Class 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()