Package org.snpeff.snpEffect.testCases.unity

Class TestCasesSequenceIndexer

java.lang.Object
org.snpeff.snpEffect.testCases.unity.TestCasesBase
org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer
public class TestCasesSequenceIndexer extends TestCasesBase

  • Field Details

    • NMER_SIZE

      public static final int NMER_SIZE
      See Also:

    • NUMBER_OF_COMPARISSONS

      public static int NUMBER_OF_COMPARISSONS

  • Constructor Details

    • TestCasesSequenceIndexer

      public TestCasesSequenceIndexer()

  • Method Details

    • test_01

      @Test public void test_01()
      Sequence comparison test

    • test_02

      @Test public void test_02()
      Sequence ordering test

    • test_03

      @Test public void test_03()
      Sequence indexer test (add sequences)

    • test_04

      @Test public void test_04()
      Sequence indexer test (overlap sequences)

    • test_05

      @Test public void test_05()
      Sequence indexer test (trivial assembly)

    • test_06

      @Test public void test_06()
      'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA' bug Sequences with nmers '0' were not being indexed

    • test_07

      @Test public void test_07()
      Sequence length = Nmer size (bug) Sequences with same length as nmers were not being indexed properly

    • test_08

      @Test public void test_08()
      Sequence "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa" + "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaac"

    • test_09

      @Test public void test_09()
      Sequence "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa" + "caaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa"

    • test_10

      @Test public void test_10()
      Sequence "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa" + "caaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaag"