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See:
          Description
| Interface Summary | |
| Matrix | This interface defines a minimal set of operations that a matrix must implement. | 
| Class Summary | |
| AlignmentBlock | This class is used by the CrochemoreLandauZivUkelson algorithm to store the information of an alignment block. | 
| BasicScoringScheme | This class implements a basic scoring scheme. | 
| CharSequence | This class implements a sequence of characters stored as an array that provides random access to any position in constant time. | 
| CrochemoreLandauZivUkelson | This abstract class is the superclass of both global and local sequence alignment algorithms (with linear gap penalty function) due to Maxime Crochemore, Gad Landau and Michal Ziv-Ukelson (2002). | 
| CrochemoreLandauZivUkelsonGlobalAlignment | This class implements the global pairwise sequence alignment algorithm (with linear gap penalty function) due to Maxime Crochemore, Gad Landau and Michal Ziv-Ukelson (2002). | 
| CrochemoreLandauZivUkelsonLocalAlignment | This class implements the local pairwise sequence alignment algorithm (with linear gap penalty function) due to Maxime Crochemore, Gad Landau and Michal Ziv-Ukelson (2002). | 
| Factor | This class is used by FactorSequence to create a linked list of factors of a text as induced by its Lempel-Ziv (LZ78) factorisation. | 
| FactorSequence | This class builds a list of factors of a character sequence as induced by its Lempel-Ziv (LZ78) factorisation. | 
| LocalAlignmentBlock | This class is used by the CrochemoreLandauZivUkelsonLocalAlignment algorithm to store the information of an alignment block. | 
| NeedlemanWunsch | This class implements the classic global alignment algorithm (with linear gap penalty function) due to S.B.Needleman and C.D.Wunsch (1970). | 
| OutMatrix | Implements an interface to the OUT matrix of a block. | 
| PairwiseAlignment | This class is the product of a pairwise alignment, generated by one subclasses of PairwiseAlignmentAlgorithm. | 
| PairwiseAlignmentAlgorithm | This abstract class is the superclass of all classes implementing pairwise sequence alignment algorithms. | 
| ScoringMatrix | This class implements a scoring scheme based on a substitution matrix. | 
| ScoringScheme | This abstract class is the superclass of all scoring schemes. | 
| Smawk | This class implement the SMAWK algorithm to compute column maxima on a totally monotone matrix as described. | 
| SmithWaterman | This class implement the classic local alignment algorithm (with linear gap penalty function) due to T.F.Smith and M.S.Waterman (1981). | 
| Trie | This class implements a trie, or a digital search tree. | 
| Exception Summary | |
| IncompatibleScoringSchemeException | Signals that an scoring scheme is not compatible with the sequences being aligned. | 
| InvalidScoringMatrixException | Signals that the substitution matrix does not comply with the specification (see ScoringMatrix for details). | 
| InvalidSequenceException | Signals that the sequence does not comply with the specification (see CharSequence or FactorSequence for details). | 
Provides implementation of sequence alignment algorithms.
All algorithms use linear gap penalty functions (additive gap costs).
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