Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
AlignedCodonFrameTest	39	177	11	0	1.0100%	Show methods

Class AlignedCodonFrameTest

Class AlignedCodonFrameTest	Line # 39	Total Statements 177	Complexity 11	Uncovered Elements 0	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4242	2.02	1.01	0.00	1.0 1.0100%
testFindAlignedSequence() : void   testFindAlignedSequence() : void	5252	21.021	1.01	0.00	1.0 1.0100%
testGetMappedRegion() : void   testGetMappedRegion() : void	9797	20.020	1.01	0.00	1.0 1.0100%
testGetMappedCodons() : void   testGetMappedCodons() : void	149149	11.011	1.01	0.00	1.0 1.0100%
testGetMappedCodons_dnaVariants() : void   testGetMappedCodons_dnaVariants() : void	187187	17.017	1.01	0.00	1.0 1.0100%
testGetMappedCodons_forSubSequences() : void   testGetMappedCodons_forSubSequences() : void	222222	9.09	1.01	0.00	1.0 1.0100%
testCouldReplaceSequence() : void   testCouldReplaceSequence() : void	249249	17.017	1.01	0.00	1.0 1.0100%
testIsRealisableWith() : void   testIsRealisableWith() : void	305305	26.026	1.01	0.00	1.0 1.0100%
testRealiseWith() : void   testRealiseWith() : void	360360	21.021	1.01	0.00	1.0 1.0100%
testGetMappedRegion_eitherWay() : void   testGetMappedRegion_eitherWay() : void	406406	21.021	1.01	0.00	1.0 1.0100%
testAddMap() : void   testAddMap() : void	467467	12.012	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.14361702	jalview.datamodel.AlignedCodonFrameTest.testIsRealisableWithjalview.datamodel.AlignedCodonFrameTest.testIsRealisableWith	1PASS
	0.11702128	jalview.datamodel.AlignedCodonFrameTest.testRealiseWithjalview.datamodel.AlignedCodonFrameTest.testRealiseWith	1PASS
	0.11702128	jalview.datamodel.AlignedCodonFrameTest.testGetMappedRegion_eitherWayjalview.datamodel.AlignedCodonFrameTest.testGetMappedRegion_eitherWay	1PASS
	0.11702128	jalview.datamodel.AlignedCodonFrameTest.testFindAlignedSequencejalview.datamodel.AlignedCodonFrameTest.testFindAlignedSequence	1PASS
	0.11170213	jalview.datamodel.AlignedCodonFrameTest.testGetMappedRegionjalview.datamodel.AlignedCodonFrameTest.testGetMappedRegion	1PASS
	0.095744684	jalview.datamodel.AlignedCodonFrameTest.testGetMappedCodons_dnaVariantsjalview.datamodel.AlignedCodonFrameTest.testGetMappedCodons_dnaVariants	1PASS
	0.095744684	jalview.datamodel.AlignedCodonFrameTest.testCouldReplaceSequencejalview.datamodel.AlignedCodonFrameTest.testCouldReplaceSequence	1PASS
	0.069148935	jalview.datamodel.AlignedCodonFrameTest.testAddMapjalview.datamodel.AlignedCodonFrameTest.testAddMap	1PASS
	0.06382979	jalview.datamodel.AlignedCodonFrameTest.testGetMappedCodonsjalview.datamodel.AlignedCodonFrameTest.testGetMappedCodons	1PASS
	0.05319149	jalview.datamodel.AlignedCodonFrameTest.testGetMappedCodons_forSubSequencesjalview.datamodel.AlignedCodonFrameTest.testGetMappedCodons_forSubSequences	1PASS

 

Source view

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.AssertJUnit.assertEquals;
24		import static org.testng.AssertJUnit.assertFalse;
25		import static org.testng.AssertJUnit.assertNull;
26		import static org.testng.AssertJUnit.assertSame;
27		import static org.testng.AssertJUnit.assertTrue;
28		import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
29
30		import jalview.gui.JvOptionPane;
31		import jalview.util.MapList;
32
33		import java.util.Arrays;
34		import java.util.List;
35
36		import org.testng.annotations.BeforeClass;
37		import org.testng.annotations.Test;
38
		100% Uncovered Elements: 0 (188) Complexity: 11 Complexity Density: 0.06
39		public class AlignedCodonFrameTest
40		{
41
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
42	1	@BeforeClass(alwaysRun = true)...
