Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ContactGeometryTest	43	77	8	0.9888888698.9%	Show methods

Class ContactGeometryTest

Class ContactGeometryTest	Line # 43	Total Statements 77	Complexity 8	TOTAL Coverage 0.9888888698.9%
testCoverageofRange() : void   testCoverageofRange() : void	4545	12.012	4.04	1.0 1.0100%
testContactGeometry() : void   testContactGeometry() : void	7070	7.07	1.01	1.0 1.0100%
checkConsistencyFor(SequenceI,AlignmentAnnotation) : void   checkConsistencyFor(SequenceI,AlignmentAnnotation) : void	8686	58.058	3.03	0.983871 0.98387198.4%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.7777778	jalview.renderer.ContactGeometryTest.testContactGeometryjalview.renderer.ContactGeometryTest.testContactGeometry	1PASS
	0.21111111	jalview.renderer.ContactGeometryTest.testCoverageofRangejalview.renderer.ContactGeometryTest.testCoverageofRange	1PASS

 

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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.renderer;
22
23		import static org.testng.Assert.assertEquals;
24		import static org.testng.Assert.assertFalse;
25		import static org.testng.Assert.assertNotEquals;
26		import static org.testng.Assert.assertNotNull;
27		import static org.testng.Assert.assertTrue;
28
29		import org.testng.annotations.Test;
30
31		import jalview.datamodel.AlignmentAnnotation;
32		import jalview.datamodel.ColumnSelection;
33		import jalview.datamodel.ContactListI;
34		import jalview.datamodel.ContactRange;
35		import jalview.datamodel.Mapping;
36		import jalview.datamodel.SeqDistanceContactMatrix;
37		import jalview.datamodel.Sequence;
38		import jalview.datamodel.SequenceI;
39		import jalview.util.MapList;
40		import jalview.util.StringUtils;
41		import jalview.ws.datamodel.MappableContactMatrixI;
42
		98.9% Uncovered Elements: 1 (90) Complexity: 8 Complexity Density: 0.1
43		public class ContactGeometryTest
44		{
		100% Uncovered Elements: 0 (18) Complexity: 4 Complexity Density: 0.33 1PASS
45	1	@Test(groups = "Functional")...
46		public void testCoverageofRange()
47		{
48		// a really dumb test to make sure we really cover the requested pixel and
49		// contactList range for any dimension of each
50	58	for (int range = 12; range < 2000; range += 35)
51		{
52	57	StringBuilder sb = new StringBuilder();
53	56601	while (sb.length() < range)
54		{
55	56544	sb.append("c");
56		}
57	57	SequenceI sq = new Sequence("a", sb.toString());
58	57	MappableContactMatrixI cm = new SeqDistanceContactMatrix(range);
59	57	AlignmentAnnotation cm_aan = sq.addContactList(cm);
60	57	ContactListI cl = sq.getContactListFor(cm_aan, 10);
61	57	assertNotNull(cl);
62	141431	for (int ht = range / 2; ht < range * 3; ht++)
63		{
64	141374	ContactGeometry clgeom = new ContactGeometry(cl, ht);
65	141374	assertNotNull(clgeom.allSteps());
66		}
67		}
68		}
69
		100% Uncovered Elements: 0 (7) Complexity: 1 Complexity Density: 0.14 1PASS
70	1	@Test(groups = "Functional")...
71		public void testContactGeometry()
72		{
73	1	SequenceI sq = new Sequence("a", "SSSQ");
74	1	MappableContactMatrixI cm = new SeqDistanceContactMatrix(4);
75	1	AlignmentAnnotation cm_aan = sq.addContactList(cm);
76	1	checkConsistencyFor(sq, cm_aan);
77		// Also check all is good when there's a sequence mapping involved
78	1	MappableContactMatrixI newcm = cm.liftOver(sq,
79		new Mapping(sq, new MapList(new int[]
80		{ 1, 4 }, new int[] { 1, 4 }, 1, 1)));
81	1	AlignmentAnnotation mapped_cm = sq.addContactList(newcm);
82	1	checkConsistencyFor(sq, mapped_cm);
83		}
84
85		// Do some asserts for a sequence and a contact matrix
		98.4% Uncovered Elements: 1 (62) Complexity: 3 Complexity Density: 0.05
86	2	private void checkConsistencyFor(SequenceI sq, AlignmentAnnotation cm_aan)...
87		{
88	2	int col = 1;
