Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
CigarArrayTest	30	59	2	0.00%	Show methods

Class CigarArrayTest

Class CigarArrayTest	Line # 30	Total Statements 59	Complexity 2	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	3232	2.02	1.01	0.0 0.00%
testConstructor() : void   testConstructor() : void	3939	57.057	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.datamodel;
22
23		import static org.testng.Assert.assertEquals;
24
25		import jalview.gui.JvOptionPane;
26
27		import org.testng.annotations.BeforeClass;
28		import org.testng.annotations.Test;
29
		0% Uncovered Elements: 61 (61) Complexity: 2 Complexity Density: 0.03
30		public class CigarArrayTest
31		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
32	0	@BeforeClass(alwaysRun = true)...
33		public void setUpJvOptionPane()
34		{
35	0	JvOptionPane.setInteractiveMode(false);
36	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
37		}
38
		0% Uncovered Elements: 57 (57) Complexity: 1 Complexity Density: 0.02 4-
39	0	@Test(groups = "Functional")...
40		public void testConstructor()
41		{
42	0	SequenceI seq1 = new Sequence("sq1",
43		"ASFDDABACBACBACBACBACBACBABCABCBACBABCAB");
44	0	Sequence seq2 = new Sequence("sq2",
45		"TTTTTTACBCBABCABCABCABCBACBACBABCABCABCBA");
46
47		// construct alignment
48	0	AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
49
50		// hide columns
51	0	HiddenColumns hc = new HiddenColumns();
52	0	hc.hideColumns(3, 6);
53	0	hc.hideColumns(16, 20);
54
55		// select group
56	0	SequenceGroup sg1 = new SequenceGroup();
57	0	sg1.addSequence(seq1, false);
58	0	sg1.setStartRes(2);
59	0	sg1.setEndRes(23);
60
61		// Cigar array meanings:
62		// M = match
63		// D = deletion
64		// I = insertion
65		// number preceding M/D/I is the number of residues which
66		// match/are deleted/are inserted
67		// In the CigarArray constructor only matches or deletions are created, as
68		// we are comparing a sequence to its own subsequence (the group) + hidden
69		// columns.
70
71		// no hidden columns case
72	0	CigarArray cig = new CigarArray(al, null, sg1);
73	0	String result = cig.getCigarstring();
74	0	assertEquals(result, "22M");
75
76	0	cig = new CigarArray(al, hc, sg1);
77	0	result = cig.getCigarstring();
78	0	assertEquals(result, "1M4D9M5D3M");
79
80		// group starts at hidden cols
81	0	sg1.setStartRes(3);
82	0	cig = new CigarArray(al, hc, sg1);
83	0	result = cig.getCigarstring();
84	0	assertEquals(result, "4D9M5D3M");
85
86		// group starts at last but 1 hidden col
87	0	sg1.setStartRes(5);
88	0	cig = new CigarArray(al, hc, sg1);
89	0	result = cig.getCigarstring();
90	0	assertEquals(result, "2D9M5D3M");
91
92		// group starts at last hidden col
93	0	sg1.setStartRes(6);
94	0	cig = new CigarArray(al, hc, sg1);
95	0	result = cig.getCigarstring();
96	0	assertEquals(result, "1D9M5D3M");
97
98		// group starts just after hidden region
99	0	sg1.setStartRes(7);
100	0	cig = new CigarArray(al, hc, sg1);
101	0	result = cig.getCigarstring();
102	0	assertEquals(result, "9M5D3M");
103
104		// group ends just before start of hidden region
105	0	sg1.setStartRes(5);
106	0	sg1.setEndRes(15);
107	0	cig = new CigarArray(al, hc, sg1);
108	0	result = cig.getCigarstring();
109	0	assertEquals(result, "2D9M");
110
111		// group ends at start of hidden region
112	0	sg1.setEndRes(16);
113	0	cig = new CigarArray(al, hc, sg1);
114	0	result = cig.getCigarstring();
115	0	assertEquals(result, "2D9M1D");
116
117		// group ends 1 after start of hidden region
118	0	sg1.setEndRes(17);
119	0	cig = new CigarArray(al, hc, sg1);
120	0	result = cig.getCigarstring();
121	0	assertEquals(result, "2D9M2D");
122
123		// group ends at end of hidden region
124	0	sg1.setEndRes(20);
125	0	cig = new CigarArray(al, hc, sg1);
126	0	result = cig.getCigarstring();
127	0	assertEquals(result, "2D9M5D");
128
129		// group ends just after end of hidden region
130	0	sg1.setEndRes(21);
131	0	cig = new CigarArray(al, hc, sg1);
132	0	result = cig.getCigarstring();
133	0	assertEquals(result, "2D9M5D1M");
134
135		// group ends 2 after end of hidden region
136	0	sg1.setEndRes(22);
137	0	cig = new CigarArray(al, hc, sg1);
138	0	result = cig.getCigarstring();
139	0	assertEquals(result, "2D9M5D2M");
140		}
141		}