tests
Class TestAlignement

java.lang.Object
  junit.framework.Assert
      junit.framework.TestCase
          tests.TestAlignement

All Implemented Interfaces:

junit.framework.Test

public class TestAlignement
extends junit.framework.TestCase

Test class about modele.Alignement class.
Some factorization was useful because of max size of memory of JVM and make easier to understand some tests when are opposite tests.
Some tests here are a little bit long because of matrix constructions and comparisons, not others way to do these tests.
Nucleotids T and U are considered as same (AU == AT for example).
getPalindrome(score) and getPalindrome(i,j) are not tested : useless ?!
Tests with true sequences would be interesting : if you see this comment it may not be implemented yet, buts it's easy to do !

Author:

Gabriel Chandesris (2008)

Field Summary

private Alignement	basetest1
private Alignement	basetest2
private Sequence	sequence1
private Sequence	sequence2

Constructor Summary

TestAlignement()

Method Summary

protected void	setUp()
void	testEqualsSequenceListeFalseDe()
void	testEqualsSequenceListeFalseUn()
void	testEqualsSequenceListeTrueDe()
void	testEqualsSequenceListeTrueUn()
void	testGeneral01()
void	testGetHasSameSequenceFalse1()
void	testGetHasSameSequenceFalse2()
void	testGetHasSameSequenceTrue1()
void	testGetHasSameSequenceTrue2()
void	testGetLbmin01()
void	testGetLbmin02()
void	testGetLbmin03()
void	testGetLpmin01()
void	testGetLpmin02()
void	testGetLpmin03()
void	testGetMatriceDe()
void	testGetMatriceScoreDe()
void	testGetMatriceScoreUn()
void	testGetMatriceUn()
void	testGetPalindromesREALecolihainf()
void	testGetPalindromesREALecolivchol()
void	testGetSequence1DeFalse()
void	testGetSequence1DeTrue()
void	testGetSequence1UnFalse()
void	testGetSequence1UnTrue()
void	testGetSequence2DeFalse()
void	testGetSequence2DeTrue()
void	testGetSequence2UnFalse()
void	testGetSequence2UnTrue()
void	testIsGoodPalindrome01()
void	testIsGoodPalindrome02()
void	testIsGoodPalindrome03()
void	testIsGoodPalindrome04()
void	testIsGoodPalindrome05()
void	testIsGoodPalindrome06()
void	testIsGoodPalindrome07()
void	testIsGoodPalindrome08()
void	testIsGoodPalindrome09()
void	testIsGoodPalindrome10()
void	testIsGoodPalindrome11()
void	testIsGoodPalindrome12()
void	testIsGoodPalindrome13()
void	testMaxInt1()
void	testMaxInt2()
void	testMaxInt3()
void	testMaxInt4()
void	testScoreAAthenHelixAUorUA() Not [...] because of impact before helix
void	testScoreAAthenHelixGCorCG()
void	testScoreAAthenHelixGU()
void	testScoreAAthenHelixUG()
void	testScoreAUandUA()
void	testScoreBaseGap()
void	testScoreGapBase()
void	testScoreGAthenHelixAUorUA()
void	testScoreGAthenHelixGCorCG()
void	testScoreGAthenHelixGU()
void	testScoreGAthenHelixUG()
void	testScoreGCandCG()
void	testScoreNOTHINGthenHelixAUorUA()
void	testScoreNOTHINGthenHelixGCorCG()
void	testScoreNOTHINGthenHelixGU()
void	testScoreNOTHINGthenHelixUG()
void	testScoreNOTR5GURYthenGUorUG()
void	testScoreNOTR5GUYRthenGU()
void	testScoreNullCombination()
void	testScoreR5GUYRthenGU()
void	testScoreUGandGU()
void	testScoreXX()
void	testSetLbmin()
void	testSetLpmin()

Methods inherited from class junit.framework.TestCase

countTestCases, createResult, getName, run, run, runBare, runTest, setName, tearDown, toString

Methods inherited from class junit.framework.Assert

assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertFalse, assertFalse, assertNotNull, assertNotNull, assertNotSame, assertNotSame, assertNull, assertNull, assertSame, assertSame, assertTrue, assertTrue, fail, fail

Methods inherited from class java.lang.Object

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

Field Detail

basetest1

private Alignement basetest1

basetest2

private Alignement basetest2

sequence1

private Sequence sequence1

sequence2

private Sequence sequence2

Constructor Detail

TestAlignement

public TestAlignement()

