
NeoBio API  
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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 ZivUkelson (2002). 
CrochemoreLandauZivUkelsonGlobalAlignment  This class implements the global pairwise sequence alignment algorithm (with linear gap penalty function) due to Maxime Crochemore, Gad Landau and Michal ZivUkelson (2002). 
CrochemoreLandauZivUkelsonLocalAlignment  This class implements the local pairwise sequence alignment algorithm (with linear gap penalty function) due to Maxime Crochemore, Gad Landau and Michal ZivUkelson (2002). 
Factor  This class is used by FactorSequence to create a linked list of factors of a text as induced by its LempelZiv (LZ78) factorisation. 
FactorSequence  This class builds a list of factors of a character sequence as induced by its LempelZiv (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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