89	2	ContactListI cl = sq.getContactListFor(cm_aan, col);
90	2	assertNotNull(cl);
91	2	assertEquals(cl.getContactHeight(), 4);
92
93		// Map contacts 0 to 3 to a tiny range and check
94	2	ContactGeometry testee = new ContactGeometry(cl, 2);
95	2	assertEquals(testee.contacts_per_pixel, 2d);
96	2	ContactGeometry.contactInterval lastInterval = testee.mapFor(1);
97	2	assertEquals(lastInterval.cStart, 2);
98	2	assertEquals(lastInterval.cEnd, 3);
99	2	assertEquals(lastInterval.pStart, 1);
100	2	assertEquals(lastInterval.pEnd, 1);
101	2	ContactGeometry.contactInterval another = testee.mapFor(1, 2);
102	2	assertEquals(lastInterval, another);
103		// Also check for a big pixel range
104	2	testee = new ContactGeometry(cl, 395);
105	2	lastInterval = testee.mapFor(390, 395); // 395 is one over limit.
106	2	assertNotNull(lastInterval);
107	2	assertEquals(lastInterval.cEnd, 3);
108	2	assertEquals(lastInterval.pEnd, 394);
109		// Map contacts 0 to 3 to Pixels 0-9, 10-19, 20-29, 30-39
110	2	testee = new ContactGeometry(cl, 40);
111
112		// verify mapping from pixel to contacts
113
114		// renderer thinks base 0 for pixel coordinates
115		// contact coordinates are base 1
116	82	for (int p = 0; p < 40; p++)
117		{
118	80	int expectC = (p / 10);
119	80	int expectP = (expectC) * 10;
120	80	ContactGeometry.contactInterval ci_at = testee.mapFor(p),
121		ci_from = testee.mapFor(p, p);
122	80	assertNotNull(ci_at);
123		// mapFor and map should locate the same pixel window
124	80	assertEquals(ci_at.cStart, expectC,
125		"Different cStart at position " + p);
126	80	assertEquals(ci_at.cEnd, expectC, "Different cEnd at position " + p);
127	80	assertEquals(ci_at.pStart, expectP,
128		"Different pStart at position " + p);
129	80	assertEquals(ci_at.pEnd, expectP + 9,
130		"Different pEnd at position " + p);
131
132	80	assertEquals(ci_from, ci_at,
133		"Different contactIntervals at position " + p);
134		// also test getRangeFor
135	80	ContactRange cr = cl.getRangeFor(ci_at.cStart, ci_at.cEnd);
136	80	assertEquals(cr.getFrom_column(), cr.getTo_column());
137	80	assertEquals((double) cr.getMean(),
138		(double) Math.abs(col - cr.getFrom_column()),
139		"Didn't resolve expected value at position " + p);
140		}
141
142	2	ContactGeometry.contactInterval ci_at0 = testee.mapFor(0);
143	2	ContactGeometry.contactInterval ci_at9 = testee.mapFor(9);
144	2	assertNotNull(ci_at9);
145
146	2	assertEquals(ci_at0, ci_at9);
147
148		// Adjacent cell
149	2	ContactGeometry.contactInterval ci_at10 = testee.mapFor(10);
150	2	assertNotNull(ci_at10);
151	2	ContactGeometry.contactInterval ci_at11 = testee.mapFor(11);
152	2	assertNotNull(ci_at11);
153
154	2	assertEquals(ci_at11, ci_at10,
155		"Off-by-one in ContactGeometry mapping.");
156
157	2	assertNotEquals(ci_at0, ci_at10,
158		"Expected adjacent cells to be not equal.");
159
160		// verify adjacent window is mapped
161	2	assertEquals(ci_at11.cStart, ci_at9.cStart + 1);
162
163	2	assertEquals(ci_at9.cEnd + 1, ci_at11.cStart);
164	2	assertEquals(ci_at9.cEnd + 1, ci_at11.cEnd);
165
166		// verify interval/intersection
167		// column selection is base 0
168	2	ColumnSelection cs = new ColumnSelection();
169	2	cs.addElement(2);
170
171	2	boolean mask = false;
172	2	do
173		{
174	2	assertFalse(testee.intersects(ci_at0, cs, null, mask));
175	2	assertFalse(testee.intersects(ci_at11, cs, null, mask));
176	2	assertTrue(testee.intersects(testee.mapFor(21), cs, null, mask));
177	2	assertFalse(testee.intersects(testee.mapFor(31), cs, null, mask));
178	2	cs.addElement(3);
179	2	assertTrue(testee.intersects(testee.mapFor(31), cs, null, mask));
180	2	cs.removeElement(2);
181	2	assertFalse(testee.intersects(testee.mapFor(21), cs, null, mask));
182	2	mask = !mask;
183	2	} while (!mask);
184
185		}
186		}