Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AlignedCodonFrameTest	41	285	14	1.0100%	Show methods

Class AlignedCodonFrameTest

Class AlignedCodonFrameTest	Line # 41	Total Statements 285	Complexity 14	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void   setUpJvOptionPane() : void	4444	2.02	1.01	1.0 1.0100%
testFindAlignedSequence() : void   testFindAlignedSequence() : void	5454	21.021	1.01	1.0 1.0100%
testGetMappedRegion() : void   testGetMappedRegion() : void	9999	24.024	1.01	1.0 1.0100%
testGetMappedCodons() : void   testGetMappedCodons() : void	168168	11.011	1.01	1.0 1.0100%
testGetMappedCodons_dnaVariants() : void   testGetMappedCodons_dnaVariants() : void	203203	17.017	1.01	1.0 1.0100%
testGetMappedCodons_forSubSequences() : void   testGetMappedCodons_forSubSequences() : void	239239	9.09	1.01	1.0 1.0100%
testCouldReplaceSequence() : void   testCouldReplaceSequence() : void	263263	17.017	1.01	1.0 1.0100%
testIsRealisableWith() : void   testIsRealisableWith() : void	320320	26.026	1.01	1.0 1.0100%
testRealiseWith() : void   testRealiseWith() : void	375375	21.021	1.01	1.0 1.0100%
testGetMappedRegion_eitherWay() : void   testGetMappedRegion_eitherWay() : void	421421	21.021	1.01	1.0 1.0100%
testAddMap() : void   testAddMap() : void	483483	12.012	1.01	1.0 1.0100%
testGetCoveringMapping() : void   testGetCoveringMapping() : void	507507	31.031	1.01	1.0 1.0100%
testMarkMappedRegion() : void   testMarkMappedRegion() : void	566566	39.039	1.01	1.0 1.0100%
testGetCoveringCodonMapping() : void   testGetCoveringCodonMapping() : void	654654	34.034	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.13377926	jalview.datamodel.AlignedCodonFrameTest.testMarkMappedRegionjalview.datamodel.AlignedCodonFrameTest.testMarkMappedRegion	1PASS
	0.117056854	jalview.datamodel.AlignedCodonFrameTest.testGetCoveringCodonMappingjalview.datamodel.AlignedCodonFrameTest.testGetCoveringCodonMapping	1PASS
	0.10702341	jalview.datamodel.AlignedCodonFrameTest.testGetCoveringMappingjalview.datamodel.AlignedCodonFrameTest.testGetCoveringMapping	1PASS
	0.09030101	jalview.datamodel.AlignedCodonFrameTest.testIsRealisableWithjalview.datamodel.AlignedCodonFrameTest.testIsRealisableWith	1PASS
	0.08361204	jalview.datamodel.AlignedCodonFrameTest.testGetMappedRegionjalview.datamodel.AlignedCodonFrameTest.testGetMappedRegion	1PASS
	0.073578596	jalview.datamodel.AlignedCodonFrameTest.testRealiseWithjalview.datamodel.AlignedCodonFrameTest.testRealiseWith	1PASS
	0.073578596	jalview.datamodel.AlignedCodonFrameTest.testFindAlignedSequencejalview.datamodel.AlignedCodonFrameTest.testFindAlignedSequence	1PASS
	0.073578596	jalview.datamodel.AlignedCodonFrameTest.testGetMappedRegion_eitherWayjalview.datamodel.AlignedCodonFrameTest.testGetMappedRegion_eitherWay	1PASS
	0.06020067	jalview.datamodel.AlignedCodonFrameTest.testCouldReplaceSequencejalview.datamodel.AlignedCodonFrameTest.testCouldReplaceSequence	1PASS
	0.06020067	jalview.datamodel.AlignedCodonFrameTest.testGetMappedCodons_dnaVariantsjalview.datamodel.AlignedCodonFrameTest.testGetMappedCodons_dnaVariants	1PASS
	0.04347826	jalview.datamodel.AlignedCodonFrameTest.testAddMapjalview.datamodel.AlignedCodonFrameTest.testAddMap	1PASS
	0.040133778	jalview.datamodel.AlignedCodonFrameTest.testGetMappedCodonsjalview.datamodel.AlignedCodonFrameTest.testGetMappedCodons	1PASS
	0.033444814	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.assertNotNull;
26		import static org.testng.AssertJUnit.assertNull;
27		import static org.testng.AssertJUnit.assertSame;
28		import static org.testng.AssertJUnit.assertTrue;
29		import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
30
31		import java.util.Arrays;
32		import java.util.List;
33
34		import org.testng.annotations.BeforeClass;
35		import org.testng.annotations.Test;
36
37		import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
38		import jalview.gui.JvOptionPane;
39		import jalview.util.MapList;
40
		100% Uncovered Elements: 0 (299) Complexity: 14 Complexity Density: 0.05
41		public class AlignedCodonFrameTest
42		{
43
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
44	1	@BeforeClass(alwaysRun = true)...
