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#Org.jscience.biology.alignment Classes and Interfaces - 22 results found.
NameDescriptionTypePackageFramework
AlignmentBlockThis class is used by the CrochemoreLandauZivUkelson algorithm to store the information of an alignment block.Classorg.jscience.biology.alignmentJScience
BasicScoringSchemeThis class implements a basic scoring scheme.Classorg.jscience.biology.alignmentJScience
CharSequenceThis class implements a sequence of characters stored as an array that provides random access to any position in constant time.Classorg.jscience.biology.alignmentJScience
CrochemoreLandauZivUkelsonThis abstract class is the superclass of both global and local sequence alignment algorithms (with linear gap penalty function) due to Maxime Crochemore, Gad Landau andClassorg.jscience.biology.alignmentJScience
CrochemoreLandauZivUkelsonGlobalAlignmentThis class implements the global pairwise sequence alignment algorithm (with linear gap penalty function) due to Maxime Crochemore, Gad Landau and MichalClassorg.jscience.biology.alignmentJScience
CrochemoreLandauZivUkelsonLocalAlignmentThis class implements the local pairwise sequence alignment algorithm (with linear gap penalty function) due to Maxime Crochemore, Gad Landau and MichalClassorg.jscience.biology.alignmentJScience
FactorThis class is used by FactorSequence to create a linked list of factors of a text as induced by its Lempel-Ziv (LZ78) factorisation.Classorg.jscience.biology.alignmentJScience
FactorSequenceThis class builds a list of factors of a character sequence as induced by its Lempel-Ziv (LZ78) factorisation.Classorg.jscience.biology.alignmentJScience
IncompatibleScoringSchemeExceptionSignals that an scoring scheme is not compatible with the sequencesSee Also:ScoringScheme, Classorg.jscience.biology.alignmentJScience
InvalidScoringMatrixExceptionSignals that the substitution matrix does not comply with the specification (see for details).Classorg.jscience.biology.alignmentJScience
InvalidSequenceExceptionSignals that the sequence does not comply with the specification (seeSee Also:CharSequence, Classorg.jscience.biology.alignmentJScience
LocalAlignmentBlockThis class is used by the CrochemoreLandauZivUkelsonLocalAlignment algorithm to store the information of an alignment block.Classorg.jscience.biology.alignmentJScience
MatrixThis interface defines a minimal set of operations that a matrix must implement.Interfaceorg.jscience.biology.alignmentJScience
NeedlemanWunschThis class implements the classic global alignment algorithm (with linear gap penalty function) due to S.Classorg.jscience.biology.alignmentJScience
OutMatrix CrochemoreLandauZivUkelson and subclasses to enconde the OUT matrix from the input border and DIST matrix of an AlignmentBlock.Classorg.jscience.biology.alignmentJScience
PairwiseAlignmentThis class is the product of a pairwise alignment, generated by one subclasses of PairwiseAlignmentAlgorithm.Classorg.jscience.biology.alignmentJScience
PairwiseAlignmentAlgorithmThis abstract class is the superclass of all classes implementing pairwise sequence alignment algorithms.Classorg.jscience.biology.alignmentJScience
ScoringMatrixThis class implements a scoring scheme based on a substitution matrix.Classorg.jscience.biology.alignmentJScience
ScoringSchemeThis abstract class is the superclass of all scoring schemes.Classorg.jscience.biology.alignmentJScience
SmawkThis class implement the SMAWK algorithm to compute column maxima on a totally monotone matrix as described.Classorg.jscience.biology.alignmentJScience
SmithWatermanThis class implement the classic local alignment algorithm (with linear gap penalty function) due to T.Classorg.jscience.biology.alignmentJScience
TrieThis class implements a trie, or a digital search tree.Classorg.jscience.biology.alignmentJScience