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 Object
Test case for interval tree structure

  • Field Details

    • 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 Random rand

    • genome

      protected Genome genome

    • chromosome

      protected Chromosome chromosome

    • markers

      protected Markers markers

  • Constructor Details

    • TestCasesIntervalTree

      public TestCasesIntervalTree()

  • Method Details

    • 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