43		public void setUpJvOptionPane()
44		{
45	1	JvOptionPane.setInteractiveMode(false);
46	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
47		}
48
49		/**
50		* Test the method that locates the first aligned sequence that has a mapping.
51		*/
		100% Uncovered Elements: 0 (21) Complexity: 1 Complexity Density: 0.05 1PASS
52	1	@Test(groups = { "Functional" })...
53		public void testFindAlignedSequence()
54		{
55	1	AlignmentI cdna = new Alignment(new SequenceI[] {});
56	1	final Sequence seq1 = new Sequence("Seq1", "C-G-TA-GC");
57	1	seq1.createDatasetSequence();
58	1	cdna.addSequence(seq1);
59	1	final Sequence seq2 = new Sequence("Seq2", "-TA-GG-GG");
60	1	seq2.createDatasetSequence();
61	1	cdna.addSequence(seq2);
62
63	1	AlignmentI aa = new Alignment(new SequenceI[] {});
64	1	final Sequence aseq1 = new Sequence("Seq1", "-P-R");
65	1	aseq1.createDatasetSequence();
66	1	aa.addSequence(aseq1);
67	1	final Sequence aseq2 = new Sequence("Seq2", "-LY-");
68	1	aseq2.createDatasetSequence();
69	1	aa.addSequence(aseq2);
70
71		/*
72		* Mapping from first DNA sequence to second AA sequence.
73		*/
74	1	AlignedCodonFrame acf = new AlignedCodonFrame();
75
76	1	assertNull(acf.findAlignedSequence(seq1, aa));
77
78	1	MapList map = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, 3, 1);
79	1	acf.addMap(seq1.getDatasetSequence(), aseq2.getDatasetSequence(), map);
80
81		/*
82		* DNA seq1 maps to AA seq2
83		*/
84	1	assertEquals(aa.getSequenceAt(1), acf.findAlignedSequence(cdna
85		.getSequenceAt(0).getDatasetSequence(), aa));
86		// can also find this from the dna aligned sequence
87	1	assertEquals(aa.getSequenceAt(1),
88		acf.findAlignedSequence(cdna.getSequenceAt(0), aa));
89
90	1	assertEquals(cdna.getSequenceAt(0), acf.findAlignedSequence(aa
91		.getSequenceAt(1).getDatasetSequence(), cdna));
92		}
93
94		/**
95		* Test the method that locates the mapped codon for a protein position.
96		*/
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
97	1	@Test(groups = { "Functional" })...
