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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_costThe cost of a gap (an insertion or deletion of a character). | 
| protected  int | match_rewardThe reward for a match (a substitution of equal characters). | 
| protected  int | max_absolute_scoreThe maximum absolute score that this scoring scheme can return, which is the maximum absolute value among match_reward,mismatch_penaltyandgap_cost. | 
| protected  int | mismatch_penaltyThe 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_penaltyandgap_cost. | 
|  int | scoreDeletion(char a)Always returns gap_costfor the deletion of any character. | 
|  int | scoreInsertion(char a)Always returns gap_costfor the insertion of any character. | 
|  int | scoreSubstitution(char a,
                                   char b)Returns the score of a substitution of character afor characterbaccording 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 character
public 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 otherwise| Method 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 ScoringSchemea - 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 ScoringSchemea - the character to be inserted
gap_costpublic int scoreDeletion(char a)
gap_cost for the deletion of any character.
scoreDeletion in class ScoringSchemea - the character to be deleted
gap_costpublic int maxAbsoluteScore()
match_reward, mismatch_penalty and
 gap_cost.
maxAbsoluteScore in class ScoringSchemematch_reward,
 mismatch_penalty and gap_cost.public boolean isPartialMatchSupported()
isPartialMatchSupported in class ScoringSchemefalsepublic java.lang.String toString()
toString in class java.lang.Object| 
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