de.jstacs.data
Class DNADataSet

java.lang.Object
  de.jstacs.data.DataSet
      de.jstacs.data.DNADataSet

All Implemented Interfaces:

Iterable<Sequence>

public class DNADataSet
extends DataSet

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

Author:

Jan Grau, Jens Keilwagen

Nested Class Summary

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

DataSet.ElementEnumerator, DataSet.PartitionMethod, DataSet.WeightedDataSetFactory

Constructor Summary

DNADataSet(String fName)
Creates a new data set of DNA sequence from a FASTA file with file name fName.

DNADataSet(String fName, char ignore)
Creates a new data set of DNA sequence from a file with file name fName.

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

Method Summary

Methods inherited from class de.jstacs.data.DataSet

diff, getAllElements, getAlphabetContainer, getAnnotation, getAnnotation, getAnnotationTypesAndIdentifier, getAverageElementLength, getCompositeDataSet, getElementAt, getElementLength, getInfixDataSet, getMaximalElementLength, getMinimalElementLength, getNumberOfElements, getNumberOfElementsWithLength, getNumberOfElementsWithLength, getPartialDataSet, getPartialDataSet, getReverseComplementaryDataSet, getSequenceAnnotationIndexMatrix, getSuffixDataSet, intersection, isDiscreteDataSet, isSimpleDataSet, iterator, partition, partition, partition, partition, resize, save, save, subSampling, subSampling, toString, union, union, union

Methods inherited from class java.lang.Object

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

Constructor Detail

DNADataSet

public DNADataSet(String fName)
           throws FileNotFoundException,
                  WrongAlphabetException,
                  EmptyDataSetException,
                  WrongLengthException,
                  IOException

Creates a new data set 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

EmptyDataSetException - if the DataSet would be empty

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

See Also:

AbstractStringExtractor.FASTA, DNADataSet(String, char)

DNADataSet

public DNADataSet(String fName,
                  char ignore)
           throws FileNotFoundException,
                  WrongAlphabetException,
                  EmptyDataSetException,
                  WrongLengthException,
                  IOException

Creates a new data set 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

EmptyDataSetException - if the DataSet would be empty

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

See Also:

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

DNADataSet

public DNADataSet(String fName,
                  char ignore,
                  SequenceAnnotationParser parser)
           throws FileNotFoundException,
                  WrongAlphabetException,
                  EmptyDataSetException,
                  WrongLengthException,
                  IOException

Creates a new data set 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

EmptyDataSetException - if the DataSet would be empty

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

See Also:

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