File ExonerateHelperTest.java

Branches:

Statements:

126

Methods:

Classes:

LOC:

323

NCLOC:

210

Total complexity:

Complexity density:

0.06

Statements/Method:

Methods/Class:

Average method complexity:

Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ExonerateHelperTest	51	126	7	1.0100%

Class ExonerateHelperTest

Class ExonerateHelperTest	Line # 51	Total Statements 126	Complexity 7	TOTAL Coverage 1.0100%
setUpJvOptionPane() : void setUpJvOptionPane() : void	5454	2.02	1.01	1.0 1.0100%
testGetMappingType() : void testGetMappingType() : void	6161	7.07	1.01	1.0 1.0100%
testProcessGffSimilarity_protein2dna_forward_querygff() : void testProcessGffSimilarity_protein2dna_forward_querygff() : void	9090	22.022	1.01	1.0 1.0100%
testProcessGffSimilarity_protein2dna_reverse_querygff() : void testProcessGffSimilarity_protein2dna_reverse_querygff() : void	133133	22.022	1.01	1.0 1.0100%
testProcessGffSimilarity_protein2dna_forward_targetgff() : void testProcessGffSimilarity_protein2dna_forward_targetgff() : void	176176	22.022	1.01	1.0 1.0100%
testProcessGffSimilarity_protein2dna_reverse_targetgff() : void testProcessGffSimilarity_protein2dna_reverse_targetgff() : void	222222	22.022	1.01	1.0 1.0100%
testAddExonerateGffToAlignment() : void testAddExonerateGffToAlignment() : void	265265	29.029	1.01	1.0 1.0100%

Contributing tests

This file is covered by 6 tests. .

Contributing tests

Test contribution	Test	Result
0.22556391	jalview.io.gff.ExonerateHelperTest.testAddExonerateGffToAlignmentjalview.io.gff.ExonerateHelperTest.testAddExonerateGffToAlignment	1PASS
0.17293233	jalview.io.gff.ExonerateHelperTest.testProcessGffSimilarity_protein2dna_reverse_targetgffjalview.io.gff.ExonerateHelperTest.testProcessGffSimilarity_protein2dna_reverse_targetgff	1PASS
0.17293233	jalview.io.gff.ExonerateHelperTest.testProcessGffSimilarity_protein2dna_forward_querygffjalview.io.gff.ExonerateHelperTest.testProcessGffSimilarity_protein2dna_forward_querygff	1PASS
0.17293233	jalview.io.gff.ExonerateHelperTest.testProcessGffSimilarity_protein2dna_forward_targetgffjalview.io.gff.ExonerateHelperTest.testProcessGffSimilarity_protein2dna_forward_targetgff	1PASS
0.17293233	jalview.io.gff.ExonerateHelperTest.testProcessGffSimilarity_protein2dna_reverse_querygffjalview.io.gff.ExonerateHelperTest.testProcessGffSimilarity_protein2dna_reverse_querygff	1PASS
0.060150377	jalview.io.gff.ExonerateHelperTest.testGetMappingTypejalview.io.gff.ExonerateHelperTest.testGetMappingType	1PASS

Source view

* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)

* Copyright (C) $$Year-Rel$$ The Jalview Authors

* This file is part of Jalview.

* Jalview is free software: you can redistribute it and/or

* modify it under the terms of the GNU General Public License

* as published by the Free Software Foundation, either version 3

* of the License, or (at your option) any later version.

* Jalview is distributed in the hope that it will be useful, but

* WITHOUT ANY WARRANTY; without even the implied warranty

* of MERCHANTABILITY or FITNESS FOR A PARTICULAR

* PURPOSE. See the GNU General Public License for more details.

* You should have received a copy of the GNU General Public License

* along with Jalview. If not, see <http://www.gnu.org/licenses/>.

* The Jalview Authors are detailed in the 'AUTHORS' file.

package jalview.io.gff;

import static org.testng.AssertJUnit.assertEquals;

import static org.testng.AssertJUnit.assertNull;

import static org.testng.AssertJUnit.assertSame;

import static org.testng.AssertJUnit.assertTrue;

import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;

import jalview.datamodel.AlignedCodonFrame;

import jalview.datamodel.Alignment;

import jalview.datamodel.AlignmentI;

import jalview.datamodel.Mapping;

import jalview.datamodel.MappingType;

import jalview.datamodel.Sequence;

import jalview.datamodel.SequenceDummy;

import jalview.datamodel.SequenceI;

import jalview.gui.AlignFrame;

import jalview.gui.JvOptionPane;

import jalview.io.DataSourceType;

import jalview.io.FileLoader;

import java.io.IOException;

import java.util.ArrayList;

import java.util.Iterator;

import java.util.List;

import java.util.Map;

import org.testng.annotations.BeforeClass;

import org.testng.annotations.Test;

public class ExonerateHelperTest

{

@BeforeClass(alwaysRun = true)

public void setUpJvOptionPane()

