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java.lang.Object  +neobio.alignment.ScoringScheme  +neobio.alignment.BasicScoringScheme
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.
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 
protected int match_reward
protected int mismatch_penalty
protected int gap_cost
protected int max_absolute_score
match_reward
,
mismatch_penalty
and gap_cost
.
Constructor Detail 
public BasicScoringScheme(int match_reward, int mismatch_penalty, int gap_cost)
match_reward
 reward for a substitution of equal charactersmismatch_penalty
 penalty for a substitution of different charactersgap_cost
 cost of an insertion or deletion of any characterpublic BasicScoringScheme(int match_reward, int mismatch_penalty, int gap_cost, boolean case_sensitive)
case_sensitive
is
true
, the case of characters is significant when subsequently
computing their score; otherwise the case is ignored.
match_reward
 reward for a substitution of equal charactersmismatch_penalty
 penalty for a substitution of different charactersgap_cost
 cost of an insertion or deletion of any charactercase_sensitive
 true
if the case of characters must be
significant, false
otherwiseMethod Detail 
public int scoreSubstitution(char a, char b)
a
for character
b
according to this scoring scheme. It is match_reward
if a
equals b
, mismatch_penalty
otherwise.
scoreSubstitution
in class ScoringScheme
a
 first characterb
 second character
match_reward
if a
equals b
,
mismatch_penalty
otherwise.public int scoreInsertion(char a)
gap_cost
for the insertion of any character.
scoreInsertion
in class ScoringScheme
a
 the character to be inserted
gap_cost
public int scoreDeletion(char a)
gap_cost
for the deletion of any character.
scoreDeletion
in class ScoringScheme
a
 the character to be deleted
gap_cost
public int maxAbsoluteScore()
match_reward
, mismatch_penalty
and
gap_cost
.
maxAbsoluteScore
in class ScoringScheme
match_reward
,
mismatch_penalty
and gap_cost
.public boolean isPartialMatchSupported()
isPartialMatchSupported
in class ScoringScheme
false
public java.lang.String toString()
toString
in class java.lang.Object


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