98		public void testGetMappedRegion()
99		{
100		// introns lower case, exons upper case
101	1	final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T");
102	1	seq1.createDatasetSequence();
103	1	final Sequence seq2 = new Sequence("Seq2", "-TA-gG-Gg-CG-a");
104	1	seq2.createDatasetSequence();
105
106	1	final Sequence aseq1 = new Sequence("Seq1", "-P-R");
107	1	aseq1.createDatasetSequence();
108	1	final Sequence aseq2 = new Sequence("Seq2", "-LY-Q");
109	1	aseq2.createDatasetSequence();
110
111		/*
112		* First with no mappings
113		*/
114	1	AlignedCodonFrame acf = new AlignedCodonFrame();
115
116	1	assertNull(acf.getMappedRegion(seq1, aseq1, 1));
117
118		/*
119		* Set up the mappings for the exons (upper-case bases)
120		* Note residue Q is unmapped
121		*/
122	1	MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 }, new int[] {
123		1, 2 }, 3, 1);
124	1	acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
125	1	map = new MapList(new int[] { 1, 2, 4, 5, 7, 8 }, new int[] { 1, 2 },
126		3, 1);
127	1	acf.addMap(seq2.getDatasetSequence(), aseq2.getDatasetSequence(), map);
128
129	1	assertArrayEquals(new int[] { 2, 4 },
130		acf.getMappedRegion(seq1, aseq1, 1));
131	1	assertArrayEquals(new int[] { 6, 6, 8, 9 },
132		acf.getMappedRegion(seq1, aseq1, 2));
133	1	assertArrayEquals(new int[] { 1, 2, 4, 4 },
134		acf.getMappedRegion(seq2, aseq2, 1));
135	1	assertArrayEquals(new int[] { 5, 5, 7, 8 },
136		acf.getMappedRegion(seq2, aseq2, 2));
137
138		/*
139		* No mapping from seq2 to Q
140		*/
141	1	assertNull(acf.getMappedRegion(seq2, aseq2, 3));
142
143		/*
144		* No mapping from sequence 1 to sequence 2
145		*/
146	1	assertNull(acf.getMappedRegion(seq1, aseq2, 1));
147		}
148
		100% Uncovered Elements: 0 (11) Complexity: 1 Complexity Density: 0.09 1PASS
149	1	@Test(groups = { "Functional" })...
150		public void testGetMappedCodons()
151		{
152	1	final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T");
153	1	seq1.createDatasetSequence();
154	1	final Sequence aseq1 = new Sequence("Seq1", "-V-L");
155	1	aseq1.createDatasetSequence();
156
157		/*
158		* First with no mappings
159		*/
160	1	AlignedCodonFrame acf = new AlignedCodonFrame();
161
162	1	assertNull(acf.getMappedCodons(seq1.getDatasetSequence(), 0));
163
164		/*
165		* Set up the mappings for the exons (upper-case bases)
166		*/
167	1	MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 }, new int[] {
168		1, 2 }, 3, 1);
169	1	acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
170
171	1	assertEquals(1, acf.getMappedCodons(aseq1.getDatasetSequence(), 1)
172		.size());
173	1	assertEquals(
174		"[G, T, A]",
175		Arrays.toString(acf.getMappedCodons(aseq1.getDatasetSequence(),
176		1).get(0)));
177	1	assertEquals(
178		"[C, T, T]",
179		Arrays.toString(acf.getMappedCodons(aseq1.getDatasetSequence(),
180		2).get(0)));
181		}
182
183		/**
184		* Test for the case where there is more than one variant of the DNA mapping
185		* to a protein sequence
186		*/
		100% Uncovered Elements: 0 (17) Complexity: 1 Complexity Density: 0.06 1PASS
187	1	@Test(groups = { "Functional" })...
188		public void testGetMappedCodons_dnaVariants()
189		{
190	1	final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T");
191	1	seq1.createDatasetSequence();
192	1	final Sequence seq2 = new Sequence("Seq2", "c-G-TT-gT-gT-A");
193	1	seq2.createDatasetSequence();
194	1	final Sequence aseq1 = new Sequence("Seq1", "-V-L");
195	1	aseq1.createDatasetSequence();
196
197	1	AlignedCodonFrame acf = new AlignedCodonFrame();
198
199		/*
200		* Set up the mappings for the exons (upper-case bases)
201		*/
202	1	MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 }, new int[] {
203		1, 2 }, 3, 1);
204	1	acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
205	1	acf.addMap(seq2.getDatasetSequence(), aseq1.getDatasetSequence(), map);
206
207	1	assertEquals(2, acf.getMappedCodons(aseq1.getDatasetSequence(), 1)
208		.size());
209	1	List<char[]> codonsForV = acf.getMappedCodons(
210		aseq1.getDatasetSequence(), 1);
211	1	assertEquals("[G, T, A]", Arrays.toString(codonsForV.get(0)));
212	1	assertEquals("[G, T, T]", Arrays.toString(codonsForV.get(1)));
213	1	List<char[]> codonsForL = acf.getMappedCodons(
214		aseq1.getDatasetSequence(), 2);
215	1	assertEquals("[C, T, T]", Arrays.toString(codonsForL.get(0)));
216	1	assertEquals("[T, T, A]", Arrays.toString(codonsForL.get(1)));
217		}
218
219		/**
220		* Test for the case where sequences have start > 1
221		*/
		100% Uncovered Elements: 0 (9) Complexity: 1 Complexity Density: 0.11 1PASS
222	1	@Test(groups = { "Functional" })...
