvOptionPane;
28
29		import org.testng.annotations.BeforeClass;
30		import org.testng.annotations.Test;
31
		0% Uncovered Elements: 32 (32) Complexity: 2 Complexity Density: 0.07
32		public class GffHelperFactoryTest
33		{
34
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
35	0	@BeforeClass(alwaysRun = true)...
36		public void setUpJvOptionPane()
37		{
38	0	JvOptionPane.setInteractiveMode(false);
39	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
40		}
41
		0% Uncovered Elements: 28 (28) Complexity: 1 Complexity Density: 0.04 4-
42	0	@Test(groups = "Functional")...
43		public void testGetHelper()
44		{
45	0	assertNull(GffHelperFactory.getHelper(null));
46
47	0	String tabRegex = "\\t";
48
49		/*
50		* column 3 = 'similarity' indicates exonerate GFF alignment data
51		*/
52	0	String gff = "submitted\taffine:local\tsimilarity\t20\t30\t99\t+\t.\t";
53		// no attributes (column 9 data):
54	0	assertTrue(GffHelperFactory
55		.getHelper(gff.split(tabRegex)) instanceof Gff2Helper);
56
57		// attributes set but unhandled featureGroup - get generic handler
58	0	gff = "submitted\taffine:local\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
59	0	assertSame(GffHelperFactory.getHelper(gff.split(tabRegex)).getClass(),
60		Gff3Helper.class);
61
62		// handled featureGroup (exonerate model) values
63	0	gff = "submitted\texonerate:protein2dna:local\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
64	0	assertTrue(GffHelperFactory
65		.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
66
67	0	gff = "submitted\tprotein2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
68	0	assertTrue(GffHelperFactory
69		.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
70
71	0	gff = "submitted\tcoding2coding\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
72	0	assertTrue(GffHelperFactory
73		.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
74
75	0	gff = "submitted\tcoding2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
76	0	assertTrue(GffHelperFactory
77		.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
78
79	0	gff = "submitted\tcdna2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
80	0	assertTrue(GffHelperFactory
81		.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
82
83	0	gff = "submitted\tgenome2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
84	0	assertTrue(GffHelperFactory
85		.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
86
87		// not case-sensitive:
88	0	gff = "submitted\tgenome2genome\tSIMILARITY\t20\t30\t99\t+\t.\tID=$1";
89	0	assertTrue(GffHelperFactory
90		.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
91
92		/*
93		* InterProScan has 'protein_match' in column 3
94		*/
95	0	gff = "Submitted\tPANTHER\tprotein_match\t1\t1174\t0.0\t+\t.\tName=PTHR32154";
96	0	assertTrue(GffHelperFactory
97		.getHelper(gff.split(tabRegex)) instanceof InterProScanHelper);
98
99		/*
100		* nothing specific - return the generic GFF3 class if Name=Value is present in col9
101		*/
102	0	gff = "nothing\tinteresting\there\t20\t30\t99\t+\t.\tID=1";
103	0	GffHelperI helper = GffHelperFactory.getHelper(gff.split(tabRegex));
104	0	assertSame(helper.getClass(), Gff3Helper.class);
105
106		// return the generic GFF2 class if "Name Value" is present in col9
107	0	gff = "nothing\tinteresting\there\t20\t30\t99\t+\t.\tID 1";
108	0	helper = GffHelperFactory.getHelper(gff.split(tabRegex));
109	0	assertSame(helper.getClass(), Gff2Helper.class);
110		}
111		}