45		public void setUpJvOptionPane()
46		{
47	1	JvOptionPane.setInteractiveMode(false);
48	1	JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
49		}
50
51		/**
52		* Test the method that locates the first aligned sequence that has a mapping.
53		*/
		100% Uncovered Elements: 0 (21) Complexity: 1 Complexity Density: 0.05 1PASS
54	1	@Test(groups = { "Functional" })...
55		public void testFindAlignedSequence()
56		{
57	1	AlignmentI cdna = new Alignment(new SequenceI[] {});
58	1	final Sequence seq1 = new Sequence("Seq1", "C-G-TA-GC");
59	1	seq1.createDatasetSequence();
60	1	cdna.addSequence(seq1);
61	1	final Sequence seq2 = new Sequence("Seq2", "-TA-GG-GG");
62	1	seq2.createDatasetSequence();
63	1	cdna.addSequence(seq2);
64
65	1	AlignmentI aa = new Alignment(new SequenceI[] {});
66	1	final Sequence aseq1 = new Sequence("Seq1", "-P-R");
67	1	aseq1.createDatasetSequence();
68	1	aa.addSequence(aseq1);
69	1	final Sequence aseq2 = new Sequence("Seq2", "-LY-");
70	1	aseq2.createDatasetSequence();
71	1	aa.addSequence(aseq2);
72
73		/*
74		* Mapping from first DNA sequence to second AA sequence.
75		*/
76	1	AlignedCodonFrame acf = new AlignedCodonFrame();
77
78	1	assertNull(acf.findAlignedSequence(seq1, aa));
79
80	1	MapList map = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 }, 3, 1);
81	1	acf.addMap(seq1.getDatasetSequence(), aseq2.getDatasetSequence(), map);
82
83		/*
84		* DNA seq1 maps to AA seq2
85		*/
86	1	assertEquals(aa.getSequenceAt(1), acf.findAlignedSequence(
87		cdna.getSequenceAt(0).getDatasetSequence(), aa));
88		// can also find this from the dna aligned sequence
89	1	assertEquals(aa.getSequenceAt(1),
90		acf.findAlignedSequence(cdna.getSequenceAt(0), aa));
91
92	1	assertEquals(cdna.getSequenceAt(0), acf.findAlignedSequence(
93		aa.getSequenceAt(1).getDatasetSequence(), cdna));
94		}
95
96		/**
97		* Test the method that locates the mapped codon for a protein position.
98		*/
		100% Uncovered Elements: 0 (24) Complexity: 1 Complexity Density: 0.04 1PASS
99	1	@Test(groups = { "Functional" })...
