neobio.alignment
Class BasicScoringScheme

java.lang.Object
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  +--neobio.alignment.ScoringScheme
        |
        +--neobio.alignment.BasicScoringScheme

public class BasicScoringScheme

extends ScoringScheme

This class implements a basic scoring scheme. At least three parameters must be provided to the constructor: the reward for a match (a substitution of equal characters), the penalty for a mismatch (a substitution of different characters) and the cost of a gap (an insertion or deletion of a character). Note that it only supports an additive gap cost function.

Although the match reward is expected to be a positive value, and the mismatch penalty and the gap cost are expected to be negative, no attempt is made to enforce these behaviour.

Author:

Sergio A. de Carvalho Jr.

Field Summary

protected int	gap_cost The cost of a gap (an insertion or deletion of a character).
protected int	match_reward The reward for a match (a substitution of equal characters).
protected int	max_absolute_score The maximum absolute score that this scoring scheme can return, which is the maximum absolute value among match_reward, mismatch_penalty and gap_cost.
protected int	mismatch_penalty The penalty for a mismatch (a substitution of different characters).

Fields inherited from class neobio.alignment.ScoringScheme

case_sensitive

Constructor Summary

BasicScoringScheme(int match_reward, int mismatch_penalty, int gap_cost)
Creates a new instance of a basic scoring scheme with the specified values of match reward, mismatch penalty and gap cost.

BasicScoringScheme(int match_reward, int mismatch_penalty, int gap_cost, boolean case_sensitive)
Creates a new instance of basic scoring scheme with the specified values of match reward, mismatch penalty and gap cost.

Method Summary

boolean	isPartialMatchSupported() Tells whether this scoring scheme supports partial matches, which it does not.
int	maxAbsoluteScore() Returns the maximum absolute score that this scoring scheme can return for any substitution, deletion or insertion, which is the maximum absolute value among match_reward, mismatch_penalty and gap_cost.
int	scoreDeletion(char a) Always returns gap_cost for the deletion of any character.
int	scoreInsertion(char a) Always returns gap_cost for the insertion of any character.
int	scoreSubstitution(char a, char b) Returns the score of a substitution of character a for character b according to this scoring scheme.
java.lang.String	toString() Returns a String representation of this scoring scheme.

Methods inherited from class neobio.alignment.ScoringScheme

isCaseSensitive

Methods inherited from class java.lang.Object

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

Field Detail

match_reward

protected int match_reward

The reward for a match (a substitution of equal characters).

mismatch_penalty

protected int mismatch_penalty

The penalty for a mismatch (a substitution of different characters).

gap_cost

protected int gap_cost

The cost of a gap (an insertion or deletion of a character).

max_absolute_score

protected int max_absolute_score

The maximum absolute score that this scoring scheme can return, which is the maximum absolute value among match_reward, mismatch_penalty and gap_cost.

Constructor Detail

BasicScoringScheme

public BasicScoringScheme(int match_reward,
                          int mismatch_penalty,
                          int gap_cost)

Creates a new instance of a basic scoring scheme with the specified values of match reward, mismatch penalty and gap cost. The case of characters is significant when subsequently computing their score.

Parameters:

match_reward - reward for a substitution of equal characters

mismatch_penalty - penalty for a substitution of different characters

gap_cost - cost of an insertion or deletion of any character

BasicScoringScheme

public BasicScoringScheme(int match_reward,
                          int mismatch_penalty,
                          int gap_cost,
                          boolean case_sensitive)

Creates a new instance of basic scoring scheme with the specified values of match reward, mismatch penalty and gap cost. If case_sensitive is true, the case of characters is significant when subsequently computing their score; otherwise the case is ignored.

Parameters:

match_reward - reward for a substitution of equal characters

mismatch_penalty - penalty for a substitution of different characters

gap_cost - cost of an insertion or deletion of any character

case_sensitive - true if the case of characters must be significant, false otherwise

Method Detail

scoreSubstitution

public int scoreSubstitution(char a,
                             char b)

Returns the score of a substitution of character a for character b according to this scoring scheme. It is match_reward if a equals b, mismatch_penalty otherwise.

Specified by:

scoreSubstitution in class ScoringScheme

Parameters:

a - first character

b - second character

Returns:

match_reward if a equals b, mismatch_penalty otherwise.

scoreInsertion

public int scoreInsertion(char a)

Always returns gap_cost for the insertion of any character.

Specified by:

scoreInsertion in class ScoringScheme

Parameters:

a - the character to be inserted

Returns:

gap_cost

scoreDeletion

public int scoreDeletion(char a)

Always returns gap_cost for the deletion of any character.

Specified by:

scoreDeletion in class ScoringScheme

Parameters:

a - the character to be deleted

Returns:

gap_cost

maxAbsoluteScore

public int maxAbsoluteScore()

Returns the maximum absolute score that this scoring scheme can return for any substitution, deletion or insertion, which is the maximum absolute value among match_reward, mismatch_penalty and gap_cost.

Specified by:

maxAbsoluteScore in class ScoringScheme

Returns:

the maximum absolute value among match_reward, mismatch_penalty and gap_cost.

isPartialMatchSupported

public boolean isPartialMatchSupported()

Tells whether this scoring scheme supports partial matches, which it does not.

Specified by:

isPartialMatchSupported in class ScoringScheme

Returns:

always return false

toString

public java.lang.String toString()

Returns a String representation of this scoring scheme.

Overrides:

toString in class java.lang.Object

Returns:

a String representation of this scoring scheme