Class TestCasesDnaSequence
- java.lang.Object
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- org.snpeff.snpEffect.testCases.unity.TestCasesBase
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- org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence
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public class TestCasesDnaSequence extends TestCasesBase
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Field Summary
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Fields inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase
addUtrs, BASE_DIR, chromoBases, chromoSequence, chromosome, codonTable, config, debug, gene, genome, genomeName, maxExons, maxGeneLen, maxTranscripts, minExons, numGenes, onlyMinusStrand, onlyPlusStrand, prefixes, rand, randSeed, shiftHgvs, snpEffectPredictor, spliceRegionExonSize, spliceRegionIntronMax, spliceRegionIntronMin, testType, transcript, verbose
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Constructor Summary
Constructors Constructor Description TestCasesDnaSequence()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
randDnaSeqGetBasesTest(int numTests, int numTestsPerSeq, int lenMask, long seed)
Create random sequences and store them in a DnaSequence.void
randDnaSeqGetBaseTest(int numTests, int numTestsPerSeq, int lenMask, long seed)
Create random sequences and store them in a DnaSequence.void
randDnaSeqTest(int numTests, int lenMask, long seed)
Create random sequences and compare to storing them in a DnaSequencevoid
randReplaceBaseTest(int numTests, int numTestsPerSeq, int lenMask, long seed)
Create random sequences and store them in a DnaSequence.void
randTestQual(int numTests, int lenMask, long seed)
Create random sequences (and qualities) and compare to storing them in a DnaAndQualityvoid
test_01_short()
void
test_01_short_getBase()
void
test_01_short_getBases()
void
test_01_short_replaceBase()
void
test_02_long()
void
test_02_long_getBase()
void
test_02_long_getBases()
void
test_02_long_replaceBase()
void
test_04_Pe()
void
test_05_fastqReader()
void
test_05_quality_short()
void
test_06_quality_long()
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Methods inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase
after, before, checkApply, checkApplyDel, checkApplyIns, checkApplyMixed, checkApplyMnp, checkApplySnp, checkEffect, checkEffect, formatVersion, hasEffect, init, initRand, initSnpEffPredictor, initSnpEffPredictor, path, pathClassName, prependSequenceToFirstExon
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Method Detail
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randDnaSeqGetBasesTest
public void randDnaSeqGetBasesTest(int numTests, int numTestsPerSeq, int lenMask, long seed)
Create random sequences and store them in a DnaSequence. Compare getting a few random bases from the original and DnaSequence sequences.
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randDnaSeqGetBaseTest
public void randDnaSeqGetBaseTest(int numTests, int numTestsPerSeq, int lenMask, long seed)
Create random sequences and store them in a DnaSequence. Compare getting a single random base from the original and DnaSequence sequences.
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randDnaSeqTest
public void randDnaSeqTest(int numTests, int lenMask, long seed)
Create random sequences and compare to storing them in a DnaSequence
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randReplaceBaseTest
public void randReplaceBaseTest(int numTests, int numTestsPerSeq, int lenMask, long seed)
Create random sequences and store them in a DnaSequence. Compare after replacing random bases from the original and DnaSequence sequences.
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randTestQual
public void randTestQual(int numTests, int lenMask, long seed)
Create random sequences (and qualities) and compare to storing them in a DnaAndQuality
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test_01_short
@Test public void test_01_short()
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test_01_short_getBase
@Test public void test_01_short_getBase()
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test_01_short_getBases
@Test public void test_01_short_getBases()
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test_01_short_replaceBase
@Test public void test_01_short_replaceBase()
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test_02_long
@Test public void test_02_long()
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test_02_long_getBase
@Test public void test_02_long_getBase()
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test_02_long_getBases
@Test public void test_02_long_getBases()
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test_02_long_replaceBase
@Test public void test_02_long_replaceBase()
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test_04_Pe
@Test public void test_04_Pe()
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test_05_fastqReader
@Test public void test_05_fastqReader()
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test_05_quality_short
@Test public void test_05_quality_short()
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test_06_quality_long
@Test public void test_06_quality_long()
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