Method Detail

setUp

protected void setUp()
              throws java.lang.Exception

Overrides:

setUp in class junit.framework.TestCase

Throws:

java.lang.Exception

testEqualsSequenceListeFalseUn

public void testEqualsSequenceListeFalseUn()

testEqualsSequenceListeFalseDe

public void testEqualsSequenceListeFalseDe()

testEqualsSequenceListeTrueUn

public void testEqualsSequenceListeTrueUn()

testEqualsSequenceListeTrueDe

public void testEqualsSequenceListeTrueDe()

testGetSequence1UnTrue

public void testGetSequence1UnTrue()

testGetSequence1UnFalse

public void testGetSequence1UnFalse()

testGetSequence1DeTrue

public void testGetSequence1DeTrue()

testGetSequence1DeFalse

public void testGetSequence1DeFalse()

testGetSequence2UnTrue

public void testGetSequence2UnTrue()

testGetSequence2UnFalse

public void testGetSequence2UnFalse()

testGetSequence2DeTrue

public void testGetSequence2DeTrue()

testGetSequence2DeFalse

public void testGetSequence2DeFalse()

testGetLpmin01

public void testGetLpmin01()

testGetLpmin02

public void testGetLpmin02()

testGetLpmin03

public void testGetLpmin03()

testSetLpmin

public void testSetLpmin()

testGetLbmin01

public void testGetLbmin01()

testGetLbmin02

public void testGetLbmin02()

testGetLbmin03

public void testGetLbmin03()

testSetLbmin

public void testSetLbmin()

testGetHasSameSequenceTrue1

public void testGetHasSameSequenceTrue1()

testGetHasSameSequenceTrue2

public void testGetHasSameSequenceTrue2()

testGetHasSameSequenceFalse1

public void testGetHasSameSequenceFalse1()

testGetHasSameSequenceFalse2

public void testGetHasSameSequenceFalse2()

testScoreAUandUA

public void testScoreAUandUA()

testScoreUGandGU

public void testScoreUGandGU()

testScoreGCandCG

public void testScoreGCandCG()

testScoreXX

public void testScoreXX()

testScoreBaseGap

public void testScoreBaseGap()

testScoreGapBase

public void testScoreGapBase()

testScoreNullCombination

public void testScoreNullCombination()

testScoreR5GUYRthenGU

public void testScoreR5GUYRthenGU()

testScoreNOTR5GURYthenGUorUG

public void testScoreNOTR5GURYthenGUorUG()

testScoreNOTR5GUYRthenGU

public void testScoreNOTR5GUYRthenGU()

testScoreAAthenHelixAUorUA

public void testScoreAAthenHelixAUorUA()

Not [...] because of impact before helix

testScoreAAthenHelixGU

public void testScoreAAthenHelixGU()

testScoreAAthenHelixUG

public void testScoreAAthenHelixUG()

testScoreAAthenHelixGCorCG

public void testScoreAAthenHelixGCorCG()

testScoreGAthenHelixAUorUA

public void testScoreGAthenHelixAUorUA()

testScoreGAthenHelixGU

public void testScoreGAthenHelixGU()

testScoreGAthenHelixUG

public void testScoreGAthenHelixUG()

testScoreGAthenHelixGCorCG

public void testScoreGAthenHelixGCorCG()

testScoreNOTHINGthenHelixAUorUA

public void testScoreNOTHINGthenHelixAUorUA()

testScoreNOTHINGthenHelixGCorCG

public void testScoreNOTHINGthenHelixGCorCG()

testScoreNOTHINGthenHelixGU

public void testScoreNOTHINGthenHelixGU()

testScoreNOTHINGthenHelixUG

public void testScoreNOTHINGthenHelixUG()

testMaxInt1

public void testMaxInt1()

testMaxInt2

public void testMaxInt2()

testMaxInt3

public void testMaxInt3()

testMaxInt4

public void testMaxInt4()

testGetMatriceUn

public void testGetMatriceUn()

testGetMatriceDe

public void testGetMatriceDe()

testGetMatriceScoreUn

public void testGetMatriceScoreUn()

testGetMatriceScoreDe

public void testGetMatriceScoreDe()

testIsGoodPalindrome01

public void testIsGoodPalindrome01()

testIsGoodPalindrome02

public void testIsGoodPalindrome02()

testIsGoodPalindrome03

public void testIsGoodPalindrome03()

testIsGoodPalindrome04

public void testIsGoodPalindrome04()

testIsGoodPalindrome05

public void testIsGoodPalindrome05()

testIsGoodPalindrome06

public void testIsGoodPalindrome06()

testIsGoodPalindrome07

public void testIsGoodPalindrome07()

testIsGoodPalindrome08

public void testIsGoodPalindrome08()

testIsGoodPalindrome09

public void testIsGoodPalindrome09()

testIsGoodPalindrome10

public void testIsGoodPalindrome10()

testIsGoodPalindrome11

public void testIsGoodPalindrome11()

testIsGoodPalindrome12

public void testIsGoodPalindrome12()

testIsGoodPalindrome13

public void testIsGoodPalindrome13()

testGeneral01

public void testGeneral01()

testGetPalindromesREALecolivchol

public void testGetPalindromesREALecolivchol()

testGetPalindromesREALecolihainf

public void testGetPalindromesREALecolihainf()