{

JvOptionPane.setInteractiveMode(false);

JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);

}

@Test(groups = "Functional")

public void testGetMappingType()

{

// protein-to-dna:

assertSame(MappingType.PeptideToNucleotide, ExonerateHelper

.getMappingType("exonerate:protein2genome:local"));

assertSame(MappingType.PeptideToNucleotide,

ExonerateHelper.getMappingType("exonerate:protein2dna:local"));

// dna-to-dna:

assertSame(MappingType.NucleotideToNucleotide,

ExonerateHelper.getMappingType("coding2coding"));

assertSame(MappingType.NucleotideToNucleotide,

ExonerateHelper.getMappingType("coding2genome"));

assertSame(MappingType.NucleotideToNucleotide,

ExonerateHelper.getMappingType("cdna2genome"));

assertSame(MappingType.NucleotideToNucleotide,

ExonerateHelper.getMappingType("genome2genome"));

assertNull(ExonerateHelper.getMappingType("affine:local"));

}

/**

* Test processing one exonerate GFF line for the case where the mapping is

* protein2dna, similarity feature is on the query (the protein), match to the

* forward strand, target sequence is in neither the alignment nor the 'new

* sequences'

* @throws IOException

@Test(groups = "Functional")

public void testProcessGffSimilarity_protein2dna_forward_querygff()

throws IOException

{

ExonerateHelper testee = new ExonerateHelper();

List<SequenceI> newseqs = new ArrayList<SequenceI>();

String[] gff = "Seq\texonerate:protein2dna:local\tsimilarity\t3\t10\t.\t+\t.\talignment_id 0 ; Target dna1 ; Align 3 400 8"

.split("\\t");

SequenceI seq = new Sequence("Seq", "PQRASTGKEEDVMIWCHQN");

seq.createDatasetSequence();

100

AlignmentI align = new Alignment(new SequenceI[] {});

101

Map<String, List<String>> set = Gff2Helper.parseNameValuePairs(gff[8]);

102

103

104

* this should create a mapping from Seq2/3-10 to virtual sequence

105

* dna1 (added to newseqs) positions 400-423

106

107

testee.processGffSimilarity(set, seq, gff, align, newseqs, false);

108

assertEquals(1, newseqs.size());

109

assertTrue(newseqs.get(0) instanceof SequenceDummy);

110

assertEquals("dna1", newseqs.get(0).getName());

111

assertEquals(1, align.getCodonFrames().size());

112

AlignedCodonFrame mapping = align.getCodonFrames().iterator().next();

113

assertEquals(1, mapping.getAaSeqs().length);

114

assertSame(seq.getDatasetSequence(), mapping.getAaSeqs()[0]);

115

assertEquals(1, mapping.getdnaSeqs().length);

116

assertSame(newseqs.get(0), mapping.getdnaSeqs()[0]);

117

assertEquals(1, mapping.getdnaToProt().length);

118

assertEquals(1, mapping.getdnaToProt()[0].getFromRanges().size());

119

assertArrayEquals(new int[] { 400, 423 },

120

mapping.getdnaToProt()[0].getFromRanges().get(0));

121

assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());

122

assertArrayEquals(new int[] { 3, 10 },

123

mapping.getdnaToProt()[0].getToRanges().get(0));

}

/**

* Test processing one exonerate GFF line for the case where the mapping is

128

* protein2dna, similarity feature is on the query (the protein), match to the

129

* reverse strand

130

131

* @throws IOException

132

133

@Test(groups = "Functional")

134

public void testProcessGffSimilarity_protein2dna_reverse_querygff()

135

throws IOException

136

{

137

ExonerateHelper testee = new ExonerateHelper();

138

List<SequenceI> newseqs = new ArrayList<SequenceI>();

139

String[] gff = "Seq\texonerate:protein2dna:local\tsimilarity\t3\t10\t0\t-\t.\talignment_id 0 ; Target dna1 ; Align 3 400 8"

140

.split("\\t");

141

SequenceI seq = new Sequence("Seq", "PQRASTGKEEDVMIWCHQN");

142

seq.createDatasetSequence();

143

AlignmentI align = new Alignment(new SequenceI[] {});

144

Map<String, List<String>> set = Gff2Helper.parseNameValuePairs(gff[8]);

