Class TestCasesIntegrationBuildPdb
java.lang.Object
org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBuildPdb
Test cases for annotation of protein interaction loci
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Field Summary
Fields inherited from class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
BASE_DIR, debug, ignoreErrors, prefixes, shiftHgvs, SHOW_EVERY, testsDir, testType, verbose
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
test_01()
Interaction within protein using PDB entry '1A12'void
test_02()
Interaction between two proteins PDB entry 4OVU should have an interaction between chains 'A' and 'B' (Min distance :2.45 Angstrom) AA.pos AA chr:pos transcript 22 E 3:178916679 NM_006218.2 533 R 5:67591006 NM_181523.2Methods inherited from class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
applyTranscript, before, build, buildAndCompare, buildEmbl, buildGeneBank, buildGeneBank, buildGetBuildCmd, buildGff3AndCompare, buildGtfAndCompare, checkHgvs, checkNoChange, checkTranscriptError, compareHgvs, compareHgvs, compareVep, compareVepSO, init, loadSnpEffectPredictor, path, pathClassName, pathMigrate, showTranscripts, showTranscripts, snpEffect, snpEffect, snpEffectCancer
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Constructor Details
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TestCasesIntegrationBuildPdb
public TestCasesIntegrationBuildPdb()
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Method Details
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test_01
@Test public void test_01()Interaction within protein using PDB entry '1A12' -
test_02
@Test public void test_02()Interaction between two proteins PDB entry 4OVU should have an interaction between chains 'A' and 'B' (Min distance :2.45 Angstrom) AA.pos AA chr:pos transcript 22 E 3:178916679 NM_006218.2 533 R 5:67591006 NM_181523.2
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