Package org.jscience.biology.alignment

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 for details).
InvalidSequenceException Signals that the sequence does not comply with the specification (see or for details).