100		public void testGetMappedRegion()
101		{
102		// introns lower case, exons upper case
103	1	final Sequence dna1 = new Sequence("Seq1/10-18", "c-G-TA-gC-gT-T");
104	1	dna1.createDatasetSequence();
105	1	final Sequence dna2 = new Sequence("Seq2/20-28", "-TA-gG-Gg-CG-a");
106	1	dna2.createDatasetSequence();
107
108	1	final Sequence pep1 = new Sequence("Seq1/3-4", "-P-R");
109	1	pep1.createDatasetSequence();
110	1	final Sequence pep2 = new Sequence("Seq2/7-9", "-LY-Q");
111	1	pep2.createDatasetSequence();
112
113		/*
114		* First with no mappings
115		*/
116	1	AlignedCodonFrame acf = new AlignedCodonFrame();
117
118	1	assertNull(acf.getMappedRegion(dna1, pep1, 3));
119
120		/*
121		* Set up the mappings for the exons (upper-case bases)
122		* Note residue Q is unmapped
123		*/
124	1	MapList map1 = new MapList(new int[] { 11, 13, 15, 15, 17, 18 },
125		new int[]
126		{ 3, 4 }, 3, 1);
127	1	acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map1);
128	1	MapList map2 = new MapList(new int[] { 20, 21, 23, 24, 26, 27 },
129		new int[]
130		{ 7, 9 }, 3, 1);
131	1	acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map2);
132
133		/*
134		* get codon positions for peptide position
135		*/
136	1	assertArrayEquals(new int[] { 11, 13 },
137		acf.getMappedRegion(dna1, pep1, 3));
138	1	assertArrayEquals(new int[] { 15, 15, 17, 18 },
139		acf.getMappedRegion(dna1, pep1, 4));
140	1	assertArrayEquals(new int[] { 20, 21, 23, 23 },
141		acf.getMappedRegion(dna2, pep2, 7));
142	1	assertArrayEquals(new int[] { 24, 24, 26, 27 },
143		acf.getMappedRegion(dna2, pep2, 8));
144
145		/*
146		* No mapping from dna2 to Q
147		*/
148	1	assertNull(acf.getMappedRegion(dna2, pep2, 9));
149
150		/*
151		* No mapping from dna1 to pep2
152		*/
153	1	assertNull(acf.getMappedRegion(dna1, pep2, 7));
154
155		/*
156		* get peptide position for codon position
157		*/
158	1	assertArrayEquals(new int[] { 3, 3 },
159		acf.getMappedRegion(pep1, dna1, 11));
160	1	assertArrayEquals(new int[] { 3, 3 },
161		acf.getMappedRegion(pep1, dna1, 12));
162	1	assertArrayEquals(new int[] { 3, 3 },
163		acf.getMappedRegion(pep1, dna1, 13));
164	1	assertNull(acf.getMappedRegion(pep1, dna1, 14)); // intron base, not mapped
165
166		}
167
		100% Uncovered Elements: 0 (11) Complexity: 1 Complexity Density: 0.09 1PASS
168	1	@Test(groups = { "Functional" })...
169		public void testGetMappedCodons()
170		{
171	1	final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T");
172	1	seq1.createDatasetSequence();
173	1	final Sequence aseq1 = new Sequence("Seq1", "-V-L");
174	1	aseq1.createDatasetSequence();
175
176		/*
177		* First with no mappings
178		*/
179	1	AlignedCodonFrame acf = new AlignedCodonFrame();
180
181	1	assertNull(acf.getMappedCodons(seq1.getDatasetSequence(), 0));
182
183		/*
184		* Set up the mappings for the exons (upper-case bases)
185		*/
186	1	MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 },
187		new int[]
188		{ 1, 2 }, 3, 1);
189	1	acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
190
191	1	assertEquals(1,
192		acf.getMappedCodons(aseq1.getDatasetSequence(), 1).size());
193	1	assertEquals("[G, T, A]", Arrays.toString(
194		acf.getMappedCodons(aseq1.getDatasetSequence(), 1).get(0)));
195	1	assertEquals("[C, T, T]", Arrays.toString(
196		acf.getMappedCodons(aseq1.getDatasetSequence(), 2).get(0)));
197		}
198
199		/**
200		* Test for the case where there is more than one variant of the DNA mapping
201		* to a protein sequence
202		*/
		100% Uncovered Elements: 0 (17) Complexity: 1 Complexity Density: 0.06 1PASS
203	1	@Test(groups = { "Functional" })...
204		public void testGetMappedCodons_dnaVariants()
205		{
206	1	final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T");
207	1	seq1.createDatasetSequence();
208	1	final Sequence seq2 = new Sequence("Seq2", "c-G-TT-gT-gT-A");
209	1	seq2.createDatasetSequence();
210	1	final Sequence aseq1 = new Sequence("Seq1", "-V-L");
211	1	aseq1.createDatasetSequence();
212
213	1	AlignedCodonFrame acf = new AlignedCodonFrame();
214
215		/*
216		* Set up the mappings for the exons (upper-case bases)
217		*/
218	1	MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 },
219		new int[]
220		{ 1, 2 }, 3, 1);
221	1	acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
222	1	acf.addMap(seq2.getDatasetSequence(), aseq1.getDatasetSequence(), map);
223
224	1	assertEquals(2,
225		acf.getMappedCodons(aseq1.getDatasetSequence(), 1).size());
226	1	List<char[]> codonsForV = acf
227		.getMappedCodons(aseq1.getDatasetSequence(), 1);
228	1	assertEquals("[G, T, A]", Arrays.toString(codonsForV.get(0)));
229	1	assertEquals("[G, T, T]", Arrays.toString(codonsForV.get(1)));
230	1	List<char[]> codonsForL = acf
231		.getMappedCodons(aseq1.getDatasetSequence(), 2);
232	1	assertEquals("[C, T, T]", Arrays.toString(codonsForL.get(0)));
233	1	assertEquals("[T, T, A]", Arrays.toString(codonsForL.get(1)));
234		}
235
236		/**
237		* Test for the case where sequences have start > 1
238		*/
		100% Uncovered Elements: 0 (9) Complexity: 1 Complexity Density: 0.11 1PASS
239	1	@Test(groups = { "Functional" })...
