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. |