modele
Class Base

java.lang.Object
  modele.Base

public class Base
extends java.lang.Object

A class for codification and input memory sequences. At start, it was only for cible sequences (original sequences were used as test char sequences in some parts of algorithms - profil computed data).

Author:

Stéfan Engelen (2006), Gabriel Chandesris (2008)

See Also:

Sequence

Field Summary

private char	acgt
private int	position

Constructor Summary

Base(char base, int position)
Standard constructor to record a sequence in Base structure without gaps for example.

Method Summary

boolean	equals(Base toCompare) To know if instance of the class and an other are the same.
char	getBase()
int	getPosition()
static boolean	isBase(char base) To test if a char symbolize a nucleotids, all nucleotidic code is tested as UPPERCASE.
static boolean	isBaseOrGap(char base) To test if nucleotids or gap / indel symbolized with '-'.
static boolean	matchBases(Base x, Base y) To know if two Base's can go together.
static boolean	matchBases(char x, char y) To know if two nucleotids (char) can go together.
static boolean	matchBasesGap(Base x, Base y) To know if two Base's can go together (including gap's).
static boolean	matchBasesGap(char x, char y) To know if two nucleotids (char) can go together (including gap's).
static int	scoreBases(char x, char y) Score for two nuleotids (char): Watson-Cricks and Wooble accepted.
void	setBase(char base)
void	setPosition(int pos)

Methods inherited from class java.lang.Object

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

Field Detail

acgt

private char acgt

position

private int position

Constructor Detail

Base

public Base(char base,
            int position)

Standard constructor to record a sequence in Base structure without gaps for example. (structure could be table, List, Vector...).

Parameters:

base - char

position - int

Method Detail

getBase

public char getBase()

getPosition

public int getPosition()

setBase

public void setBase(char base)

setPosition

public void setPosition(int pos)

equals

public boolean equals(Base toCompare)

To know if instance of the class and an other are the same.

Parameters:

toCompare - An other Base.

Returns:

boolean

isBase

public static boolean isBase(char base)

To test if a char symbolize a nucleotids, all nucleotidic code is tested as UPPERCASE.
Table below is given as information, only bold bases are used in computing in algorithms and should be completed.

Adenine	A
Thymine	T
Guanine	G
Cytosine	C
Uracile	U
Inosine	I
Purine : Adenine or Guanine	R
Pyrimidine : Thymine or Cytosine	Y
Weak Hydrogen bonds : Adenine or Thymine	W
Keto in major groove : Thymine or Guanine	K
Strong hydrogen bonds : Cytosine or Guanine	S
Amino in major groove : Adenine or Cytosine	M
Not Adenine	B
Not Thymine	V
Not Cytosine	D
Not Guanine	H
Any	N
Gap / Indel	-

Parameters:

base - char

Returns:

boolean

isBaseOrGap

public static boolean isBaseOrGap(char base)

To test if nucleotids or gap / indel symbolized with '-'.

Parameters:

base - char

scoreBases

public static int scoreBases(char x,
                             char y)

Score for two nuleotids (char): Watson-Cricks and Wooble accepted.
1 pour GU/UG ; 2 pour AU/UA ; 3 pour CG/GC.

Parameters:

x - char

y - char

Returns:

int

matchBases

public static boolean matchBases(char x,
                                 char y)

To know if two nucleotids (char) can go together.

Parameters:

x - char

y - char

Returns:

boolean

matchBasesGap

public static boolean matchBasesGap(char x,
                                    char y)

To know if two nucleotids (char) can go together (including gap's).

Parameters:

x - char

y - char

Returns:

boolean

matchBases

public static boolean matchBases(Base x,
                                 Base y)

To know if two Base's can go together.

Parameters:

x - Base

y - Base

Returns:

boolean

matchBasesGap

public static boolean matchBasesGap(Base x,
                                    Base y)

To know if two Base's can go together (including gap's).

Parameters:

x - Base

y - Base

Returns:

boolean