neobio.alignment
Class Factor

java.lang.Object
  |
  +--neobio.alignment.Factor

public class Factor

extends java.lang.Object

This class is used by FactorSequence to create a linked list of factors of a text as induced by its Lempel-Ziv (LZ78) factorisation.

Each instance of this class represent a string composed of its an ancestor factor's string plus one character, and contains:

• a pointer to its ancestor factor (the longest factor previously seen in the text during its LZ78 factorisation);
• the new character;
• a serial number (which represents its order in the text)
• a pointer to the next factor of the text
• its length (number of characters, which is equal to its ancestor's length plus one)

Author:

Sergio A. de Carvalho Jr.

See Also:

FactorSequence

Field Summary

protected Factor	ancestor A pointer to this factor's ancestor, which represents a prefix of this factor's text.
protected int	length The number of characters of the text represented by this factor.
protected char	new_char The new character of this factor.
protected Factor	next A pointer to the next factor.
protected int	serial_number This factor's serial number, which indicates the order of this factor inside the linked list of factors of a text.

Constructor Summary

Factor()
Creates a new empty Factor.

Factor(Factor ancestor, int serial_number, char new_char)
Creates a new Factor instance with the specified serial number and new character, and pointing to the given ancestor.

Method Summary

Factor	getAncestor() Returns this factor's ancestor factor.
int	getAncestorSerialNumber() This method is a shorthand to return the serial number of this factor's ancestor.
char	getNewChar() Returns this factor's new character.
Factor	getNext() Returns this factor's next factor.
int	getSerialNumber() Returns this factor's serial number.
int	length() Returns this factor's length.
void	setNext(Factor next) Sets this factor's next pointer to point to the specified factor.
java.lang.String	toString() Returns a string representation of the text represented by this factor.

Methods inherited from class java.lang.Object

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

Field Detail

ancestor

protected Factor ancestor

A pointer to this factor's ancestor, which represents a prefix of this factor's text.

next

protected Factor next

A pointer to the next factor.

serial_number

protected int serial_number

This factor's serial number, which indicates the order of this factor inside the linked list of factors of a text.

length

protected int length

The number of characters of the text represented by this factor.

new_char

protected char new_char

The new character of this factor.

Constructor Detail

Factor

public Factor()

Creates a new empty Factor. It has no ancestor and no character (both are set to null). Its serial number is set to zero as well as its length.

This constructor is used to initiate the a linked list of factors of a text. Its next pointer is initially null, but it is typically set to point to the first factor afterwards (with the setNext method).

See Also:

setNext(neobio.alignment.Factor)

Factor

public Factor(Factor ancestor,
              int serial_number,
              char new_char)

Creates a new Factor instance with the specified serial number and new character, and pointing to the given ancestor. Its length is set to its ancestor's length plus 1.

Its next pointer is initially null, but it is typically set to point to the next factor afterwards (with the setNext method).

Parameters:

ancestor - this factor's ancestor

serial_number - this factor's serial number

new_char - this factor's new character

See Also:

setNext(neobio.alignment.Factor)

Method Detail

setNext

public void setNext(Factor next)

Sets this factor's next pointer to point to the specified factor. Although the next factor has typically a serial number equal to this factor's serial number plus 1, no attempt is made to guarantee this rule. This allows special constructs or a different order in the factorisation.

Parameters:

next - the factor that will be pointed to

See Also:

getNext()

getAncestor

public Factor getAncestor()

Returns this factor's ancestor factor.

Returns:

this factor's ancestor factor

getAncestorSerialNumber

public int getAncestorSerialNumber()

This method is a shorthand to return the serial number of this factor's ancestor. Note that it does not check if this factor has an ancestor or not, therefore, if it is called on the root factor, a NullPointerException is raised.

Returns:

the serial number of this factor's ancestor

getNext

public Factor getNext()

Returns this factor's next factor.

Returns:

this factor's next factor

See Also:

setNext(neobio.alignment.Factor)

getSerialNumber

public int getSerialNumber()

Returns this factor's serial number.

Returns:

this factor's serial number

length

public int length()

Returns this factor's length.

Returns:

this factor's length

getNewChar

public char getNewChar()

Returns this factor's new character.

Returns:

this factor's new character

toString

public java.lang.String toString()

Returns a string representation of the text represented by this factor. It inspects its chain of ancestors up until as far as the root factor, spelling their new characters out.

Overrides:

toString in class java.lang.Object

Returns:

a string representation of the text denoted by this factor