Class TestCasesIntervals
- java.lang.Object
-
- org.snpeff.snpEffect.testCases.unity.TestCasesBase
-
- org.snpeff.snpEffect.testCases.unity.TestCasesIntervals
-
public class TestCasesIntervals extends TestCasesBase
-
-
Field Summary
-
Fields inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase
addUtrs, BASE_DIR, chromoBases, chromoSequence, chromosome, codonTable, config, debug, gene, genomeName, maxExons, maxGeneLen, maxTranscripts, minExons, numGenes, onlyMinusStrand, onlyPlusStrand, prefixes, rand, randSeed, shiftHgvs, snpEffectPredictor, spliceRegionExonSize, spliceRegionIntronMax, spliceRegionIntronMin, testType, transcript, verbose
-
-
Constructor Summary
Constructors Constructor Description TestCasesIntervals()
-
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 DnaSequenceprotected void
initRand()
Markers
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()
-
Methods inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase
after, before, checkApply, checkApplyDel, checkApplyIns, checkApplyMixed, checkApplyMnp, checkApplySnp, checkEffect, checkEffect, formatVersion, hasEffect, init, initSnpEffPredictor, initSnpEffPredictor, path, pathClassName, prependSequenceToFirstExon
-
-
-
-
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
-
initRand
protected void initRand()
- Overrides:
initRand
in classTestCasesBase
-
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()
-
-