Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PAEContactMatrixTest	36	122	6	1.0100%	Show methods

Class PAEContactMatrixTest

Class PAEContactMatrixTest	Line # 36	Total Statements 122	Complexity 6	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	3838	2.02	1.01	1.0 1.0100%
testSeqAssociatedPAEMatrix() : void   testSeqAssociatedPAEMatrix() : void	5454	77.077	1.01	1.0 1.0100%
verify_mapping(SequenceI,AlignmentAnnotation) : void   verify_mapping(SequenceI,AlignmentAnnotation) : void	196196	9.09	1.01	1.0 1.0100%
verifyPAEmatrix(SequenceI,AlignmentAnnotation,int,int,int) : void   verifyPAEmatrix(SequenceI,AlignmentAnnotation,int,int,int) : void	216216	10.010	2.02	1.0 1.0100%
testMappableContactMatrix() : void   testMappableContactMatrix() : void	238238	24.024	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.78294575	jalview.datamodel.PAEContactMatrixTest.testSeqAssociatedPAEMatrixjalview.datamodel.PAEContactMatrixTest.testSeqAssociatedPAEMatrix	1PASS
	0.19379845	jalview.datamodel.PAEContactMatrixTest.testMappableContactMatrixjalview.datamodel.PAEContactMatrixTest.testMappableContactMatrix	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.datamodel;
22
23		import static org.testng.Assert.*;
24
25		import org.testng.Assert;
26		import org.testng.annotations.BeforeClass;
27		import org.testng.annotations.Test;
28
29		import jalview.analysis.AlignmentUtils;
30		import jalview.analysis.SeqsetUtils;
31		import jalview.gui.JvOptionPane;
32		import jalview.util.MapList;
33		import jalview.ws.datamodel.MappableContactMatrixI;
34		import jalview.ws.datamodel.alphafold.PAEContactMatrix;
35
		100% Uncovered Elements: 0 (129) Complexity: 6 Complexity Density: 0.05
36		public class PAEContactMatrixTest
37		{
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
38	1	@BeforeClass(alwaysRun = true)...
39		public void setUpJvOptionPane()
40		{
41	1	JvOptionPane.setInteractiveMode(false);
42	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
43		}
44
45		static float[][] PAEdata = { { 1.0f, 2.0f, 3.0f, 4.0f, 5.0f },
46		{ 2.0f, 1.0f, 2.0f, 3.0f, 4.0f },
47		{ 3.0f, 2.0f, 1.0f, 2.0f, 3.0f },
48		{ 4.0f, 3.0f, 2.0f, 1.0f, 2.0f },
49		{ 5.0f, 4.0f, 3.0f, 2.0f, 1.0f } };
50
51		/**
52		* test associations for a PAE matrix
53		*/
		100% Uncovered Elements: 0 (77) Complexity: 1 Complexity Density: 0.01 1PASS
54	1	@Test(groups = { "Functional" })...
55		public void testSeqAssociatedPAEMatrix()
56		{
57	1	Sequence seq = new Sequence("Seq", "ASDQE");
58	1	AlignmentAnnotation aa = seq
59		.addContactList(new PAEContactMatrix(seq, PAEdata));
60	1	assertNotNull(seq.getContactListFor(aa, 0));
61	1	assertEquals(seq.getContactListFor(aa, 0).getContactAt(0), 1.0);
62	1	assertNotNull(seq.getContactListFor(aa, 1));
63	1	assertEquals(seq.getContactListFor(aa, 1).getContactAt(1), 1.0);
64	1	assertNotNull(seq.getContactListFor(aa, 2));
65	1	assertEquals(seq.getContactListFor(aa, 2).getContactAt(2), 1.0);
66	1	assertNotNull(seq.getContactListFor(aa, 3));
67	1	assertEquals(seq.getContactListFor(aa, 3).getContactAt(3), 1.0);
68	1	assertNotNull(seq.getContactListFor(aa, 4));
69	1	assertEquals(seq.getContactListFor(aa, 4).getContactAt(4), 1.0);
70
71	1	assertNotNull(seq.getContactListFor(aa, seq.getEnd() - 1));
72	1	assertNull(seq.getContactListFor(aa, seq.getEnd()));
73
74	1	ContactListI cm = seq.getContactListFor(aa, seq.getStart());
75	1	assertEquals(cm.getContactAt(seq.getStart()), 1d);
76	1	verifyPAEmatrix(seq, aa, 0, 0, 4);
77
78		// Now associated with sequence not starting at 1
79	1	seq = new Sequence("Seq/5-9", "ASDQE");
80	1	ContactMatrixI paematrix = new PAEContactMatrix(seq, PAEdata);
81	1	aa = seq.addContactList(paematrix);
82	1	assertNotNull(aa);
83		// individual annotation elements need to be distinct for Matrix associated
84		// rows
85	1	Annotation ae5 = aa.getAnnotationForPosition(5);
86	1	Annotation ae6 = aa.getAnnotationForPosition(6);
87	1	assertNotNull(ae5);
88	1	assertNotNull(ae6);
89	1	assertTrue(ae5 != ae6);
90
