Class TestCasesIntervals

java.lang.Object
org.snpeff.snpEffect.testCases.unity.TestCasesBase
org.snpeff.snpEffect.testCases.unity.TestCasesIntervals

public class TestCasesIntervals extends TestCasesBase
  • Constructor Details

    • TestCasesIntervals

      public TestCasesIntervals()
  • Method Details

    • compareToFile

      public void compareToFile(String result, String fileName)
      Compare a string and a file. Throw an exception if they don't match
      Parameters:
      result -
      fileName -
    • DnaSequenceBaseAt

      public void DnaSequenceBaseAt(int len)
      Tests 'baseAt' method in DnaSequence
    • initRand

      protected void initRand()
      Overrides:
      initRand in class TestCasesBase
    • intersects

      public Markers intersects(Markers interval1, Marker intervals)
    • randomIntervals

      public Markers randomIntervals(int numIntervals, int maxStart, int maxLength, int numChromo)
      Create a random set of intervals
      Parameters:
      numIntervals -
      maxStart -
      maxLength -
      Returns:
    • test_00

      @Test public void test_00()
    • test_01

      @Test public void test_01()
      Read file
    • test_02

      @Test public void test_02()
      Sort test
    • test_03

      @Test public void test_03()
      Sort (by end) test
    • test_04

      @Test public void test_04()
      Merge intervals
    • test_05

      @Test public void test_05()
      Adding intervals
    • test_06

      @Test public void test_06()
      Intersect of 2 intervals We have 2 implementation (brute force and interval trees), so we can compare them.
    • test_07_01

      @Test public void test_07_01()
      Minus operation for intervals
    • test_07_02

      @Test public void test_07_02()
      Minus operation for intervals
    • test_07_03

      @Test public void test_07_03()
      Minus operation for intervals
    • test_07_04

      @Test public void test_07_04()
      Minus operation for intervals
    • test_07_05

      @Test public void test_07_05()
      Minus operation for intervals
    • test_08

      @Test public void test_08()
      Test distance (in bases) from a list of markers
    • test_08_02

      @Test public void test_08_02()
      Test distance (in bases) from a list of markers
    • test_08_03

      @Test public void test_08_03()
      Test distance (in bases) from a list of markers
    • test_09_chrOrder

      @Test public void test_09_chrOrder()
    • test_10_chrOrder

      @Test public void test_10_chrOrder()