de.jstacs.data.sequences.annotation

Class SinglePositionSequenceAnnotation

java.lang.Object

de.jstacs.results.ResultSet

de.jstacs.data.sequences.annotation.SequenceAnnotation

de.jstacs.data.sequences.annotation.LocatedSequenceAnnotation

de.jstacs.data.sequences.annotation.SinglePositionSequenceAnnotation

All Implemented Interfaces:

Storable

public class SinglePositionSequenceAnnotation
extends LocatedSequenceAnnotation

Class for some annotations that consist mainly of one position on a sequence. This includes transcription start sites, translation start sites, splice donor sites and splice acceptor sites.

Author:

Jan Grau

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SinglePositionSequenceAnnotation.Type This enum defines possible types of a SinglePositionSequenceAnnotation.

Field Summary

Fields inherited from class de.jstacs.results.ResultSet

results

Constructor Summary

Constructors

Constructor and Description
SinglePositionSequenceAnnotation(SinglePositionSequenceAnnotation.Type type, String identifier, int position) Creates a new SinglePositionSequenceAnnotation of type type with identifier identifier and position position.
SinglePositionSequenceAnnotation(SinglePositionSequenceAnnotation.Type type, String identifier, int position, Result... additionalAnnotation) Creates a new SinglePositionSequenceAnnotation of type type with identifier identifier, position position and additional annotations additionalAnnotation.
SinglePositionSequenceAnnotation(StringBuffer representation) The standard constructor for the interface Storable.

Method Summary

Methods inherited from class de.jstacs.data.sequences.annotation.LocatedSequenceAnnotation

fromXML, getPosition, toString, toXML

Methods inherited from class de.jstacs.data.sequences.annotation.SequenceAnnotation

getAnnotations, getIdentifier, getSubAnnotations, getType, hashCode

Methods inherited from class de.jstacs.results.ResultSet

findColumn, getNumberOfResults, getResultAt, getResultForName, getResults

Methods inherited from class java.lang.Object

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

Constructor Detail

SinglePositionSequenceAnnotation

public SinglePositionSequenceAnnotation(SinglePositionSequenceAnnotation.Type type,
                                String identifier,
                                int position)

Creates a new SinglePositionSequenceAnnotation of type type with identifier identifier and position position.

Parameters:

position - the position of the SinglePositionSequenceAnnotation on the sequence

type - the type of the annotation

identifier - the identifier of the annotation

See Also:

LocatedSequenceAnnotation.LocatedSequenceAnnotation(int, String, String, Result...)

SinglePositionSequenceAnnotation

public SinglePositionSequenceAnnotation(SinglePositionSequenceAnnotation.Type type,
                                String identifier,
                                int position,
                                Result... additionalAnnotation)

Creates a new SinglePositionSequenceAnnotation of type type with identifier identifier, position position and additional annotations additionalAnnotation.

Parameters:

position - the position of the SinglePositionSequenceAnnotation on the sequence

type - the type of the annotation

identifier - the identifier of the annotation

additionalAnnotation - the additional annotation

See Also:

LocatedSequenceAnnotation.LocatedSequenceAnnotation(int, String, String, Result...)

SinglePositionSequenceAnnotation

public SinglePositionSequenceAnnotation(StringBuffer representation)
                                 throws NonParsableException

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

Parameters:

representation - the XML representation as StringBuffer

Throws:

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

See Also:

LocatedSequenceAnnotation.LocatedSequenceAnnotation(StringBuffer), Storable