145

146

147

* this should create a mapping from Seq2/3-10 to virtual sequence

148

* dna1 (added to newseqs) positions 400-377 (reverse)

149

150

testee.processGffSimilarity(set, seq, gff, align, newseqs, false);

151

assertEquals(1, newseqs.size());

152

assertTrue(newseqs.get(0) instanceof SequenceDummy);

153

assertEquals("dna1", newseqs.get(0).getName());

154

assertEquals(1, align.getCodonFrames().size());

155

AlignedCodonFrame mapping = align.getCodonFrames().iterator().next();

156

assertEquals(1, mapping.getAaSeqs().length);

157

assertSame(seq.getDatasetSequence(), mapping.getAaSeqs()[0]);

158

assertEquals(1, mapping.getdnaSeqs().length);

159

assertSame(newseqs.get(0), mapping.getdnaSeqs()[0]);

160

assertEquals(1, mapping.getdnaToProt().length);

161

assertEquals(1, mapping.getdnaToProt()[0].getFromRanges().size());

162

assertArrayEquals(new int[] { 400, 377 },

163

mapping.getdnaToProt()[0].getFromRanges().get(0));

164

assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());

165

assertArrayEquals(new int[] { 3, 10 },

166

mapping.getdnaToProt()[0].getToRanges().get(0));

}

/**

* Test processing one exonerate GFF line for the case where the mapping is

171

* protein2dna, similarity feature is on the target (the dna), match to the

172

* forward strand

173

174

* @throws IOException

175

176

@Test(groups = "Functional")

177

public void testProcessGffSimilarity_protein2dna_forward_targetgff()

178

throws IOException

179

{

180

ExonerateHelper testee = new ExonerateHelper();

181

List<SequenceI> newseqs = new ArrayList<SequenceI>();

182

String[] gff = "dna1\texonerate:protein2dna:local\tsimilarity\t400\t423\t0\t+\t.\talignment_id 0 ; Query Prot1 ; Align 400 3 24"

183

.split("\\t");

184

SequenceI seq = new Sequence("dna1/391-430",

185

"CGATCCGATCCGATCCGATCCGATCCGATCCGATCCGATC");

186

seq.createDatasetSequence();

187

AlignmentI align = new Alignment(new SequenceI[] { seq });

188

// GFF feature on the target describes mapping from base 400 for

189

// count 24 to position 3

190

Map<String, List<String>> set = Gff2Helper.parseNameValuePairs(gff[8]);

191

192

193

* this should create a mapping from virtual sequence dna1 (added to

194

* newseqs) positions 400-423 to Prot1/3-10

195

196

testee.processGffSimilarity(set, seq, gff, align, newseqs, false);

197

assertEquals(1, newseqs.size());

198

assertTrue(newseqs.get(0) instanceof SequenceDummy);

199

assertEquals("Prot1", newseqs.get(0).getName());

200

assertEquals(1, align.getCodonFrames().size());

201

AlignedCodonFrame mapping = align.getCodonFrames().iterator().next();

202

assertEquals(1, mapping.getAaSeqs().length);

203

assertSame(newseqs.get(0), mapping.getAaSeqs()[0]);

204

assertSame(seq.getDatasetSequence(), mapping.getdnaSeqs()[0]);

205

assertEquals(1, mapping.getdnaSeqs().length);

206

assertEquals(1, mapping.getdnaToProt().length);

207

assertEquals(1, mapping.getdnaToProt()[0].getFromRanges().size());

208

assertArrayEquals(new int[] { 400, 423 },

209

mapping.getdnaToProt()[0].getFromRanges().get(0));

210

assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());

211

assertArrayEquals(new int[] { 3, 10 },

212

mapping.getdnaToProt()[0].getToRanges().get(0));

}

/**

* Test processing one exonerate GFF line for the case where the mapping is

217

* protein2dna, similarity feature is on the target (the dna), match to the

218

* reverse strand

219

220

* @throws IOException

221

222

@Test(groups = "Functional")

223

public void testProcessGffSimilarity_protein2dna_reverse_targetgff()

224

throws IOException

225

{

226

ExonerateHelper testee = new ExonerateHelper();

227

List<SequenceI> newseqs = new ArrayList<SequenceI>();

228

String[] gff = "dna1\texonerate:protein2dna:local\tsimilarity\t377\t400\t0\t-\t.\talignment_id 0 ; Query Prot1 ; Align 400 3 24"

229

.split("\\t");

230

SequenceI seq = new Sequence("dna1/371-410",

231

"CGATCCGATCCGATCCGATCCGATCCGATCCGATCCGATC");

232

seq.createDatasetSequence();

