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CharSequence, loading the sequence data
 from the Reader input stream.
computeBlockTable for details) and requests subclasses to retrieve an
 optimal alignment between the loaded sequences. 
computeBlockTable for details) and requests subclasses to locate the
 score of the highest scoring alignment between the two sequences in the block
 table. 
col
 array of indexes. 
reduce operation. 
Factor. 
Factor instance with the specified serial number and
 new character, and pointing to the given ancestor. 
FactorSequence, loading the sequence data
 from the Reader input stream. 
computePairwiseAlignment method. 
computeScore method.
 
IncompatibleScoringSchemeException with null as its
 error detail message.
IncompatibleScoringSchemeException with the specified
 detail message.
IncompatibleScoringSchemeException with the specified
 detail message and cause.
IncompatibleScoringSchemeException with the specified
 cause (and a detail message that typically contains the class and detail message
 of cause).
InvalidScoringMatrixException with null as its error
 detail message.
InvalidScoringMatrixException with the specified detail
 message.
InvalidScoringMatrixException with the specified detail
 message and cause.
InvalidScoringMatrixException with the specified cause
 (and a detail message that typically contains the class and detail message of
 cause).
InvalidSequenceException with null as its
 error detail message.
InvalidSequenceException with the specified
 detail message.
InvalidSequenceException with the specified
 detail message and cause.
InvalidSequenceException with the specified
 cause (and a detail message that typically contains the class and detail message
 of cause).
true if this scoring scheme supports partial matches,
 false otherwise. 
FactorSequence instances. 
match_reward,
 mismatch_penalty and gap_cost.
match_reward, mismatch_penalty and
 gap_cost.
OutMatrix class that encodes the OUT matrix of a
 block when supplied with the DIST matrix and the input border array of a block.
 
PairwiseAlignment instance with the specified gapped
 sequences, score tag line and score value.
col array of indexes to the state it was before the
 deleteOddColumns method was called. 
row array of indexes to the state it was before the
 reduce method was called. 
row array.
score_computed flag is set to true). 
a according to this
 scoring matrix.
scoreDeletion method of the scoring scheme
 set to this algorithm.
a according to this
 scoring scheme. 
gap_cost for the deletion of any character.
a according to this
 scoring matrix.
scoreInsertion method of the scoring
 scheme set to this algorithm.
a according to this
 scoring scheme. 
gap_cost for the insertion of any character.
a for character
 b according to this scoring matrix.
scoreSubstitution method of the scoring
 scheme set to this algorithm.
a for character
 b according to this scoring scheme. 
a for character
 b according to this scoring scheme. 
next pointer to point to the specified factor.
 
Smawk class that implements the SMAWK algorithm to
 compute the column maxima of a totally monotone matrix. 
sibling.
son.
MATCH_TAG tag should be used or not. 
MATCH_TAG tag should be used or not. 
valueAt method
 of the matrix. 
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