Package org.snpeff.snpEffect.testCases.unity

Class TestCasesIntervalTree

java.lang.Object

org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree

Direct Known Subclasses:

TestCasesIntervalTreeArray, TestCasesIntervalTreeOri

public class TestCasesIntervalTree
extends java.lang.Object

Test case for interval tree structure

Field Summary

Fields

Modifier and Type	Field	Description
static int	CHR_SIZE
protected Chromosome	chromosome
protected boolean	debug
protected Genome	genome
protected Markers	markers
static int	MAX_SMALL_MARKER_SIZE
static int	NUM_LARGE_INTERVALS
static int	NUM_SMALL_INTERVALS
protected java.util.Random	rand
protected boolean	verbose

Constructor Summary

Constructors

Constructor	Description
TestCasesIntervalTree()

Method Summary

Modifier and Type	Method	Description
void	before()
protected int	compareQuery(Marker m, Itree intTree)	Perform a query using 'naive' lookup and interval forest.
protected Markers	createRandomLargeMarkers(Chromosome chr, int num)
protected Markers	createRandomMarkers()
protected Markers	createRandomSmallMarkers(Chromosome chr, int num)
protected Itree	newItree(Markers markers)
protected Markers	queryNaive(Marker query)	Naively find all intervals intersecting 'marker'
void	test_01()	Test small intervals
void	test_02()	Test large intervals

Methods inherited from class java.lang.Object

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

Field Detail

MAX_SMALL_MARKER_SIZE

public static int MAX_SMALL_MARKER_SIZE

NUM_LARGE_INTERVALS

public static int NUM_LARGE_INTERVALS

NUM_SMALL_INTERVALS

public static int NUM_SMALL_INTERVALS

CHR_SIZE

public static int CHR_SIZE

debug

protected boolean debug

verbose

protected boolean verbose

rand

protected java.util.Random rand

genome

protected Genome genome

chromosome

protected Chromosome chromosome

markers

protected Markers markers

Constructor Detail

TestCasesIntervalTree

public TestCasesIntervalTree()

Method Detail

before

@BeforeEach
public void before()

compareQuery

protected int compareQuery(Marker m,
                           Itree intTree)

Perform a query using 'naive' lookup and interval forest. Compare results and throw an exception if any difference exists

createRandomLargeMarkers

protected Markers createRandomLargeMarkers(Chromosome chr,
                                           int num)

createRandomMarkers

protected Markers createRandomMarkers()

createRandomSmallMarkers

protected Markers createRandomSmallMarkers(Chromosome chr,
                                           int num)

newItree

protected Itree newItree(Markers markers)

queryNaive

protected Markers queryNaive(Marker query)

Naively find all intervals intersecting 'marker'

test_01

@Test
public void test_01()

Test small intervals

test_02

@Test
public void test_02()

Test large intervals