240		public void testGetMappedCodons_forSubSequences()
241		{
242	1	final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T", 27, 35);
243	1	seq1.createDatasetSequence();
244
245	1	final Sequence aseq1 = new Sequence("Seq1", "-V-L", 12, 13);
246	1	aseq1.createDatasetSequence();
247
248		/*
249		* Set up the mappings for the exons (upper-case bases)
250		*/
251	1	AlignedCodonFrame acf = new AlignedCodonFrame();
252	1	MapList map = new MapList(new int[] { 28, 30, 32, 32, 34, 35 },
253		new int[]
254		{ 12, 13 }, 3, 1);
255	1	acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
256
257	1	assertEquals("[G, T, A]", Arrays.toString(
258		acf.getMappedCodons(aseq1.getDatasetSequence(), 12).get(0)));
259	1	assertEquals("[C, T, T]", Arrays.toString(
260		acf.getMappedCodons(aseq1.getDatasetSequence(), 13).get(0)));
261		}
262
		100% Uncovered Elements: 0 (17) Complexity: 1 Complexity Density: 0.06 1PASS
263	1	@Test(groups = { "Functional" })...
264		public void testCouldReplaceSequence()
265		{
266	1	SequenceI seq1 = new Sequence("Seq1/10-21", "aaacccgggttt");
267	1	SequenceI seq1proxy = new SequenceDummy("Seq1");
268
269		// map to region within sequence is ok
270	1	assertTrue(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 12,
271		17));
272		// map to region overlapping sequence is ok
273	1	assertTrue(
274		AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 5, 10));
275	1	assertTrue(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 21,
276		26));
277		// map to region before sequence is not ok
278	1	assertFalse(
279		AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 4, 9));
280		// map to region after sequence is not ok
281	1	assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 22,
282		27));
283
284		/*
285		* test should fail if name doesn't match
286		*/
287	1	seq1proxy.setName("Seq1a");
288	1	assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 12,
289		17));
290	1	seq1proxy.setName("Seq1");
291	1	seq1.setName("Seq1a");
292	1	assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 12,
293		17));
294
295		/*
296		* a dummy sequence can't replace a real one
297		*/
298	1	assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1, seq1proxy, 12,
299		17));
300
301		/*
302		* a dummy sequence can't replace a dummy sequence
303		*/
304	1	SequenceI seq1proxy2 = new SequenceDummy("Seq1");
305	1	assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1proxy,
306		seq1proxy2, 12, 17));
307
308		/*
309		* a real sequence can't replace a real one
310		*/
311	1	SequenceI seq1a = new Sequence("Seq1/10-21", "aaacccgggttt");
312	1	assertFalse(
313		AlignedCodonFrame.couldRealiseSequence(seq1, seq1a, 12, 17));
314		}
315
316		/**
317		* Tests for the method that tests whether any mapping to a dummy sequence can
318		* be 'realised' to a given real sequence
319		*/
		100% Uncovered Elements: 0 (26) Complexity: 1 Complexity Density: 0.04 1PASS
320	1	@Test(groups = { "Functional" })...
