de.jstacs.data
Class DNASample

java.lang.Object
  de.jstacs.data.Sample
      de.jstacs.data.DNASample

All Implemented Interfaces:

Iterable<Sequence>

public class DNASample
extends Sample

This class exist for convenience to allow the user an easy creation of Samples of DNA Sequences.

Author:

Jan Grau, Jens Keilwagen

Nested Class Summary

Nested classes/interfaces inherited from class de.jstacs.data.Sample

Sample.ElementEnumerator, Sample.PartitionMethod, Sample.WeightedSampleFactory

Constructor Summary

DNASample(String fName)
Creates a new sample of DNA sequence from a FASTA file with file name fName.

DNASample(String fName, char ignore)
Creates a new sample of DNA sequence from a file with file name fName.

DNASample(String fName, char ignore, SequenceAnnotationParser parser)
Creates a new sample of DNA sequence from a file with file name fName using the given parser.

Method Summary

Methods inherited from class de.jstacs.data.Sample

diff, getAllElements, getAlphabetContainer, getAnnotation, getAnnotation, getAnnotationTypesAndIdentifier, getCompositeSample, getElementAt, getElementLength, getInfixSample, getMaximalElementLength, getMinimalElementLength, getNumberOfElements, getNumberOfElementsWithLength, getNumberOfElementsWithLength, getReverseComplementarySample, getSequenceAnnotationIndexMatrix, getSuffixSample, intersection, isDiscreteSample, isSimpleSample, iterator, partition, partition, partition, partition, partition, save, save, subSampling, toString, union, union, union, union

Methods inherited from class java.lang.Object

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

Constructor Detail

DNASample

public DNASample(String fName)
          throws FileNotFoundException,
                 WrongAlphabetException,
                 EmptySampleException,
                 WrongLengthException,
                 IOException

Creates a new sample of DNA sequence from a FASTA file with file name fName.

Parameters:

fName - the file name

Throws:

IOException - if the File could not be read

FileNotFoundException - if the File could not be found

WrongAlphabetException - if the DNA AlphabetContainer is not suitable

EmptySampleException - if the Sample would be empty

WrongLengthException - never happens (forwarded from Sample.Sample(AlphabetContainer, de.jstacs.io.AbstractStringExtractor, String, int) )

See Also:

AbstractStringExtractor.FASTA, DNASample(String, char)

DNASample

public DNASample(String fName,
                 char ignore)
          throws FileNotFoundException,
                 WrongAlphabetException,
                 EmptySampleException,
                 WrongLengthException,
                 IOException

Creates a new sample of DNA sequence from a file with file name fName.

Parameters:

fName - the file name

ignore - the first character of lines that should be treated as comments

Throws:

IOException - if the File could not be read

FileNotFoundException - if the File could not be found

WrongAlphabetException - if the DNA AlphabetContainer is not suitable

EmptySampleException - if the Sample would be empty

WrongLengthException - never happens (forwarded from Sample.Sample(AlphabetContainer, de.jstacs.io.AbstractStringExtractor, String, int) )

See Also:

SparseStringExtractor, AbstractStringExtractor.FASTA, AbstractStringExtractor.USUALLY, DNASample(String, char, SequenceAnnotationParser)

DNASample

public DNASample(String fName,
                 char ignore,
                 SequenceAnnotationParser parser)
          throws FileNotFoundException,
                 WrongAlphabetException,
                 EmptySampleException,
                 WrongLengthException,
                 IOException

Creates a new sample of DNA sequence from a file with file name fName using the given parser.

Parameters:

fName - the file name

ignore - the first character of lines that should be treated as comments

parser - the parser for the SequenceAnnotation

Throws:

IOException - if the File could not be read

FileNotFoundException - if the File could not be found

WrongAlphabetException - if the DNA AlphabetContainer is not suitable

EmptySampleException - if the Sample would be empty

WrongLengthException - never happens (forwarded from Sample.Sample(AlphabetContainer, de.jstacs.io.AbstractStringExtractor, String, int) )

See Also:

SparseStringExtractor, AbstractStringExtractor.FASTA, AbstractStringExtractor.USUALLY, Sample.Sample(AlphabetContainer, de.jstacs.io.AbstractStringExtractor)