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Packages that use SequenceAnnotationParser | |
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de.jstacs.data | Provides classes for the representation of data. |
de.jstacs.data.sequences | Provides classes for representing sequences. |
de.jstacs.data.sequences.annotation | Provides the facilities to annotate Sequence s 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 Storable s to an XML-representation |
de.jstacs.results | This package provides classes for results and sets of results. |
Uses of SequenceAnnotationParser in de.jstacs.data |
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Methods in de.jstacs.data with parameters of type SequenceAnnotationParser | |
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void |
DataSet.save(OutputStream stream,
char commentChar,
SequenceAnnotationParser p)
This method allows to write all Sequence s including their
SequenceAnnotation s into a OutputStream . |
Constructors in de.jstacs.data with parameters of type SequenceAnnotationParser | |
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DNADataSet(String fName,
char ignore,
SequenceAnnotationParser parser)
Creates a new sample of DNA sequence from a file with file name fName using the given parser . |
Uses of SequenceAnnotationParser in de.jstacs.data.sequences |
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Methods in de.jstacs.data.sequences with parameters of type SequenceAnnotationParser | |
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static DataSet |
SparseSequence.getDataSet(AlphabetContainer con,
String filename,
SequenceAnnotationParser parser)
This method allows to create a DataSet containing SparseSequence s using
a file name. |
static DataSet |
ArbitraryFloatSequence.getDataSet(AlphabetContainer con,
String filename,
SequenceAnnotationParser parser)
This method allows to create a DataSet containing ArbitraryFloatSequence s using
a file name. |
Uses of SequenceAnnotationParser in de.jstacs.data.sequences.annotation |
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Classes in de.jstacs.data.sequences.annotation that implement SequenceAnnotationParser | |
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class |
MotifAnnotationParser
Annotation parser for MotifAnnotation s. |
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 |
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Fields in de.jstacs.io declared as SequenceAnnotationParser | |
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protected SequenceAnnotationParser |
SparseStringExtractor.annotationParser
A parser for the sequence annotation. |
Constructors in de.jstacs.io with parameters of type SequenceAnnotationParser | |
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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 . |
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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 . |
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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 . |
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SparseStringExtractor(String fName,
SequenceAnnotationParser parser)
A constructor that reads the lines from a file. |
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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 |
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Methods in de.jstacs.results that return SequenceAnnotationParser | |
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SequenceAnnotationParser |
DataSetResult.getParser()
Returns the SequenceAnnotationParser that can be used to
write this DataSetResult including annotations on the contained Sequence s
to a file. |
Methods in de.jstacs.results with parameters of type SequenceAnnotationParser | |
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void |
DataSetResult.setParser(SequenceAnnotationParser parser)
Sets the SequenceAnnotationParser that can be used to
write this DataSetResult including annotations on the contained Sequence s
to a file |
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