Class TestCasesIntervalTree
java.lang.Object
org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree
- Direct Known Subclasses:
TestCasesIntervalTreeArray
,TestCasesIntervalTreeOri
Test case for interval tree structure
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic int
protected Chromosome
protected boolean
protected Genome
protected Markers
static int
static int
static int
protected Random
protected boolean
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
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
protected Markers
createRandomSmallMarkers
(Chromosome chr, int num) protected Itree
protected Markers
queryNaive
(Marker query) Naively find all intervals intersecting 'marker'void
test_01()
Test small intervalsvoid
test_02()
Test large intervals
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Field Details
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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
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genome
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chromosome
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markers
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Constructor Details
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TestCasesIntervalTree
public TestCasesIntervalTree()
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Method Details
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before
@BeforeEach public void before() -
compareQuery
Perform a query using 'naive' lookup and interval forest. Compare results and throw an exception if any difference exists -
createRandomLargeMarkers
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createRandomMarkers
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createRandomSmallMarkers
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newItree
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queryNaive
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
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