DataSet.ElementEnumerator, DataSet.PartitionMethod, DataSet.WeightedDataSetFactory
Constructor and Description |
---|
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 . |
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
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
forEach, spliterator
public DNADataSet(String fName) throws FileNotFoundException, WrongAlphabetException, EmptyDataSetException, WrongLengthException, IOException
fName
.fName
- the file nameIOException
- if the File
could not be readFileNotFoundException
- if the File
could not be foundWrongAlphabetException
- if the DNA AlphabetContainer
is not suitableEmptyDataSetException
- if the DataSet
would be emptyWrongLengthException
- never happens (forwarded from
DataSet.DataSet(AlphabetContainer, de.jstacs.io.AbstractStringExtractor, String, int)
)AbstractStringExtractor.FASTA
,
DNADataSet(String, char)
public DNADataSet(String fName, char ignore) throws FileNotFoundException, WrongAlphabetException, EmptyDataSetException, WrongLengthException, IOException
fName
.fName
- the file nameignore
- the first character of lines that should be treated as commentsIOException
- if the File
could not be readFileNotFoundException
- if the File
could not be foundWrongAlphabetException
- if the DNA AlphabetContainer
is not suitableEmptyDataSetException
- if the DataSet
would be emptyWrongLengthException
- never happens (forwarded from
DataSet.DataSet(AlphabetContainer, de.jstacs.io.AbstractStringExtractor, String, int)
)SparseStringExtractor
,
AbstractStringExtractor.FASTA
,
AbstractStringExtractor.USUALLY
,
DNADataSet(String, char, SequenceAnnotationParser)
public DNADataSet(String fName, char ignore, SequenceAnnotationParser parser) throws FileNotFoundException, WrongAlphabetException, EmptyDataSetException, WrongLengthException, IOException
fName
using the given parser
.fName
- the file nameignore
- the first character of lines that should be treated as commentsparser
- the parser for the SequenceAnnotation
IOException
- if the File
could not be readFileNotFoundException
- if the File
could not be foundWrongAlphabetException
- if the DNA AlphabetContainer
is not suitableEmptyDataSetException
- if the DataSet
would be emptyWrongLengthException
- never happens (forwarded from
DataSet.DataSet(AlphabetContainer, de.jstacs.io.AbstractStringExtractor, String, int)
)SparseStringExtractor
,
AbstractStringExtractor.FASTA
,
AbstractStringExtractor.USUALLY
,
DataSet.DataSet(AlphabetContainer, de.jstacs.io.AbstractStringExtractor)