de.jstacs.results
Class SampleResult

java.lang.Object
  de.jstacs.results.Result
      de.jstacs.results.SampleResult

All Implemented Interfaces:

Storable

public class SampleResult
extends Result

Result that contains a Sample. This Sample e.g. may have been created by Model.emitSample(int, int...), or maybe a Sample that has been annotated in a classification.

Author:

Jan Grau

Field Summary

Fields inherited from class de.jstacs.results.Result

comment, datatype, name

Constructor Summary

SampleResult(StringBuffer source)
The standard constructor for the interface Storable.

SampleResult(String name, String comment, Sample data)
Creates a new SampleResult from a Sample with the annotation name and comment.

SampleResult(String name, String comment, Sample data, SequenceAnnotationParser parser)
Creates a new SampleResult from a Sample with the annotation name and comment.

Method Summary

protected void	fromXML(StringBuffer rep) This method is used in Result.Result(StringBuffer) to extract the information.
SequenceAnnotationParser	getParser() Returns the SequenceAnnotationParser that can be used to write this SampleResult including annotations on the contained Sequences to a file.
Sample	getResult() Returns the value of the Result.
void	setParser(SequenceAnnotationParser parser) Sets the SequenceAnnotationParser that can be used to write this SampleResult including annotations on the contained Sequences to a file
StringBuffer	toXML() This method returns an XML representation as StringBuffer of an instance of the implementing class.

Methods inherited from class de.jstacs.results.Result

appendMainInfo, checkDatatype, createResult, extractMainInfo, getComment, getDatatype, getName, isCastableResult, isComparableResult

Methods inherited from class java.lang.Object

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

Constructor Detail

SampleResult

public SampleResult(String name,
                    String comment,
                    Sample data)

Creates a new SampleResult from a Sample with the annotation name and comment.

Parameters:

name - the name of the Result

comment - the comment on the Result

data - the Sample that is the result of some computation

SampleResult

public SampleResult(String name,
                    String comment,
                    Sample data,
                    SequenceAnnotationParser parser)

Creates a new SampleResult from a Sample with the annotation name and comment.

Parameters:

name - the name of the Result

comment - the comment on the Result

data - the Sample that is the result of some computation

parser - a SequenceAnnotationParser that can be used to store and parse the annotations of data

SampleResult

public SampleResult(StringBuffer source)
             throws NonParsableException

The standard constructor for the interface Storable. Recreates a SampleResult from its XML representation as returned by toXML().

Parameters:

source - the XML representation as StringBuffer

Throws:

NonParsableException - if the XML code could not be parsed

Method Detail

fromXML

protected void fromXML(StringBuffer rep)
                throws NonParsableException

Description copied from class: Result

This method is used in Result.Result(StringBuffer) to extract the information. The method can be seen as opposite of Storable.toXML() and should not be made public.

Specified by:

fromXML in class Result

Parameters:

rep - the XML represenation of the Result to be parsed

Throws:

NonParsableException - if the XML representation is not parsable

See Also:

Result.extractMainInfo(StringBuffer)

getResult

public Sample getResult()

Description copied from class: Result

Returns the value of the Result.

Specified by:

getResult in class Result

Returns:

the value of the Result

toXML

public StringBuffer toXML()

Description copied from interface: Storable

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

Returns:

the XML representation

getParser

public SequenceAnnotationParser getParser()

Returns the SequenceAnnotationParser that can be used to write this SampleResult including annotations on the contained Sequences to a file.

Returns:

the SequenceAnnotationParser

setParser

public void setParser(SequenceAnnotationParser parser)

Sets the SequenceAnnotationParser that can be used to write this SampleResult including annotations on the contained Sequences to a file

Parameters:

parser - the new SequenceAnnotationParser