de.jstacs.data.sequences.annotation
Class SequenceAnnotation

java.lang.Object
  de.jstacs.results.ResultSet
      de.jstacs.data.sequences.annotation.SequenceAnnotation

All Implemented Interfaces:

Storable

Direct Known Subclasses:

CisRegulatoryModuleAnnotation, LocatedSequenceAnnotation, ReferenceSequenceAnnotation

public class SequenceAnnotation
extends ResultSet

Class for a general annotation of a Sequence. Annotations may be e.g. exons, introns, coding sequences or splice sites.

Author:

Jan Grau

Field Summary

Fields inherited from class de.jstacs.results.ResultSet

results

Constructor Summary

SequenceAnnotation(StringBuffer representation)
The standard constructor for the interface Storable.

SequenceAnnotation(String type, String identifier, Collection<? extends Result> results)
Creates a new SequenceAnnotation of type type with identifier identifier and additional annotation (that does not fit the SequenceAnnotation definitions) given as a Collection of Results results.

SequenceAnnotation(String type, String identifier, Result result)
Creates a new SequenceAnnotation of type type with identifier identifier and additional annotation (that does not fit the SequenceAnnotation definitions) given as a Result result.

SequenceAnnotation(String type, String identifier, Result[]... results)
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 Results results.

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 Results additionalAnnotation.

Method Summary

protected void	fromXML(StringBuffer source) Parses the contents of a ResultSet from its XML representation as returned by ResultSet.toXML().
Result[]	getAnnotations() Returns the additional annotations of this SequenceAnnotation as given in the constructor.
String	getIdentifier() Returns the identifier of this SequenceAnnotation as given in the constructor.
SequenceAnnotation[]	getSubAnnotations() Returns the sub-annotations of this SequenceAnnotation as given in the constructor.
String	getType() Returns the type of this SequenceAnnotation as given in the constructor.
String	toString()
StringBuffer	toXML() This method returns an XML representation as StringBuffer of an instance of the implementing class.

Methods inherited from class de.jstacs.results.ResultSet

findColumn, getNumberOfResults, getResultAt, getResultForName, getResults

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

SequenceAnnotation

public SequenceAnnotation(String type,
                          String identifier,
                          Result result)

Creates a new SequenceAnnotation of type type with identifier identifier and additional annotation (that does not fit the SequenceAnnotation definitions) given as a Result result.

Parameters:

type - the type of the annotation

identifier - the identifier of the annotation

result - the additional annotation

See Also:

ResultSet.ResultSet(Result)

SequenceAnnotation

public SequenceAnnotation(String type,
                          String identifier,
                          Result[]... results)

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 Results results.

Parameters:

type - the type of the annotation

identifier - the identifier of the annotation

results - the additional annotation

See Also:

ResultSet.ResultSet(Result[][])

SequenceAnnotation

public 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 Results additionalAnnotation. This SequenceAnnotation may contain sub-annotations subAnnotations, this may be e.g. the donor and acceptor site for splice sites or the exons for a gene.

Parameters:

type - the type of the annotation

identifier - the identifier of the annotation

subAnnotations - the sub-annotation

additionalAnnotation - the additional annotation

See Also:

ResultSet.ResultSet(Result[][])

SequenceAnnotation

public SequenceAnnotation(String type,
                          String identifier,
                          Collection<? extends Result> results)

Creates a new SequenceAnnotation of type type with identifier identifier and additional annotation (that does not fit the SequenceAnnotation definitions) given as a Collection of Results results.

Parameters:

type - the type of the annotation

identifier - the identifier of the annotation

results - the additional annotation

See Also:

ResultSet.ResultSet(Collection)

SequenceAnnotation

public SequenceAnnotation(StringBuffer representation)
                   throws NonParsableException

The standard constructor for the interface Storable. Creates a new SequenceAnnotation out of its XML representation.

Parameters:

representation - the XML representation as StringBuffer

Throws:

NonParsableException - if the SequenceAnnotation could not be reconstructed out of the XML representation (the StringBuffer representation could not be parsed)

See Also:

ResultSet.ResultSet(StringBuffer), Storable

Method Detail

getType

public String getType()

Returns the type of this SequenceAnnotation as given in the constructor.

Returns:

the type of this SequenceAnnotation

getAnnotations

public Result[] getAnnotations()

Returns the additional annotations of this SequenceAnnotation as given in the constructor.

Returns:

the additional annotations of this SequenceAnnotation

getSubAnnotations

public SequenceAnnotation[] getSubAnnotations()

Returns the sub-annotations of this SequenceAnnotation as given in the constructor.

Returns:

the sub-annotations of this SequenceAnnotation

toString

public String toString()

Overrides:

toString in class ResultSet

fromXML

protected void fromXML(StringBuffer source)
                throws NonParsableException

Description copied from class: ResultSet

Parses the contents of a ResultSet from its XML representation as returned by ResultSet.toXML().

Overrides:

fromXML in class ResultSet

Parameters:

source - the XML representation as StringBuffer

Throws:

NonParsableException - if the XML code could not be parsed

toXML

public StringBuffer toXML()

Description copied from interface: Storable

This method returns an XML representation as StringBuffer of an instance of the implementing class.

Specified by:

toXML in interface Storable

Overrides:

toXML in class ResultSet

Returns:

the XML representation

getIdentifier

public String getIdentifier()

Returns the identifier of this SequenceAnnotation as given in the constructor.

Returns:

the identifier of this SequenceAnnotation