321		public void testIsRealisableWith()
322		{
323	1	SequenceI seq1 = new Sequence("Seq1", "tttaaaCCCGGGtttaaa");
324	1	SequenceI seq2 = new Sequence("Seq2", "PG");
325	1	SequenceI seq1proxy = new SequenceDummy("Seq1");
326	1	seq1.createDatasetSequence();
327	1	seq2.createDatasetSequence();
328	1	MapList mapList = new MapList(new int[] { 7, 12 }, new int[] { 2, 3 },
329		3, 1);
330	1	AlignedCodonFrame acf = new AlignedCodonFrame();
331	1	acf.addMap(seq1proxy, seq2, mapList);
332
333		/*
334		* Seq2 is mapped to SequenceDummy seq1proxy bases 4-9
335		* This is 'realisable' from real sequence Seq1
336		*/
337	1	assertTrue(acf.isRealisableWith(seq1));
338
339		/*
340		* test should fail if name doesn't match
341		*/
342	1	seq1proxy.setName("Seq1a");
343	1	assertFalse(acf.isRealisableWith(seq1));
344	1	seq1proxy.setName("Seq1");
345
346	1	SequenceI seq1ds = seq1.getDatasetSequence();
347	1	seq1ds.setName("Seq1a");
348	1	assertFalse(acf.isRealisableWith(seq1));
349	1	seq1ds.setName("Seq1");
350
351		/*
352		* test should fail if no sequence overlap with mapping of bases 7-12
353		* use artificial start/end values to test this
354		*/
355	1	seq1ds.setStart(1);
356	1	seq1ds.setEnd(6);
357		// seq1 precedes mapped region:
358	1	assertFalse(acf.isRealisableWith(seq1));
359	1	seq1ds.setEnd(7);
360		// seq1 includes first mapped base:
361	1	assertTrue(acf.isRealisableWith(seq1));
362	1	seq1ds.setStart(13);
363	1	seq1ds.setEnd(18);
364		// seq1 follows mapped region:
365	1	assertFalse(acf.isRealisableWith(seq1));
366	1	seq1ds.setStart(12);
367		// seq1 includes last mapped base:
368	1	assertTrue(acf.isRealisableWith(seq1));
369		}
370
371		/**
372		* Tests for the method that converts mappings to a dummy sequence to mappings
373		* to a compatible real sequence
374		*/
		100% Uncovered Elements: 0 (21) Complexity: 1 Complexity Density: 0.05 1PASS
375	1	@Test(groups = { "Functional" })...
376		public void testRealiseWith()
377		{
378	1	SequenceI seq1 = new Sequence("Seq1", "tttCAACCCGGGtttaaa");
379	1	SequenceI seq2 = new Sequence("Seq2", "QPG");
380	1	SequenceI seq2a = new Sequence("Seq2a", "QPG");
381	1	SequenceI seq1proxy = new SequenceDummy("Seq1");
382	1	seq1.createDatasetSequence();
383	1	seq2.createDatasetSequence();
384	1	seq2a.createDatasetSequence();
385
386		/*
387		* Make mappings from Seq2 and Seq2a peptides to dummy sequence Seq1
388		*/
389	1	AlignedCodonFrame acf = new AlignedCodonFrame();
390
391		// map PG to codons 7-12 (CCCGGG)
392	1	MapList mapping1 = new MapList(new int[] { 7, 12 }, new int[] { 2, 3 },
393		3, 1);
394	1	acf.addMap(seq1proxy, seq2, mapping1);
395	1	acf.addMap(seq1proxy, seq2a, mapping1);
396
397		// map QP to codons 4-9 (CAACCC)
398	1	MapList mapping2 = new MapList(new int[] { 4, 9 }, new int[] { 1, 2 },
399		3, 1);
400	1	acf.addMap(seq1proxy, seq2, mapping2);
401	1	acf.addMap(seq1proxy, seq2a, mapping2);
402
403		/*
404		* acf now has two mappings one from Seq1 to Seq2, one from Seq1 to Seq2a
405		*/
406	1	assertEquals(2, acf.getdnaSeqs().length);
407	1	assertSame(seq1proxy, acf.getdnaSeqs()[0]);
408	1	assertSame(seq1proxy, acf.getdnaSeqs()[1]);
409	1	assertEquals(2, acf.getProtMappings().length);
410
411		// 'realise' these mappings with the compatible sequence seq1
412		// two mappings should be updated:
413	1	assertEquals(2, acf.realiseWith(seq1));
414	1	assertSame(seq1.getDatasetSequence(), acf.getdnaSeqs()[0]);
415	1	assertSame(seq1.getDatasetSequence(), acf.getdnaSeqs()[1]);
416		}
417
418		/**
419		* Test the method that locates the mapped codon for a protein position.
420		*/
		100% Uncovered Elements: 0 (21) Complexity: 1 Complexity Density: 0.05 1PASS
421	1	@Test(groups = { "Functional" })...
