Package org.snpeff.snpEffect.testCases.unity

Class TestCasesDnaSequence

java.lang.Object

org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence

public class TestCasesDnaSequence
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field	Description
static boolean	verbose

Constructor Summary

Constructors

Constructor	Description
TestCasesDnaSequence()

Method Summary

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 DnaSequence
void	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 DnaAndQuality
void	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()

Methods inherited from class java.lang.Object

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

Field Detail

verbose

public static boolean verbose

Constructor Detail

TestCasesDnaSequence

public TestCasesDnaSequence()

Method Detail

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.

Parameters:

numTests -

lenMask -

seed -

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.

Parameters:

numTests -

lenMask -

seed -

randDnaSeqTest

public void randDnaSeqTest(int numTests,
                           int lenMask,
                           long seed)

Create random sequences and compare to storing them in a DnaSequence

Parameters:

numTests -

lenMask -

seed -

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.

Parameters:

numTests -

lenMask -

seed -

randTestQual

public void randTestQual(int numTests,
                         int lenMask,
                         long seed)

Create random sequences (and qualities) and compare to storing them in a DnaAndQuality

Parameters:

numTests -

lenMask -

seed -

test_01_short

public void test_01_short()

test_01_short_getBase

public void test_01_short_getBase()

test_01_short_getBases

public void test_01_short_getBases()

test_01_short_replaceBase

public void test_01_short_replaceBase()

test_02_long

public void test_02_long()

test_02_long_getBase

public void test_02_long_getBase()

test_02_long_getBases

public void test_02_long_getBases()

test_02_long_replaceBase

public void test_02_long_replaceBase()

test_04_Pe

public void test_04_Pe()

test_05_fastqReader

public void test_05_fastqReader()

test_05_quality_short

public void test_05_quality_short()

test_06_quality_long

public void test_06_quality_long()