Class TestCasesIntervalTree

    • 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
      • 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)
      • 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