Class TestCasesIntervals
java.lang.Object
org.snpeff.snpEffect.testCases.unity.TestCasesBase
org.snpeff.snpEffect.testCases.unity.TestCasesIntervals
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Field Summary
Fields inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase
addUtrs, BASE_DIR, chromoBases, chromoSequence, chromosome, codonTable, config, debug, gene, 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
compareToFile
(String result, String fileName) Compare a string and a file.void
DnaSequenceBaseAt
(int len) Tests 'baseAt' method in DnaSequenceprotected void
initRand()
intersects
(Markers interval1, Marker intervals) randomIntervals
(int numIntervals, int maxStart, int maxLength, int numChromo) Create a random set of intervalsvoid
test_00()
void
test_01()
Read filevoid
test_02()
Sort testvoid
test_03()
Sort (by end) testvoid
test_04()
Merge intervalsvoid
test_05()
Adding intervalsvoid
test_06()
Intersect of 2 intervals We have 2 implementation (brute force and interval trees), so we can compare them.void
Minus operation for intervalsvoid
Minus operation for intervalsvoid
Minus operation for intervalsvoid
Minus operation for intervalsvoid
Minus operation for intervalsvoid
test_08()
Test distance (in bases) from a list of markersvoid
Test distance (in bases) from a list of markersvoid
Test distance (in bases) from a list of markersvoid
void
Methods inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase
after, before, checkApply, checkApplyDel, checkApplyIns, checkApplyMixed, checkApplyMnp, checkApplySnp, checkEffect, checkEffect, formatVersion, hasEffect, init, initSnpEffPredictor, initSnpEffPredictor, path, pathClassName, prependSequenceToFirstExon
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Constructor Details
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TestCasesIntervals
public TestCasesIntervals()
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Method Details
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compareToFile
Compare a string and a file. Throw an exception if they don't match- Parameters:
result
-fileName
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DnaSequenceBaseAt
public void DnaSequenceBaseAt(int len) Tests 'baseAt' method in DnaSequence -
initRand
protected void initRand()- Overrides:
initRand
in classTestCasesBase
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intersects
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randomIntervals
Create a random set of intervals- Parameters:
numIntervals
-maxStart
-maxLength
-- Returns:
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test_00
@Test public void test_00() -
test_01
@Test public void test_01()Read file -
test_02
@Test public void test_02()Sort test -
test_03
@Test public void test_03()Sort (by end) test -
test_04
@Test public void test_04()Merge intervals -
test_05
@Test public void test_05()Adding intervals -
test_06
@Test public void test_06()Intersect of 2 intervals We have 2 implementation (brute force and interval trees), so we can compare them. -
test_07_01
@Test public void test_07_01()Minus operation for intervals -
test_07_02
@Test public void test_07_02()Minus operation for intervals -
test_07_03
@Test public void test_07_03()Minus operation for intervals -
test_07_04
@Test public void test_07_04()Minus operation for intervals -
test_07_05
@Test public void test_07_05()Minus operation for intervals -
test_08
@Test public void test_08()Test distance (in bases) from a list of markers -
test_08_02
@Test public void test_08_02()Test distance (in bases) from a list of markers -
test_08_03
@Test public void test_08_03()Test distance (in bases) from a list of markers -
test_09_chrOrder
@Test public void test_09_chrOrder() -
test_10_chrOrder
@Test public void test_10_chrOrder()
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