233

AlignmentI align = new Alignment(new SequenceI[] { seq });

234

// GFF feature on the target describes mapping from base 400 for

235

// count 24 to position 3

236

Map<String, List<String>> set = Gff2Helper.parseNameValuePairs(gff[8]);

237

238

239

* this should create a mapping from virtual sequence dna1 (added to

240

* newseqs) positions 400-377 (reverse) to Prot1/3-10

241

242

testee.processGffSimilarity(set, seq, gff, align, newseqs, false);

243

assertEquals(1, newseqs.size());

244

assertTrue(newseqs.get(0) instanceof SequenceDummy);

245

assertEquals("Prot1", newseqs.get(0).getName());

246

assertEquals(1, align.getCodonFrames().size());

247

AlignedCodonFrame mapping = align.getCodonFrames().iterator().next();

248

assertEquals(1, mapping.getAaSeqs().length);

249

assertSame(newseqs.get(0), mapping.getAaSeqs()[0]);

250

assertSame(seq.getDatasetSequence(), mapping.getdnaSeqs()[0]);

251

assertEquals(1, mapping.getdnaSeqs().length);

252

assertEquals(1, mapping.getdnaToProt().length);

253

assertEquals(1, mapping.getdnaToProt()[0].getFromRanges().size());

254

assertArrayEquals(new int[] { 400, 377 },

255

mapping.getdnaToProt()[0].getFromRanges().get(0));

256

assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());

257

assertArrayEquals(new int[] { 3, 10 },

258

mapping.getdnaToProt()[0].getToRanges().get(0));

}

/**

* Tests loading exonerate GFF2 output, including 'similarity' alignment

263

* feature, on to sequences

264

265

@Test(groups = { "Functional" })

266

public void testAddExonerateGffToAlignment()

267

{

268

FileLoader loader = new FileLoader(false);

269

AlignFrame af = loader.LoadFileWaitTillLoaded(

270

"examples/testdata/exonerateseqs.fa", DataSourceType.FILE);

271

272

af.loadJalviewDataFile("examples/testdata/exonerateoutput.gff",

273

DataSourceType.FILE, null, null);

274

275

276

* verify one mapping to a dummy sequence, one to a real one

277

278

List<AlignedCodonFrame> mappings = af.getViewport().getAlignment()

279

.getDataset().getCodonFrames();

280

assertEquals(2, mappings.size());

281

Iterator<AlignedCodonFrame> iter = mappings.iterator();

282

283

// first mapping is to dummy sequence

284

AlignedCodonFrame mapping = iter.next();

285

Mapping[] mapList = mapping.getProtMappings();

286

assertEquals(1, mapList.length);

287

assertTrue(mapList[0].getTo() instanceof SequenceDummy);

288

assertEquals("DDB_G0269124", mapList[0].getTo().getName());

289

290

// 143 in protein should map to codon [11270, 11269, 11268] in dna

291

int[] mappedRegion = mapList[0].getMap().locateInFrom(143, 143);

292

assertArrayEquals(new int[] { 11270, 11268 }, mappedRegion);

293

294

// second mapping is to a sequence in the alignment

295

mapping = iter.next();

296

mapList = mapping.getProtMappings();

297

assertEquals(1, mapList.length);

298

SequenceI proteinSeq = af.getViewport().getAlignment()

299

.findName("DDB_G0280897");

300

assertSame(proteinSeq.getDatasetSequence(), mapList[0].getTo());

301

assertEquals(1, mapping.getdnaToProt().length);

302

303

// 143 in protein should map to codon [11270, 11269, 11268] in dna

304

mappedRegion = mapList[0].getMap().locateInFrom(143, 143);

305

assertArrayEquals(new int[] { 11270, 11268 }, mappedRegion);

306

307

// 182 in protein should map to codon [11153, 11152, 11151] in dna

308

mappedRegion = mapList[0].getMap().locateInFrom(182, 182);

309

assertArrayEquals(new int[] { 11153, 11151 }, mappedRegion);

310

311

// and the reverse mapping:

312

mappedRegion = mapList[0].getMap().locateInTo(11151, 11153);

313

assertArrayEquals(new int[] { 182, 182 }, mappedRegion);

314

315

// 11150 in dna should _not_ map to protein

316

mappedRegion = mapList[0].getMap().locateInTo(11150, 11150);

317

assertNull(mappedRegion);

318

319

// similarly 183 in protein should _not_ map to dna

320

mappedRegion = mapList[0].getMap().locateInFrom(183, 183);

321

assertNull(mappedRegion);

322

}

323

}

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File ExonerateHelperTest.java

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