422		public void testGetMappedRegion_eitherWay()
423		{
424	1	final Sequence seq1 = new Sequence("Seq1", "AAACCCGGGTTT");
425	1	seq1.createDatasetSequence();
426	1	final Sequence seq2 = new Sequence("Seq2", "KPGF");
427	1	seq2.createDatasetSequence();
428	1	final Sequence seq3 = new Sequence("Seq3", "QYKPGFSW");
429	1	seq3.createDatasetSequence();
430
431		/*
432		* map Seq1 to all of Seq2 and part of Seq3
433		*/
434	1	AlignedCodonFrame acf = new AlignedCodonFrame();
435	1	MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3,
436		1);
437	1	acf.addMap(seq1.getDatasetSequence(), seq2.getDatasetSequence(), map);
438	1	map = new MapList(new int[] { 1, 12 }, new int[] { 3, 6 }, 3, 1);
439	1	acf.addMap(seq1.getDatasetSequence(), seq3.getDatasetSequence(), map);
440
441		/*
442		* map part of Seq3 to Seq2
443		*/
444	1	map = new MapList(new int[] { 3, 6 }, new int[] { 1, 4 }, 1, 1);
445	1	acf.addMap(seq3.getDatasetSequence(), seq2.getDatasetSequence(), map);
446
447		/*
448		* original case - locate mapped codon for protein position
449		*/
450	1	assertArrayEquals(new int[] { 4, 6 },
451		acf.getMappedRegion(seq1, seq2, 2));
452	1	assertArrayEquals(new int[] { 7, 9 },
453		acf.getMappedRegion(seq1, seq3, 5));
454	1	assertNull(acf.getMappedRegion(seq1, seq3, 1));
455
456		/*
457		* locate mapped protein for protein position
458		*/
459	1	assertArrayEquals(new int[] { 4, 4 },
460		acf.getMappedRegion(seq3, seq2, 2));
461
462		/*
463		* reverse location protein-to-protein
464		*/
465	1	assertArrayEquals(new int[] { 2, 2 },
466		acf.getMappedRegion(seq2, seq3, 4));
467
468		/*
469		* reverse location protein-from-nucleotide
470		* any of codon [4, 5, 6] positions map to seq2/2
471		*/
472	1	assertArrayEquals(new int[] { 2, 2 },
473		acf.getMappedRegion(seq2, seq1, 4));
474	1	assertArrayEquals(new int[] { 2, 2 },
475		acf.getMappedRegion(seq2, seq1, 5));
476	1	assertArrayEquals(new int[] { 2, 2 },
477		acf.getMappedRegion(seq2, seq1, 6));
478		}
479
480		/**
481		* Tests for addMap. See also tests for MapList.addMapList
482		*/
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08 1PASS
483	1	@Test(groups = { "Functional" })...
484		public void testAddMap()
485		{
486	1	final Sequence seq1 = new Sequence("Seq1", "c-G-TA-gC-gT-T");
487	1	seq1.createDatasetSequence();
488	1	final Sequence aseq1 = new Sequence("Seq1", "-V-L");
489	1	aseq1.createDatasetSequence();
490
491	1	AlignedCodonFrame acf = new AlignedCodonFrame();
492	1	MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 },
493		new int[]
494		{ 1, 2 }, 3, 1);
495	1	acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
496	1	assertEquals(1, acf.getMappingsFromSequence(seq1).size());
497	1	Mapping before = acf.getMappingsFromSequence(seq1).get(0);
498
499		/*
500		* add the same map again, verify it doesn't get duplicated
501		*/
502	1	acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
503	1	assertEquals(1, acf.getMappingsFromSequence(seq1).size());
504	1	assertSame(before, acf.getMappingsFromSequence(seq1).get(0));
505		}
506
		100% Uncovered Elements: 0 (31) Complexity: 1 Complexity Density: 0.03 1PASS
507	1	@Test(groups = { "Functional" })...
