See: Description
Interface | Description |
---|---|
AlignmentAlgorithm<R> |
This is the most generic AlignmentAlgorithm interface for all algorithms
that provide some sort of alignment between two input sequences.
|
AlignmentDerivativeAlgorithm |
This is an interface to provide calculation methods for the derivative of an
alignment w.r.t.
|
AlignmentMatrixEntry |
This is an interface for the entries of an alignment matrix.
|
GapAlignmentAlgorithm<R> |
This is an interface for Alignment algorithms that use gaps (insertion and
deletion operations) in the alignment.
|
LocalAlignmentAlgorithm<R> |
This is an interface for GapAlignmentAlgorithms that also use skips
(SkipDeletion, SkipInsertion) and in that way are local distance measures.
|
Class | Description |
---|---|
AbstractGapAlignmentAlgorithm<X extends AlignmentMatrixEntry,R> |
This is an abstract super class for GapAlignmentAlgorithms that provides a
generic implementation of the dynamic programming needed to efficiently
calculate the alignment.
|
AlignmentPath |
This class models an alignment path as it is given out by a strict alignment.
|
AlignmentSpecification |
The alignment specification defines which keywords of the input sequences
shall be used and which comparator is to be used to calculate the local
distance between two values for that keyword.
|
DynamicTimeWarpingAlgorithm |
Implements soft alignment DTW.
|
IndexedStochasticPriorityQueue<K extends Comparable<K>,V> |
This is a helper class, which actually extends the TreeMap to implement a
PriorityQueue that is able to poll the minimum as well as the maximum in
constanst time.
|
MatrixCoordinate |
Identifies a position in a two-dimensional matrix.
|
Operation |
This defines an applied alignment operation.
|
ParallelDerivativeEngine |
This allows parallel processing of derivative calculations.
|
ParallelProcessingEngine<R> |
This allows parallel processing of alignment calculations.
|
PathList |
This is a list-based datastructure accumulating multiple AlignmentPaths.
|
PathMap |
This is a TreeMap-based datastructure implementing a mapping from scores to
AlignmentPaths.
|
SoftAlignmentFullAlgorithm |
This calculates the soft (global) alignment of two sequences similarly to the
Needleman-Wunsch-Algorithm.
|
SoftAlignmentSamplingAlgorithm |
This calculates the soft (global) alignment of two sequences similarly to the
Needleman-Wunsch-Algorithm.
|
SoftAlignmentScoreAlgorithm |
This calculates the soft (global) alignment of two sequences similarly to the
Needleman-Wunsch-Algorithm.
|
SoftAlignmentScoreAlgorithm.ScoreEntry | |
SoftDTWModel |
storage unit for soft DTW alignment result, provides functions to calculate
the soft DTW derivatives based on the stored soft alignment
|
SoftPathModel |
This is the soft pendant to the AlignmentPath.
|
SoftPathModel.SoftMatrixEntry | |
SparseMatrix<X> |
This models a sparse matrix that does not have to be fully calculated.
|
StrictAlignmentFullAlgorithm |
This is an implementation of the Needleman-Wunsch-Algorithm for sequence
alignment.
|
StrictAlignmentFullAlgorithm.FullMatrixEntry | |
StrictAlignmentScoreAlgorithm |
This is an implementation of the Needleman-Wunsch-Algorithm for sequence
alignment.
|
StrictAlignmentScoreAlgorithm.ScoreEntry | |
StrictAllOptimalAlgorithm |
This is an implementation of the Needleman-Wunsch-Algorithm for sequence
alignment.
|
StrictAllOptimalAlgorithm.FullMatrixEntry | |
StrictKPathAlgorithm |
This is an implementation of the Needleman-Wunsch-Algorithm for sequence
alignment.
|
Enum | Description |
---|---|
OperationType |
This defines the possible types of operations that may be used in an
alignment within this Toolbox.
|
ScoreBasedWeighting |
This is a helper class to enable users to weight a collection of scores based
on different schemes specified below.
|
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