223		public void testGetMappedCodons_forSubSequences()
224		{
225	1	final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T", 27, 35);
226	1	seq1.createDatasetSequence();
227
228	1	final Sequence aseq1 = new Sequence("Seq1", "-V-L", 12, 13);
229	1	aseq1.createDatasetSequence();
230
231		/*
232		* Set up the mappings for the exons (upper-case bases)
233		*/
234	1	AlignedCodonFrame acf = new AlignedCodonFrame();
235	1	MapList map = new MapList(new int[] { 28, 30, 32, 32, 34, 35 },
236		new int[] { 12, 13 }, 3, 1);
237	1	acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
238
239	1	assertEquals(
240		"[G, T, A]",
241		Arrays.toString(acf.getMappedCodons(aseq1.getDatasetSequence(),
242		12).get(0)));
243	1	assertEquals(
244		"[C, T, T]",
245		Arrays.toString(acf.getMappedCodons(aseq1.getDatasetSequence(),
246		13).get(0)));
247		}
248
		100% Uncovered Elements: 0 (17) Complexity: 1 Complexity Density: 0.06 1PASS
249	1	@Test(groups = { "Functional" })...
250		public void testCouldReplaceSequence()
251		{
252	1	SequenceI seq1 = new Sequence("Seq1/10-21", "aaacccgggttt");
253	1	SequenceI seq1proxy = new SequenceDummy("Seq1");
254
255		// map to region within sequence is ok
256	1	assertTrue(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 12,
257		17));
258		// map to region overlapping sequence is ok
259	1	assertTrue(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 5,
260		10));
261	1	assertTrue(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 21,
262		26));
263		// map to region before sequence is not ok
264	1	assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 4,
265		9));
266		// map to region after sequence is not ok
267	1	assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 22,
268		27));
269
270		/*
271		* test should fail if name doesn't match
272		*/
273	1	seq1proxy.setName("Seq1a");
274	1	assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 12,
275		17));
276	1	seq1proxy.setName("Seq1");
277	1	seq1.setName("Seq1a");
278	1	assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 12,
279		17));
280
281		/*
282		* a dummy sequence can't replace a real one
283		*/
284	1	assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1, seq1proxy, 12,
285		17));
286
287		/*
288		* a dummy sequence can't replace a dummy sequence
289		*/
290	1	SequenceI seq1proxy2 = new SequenceDummy("Seq1");
291	1	assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1proxy,
292		seq1proxy2, 12, 17));
293
294		/*
295		* a real sequence can't replace a real one
296		*/
297	1	SequenceI seq1a = new Sequence("Seq1/10-21", "aaacccgggttt");
298	1	assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1, seq1a, 12, 17));
299		}
300
301		/**
302		* Tests for the method that tests whether any mapping to a dummy sequence can
303		* be 'realised' to a given real sequence
304		*/
		100% Uncovered Elements: 0 (26) Complexity: 1 Complexity Density: 0.04 1PASS
305	1	@Test(groups = { "Functional" })...
