public class StringEditDistance extends Object
Constructor and Description |
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StringEditDistance() |
Modifier and Type | Method and Description |
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static double[][] |
calculateDerivative(AlignmentAlgorithm<? extends AlignmentDerivativeAlgorithm> algorithm,
Sequence a,
Sequence b)
Calculates the alignment derivative between the two given input sequences
using the given algorithm.
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static <R extends AlignmentDerivativeAlgorithm> |
calculateDerivatives(AlignmentAlgorithm<R> algorithm,
Sequence[] dataSpace,
int threadNum)
Calculates the pairwise alignment derivative between all given input
sequences using the given algorithm.
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static AlignmentSpecification |
setUpSpecification(Sequence[] dataSpace)
Sets up a default AlignmentSpecification for the simple
StringEditDistance problem.
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static AlignmentSpecification |
setUpSpecification(Sequence[] dataSpace,
double[][] scoringScheme)
Sets up an AlignmentSpecification for the simple
StringEditDistance problem.
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static AlignmentSpecification |
setUpSpecification(Sequence[] dataSpace,
double matchCost,
double mismatchCost,
double gapCost)
Sets up an AlignmentSpecification for the simple
StringEditDistance problem.
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static Sequence[] |
toSequences(Collection<String> strings)
Transforms the given strings to the TCSAlignmentToolbox Sequence format.
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static Sequence[] |
toSequences(Collection<String> strings,
Alphabet alphabet)
Transforms the given strings to the TCSAlignmentToolbox Sequence format
using the given alphabet.
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static Sequence[] |
toSequences(String[] strings)
Transforms the given strings to the TCSAlignmentToolbox Sequence format.
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static Sequence[] |
toSequences(String[] strings,
Alphabet alphabet)
Transforms the given strings to the TCSAlignmentToolbox Sequence format
using the given alphabet.
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public static Sequence[] toSequences(String[] strings)
strings
- your data. The input format can be either a plain string,
where each character is interpreted as a distinct symbol or a string of
symbols separated by a vertical bar '|' character.public static Sequence[] toSequences(Collection<String> strings)
strings
- your data. The input format can be either a plain string,
where each character is interpreted as a distinct symbol or a string of
symbols separated by a vertical bar '|' character.public static Sequence[] toSequences(String[] strings, Alphabet alphabet)
strings
- your data. The input format can be either a plain string,
where each character is interpreted as a distinct symbol or a string of
symbols separated by a vertical bar '|' character.alphabet
- the alphabet containing all symbols of your data space.public static Sequence[] toSequences(Collection<String> strings, Alphabet alphabet)
strings
- your data. The input format can be either a plain string,
where each character is interpreted as a distinct symbol or a string of
symbols separated by a vertical bar '|' character.alphabet
- the alphabet containing all symbols of your data space.public static AlignmentSpecification setUpSpecification(Sequence[] dataSpace)
dataSpace
- the sequences of your dataspace.public static AlignmentSpecification setUpSpecification(Sequence[] dataSpace, double matchCost, double mismatchCost, double gapCost)
dataSpace
- the sequences of your dataspace.matchCost
- the cost for aligning two equal symbols.mismatchCost
- the cost for aligning two unequal symbols.gapCost
- the cost for deleting or inserting a symbol.public static AlignmentSpecification setUpSpecification(Sequence[] dataSpace, double[][] scoringScheme)
dataSpace
- the sequences of your dataspace.scoringScheme
- a scoring scheme that defines individual replacement
and gap costs for each symbol. More formally: For each combination of
symbols a,b in Sigma u {_,skip} you have to specify
lambda(a,b), where lambda(a,b) is stored at point [i][j] in the matrix,
where i is the index of a in the alphabet and j is the index of b in the
alphabet (see also the Alphabet documentation).
deletion costs
lambda(a,_)
are stored at point [i][|Sigma|] and insertion costs
lambda(_,b)public static double[][] calculateDerivative(AlignmentAlgorithm<? extends AlignmentDerivativeAlgorithm> algorithm, Sequence a, Sequence b)
algorithm
- an algorithm that returns enough information to
calculate the alignment.a
- a sequence.b
- a sequence.public static <R extends AlignmentDerivativeAlgorithm> double[][][][] calculateDerivatives(AlignmentAlgorithm<R> algorithm, Sequence[] dataSpace, int threadNum)
algorithm
- an algorithm that returns enough information to
calculate the alignment.dataSpace
- an array of sequences.threadNum
- the number of threads that shall be used for parallel
computation.Copyright © 2014. All rights reserved.