508		public void testGetCoveringMapping()
509		{
510	1	SequenceI dna = new Sequence("dna", "acttcaATGGCGGACtaattt");
511	1	SequenceI cds = new Sequence("cds/7-15", "ATGGCGGAC");
512	1	cds.setDatasetSequence(dna);
513	1	SequenceI pep = new Sequence("pep", "MAD");
514
515		/*
516		* with null argument or no mappings
517		*/
518	1	AlignedCodonFrame acf = new AlignedCodonFrame();
519	1	assertNull(acf.getCoveringMapping(null, null));
520	1	assertNull(acf.getCoveringMapping(dna, null));
521	1	assertNull(acf.getCoveringMapping(null, pep));
522	1	assertNull(acf.getCoveringMapping(dna, pep));
523
524		/*
525		* with a non-covering mapping e.g. overlapping exon
526		*/
527	1	MapList map = new MapList(new int[] { 7, 9 }, new int[] { 1, 1 }, 3, 1);
528	1	acf.addMap(dna, pep, map);
529	1	assertNull(acf.getCoveringMapping(dna, pep));
530
531	1	acf = new AlignedCodonFrame();
532	1	MapList map2 = new MapList(new int[] { 13, 18 }, new int[] { 2, 2 }, 3,
533		1);
534	1	acf.addMap(dna, pep, map2);
535	1	assertNull(acf.getCoveringMapping(dna, pep));
536
537		/*
538		* with a covering mapping from CDS (dataset) to protein
539		*/
540	1	acf = new AlignedCodonFrame();
541	1	MapList map3 = new MapList(new int[] { 7, 15 }, new int[] { 1, 3 }, 3,
542		1);
543	1	acf.addMap(dna, pep, map3);
544	1	assertNull(acf.getCoveringMapping(dna, pep));
545	1	SequenceToSequenceMapping mapping = acf.getCoveringMapping(cds, pep);
546	1	assertNotNull(mapping);
547
548		/*
549		* with a mapping that extends to stop codon
550		*/
551	1	acf = new AlignedCodonFrame();
552	1	MapList map4 = new MapList(new int[] { 7, 18 }, new int[] { 1, 3 }, 3,
553		1);
554	1	acf.addMap(dna, pep, map4);
555	1	assertNull(acf.getCoveringMapping(dna, pep));
556	1	assertNull(acf.getCoveringMapping(cds, pep));
557	1	SequenceI cds2 = new Sequence("cds/7-18", "ATGGCGGACtaa");
558	1	cds2.setDatasetSequence(dna);
559	1	mapping = acf.getCoveringMapping(cds2, pep);
560	1	assertNotNull(mapping);
561		}
562
563		/**
564		* Test the method that adds mapped positions to SearchResults
565		*/
		100% Uncovered Elements: 0 (39) Complexity: 1 Complexity Density: 0.03 1PASS
566	1	@Test(groups = { "Functional" })...
567		public void testMarkMappedRegion()
568		{
569		// introns lower case, exons upper case
570	1	final Sequence dna1 = new Sequence("Seq1/10-18", "c-G-TA-gC-gT-T");
571	1	dna1.createDatasetSequence();
572	1	final Sequence dna2 = new Sequence("Seq2/20-28", "-TA-gG-Gg-CG-a");
573	1	dna2.createDatasetSequence();
574
575	1	final Sequence pep1 = new Sequence("Seq1/3-4", "-P-R");
576	1	pep1.createDatasetSequence();
577	1	final Sequence pep2 = new Sequence("Seq2/7-9", "-LY-Q");
578	1	pep2.createDatasetSequence();
579
580		/*
581		* First with no mappings
582		*/
583	1	AlignedCodonFrame acf = new AlignedCodonFrame();
584	1	SearchResults sr = new SearchResults();
585	1	acf.markMappedRegion(dna1, 12, sr);
586	1	assertTrue(sr.isEmpty());
587
588		/*
589		* Set up the mappings for the exons (upper-case bases)
590		* Note residue Q is unmapped
591		*/
592	1	MapList map1 = new MapList(new int[] { 11, 13, 15, 15, 17, 18 },
593		new int[]
594		{ 3, 4 }, 3, 1);
595	1	acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map1);
596	1	MapList map2 = new MapList(new int[] { 20, 21, 23, 24, 26, 27 },
597		new int[]
598		{ 7, 8 }, 3, 1);
599	1	acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map2);
600
601		/*
602		* intron bases are not mapped
603		*/
604	1	acf.markMappedRegion(dna1, 10, sr);
605	1	assertTrue(sr.isEmpty());
606
607		/*
608		* Q is not mapped
609		*/
610	1	acf.markMappedRegion(pep2, 9, sr);
611	1	assertTrue(sr.isEmpty());
612
613		/*
614		* mark peptide position for exon position (of aligned sequence)
615		*/
616	1	acf.markMappedRegion(dna1, 11, sr);
617	1	SearchResults expected = new SearchResults();
