Uses of Interface
de.jstacs.data.sequences.annotation.SequenceAnnotationParser

Packages that use SequenceAnnotationParser

Package	Description
de.jstacs.data	Provides classes for the representation of data. The base classes to represent data are Alphabet and AlphabetContainer for representing alphabets, Sequence and its sub-classes to represent continuous and discrete sequences, and DataSet to represent data sets comprising a set of sequences.
de.jstacs.data.sequences	Provides classes for representing sequences. The implementations of sequences currently include DiscreteSequences prepared for alphabets of different sizes, and ArbitrarySequences that may contain continuous values as well. As sub-package provides the facilities to annotate Sequences.
de.jstacs.data.sequences.annotation	Provides the facilities to annotate Sequences using a number of pre-defined annotation types, or additional implementations of the SequenceAnnotation class.
de.jstacs.io	Provides classes for reading data from and writing to a file and storing a number of datatypes, including all primitives, arrays of primitives, and Storables to an XML-representation.
de.jstacs.results	This package provides classes for results and sets of results.

Uses of SequenceAnnotationParser in de.jstacs.data

Methods in de.jstacs.data with parameters of type SequenceAnnotationParser

Modifier and Type	Method and Description
void	DataSet.save(OutputStream stream, char commentChar, SequenceAnnotationParser p) This method allows to write all Sequences including their SequenceAnnotations into a OutputStream.

Constructors in de.jstacs.data with parameters of type SequenceAnnotationParser

Constructor and Description
DNADataSet(String fName, char ignore, SequenceAnnotationParser parser) Creates a new data set of DNA sequence from a file with file name fName using the given parser.

Uses of SequenceAnnotationParser in de.jstacs.data.sequences

Methods in de.jstacs.data.sequences with parameters of type SequenceAnnotationParser

Modifier and Type	Method and Description
static DataSet	SparseSequence.getDataSet(AlphabetContainer con, String filename, SequenceAnnotationParser parser) This method allows to create a DataSet containing SparseSequences using a file name.
static DataSet	ArbitraryFloatSequence.getDataSet(AlphabetContainer con, String filename, SequenceAnnotationParser parser) This method allows to create a DataSet containing ArbitraryFloatSequences using a file name.

Uses of SequenceAnnotationParser in de.jstacs.data.sequences.annotation

Classes in de.jstacs.data.sequences.annotation that implement SequenceAnnotationParser

Modifier and Type	Class and Description
class	MotifAnnotationParser Annotation parser for MotifAnnotations.
class	NullSequenceAnnotationParser This SequenceAnnotationParser returns always null as SequenceAnnotation.
class	ReferenceSequenceAnnotationParser This class implements an SequenceAnnotationParser that parses a ReferenceSequenceAnnotation from the comment lines of a sequence.
class	SimpleSequenceAnnotationParser This class implements a naive SequenceAnnotationParser which simply paste the comments into SequenceAnnotation.
class	SplitSequenceAnnotationParser This class implements a simple SequenceAnnotationParser which simply splits the comments by specific delimiters.

Uses of SequenceAnnotationParser in de.jstacs.io

Fields in de.jstacs.io declared as SequenceAnnotationParser

Modifier and Type	Field and Description
protected SequenceAnnotationParser	SparseStringExtractor.annotationParser A parser for the sequence annotation.

Constructors in de.jstacs.io with parameters of type SequenceAnnotationParser

Constructor and Description
SparseStringExtractor(File f, char ignore, String annotation, SequenceAnnotationParser parser) A constructor that reads the lines from a file, ignores those starting with the comment character ignore and sets the annotation of the source to annotation.
SparseStringExtractor(Reader reader, char ignore, String annotation, SequenceAnnotationParser parser) A constructor that reads the lines from a Reader, ignores those starting with the comment character ignore and sets the annotation of the source to annotation.
SparseStringExtractor(String fName, char ignore, SequenceAnnotationParser parser) A constructor that reads the lines from a file and ignores those starting with the comment character ignore.
SparseStringExtractor(String fName, char ignore, String annotation, SequenceAnnotationParser parser) A constructor that reads the lines from a file, ignores those starting with the comment character ignore and sets the annotation of the source to annotation.
SparseStringExtractor(String fName, SequenceAnnotationParser parser) A constructor that reads the lines from a file.
SparseStringExtractor(String fName, String annotation, SequenceAnnotationParser parser) A constructor that reads the lines from a file and sets the annotation of the source to annotation.

Uses of SequenceAnnotationParser in de.jstacs.results

Methods in de.jstacs.results that return SequenceAnnotationParser

Modifier and Type	Method and Description
SequenceAnnotationParser	DataSetResult.getParser() Returns the SequenceAnnotationParser that can be used to write this DataSetResult including annotations on the contained Sequences to a file.

Methods in de.jstacs.results with parameters of type SequenceAnnotationParser

Modifier and Type	Method and Description
void	DataSetResult.setParser(SequenceAnnotationParser parser) Sets the SequenceAnnotationParser that can be used to write this DataSetResult including annotations on the contained Sequences to a file