Class TestCasesSequenceIndexer
java.lang.Object
org.snpeff.snpEffect.testCases.unity.TestCasesBase
org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer
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Field Summary
FieldsFields 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 -
Method Summary
Modifier and TypeMethodDescriptionvoid
test_01()
Sequence comparison testvoid
test_02()
Sequence ordering testvoid
test_03()
Sequence indexer test (add sequences)void
test_04()
Sequence indexer test (overlap sequences)void
test_05()
Sequence indexer test (trivial assembly)void
test_06()
'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA' bug Sequences with nmers '0' were not being indexedvoid
test_07()
Sequence length = Nmer size (bug) Sequences with same length as nmers were not being indexed properlyvoid
test_08()
Sequence "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa" + "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaac"void
test_09()
Sequence "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa" + "caaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa"void
test_10()
Sequence "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa" + "caaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaag"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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Field Details
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NMER_SIZE
public static final int NMER_SIZE- See Also:
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NUMBER_OF_COMPARISSONS
public static int NUMBER_OF_COMPARISSONS
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Constructor Details
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TestCasesSequenceIndexer
public TestCasesSequenceIndexer()
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Method Details
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test_01
@Test public void test_01()Sequence comparison test -
test_02
@Test public void test_02()Sequence ordering test -
test_03
@Test public void test_03()Sequence indexer test (add sequences) -
test_04
@Test public void test_04()Sequence indexer test (overlap sequences) -
test_05
@Test public void test_05()Sequence indexer test (trivial assembly) -
test_06
@Test public void test_06()'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA' bug Sequences with nmers '0' were not being indexed -
test_07
@Test public void test_07()Sequence length = Nmer size (bug) Sequences with same length as nmers were not being indexed properly -
test_08
@Test public void test_08()Sequence "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa" + "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaac" -
test_09
@Test public void test_09()Sequence "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa" + "caaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa" -
test_10
@Test public void test_10()Sequence "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa" + "caaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaag"
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