618	1	expected.addResult(pep1.getDatasetSequence(), 3, 3);
619	1	assertEquals(sr, expected);
620
621		/*
622		* mark peptide position for exon position of dataset sequence - same result
623		*/
624	1	sr = new SearchResults();
625	1	acf.markMappedRegion(dna1.getDatasetSequence(), 11, sr);
626	1	assertEquals(sr, expected);
627
628		/*
629		* marking the same position a second time should not create a duplicate match
630		*/
631	1	acf.markMappedRegion(dna1.getDatasetSequence(), 12, sr);
632	1	assertEquals(sr, expected);
633
634		/*
635		* mark exon positions for peptide position (of aligned sequence)
636		*/
637	1	sr = new SearchResults();
638	1	acf.markMappedRegion(pep2, 7, sr); // codon positions 20, 21, 23
639	1	expected = new SearchResults();
640	1	expected.addResult(dna2.getDatasetSequence(), 20, 21);
641	1	expected.addResult(dna2.getDatasetSequence(), 23, 23);
642	1	assertEquals(sr, expected);
643
644		/*
645		* add another codon to the same SearchResults
646		*/
647	1	acf.markMappedRegion(pep1.getDatasetSequence(), 4, sr); // codon positions
648		// 15, 17, 18
649	1	expected.addResult(dna1.getDatasetSequence(), 15, 15);
650	1	expected.addResult(dna1.getDatasetSequence(), 17, 18);
651	1	assertEquals(sr, expected);
652		}
653
		100% Uncovered Elements: 0 (34) Complexity: 1 Complexity Density: 0.03 1PASS
654	1	@Test(groups = { "Functional" })...
655		public void testGetCoveringCodonMapping()
656		{
657	1	SequenceI dna = new Sequence("dna/10-30", "acttcaATGGCGGACtaattt");
658		// CDS sequence with its own dataset sequence (JAL-3763)
659	1	SequenceI cds = new Sequence("cds/1-9", "-A--TGGC-GGAC");
660	1	cds.createDatasetSequence();
661	1	SequenceI pep = new Sequence("pep/1-3", "MAD");
662
663		/*
664		* with null argument or no mappings
665		*/
666	1	AlignedCodonFrame acf = new AlignedCodonFrame();
667	1	assertNull(acf.getCoveringCodonMapping(null));
668	1	assertNull(acf.getCoveringCodonMapping(dna));
669	1	assertNull(acf.getCoveringCodonMapping(pep));
670
671		/*
672		* with a non-covering mapping e.g. overlapping exon
673		*/
674	1	MapList map = new MapList(new int[] { 16, 18 }, new int[] { 1, 1 }, 3,
675		1);
676	1	acf.addMap(dna, pep, map);
677	1	assertNull(acf.getCoveringCodonMapping(dna));
678	1	assertNull(acf.getCoveringCodonMapping(pep));
679
680	1	acf = new AlignedCodonFrame();
681	1	MapList map2 = new MapList(new int[] { 13, 18 }, new int[] { 2, 2 }, 3,
682		1);
683	1	acf.addMap(dna, pep, map2);
684	1	assertNull(acf.getCoveringCodonMapping(dna));
685	1	assertNull(acf.getCoveringCodonMapping(pep));
686
687		/*
688		* with a covering mapping from CDS (dataset) to protein
689		*/
690	1	acf = new AlignedCodonFrame();
691	1	MapList map3 = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3,
692		1);
693	1	acf.addMap(cds.getDatasetSequence(), pep, map3);
694	1	assertNull(acf.getCoveringCodonMapping(dna));
695	1	SequenceToSequenceMapping mapping = acf.getCoveringCodonMapping(pep);
696	1	assertNotNull(mapping);
697	1	SequenceToSequenceMapping mapping2 = acf
698		.getCoveringCodonMapping(cds.getDatasetSequence());
699	1	assertSame(mapping, mapping2);
700
701		/*
702		* with a mapping that extends to stop codon
703		* (EMBL CDS location often includes the stop codon)
704		* - getCoveringCodonMapping is lenient (doesn't require exact length match)
705		*/
706	1	SequenceI cds2 = new Sequence("cds/1-12", "-A--TGGC-GGACTAA");
707	1	cds2.createDatasetSequence();
708	1	acf = new AlignedCodonFrame();
709	1	MapList map4 = new MapList(new int[] { 1, 12 }, new int[] { 1, 3 }, 3,
710		1);
711	1	acf.addMap(cds2, pep, map4);
712	1	mapping = acf.getCoveringCodonMapping(cds2.getDatasetSequence());
713	1	assertNotNull(mapping);
714	1	mapping2 = acf.getCoveringCodonMapping(pep);
715	1	assertSame(mapping, mapping2);
716		}
717		}