306		public void testIsRealisableWith()
307		{
308	1	SequenceI seq1 = new Sequence("Seq1", "tttaaaCCCGGGtttaaa");
309	1	SequenceI seq2 = new Sequence("Seq2", "PG");
310	1	SequenceI seq1proxy = new SequenceDummy("Seq1");
311	1	seq1.createDatasetSequence();
312	1	seq2.createDatasetSequence();
313	1	MapList mapList = new MapList(new int[] { 7, 12 }, new int[] { 2, 3 },
314		3, 1);
315	1	AlignedCodonFrame acf = new AlignedCodonFrame();
316	1	acf.addMap(seq1proxy, seq2, mapList);
317
318		/*
319		* Seq2 is mapped to SequenceDummy seq1proxy bases 4-9
320		* This is 'realisable' from real sequence Seq1
321		*/
322	1	assertTrue(acf.isRealisableWith(seq1));
323
324		/*
325		* test should fail if name doesn't match
326		*/
327	1	seq1proxy.setName("Seq1a");
328	1	assertFalse(acf.isRealisableWith(seq1));
329	1	seq1proxy.setName("Seq1");
330
331	1	SequenceI seq1ds = seq1.getDatasetSequence();
332	1	seq1ds.setName("Seq1a");
333	1	assertFalse(acf.isRealisableWith(seq1));
334	1	seq1ds.setName("Seq1");
335
336		/*
337		* test should fail if no sequence overlap with mapping of bases 7-12
338		* use artificial start/end values to test this
339		*/
340	1	seq1ds.setStart(1);
341	1	seq1ds.setEnd(6);
342		// seq1 precedes mapped region:
343	1	assertFalse(acf.isRealisableWith(seq1));
344	1	seq1ds.setEnd(7);
345		// seq1 includes first mapped base:
346	1	assertTrue(acf.isRealisableWith(seq1));
347	1	seq1ds.setStart(13);
348	1	seq1ds.setEnd(18);
349		// seq1 follows mapped region:
350	1	assertFalse(acf.isRealisableWith(seq1));
351	1	seq1ds.setStart(12);
352		// seq1 includes last mapped base:
353	1	assertTrue(acf.isRealisableWith(seq1));
354		}
355
356		/**
357		* Tests for the method that converts mappings to a dummy sequence to mappings
358		* to a compatible real sequence
359		*/
		100% Uncovered Elements: 0 (21) Complexity: 1 Complexity Density: 0.05 1PASS
360	1	@Test(groups = { "Functional" })...
361		public void testRealiseWith()
362		{
363	1	SequenceI seq1 = new Sequence("Seq1", "tttCAACCCGGGtttaaa");
364	1	SequenceI seq2 = new Sequence("Seq2", "QPG");
365	1	SequenceI seq2a = new Sequence("Seq2a", "QPG");
366	1	SequenceI seq1proxy = new SequenceDummy("Seq1");
367	1	seq1.createDatasetSequence();
368	1	seq2.createDatasetSequence();
369	1	seq2a.createDatasetSequence();
370
371		/*
372		* Make mappings from Seq2 and Seq2a peptides to dummy sequence Seq1
373		*/
374	1	AlignedCodonFrame acf = new AlignedCodonFrame();
375
376		// map PG to codons 7-12 (CCCGGG)
377	1	MapList mapping1 = new MapList(new int[] { 7, 12 }, new int[] { 2, 3 },
378		3, 1);
379	1	acf.addMap(seq1proxy, seq2, mapping1);
380	1	acf.addMap(seq1proxy, seq2a, mapping1);
381
382		// map QP to codons 4-9 (CAACCC)
383	1	MapList mapping2 = new MapList(new int[] { 4, 9 }, new int[] { 1, 2 },
384		3, 1);
385	1	acf.addMap(seq1proxy, seq2, mapping2);
386	1	acf.addMap(seq1proxy, seq2a, mapping2);
387
388		/*
389		* acf now has two mappings one from Seq1 to Seq2, one from Seq1 to Seq2a
390		*/
391	1	assertEquals(2, acf.getdnaSeqs().length);
392	1	assertSame(seq1proxy, acf.getdnaSeqs()[0]);
393	1	assertSame(seq1proxy, acf.getdnaSeqs()[1]);
394	1	assertEquals(2, acf.getProtMappings().length);
395
396		// 'realise' these mappings with the compatible sequence seq1
397		// two mappings should be updated:
398	1	assertEquals(2, acf.realiseWith(seq1));
399	1	assertSame(seq1.getDatasetSequence(), acf.getdnaSeqs()[0]);
400	1	assertSame(seq1.getDatasetSequence(), acf.getdnaSeqs()[1]);
401		}
402
403		/**
404		* Test the method that locates the mapped codon for a protein position.
