Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ShiftListTest	34	49	4	0.00%	Show methods

Class ShiftListTest

Class ShiftListTest	Line # 34	Total Statements 49	Complexity 4	TOTAL Coverage 0.00%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	3737	2.02	1.01	0.0 0.00%
testParseMap() : void   testParseMap() : void	4444	9.09	1.01	0.0 0.00%
testaddShiftOperations() : void   testaddShiftOperations() : void	6363	11.011	1.01	0.0 0.00%
testaddExtendShiftOperations() : void   testaddExtendShiftOperations() : void	7777	27.027	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.util;
22
23		import static org.testng.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertNull;
25
26		import jalview.gui.JvOptionPane;
27
28		import java.util.Arrays;
29		import java.util.List;
30
31		import org.testng.annotations.BeforeClass;
32		import org.testng.annotations.Test;
33
		0% Uncovered Elements: 53 (53) Complexity: 4 Complexity Density: 0.08
34		public class ShiftListTest
35		{
36
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
37	0	@BeforeClass(alwaysRun = true)...
38		public void setUpJvOptionPane()
39		{
40	0	JvOptionPane.setInteractiveMode(false);
41	0	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
42		}
43
		0% Uncovered Elements: 9 (9) Complexity: 1 Complexity Density: 0.11 4-
44	0	@Test(groups = { "Functional" })...
45		public void testParseMap()
46		{
47	0	assertNull(ShiftList.parseMap(null));
48	0	assertNull(ShiftList.parseMap(new int[] {}));
49
50		/*
51		* Gap map showing residues in aligned positions 2,3,6,8,9,10,12
52		*/
53	0	int[] gm = new int[] { 2, 3, 6, 8, 9, 10, 12 };
54	0	List<int[]> shifts = ShiftList.parseMap(gm).getShifts();
55	0	assertEquals(4, shifts.size());
56
57		// TODO are these results (which pass) correct??
58	0	assertEquals("[0, 2]", Arrays.toString(shifts.get(0)));
59	0	assertEquals("[4, 2]", Arrays.toString(shifts.get(1)));
60	0	assertEquals("[7, 1]", Arrays.toString(shifts.get(2)));
61	0	assertEquals("[11, 1]", Arrays.toString(shifts.get(3)));
62		}
		0% Uncovered Elements: 11 (11) Complexity: 1 Complexity Density: 0.09 4-
63	0	@Test(groups = { "Functional" })...
64		public void testaddShiftOperations() {
65	0	ShiftList sl = new ShiftList();
66	0	assertEquals(0,sl.shift(0));
67	0	sl.addShift(0, 0);
68	0	assertEquals(0,sl.shift(0));
69	0	sl.addShift(0, 1);
70	0	assertEquals(1,sl.shift(0));
71	0	assertEquals(2,sl.shift(1));
72	0	sl.addShift(2, 2);
73	0	assertEquals(1,sl.shift(0));
74	0	assertEquals(2,sl.shift(1)); // (0+1)
75	0	assertEquals(5,sl.shift(2)); // (0+1)(2+2): 1+2+2->5
76		}
		0% Uncovered Elements: 27 (27) Complexity: 1 Complexity Density: 0.04 4-
77	0	@Test(groups = { "Functional" })...
78		public void testaddExtendShiftOperations() {
79	0	ShiftList sl = new ShiftList();
80	0	assertEquals(0,sl.shift(0));
81	0	sl.extendShift(0, 0);
82	0	assertEquals(0,sl.shift(0));
83	0	sl.extendShift(0, 1);
84	0	assertEquals(1,sl.shift(0));
85	0	assertEquals(2,sl.shift(1));
86	0	sl.extendShift(2, 2);
87	0	assertEquals(1,sl.shift(0));
88	0	assertEquals(2,sl.shift(1)); // (0+1)
89	0	assertEquals(5,sl.shift(2)); // (0+1)(2+2): 1+2+2->5
90
91		// now check extend really does
92	0	sl.extendShift(2, 1);
93	0	assertEquals(1,sl.shift(0));
94	0	assertEquals(2,sl.shift(1)); // (0+1)
95	0	assertEquals(5,sl.shift(2)); // (0+1)(2+2): 1+2+2->5
96
97	0	sl.extendShift(2, 3);
98	0	assertEquals(1,sl.shift(0));
99	0	assertEquals(2,sl.shift(1)); // (0+1)
100	0	assertEquals(6,sl.shift(2)); // (0+1)(2+2): 1+2+2->5
101
102		// and two interssecting shifts
103	0	sl = new ShiftList();
104	0	sl.extendShift(0, 5);
105	0	sl.extendShift(5, 3);
106	0	sl.extendShift(1, 6);
107	0	sl.extendShift(3, 1);
108	0	sl.extendShift(1, 7);
109
110	0	List<int[]> shifts = sl.getShifts();
111	0	assertEquals(4,shifts.size());
112		}
113		}