91	1	cm = seq.getContactListFor(aa, 0);
92	1	assertEquals(cm.getContactAt(0), 1d);
93	1	verifyPAEmatrix(seq, aa, 0, 0, 4);
94
95		// test clustering
96	1	paematrix.setGroupSet(
97		GroupSet.makeGroups(paematrix, false, 0.1f, false));
98
99		// remap - test the MappableContactMatrix.liftOver method
100	1	SequenceI newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
101	1	Mapping sqmap = new Mapping(seq,
102		new MapList(new int[]
103		{ 5, 8, 10, 10 }, new int[] { 5, 9 }, 1, 1));
104	1	assertTrue(paematrix instanceof MappableContactMatrixI);
105
106	1	MappableContactMatrixI remapped = ((MappableContactMatrixI) paematrix)
107		.liftOver(newseq, sqmap);
108	1	assertTrue(remapped instanceof PAEContactMatrix);
109
110	1	AlignmentAnnotation newaa = newseq.addContactList(remapped);
111	1	assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(1)));
112	1	assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(4)));
113	1	assertNotNull(
114		newseq.getContactListFor(newaa, -1 + newseq.findIndex(5)));
115	1	assertNotNull(
116		newseq.getContactListFor(newaa, -1 + newseq.findIndex(6)));
117	1	assertNotNull(
118		newseq.getContactListFor(newaa, -1 + newseq.findIndex(7)));
119	1	assertNotNull(
120		newseq.getContactListFor(newaa, -1 + newseq.findIndex(8)));
121		// no mapping for position 9
122	1	assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(9)));
123		// last column
124	1	assertNotNull(
125		newseq.getContactListFor(newaa, -1 + newseq.findIndex(10)));
126
127		// verify MappedPositions includes discontinuity
128	1	int[] mappedCl = newseq.getContactListFor(newaa, 5)
129		.getMappedPositionsFor(0, 4);
130	1	assertEquals(4, mappedCl.length,
131		"getMappedPositionsFor doesn't support discontinuous mappings to contactList");
132
133		// make it harder.
134
135	1	SequenceI alseq = newseq.getSubSequence(6, 10);
136	1	alseq.insertCharAt(2, 2, '-');
137	1	AlignmentI alForSeq = new Alignment(new SequenceI[] { alseq });
138	1	newaa = AlignmentUtils.addReferenceAnnotationTo(alForSeq, alseq, newaa,
139		null);
140		// check for null on out of bounds
141	1	ContactListI alcl = alForSeq.getContactListFor(newaa,
142		newaa.annotations.length);
143	1	assertNull(alcl, "Should've gotten null!");
144		// now check for mapping
145	1	alcl = alForSeq.getContactListFor(newaa, 1);
146	1	assertNotNull(alcl);
147	1	mappedCl = alcl.getMappedPositionsFor(0, 4);
148	1	assertNotNull(mappedCl);
149	1	assertEquals(4, mappedCl.length,
150		"getMappedPositionsFor doesn't support discontinuous mappings to contactList");
151
152		// remap2 - test with original matrix map from 1-5 remapped to 5-9
153
154	1	seq = new Sequence("Seq/1-5", "ASDQE");
155	1	paematrix = new PAEContactMatrix(seq, PAEdata);
156	1	assertTrue(paematrix instanceof MappableContactMatrixI);
157	1	aa = seq.addContactList(paematrix);
158
159	1	newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
160	1	sqmap = new Mapping(seq,
161		new MapList(new int[]
162		{ 5, 9 }, new int[] { 1, 5 }, 1, 1));
163
164	1	remapped = ((MappableContactMatrixI) paematrix).liftOver(newseq, sqmap);
165	1	assertTrue(remapped instanceof PAEContactMatrix);
166
167	1	newaa = newseq.addContactList(remapped);
168	1	verify_mapping(newseq, newaa);
169
170		// remap3 - remap2 but mapping sense in liftover is reversed
171
172	1	seq = new Sequence("Seq/1-5", "ASDQE");
173	1	paematrix = new PAEContactMatrix(seq, PAEdata);
174	1	assertTrue(paematrix instanceof MappableContactMatrixI);
175	1	aa = seq.addContactList(paematrix);
176
177	1	newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
178	1	sqmap = new Mapping(newseq,
179		new MapList(new int[]
180		{ 1, 5 }, new int[] { 5, 9 }, 1, 1));
181
182	1	remapped = ((MappableContactMatrixI) paematrix).liftOver(newseq, sqmap);
183	1	assertTrue(remapped instanceof PAEContactMatrix);
184
185	1	newaa = newseq.addContactList(remapped);
186	1	verify_mapping(newseq, newaa);
187		}
188
189		/**
190		* checks that the PAE matrix is located at positions 1-9 in newseq, and
191		* columns are not truncated.