405		*/
		100% Uncovered Elements: 0 (21) Complexity: 1 Complexity Density: 0.05 1PASS
406	1	@Test(groups = { "Functional" })...
407		public void testGetMappedRegion_eitherWay()
408		{
409	1	final Sequence seq1 = new Sequence("Seq1", "AAACCCGGGTTT");
410	1	seq1.createDatasetSequence();
411	1	final Sequence seq2 = new Sequence("Seq2", "KPGF");
412	1	seq2.createDatasetSequence();
413	1	final Sequence seq3 = new Sequence("Seq3", "QYKPGFSW");
414	1	seq3.createDatasetSequence();
415
416		/*
417		* map Seq1 to all of Seq2 and part of Seq3
418		*/
419	1	AlignedCodonFrame acf = new AlignedCodonFrame();
420	1	MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1);
421	1	acf.addMap(seq1.getDatasetSequence(), seq2.getDatasetSequence(), map);
422	1	map = new MapList(new int[] { 1, 12 }, new int[] { 3, 6 }, 3, 1);
423	1	acf.addMap(seq1.getDatasetSequence(), seq3.getDatasetSequence(), map);
424
425		/*
426		* map part of Seq3 to Seq2
427		*/
428	1	map = new MapList(new int[] { 3, 6 }, new int[] { 1, 4 }, 1, 1);
429	1	acf.addMap(seq3.getDatasetSequence(), seq2.getDatasetSequence(), map);
430
431		/*
432		* original case - locate mapped codon for protein position
433		*/
434	1	assertArrayEquals(new int[] { 4, 6 },
435		acf.getMappedRegion(seq1, seq2, 2));
436	1	assertArrayEquals(new int[] { 7, 9 },
437		acf.getMappedRegion(seq1, seq3, 5));
438	1	assertNull(acf.getMappedRegion(seq1, seq3, 1));
439
440		/*
441		* locate mapped protein for protein position
442		*/
443	1	assertArrayEquals(new int[] { 4, 4 },
444		acf.getMappedRegion(seq3, seq2, 2));
445
446		/*
447		* reverse location protein-to-protein
448		*/
449	1	assertArrayEquals(new int[] { 2, 2 },
450		acf.getMappedRegion(seq2, seq3, 4));
451
452		/*
453		* reverse location protein-from-nucleotide
454		* any of codon [4, 5, 6] positions map to seq2/2
455		*/
456	1	assertArrayEquals(new int[] { 2, 2 },
457		acf.getMappedRegion(seq2, seq1, 4));
458	1	assertArrayEquals(new int[] { 2, 2 },
459		acf.getMappedRegion(seq2, seq1, 5));
460	1	assertArrayEquals(new int[] { 2, 2 },
461		acf.getMappedRegion(seq2, seq1, 6));
462		}
463
464		/**
465		* Tests for addMap. See also tests for MapList.addMapList
466		*/
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
467	1	@Test(groups = { "Functional" })...
468		public void testAddMap()
469		{
470	1	final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T");
471	1	seq1.createDatasetSequence();
472	1	final Sequence aseq1 = new Sequence("Seq1", "-V-L");
473	1	aseq1.createDatasetSequence();
474
475	1	AlignedCodonFrame acf = new AlignedCodonFrame();
476	1	MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 }, new int[] {
477		1, 2 }, 3, 1);
478	1	acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
479	1	assertEquals(1, acf.getMappingsFromSequence(seq1).size());
480	1	Mapping before = acf.getMappingsFromSequence(seq1).get(0);
481
482		/*
483		* add the same map again, verify it doesn't get duplicated
484		*/
485	1	acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
486	1	assertEquals(1, acf.getMappingsFromSequence(seq1).size());
487	1	assertSame(before, acf.getMappingsFromSequence(seq1).get(0));
488		}
489		}