Class TestCasesIntervals
- java.lang.Object
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- org.snpeff.snpEffect.testCases.unity.TestCasesIntervals
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public class TestCasesIntervals extends java.lang.Object
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Constructor Summary
Constructors Constructor Description TestCasesIntervals()
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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 DnaSequenceMarkers
intersects(Markers interval1, Marker intervals)
Markers
randomIntervals(int numIntervals, int maxStart, int maxLength, int numChromo)
Create a random set of intervalsvoid
test_00()
void
test_01()
Read filevoid
test_02()
Sort testvoid
test_03()
Sort (by end) testvoid
test_04()
Merge intervalsvoid
test_05()
Adding intervalsvoid
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 intervalsvoid
test_07_02()
Minus operation for intervalsvoid
test_07_03()
Minus operation for intervalsvoid
test_07_04()
Minus operation for intervalsvoid
test_07_05()
Minus operation for intervalsvoid
test_08()
Test distance (in bases) from a list of markersvoid
test_08_02()
Test distance (in bases) from a list of markersvoid
test_08_03()
Test distance (in bases) from a list of markersvoid
test_09_chrOrder()
void
test_10_chrOrder()
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Method Detail
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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
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DnaSequenceBaseAt
public void DnaSequenceBaseAt(int len)
Tests 'baseAt' method in DnaSequence
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randomIntervals
public Markers randomIntervals(int numIntervals, int maxStart, int maxLength, int numChromo)
Create a random set of intervals- Parameters:
numIntervals
-maxStart
-maxLength
-- Returns:
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test_00
public void test_00()
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test_01
public void test_01()
Read file
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test_02
public void test_02()
Sort test
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test_03
public void test_03()
Sort (by end) test
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test_04
public void test_04()
Merge intervals
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test_05
public void test_05()
Adding intervals
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test_06
public void test_06()
Intersect of 2 intervals We have 2 implementation (brute force and interval trees), so we can compare them.
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test_07_01
public void test_07_01()
Minus operation for intervals
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test_07_02
public void test_07_02()
Minus operation for intervals
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test_07_03
public void test_07_03()
Minus operation for intervals
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test_07_04
public void test_07_04()
Minus operation for intervals
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test_07_05
public void test_07_05()
Minus operation for intervals
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test_08
public void test_08()
Test distance (in bases) from a list of markers
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test_08_02
public void test_08_02()
Test distance (in bases) from a list of markers
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test_08_03
public void test_08_03()
Test distance (in bases) from a list of markers
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test_09_chrOrder
public void test_09_chrOrder()
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test_10_chrOrder
public void test_10_chrOrder()
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