192		*
193		* @param newseq
194		* @param newaa
195		*/
		100% Uncovered Elements: 0 (9) Complexity: 1 Complexity Density: 0.11
196	2	private void verify_mapping(SequenceI newseq, AlignmentAnnotation newaa)...
197		{
198	2	assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(1)));
199	2	assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(4)));
200	2	assertNotNull(
201		newseq.getContactListFor(newaa, -1 + newseq.findIndex(5)));
202	2	assertNotNull(
203		newseq.getContactListFor(newaa, -1 + newseq.findIndex(6)));
204	2	assertNotNull(
205		newseq.getContactListFor(newaa, -1 + newseq.findIndex(7)));
206	2	assertNotNull(
207		newseq.getContactListFor(newaa, -1 + newseq.findIndex(8)));
208	2	assertNotNull(
209		newseq.getContactListFor(newaa, -1 + newseq.findIndex(9)));
210		// last column should be null this time
211	2	assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(10)));
212
213	2	verifyPAEmatrix(newseq, newaa, 4, 4, 8);
214		}
215
		100% Uncovered Elements: 0 (12) Complexity: 2 Complexity Density: 0.2
216	4	private void verifyPAEmatrix(SequenceI seq, AlignmentAnnotation aa,...
217		int topl, int rowl, int rowr)
218		{
219	4	int[] mappedCl;
220	24	for (int f = rowl; f <= rowr; f++)
221		{
222	20	ContactListI clist = seq.getContactListFor(aa, f);
223	20	assertNotNull(clist, "No ContactListI for position " + (f));
224	20	assertEquals(clist.getContactAt(0), (double) f - topl + 1,
225		"for column " + f + " relative to " + topl);
226	20	mappedCl = clist.getMappedPositionsFor(0, 0);
227	20	assertNotNull(mappedCl);
228	20	assertEquals(mappedCl[0], mappedCl[1]);
229	20	assertEquals(mappedCl[0], seq.findIndex(seq.getStart() + topl));
230	20	assertEquals(clist.getContactAt(f - topl), 1d,
231		"for column and row " + f + " relative to " + topl);
232		}
233		}
234
235		/**
236		* check mapping and resolution methods work
237		*/
		100% Uncovered Elements: 0 (24) Complexity: 1 Complexity Density: 0.04 1PASS
238	1	@Test(groups = { "Functional" })...
239		public void testMappableContactMatrix()
240		{
241	1	SequenceI newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
242	1	MapList map = new MapList(new int[] { 5, 9 }, new int[] { 1, 5 }, 1, 1);
243	1	AlignmentAnnotation aa = newseq.addContactList(
244		new PAEContactMatrix(newseq, map, PAEdata, null));
245	1	ContactListI clist = newseq.getContactListFor(aa, 4);
246	1	assertNotNull(clist);
247	1	clist = newseq.getContactListFor(aa, 3);
248	1	assertNull(clist);
249
250	1	ContactMatrixI cm = newseq.getContactMatrixFor(aa);
251	1	MappableContactMatrixI mcm = (MappableContactMatrixI) cm;
252	1	int[] pos = mcm.getMappedPositionsFor(newseq, 0);
253	1	assertNull(pos);
254
255	1	pos = mcm.getMappedPositionsFor(newseq, 1);
256	1	assertNotNull(pos);
257	1	assertEquals(pos[0], 4 + newseq.getStart());
258
259	1	pos = mcm.getMappedPositionsFor(newseq, 6); // after end of matrix
260	1	assertNull(pos);
261	1	pos = mcm.getMappedPositionsFor(newseq, 5); // at end of matrix
262	1	assertNotNull(pos);
263	1	assertEquals(pos[0], 8 + newseq.getStart());
264	1	SequenceI alseq = newseq.deriveSequence();
265	1	alseq.insertCharAt(5, '-');
266	1	pos = mcm.getMappedPositionsFor(alseq, 5); // at end of matrix
267	1	assertNotNull(pos);
268	1	assertEquals(pos[0], 8 + newseq.getStart());
269
270		}
271		}