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 DiscreteSequence s prepared for alphabets of different sizes, and ArbitrarySequence s that may
contain continuous values as well.As sub-package provides the facilities to annotate Sequence s. |
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.
|
Modifier and Type | Method and Description |
---|---|
void |
DataSet.save(OutputStream stream,
char commentChar,
SequenceAnnotationParser p)
|
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 . |
Modifier and Type | Method and Description |
---|---|
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. |
Modifier and Type | Class and Description |
---|---|
class |
MotifAnnotationParser
Annotation parser for
MotifAnnotation s. |
class |
NullSequenceAnnotationParser
|
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. |
Modifier and Type | Field and Description |
---|---|
protected SequenceAnnotationParser |
SparseStringExtractor.annotationParser
A parser for the sequence annotation.
|
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 . |
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 Sequence s
to a file. |
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 Sequence s
to a file |