testsorigin
Class TestPDCFold00

java.lang.Object
  junit.framework.Assert
      junit.framework.TestCase
          testsorigin.TestPDCFold00

All Implemented Interfaces:

junit.framework.Test

public class TestPDCFold00
extends junit.framework.TestCase

This class to test the P-DCfold algorithm as defined in source code of Stefan Engelen and as discovered...
Tests with sequences tmRNA : 01 to 03 : tests with all sequences selected and changing variables
04 to 06 : tests with double selection of all sequences
10 to 12 : tests with six bests homologuous sequences (SSCA scores then selection)
13 to 15 : tests with two times the prediction of six best sequences...
20 to 25 (including the "Less") : tests to know and prouve that target sequence is needed is homologuous sequences to compute prediction...
Tests with sequences tRNA : 31 to 33 : similar to 01 to 03 34 to 36 : similar to 04 to 06

Since:

August 2008

Author:

Gabriel Chandesris (2008)

See Also:

ADN1cible

Field Summary

private java.util.Vector	tabsadn
private ADN1cible	target
private ADN1test[]	tests

Constructor Summary

TestPDCFold00()

Method Summary

static void	computing(java.util.Vector tabsadn, ADN1cible adncible, boolean morePrediction, boolean searchPseudoknots) Computing the main algorithm made by Stefan Engelen.
static java.lang.String	getScreenToSee(java.util.Vector tabsadn, ADN1cible adncible) Working about what will be on screen
protected void	setUp()
void	testPDCFold01()
void	testPDCFold02()
void	testPDCFold03()
void	testPDCFold04()
void	testPDCFold05()
void	testPDCFold06()
void	testPDCFold10()
void	testPDCFold11()
void	testPDCFold12()
void	testPDCFold13()
void	testPDCFold14()
void	testPDCFold15()
void	testPDCFold20()
void	testPDCFold20Less()
void	testPDCFold21()
void	testPDCFold21Less()
void	testPDCFold22()
void	testPDCFold22Less()
void	testPDCFold23()
void	testPDCFold23Less()
void	testPDCFold24()
void	testPDCFold24Less()
void	testPDCFold25()
void	testPDCFold25Less()
void	testPDCFold31()
void	testPDCFold32()
void	testPDCFold33()
void	testPDCFold34()
void	testPDCFold35()
void	testPDCFold36()

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

target

private ADN1cible target

tests

private ADN1test[] tests

tabsadn

private java.util.Vector tabsadn

Constructor Detail

TestPDCFold00

public TestPDCFold00()

Method Detail

setUp

protected void setUp()
              throws java.lang.Exception

Overrides:

setUp in class junit.framework.TestCase

Throws:

java.lang.Exception

testPDCFold01

public void testPDCFold01()

testPDCFold02

public void testPDCFold02()

testPDCFold03

public void testPDCFold03()

testPDCFold04

public void testPDCFold04()

testPDCFold05

public void testPDCFold05()

testPDCFold06

public void testPDCFold06()

testPDCFold10

public void testPDCFold10()

testPDCFold11

public void testPDCFold11()

testPDCFold12

public void testPDCFold12()

testPDCFold13

public void testPDCFold13()

testPDCFold14

public void testPDCFold14()

testPDCFold15

public void testPDCFold15()

testPDCFold20

public void testPDCFold20()

testPDCFold20Less

public void testPDCFold20Less()

testPDCFold21

public void testPDCFold21()

testPDCFold21Less

public void testPDCFold21Less()

testPDCFold22

public void testPDCFold22()

testPDCFold22Less

public void testPDCFold22Less()

testPDCFold23

public void testPDCFold23()

testPDCFold23Less

public void testPDCFold23Less()

testPDCFold24

public void testPDCFold24()

testPDCFold24Less

public void testPDCFold24Less()

testPDCFold25

public void testPDCFold25()

testPDCFold25Less

public void testPDCFold25Less()

testPDCFold31

public void testPDCFold31()

testPDCFold32

public void testPDCFold32()

testPDCFold33

public void testPDCFold33()

testPDCFold34

public void testPDCFold34()

testPDCFold35

public void testPDCFold35()

testPDCFold36

public void testPDCFold36()

getScreenToSee

public static java.lang.String getScreenToSee(java.util.Vector tabsadn,
                                              ADN1cible adncible)

Working about what will be on screen

Parameters:

tabsadn - (Vector) vector of tabs of palindromes

adncible - (ADN1cible)

Returns:

(String)

computing

public static void computing(java.util.Vector tabsadn,
                             ADN1cible adncible,
                             boolean morePrediction,
                             boolean searchPseudoknots)

Computing the main algorithm made by Stefan Engelen.
Result is structures contained by adncible.
Not static because of need of some parameters in Processsus.

Parameters:

tabsadn - (Vector) Vector of tabs of ADN1tests

adncible - (ADN1test)

morePrediction - (boolean) if more than one structure as result or not

searchPseudoknots - (boolean) Searching pseudoknots or not

See Also:

ProcessusOrigin.conversionFrom(SequenceListe[]), ProcessusOrigin.getRecordingStructures(ADN1cible), ProcessusOrigin.getScreenToSee(Vector, ADN1cible)