neobio.alignment(NeoBio API)

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## Package neobio.alignment

Provides implementation of sequence alignment algorithms.

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).

## Package neobio.alignment Description

Provides implementation of sequence alignment algorithms.

### Pairwise sequence alignment algorithms:

- Needleman & Wunsch (global alignment)
- Smith & Waterman (local alignment)
- Crochemore, Landau & Ziv-Ukelson for global alignment
- Crochemore, Landau & Ziv-Ukelson for local alignment

All algorithms use linear gap penalty functions (additive gap costs).

### Main supporting classes:

- CharSequence and FactorSequence: store information about a sequence that can be aligned with another sequence using one alignment algorithm; they wrap the main input of alignment algorithms to provide ways of reading the data.
- ScoringScheme and its subclasses: implement scoring schemes used by alignment algorithms to calculate the similary between two sequences.
- PairwiseAlignment: this is the result of an execution of a pairwise alignment algorithm. It basically contains a string representation of both sequences with gaps (represented with dashes) that produces a highest scoring alignment between them.
- Smawk: both of Crochemore, Landau & Ziv-Ukelson's algorithms rely on this class to provide an implementation of an algorithm, nicknamed SMAWK in the literature, that computes in linear time all column (or row) maxima of a totally monotone matrix.

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