Package org.snpeff.snpEffect.testCases.unity

Class TestCasesIntervals

  • public class TestCasesIntervals
extends java.lang.Object

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void compareToFile​(java.lang.String result, java.lang.String fileName)
      Compare a string and a file.
      void DnaSequenceBaseAt​(int len)
      Tests 'baseAt' method in DnaSequence
      Markers intersects​(Markers interval1, Marker intervals)  
      Markers randomIntervals​(int numIntervals, int maxStart, int maxLength, int numChromo)
      Create a random set of intervals
      void test_00()  
      void test_01()
      Read file
      void test_02()
      Sort test
      void test_03()
      Sort (by end) test
      void test_04()
      Merge intervals
      void test_05()
      Adding intervals
      void test_06()
      Intersect of 2 intervals We have 2 implementation (brute force and interval trees), so we can compare them.
      void test_07_01()
      Minus operation for intervals
      void test_07_02()
      Minus operation for intervals
      void test_07_03()
      Minus operation for intervals
      void test_07_04()
      Minus operation for intervals
      void test_07_05()
      Minus operation for intervals
      void test_08()
      Test distance (in bases) from a list of markers
      void test_08_02()
      Test distance (in bases) from a list of markers
      void test_08_03()
      Test distance (in bases) from a list of markers
      void test_09_chrOrder()  
      void test_10_chrOrder()  

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • TestCasesIntervals

        public TestCasesIntervals()

    • Method Detail

      • compareToFile

        public void compareToFile​(java.lang.String result,
                          java.lang.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

      • 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

        public void test_00()

      • test_01

        public void test_01()
        Read file

      • test_02

        public void test_02()
        Sort test

      • test_03

        public void test_03()
        Sort (by end) test

      • test_04

        public void test_04()
        Merge intervals

      • test_05

        public void test_05()
        Adding intervals

      • test_06

        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

        public void test_07_01()
        Minus operation for intervals

      • test_07_02

        public void test_07_02()
        Minus operation for intervals

      • test_07_03

        public void test_07_03()
        Minus operation for intervals

      • test_07_04

        public void test_07_04()
        Minus operation for intervals

      • test_07_05

        public void test_07_05()
        Minus operation for intervals

      • test_08

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

      • test_08_02

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

      • test_08_03

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

      • test_09_chrOrder

        public void test_09_chrOrder()

      • test_10_chrOrder

        public void test_10_chrOrder()