Package org.snpeff.snpEffect.testCases.unity

Class TestCasesIntervals

java.lang.Object

org.snpeff.snpEffect.testCases.unity.TestCasesBase

org.snpeff.snpEffect.testCases.unity.TestCasesIntervals

public class TestCasesIntervals
extends TestCasesBase

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

Constructor Summary

Constructors

Constructor	Description
TestCasesIntervals()

Method Summary

Modifier and Type	Method	Description
void	compareToFile(java.lang.String result, java.lang.String fileName)	Compare a string and a file.
void	DnaSequenceBaseAt(int len)	Tests 'baseAt' method in DnaSequence
protected void	initRand()
Markers	intersects(Markers interval1, Marker intervals)
Markers	randomIntervals(int numIntervals, int maxStart, int maxLength, int numChromo)	Create a random set of intervals
void	test_00()
void	test_01()	Read file
void	test_02()	Sort test
void	test_03()	Sort (by end) test
void	test_04()	Merge intervals
void	test_05()	Adding intervals
void	test_06()	Intersect of 2 intervals We have 2 implementation (brute force and interval trees), so we can compare them.
void	test_07_01()	Minus operation for intervals
void	test_07_02()	Minus operation for intervals
void	test_07_03()	Minus operation for intervals
void	test_07_04()	Minus operation for intervals
void	test_07_05()	Minus operation for intervals
void	test_08()	Test distance (in bases) from a list of markers
void	test_08_02()	Test distance (in bases) from a list of markers
void	test_08_03()	Test distance (in bases) from a list of markers
void	test_09_chrOrder()
void	test_10_chrOrder()

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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

TestCasesIntervals

public TestCasesIntervals()

Method Detail

compareToFile

public void compareToFile(java.lang.String result,
                          java.lang.String fileName)

Compare a string and a file. Throw an exception if they don't match

Parameters:

result -

fileName -

DnaSequenceBaseAt

public void DnaSequenceBaseAt(int len)

Tests 'baseAt' method in DnaSequence

initRand

protected void initRand()

Overrides:

initRand in class TestCasesBase

intersects

public Markers intersects(Markers interval1,
                          Marker intervals)

randomIntervals

public Markers randomIntervals(int numIntervals,
                               int maxStart,
                               int maxLength,
                               int numChromo)

Create a random set of intervals

Parameters:

numIntervals -

maxStart -

maxLength -

Returns:

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()