Package | Description |
---|---|
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. |
Modifier and Type | Field and Description |
---|---|
protected SequenceAnnotation[] |
Sequence.annotation
The annotation of the
Sequence . |
Modifier and Type | Method and Description |
---|---|
SequenceAnnotation[] |
Sequence.getAnnotation()
Returns the annotation of the
Sequence . |
SequenceAnnotation[][] |
MultiDimensionalSequence.getAnnotations()
This method returns the
SequenceAnnotation [] for each dimension of this multidimensional sequence. |
SequenceAnnotation |
Sequence.getSequenceAnnotationByType(String type,
int idx)
Returns the
SequenceAnnotation no. |
SequenceAnnotation |
Sequence.getSequenceAnnotationByTypeAndIdentifier(String type,
String identifier)
|
Modifier and Type | Method and Description |
---|---|
Sequence |
Sequence.annotate(boolean add,
SequenceAnnotation... annotation)
This method allows to append annotation to a
Sequence . |
static Sequence |
Sequence.create(AlphabetContainer con,
SequenceAnnotation[] annotation,
String sequence,
String delim)
Creates a
Sequence from a String based on the given
AlphabetContainer using the given delimiter delim
and some annotation for the Sequence . |
protected abstract MultiDimensionalSequence<T> |
MultiDimensionalSequence.getInstance(SequenceAnnotation[] seqAn,
Sequence... seqs)
Returns a new instance of a
MultiDimensionalSequence with given SequenceAnnotation s and given Sequence s. |
protected MultiDimensionalDiscreteSequence |
MultiDimensionalDiscreteSequence.getInstance(SequenceAnnotation[] seqAn,
Sequence... seqs) |
protected MultiDimensionalArbitrarySequence |
MultiDimensionalArbitrarySequence.getInstance(SequenceAnnotation[] seqAn,
Sequence... seqs) |
Modifier and Type | Class and Description |
---|---|
class |
CisRegulatoryModuleAnnotation
Annotation for a cis-regulatory module as defined by a set of
MotifAnnotation s of the motifs in the module. |
class |
IntronAnnotation
Annotation class for an intron as defined by a donor and an acceptor splice
site.
|
class |
LocatedSequenceAnnotation
Class for a
SequenceAnnotation that has a position on the sequence,
e.g for transcription start sites or intron-exon junctions. |
class |
LocatedSequenceAnnotationWithLength
Class for a
SequenceAnnotation that has a position on the sequence
and a length, e.g. |
class |
MotifAnnotation
Class for a
StrandedLocatedSequenceAnnotationWithLength that is a
motif. |
class |
ReferenceSequenceAnnotation
This class implements a
SequenceAnnotation that contains a reference
sequence. |
class |
SinglePositionSequenceAnnotation
Class for some annotations that consist mainly of one position on a sequence.
|
class |
StrandedLocatedSequenceAnnotationWithLength
Class for a
SequenceAnnotation that has a position, a length and an
orientation on the strand of a Sequence . |
Modifier and Type | Field and Description |
---|---|
protected LinkedList<SequenceAnnotation> |
SplitSequenceAnnotationParser.annot
The internal list of current
SequenceAnnotation s. |
Modifier and Type | Method and Description |
---|---|
SequenceAnnotation[] |
SplitSequenceAnnotationParser.getCurrentAnnotation() |
SequenceAnnotation[] |
SimpleSequenceAnnotationParser.getCurrentAnnotation() |
SequenceAnnotation[] |
SequenceAnnotationParser.getCurrentAnnotation()
This method returns the current
SequenceAnnotation . |
SequenceAnnotation[] |
NullSequenceAnnotationParser.getCurrentAnnotation() |
SequenceAnnotation[] |
SequenceAnnotation.getSubAnnotations()
Returns the sub-annotations of this
SequenceAnnotation as given
in the constructor. |
Modifier and Type | Method and Description |
---|---|
String |
SplitSequenceAnnotationParser.parseAnnotationToComment(char commentChar,
SequenceAnnotation... annotations) |
String |
SimpleSequenceAnnotationParser.parseAnnotationToComment(char commentChar,
SequenceAnnotation... annotations) |
String |
SequenceAnnotationParser.parseAnnotationToComment(char commentChar,
SequenceAnnotation... annotations)
This method returns a
String representation of the given
SequenceAnnotation s that can be used as comment line in a file. |
String |
ReferenceSequenceAnnotationParser.parseAnnotationToComment(char commentChar,
SequenceAnnotation... annotations) |
String |
NullSequenceAnnotationParser.parseAnnotationToComment(char commentChar,
SequenceAnnotation... annotations) |
String |
MotifAnnotationParser.parseAnnotationToComment(char commentChar,
SequenceAnnotation... annotations) |
Constructor and Description |
---|
LocatedSequenceAnnotation(int position,
String type,
String identifier,
SequenceAnnotation[] annotations,
Result... additionalAnnotation)
Creates a new
LocatedSequenceAnnotation of type type
with identifier identifier , additional annotation (that does
not fit the SequenceAnnotation definitions) given as an array of
Result s additionalAnnotation and sub-annotations
annotations . |
LocatedSequenceAnnotationWithLength(int position,
int length,
String type,
String identifier,
SequenceAnnotation[] annotations,
Result... additionalAnnotations)
Creates a new
LocatedSequenceAnnotationWithLength of type
type with identifier identifier , additional
annotation (that does not fit the SequenceAnnotation definitions)
given as an array of Result s additionalAnnotations
and sub-annotations annotations . |
SequenceAnnotation(String type,
String identifier,
SequenceAnnotation[] subAnnotations,
Result... additionalAnnotation)
Creates a new
SequenceAnnotation of type type with
identifier identifier and additional annotation (that does
not fit the SequenceAnnotation definitions) given as an array of
Result s additionalAnnotation . |
StrandedLocatedSequenceAnnotationWithLength(int position,
int length,
StrandedLocatedSequenceAnnotationWithLength.Strand strandedness,
String type,
String identifier,
SequenceAnnotation[] annotations,
Result... additionalAnnotations)
Creates a new
StrandedLocatedSequenceAnnotationWithLength of type
type with identifier identifier , additional
annotation (that does not fit the SequenceAnnotation definitions)
given as an array of Result s additionalAnnotations
and sub-annotations annotations . |
Modifier and Type | Method and Description |
---|---|
SequenceAnnotation[] |
SparseStringExtractor.getCurrentSequenceAnnotations() |
SequenceAnnotation[] |
LimitedStringExtractor.getCurrentSequenceAnnotations() |
SequenceAnnotation[] |
InfixStringExtractor.getCurrentSequenceAnnotations() |
SequenceAnnotation[] |
AbstractStringExtractor.getCurrentSequenceAnnotations()
|