Package | Description |
---|---|
de.citec.tcs.alignment.csv |
This module permits exporting and importing of Sequence objects to CSV files.
|
de.citec.tcs.alignment.sequence |
This module contains the sequence datastructure of the
TCS Alignment Toolbox.
|
de.citec.tcs.alignment.wrappers |
This module contains some wrappers to make usage of the
TCSAlignmentToolbox easier.
|
Modifier and Type | Method and Description |
---|---|
static Sequence |
CSVImporter.importSequence(NodeSpecification nodeSpec,
File csvFile)
This imports a sequence from a CSV file using the default delimiter "\t".
|
static Sequence |
CSVImporter.importSequence(NodeSpecification nodeSpec,
File csvFile,
String valueDelimiterString)
This imports a sequence from a CSV file using the given delimiter string.
|
static Sequence |
CSVImporter.importSequence(NodeSpecification nodeSpec,
Reader in)
This imports a sequence from a Reader using the default delimiter "\t".
|
static Sequence |
CSVImporter.importSequence(NodeSpecification nodeSpec,
Reader in,
String valueDelimiterString)
This imports a sequence from a Reader containing CSV data using the
given delimiter string.
|
static Sequence |
CSVImporter.importSequence(NodeSpecification nodeSpec,
String csvFileName)
This imports a sequence from a CSV file using the default delimiter "\t".
|
static Sequence |
CSVImporter.importSequence(NodeSpecification nodeSpec,
String csvFileName,
String valueDelimiterString)
This imports a sequence from a CSV file using the given delimiter string.
|
Modifier and Type | Method and Description |
---|---|
static void |
CSVExporter.exportSequence(Sequence seq,
File csvFile)
This exports a sequence to a file of comma-separated values (CSV).
|
static void |
CSVExporter.exportSequence(Sequence seq,
File csvFile,
String valueDelimiterCharacter)
This exports a sequence to a CSV file, with a specified delimiter-string.
|
static void |
CSVExporter.exportSequence(Sequence seq,
String csvFileName)
This exports a sequence to a file of comma-separated values (CSV).
|
static void |
CSVExporter.exportSequence(Sequence seq,
String csvFileName,
String valueDelimiterCharacter)
This exports a sequence to a CSV file, with a specified delimiter-string.
|
static void |
CSVExporter.exportSequence(Sequence seq,
Writer out)
This exports a sequence to a Writer as CSV data.
|
static void |
CSVExporter.exportSequence(Sequence seq,
Writer out,
String valueDelimiterCharacter)
This exports a sequence to a CSV file, with a specified delimiter-string.
|
Modifier and Type | Method and Description |
---|---|
Sequence |
Node.getSequence()
Returns the sequence this node belongs to.
|
Constructor and Description |
---|
Node(Sequence sequence) |
Modifier and Type | Method and Description |
---|---|
static Sequence[] |
RandomSequenceGenerator.generateSequences(int N,
int L,
int K)
This generates N random sequences of length L each with K keywords.
|
static Sequence[] |
RandomSequenceGenerator.generateSequences(int N,
int L,
NodeSpecification nodeSpec)
This generates N random sequences of length L each according to
the given NodeSpecification.
|
static Sequence[] |
StringEditDistance.toSequences(Collection<String> strings)
Transforms the given strings to the TCSAlignmentToolbox Sequence format.
|
static Sequence[] |
StringEditDistance.toSequences(Collection<String> strings,
Alphabet alphabet)
Transforms the given strings to the TCSAlignmentToolbox Sequence format
using the given alphabet.
|
static Sequence[] |
VectorialSequences.toSequences(double[][] arrays)
Transforms the given arrays to sequences.
|
static Sequence[] |
VectorialSequences.toSequences(double[][][] arrays)
Transforms the given arrays to sequences.
|
static Sequence[] |
VectorialSequences.toSequences(double[][][] arrays,
String[] keywords)
Transforms the given arrays to sequences.
|
static Sequence[] |
VectorialSequences.toSequences(double[][][] arrays,
String[] keywords,
int[] propertyDist)
Transforms the given arrays to sequences.
|
static Sequence[] |
StringEditDistance.toSequences(String[] strings)
Transforms the given strings to the TCSAlignmentToolbox Sequence format.
|
static Sequence[] |
StringEditDistance.toSequences(String[] strings,
Alphabet alphabet)
Transforms the given strings to the TCSAlignmentToolbox Sequence format
using the given alphabet.
|
Modifier and Type | Method and Description |
---|---|
static double[][] |
StringEditDistance.calculateDerivative(AlignmentAlgorithm<Node,Node,? extends DerivableAlignmentDistance<Node,Node>> algorithm,
Sequence a,
Sequence b)
Calculates the alignment derivative between the two given input sequences
using the given algorithm.
|
static <R extends DerivableAlignmentDistance<Node,Node>> |
StringEditDistance.calculateDerivatives(AlignmentAlgorithm<Node,Node,R> algorithm,
Sequence[] dataSpace,
int threadNum)
Calculates the pairwise alignment derivative between all given input
sequences using the given algorithm.
|
static AlignmentSpecification |
VectorialSequences.setUpSpecification(Sequence[] dataSpace)
Sets up an AlignmentSpecification for an array of vectorial sequences.
|
static AlignmentSpecification |
StringEditDistance.setUpSpecification(Sequence[] dataSpace)
Sets up a default AlignmentSpecification for the simple
StringEditDistance problem.
|
static AlignmentSpecification |
VectorialSequences.setUpSpecification(Sequence[] dataSpace,
double[] weights)
Sets up an AlignmentSpecification for an array of vectorial sequences.
|
static AlignmentSpecification |
StringEditDistance.setUpSpecification(Sequence[] dataSpace,
double[][] scoringScheme)
Sets up an AlignmentSpecification for the simple
StringEditDistance problem.
|
static AlignmentSpecification |
StringEditDistance.setUpSpecification(Sequence[] dataSpace,
double matchCost,
double mismatchCost,
double gapCost,
double skipCost)
Sets up an AlignmentSpecification for the simple
StringEditDistance problem.
|
static AlignmentSpecification |
VectorialSequences.setUpSpecification(Sequence[] dataSpace,
ValueComparator comparator)
Sets up an AlignmentSpecification for an array of vectorial sequences.
|
static AlignmentSpecification |
VectorialSequences.setUpSpecification(Sequence[] dataSpace,
ValueComparator[] comparators)
Sets up an AlignmentSpecification for an array of vectorial sequences.
|
static AlignmentSpecification |
VectorialSequences.setUpSpecification(Sequence[] dataSpace,
ValueComparator[] comparators,
double[] weights)
Sets up an AlignmentSpecification for an array of vectorial sequences.
|
static AlignmentSpecification |
VectorialSequences.setUpSpecification(Sequence[] dataSpace,
ValueComparator comparator,
double[] weights)
Sets up an AlignmentSpecification for an array of vectorial sequences.
|
Copyright (C) 2016 Benjamin Paaßen, AG Theoretical Computer Science, Centre of Excellence Cognitive Interaction Technology (CITEC), University of Bielefeld, licensed under the AGPL v. 3: http://openresearch.cit-ec.de/projects/tcs . This documentation is licensed under the conditions of CC-BY-SA 4.0: https://creativecommons.org/licenses/by-sa/4.0/