Class TestCasesIntervalTree
- java.lang.Object
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- org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree
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- Direct Known Subclasses:
TestCasesIntervalTreeArray
,TestCasesIntervalTreeOri
public class TestCasesIntervalTree extends java.lang.Object
Test case for interval tree structure
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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
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Constructor Summary
Constructors Constructor Description TestCasesIntervalTree()
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Method Summary
All Methods Instance Methods Concrete Methods 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 intervalsvoid
test_02()
Test large intervals
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Field Detail
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MAX_SMALL_MARKER_SIZE
public static int MAX_SMALL_MARKER_SIZE
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NUM_LARGE_INTERVALS
public static int NUM_LARGE_INTERVALS
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NUM_SMALL_INTERVALS
public static int NUM_SMALL_INTERVALS
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CHR_SIZE
public static int CHR_SIZE
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debug
protected boolean debug
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verbose
protected boolean verbose
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rand
protected java.util.Random rand
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genome
protected Genome genome
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chromosome
protected Chromosome chromosome
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markers
protected Markers markers
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Method Detail
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before
@BeforeEach public void before()
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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
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createRandomLargeMarkers
protected Markers createRandomLargeMarkers(Chromosome chr, int num)
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createRandomMarkers
protected Markers createRandomMarkers()
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createRandomSmallMarkers
protected Markers createRandomSmallMarkers(Chromosome chr, int num)
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queryNaive
protected Markers queryNaive(Marker query)
Naively find all intervals intersecting 'marker'
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test_01
@Test public void test_01()
Test small intervals
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test_02
@Test public void test_02()
Test large intervals
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