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java.lang.Objectde.jstacs.data.sequences.Sequence<int[]>
de.jstacs.data.sequences.SimpleDiscreteSequence
de.jstacs.data.sequences.SparseSequence
public final class SparseSequence
This class is an implementation for sequences on one alphabet with length 4.
This implementation can be used, for instance, for DNA sequences.
The symbols are encoded in the bits of the primitive type long
,
which allows to save 32 symbols in one long
. On the one hand an
instance of this class is more memory efficient than any other
SimpleDiscreteSequence
, e.g. ByteSequence
. But on the other hand
this class will be a little bit slower when accessing single positions.
Nested Class Summary |
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Nested classes/interfaces inherited from class de.jstacs.data.sequences.Sequence |
---|
Sequence.CompositeSequence<T>, Sequence.RecursiveSequence<T>, Sequence.SubSequence<T> |
Field Summary |
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Fields inherited from class de.jstacs.data.sequences.Sequence |
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alphabetCon, annotation, rc |
Constructor Summary | |
---|---|
SparseSequence(AlphabetContainer alphCon,
String seq)
Creates a new SparseSequence from a String
representation. |
|
SparseSequence(AlphabetContainer alphCon,
SymbolExtractor se)
Creates a new SparseSequence from a SymbolExtractor . |
Method Summary | |
---|---|
SparseSequence |
complement(int start,
int end)
This method returns a new instance of Sequence containing a part
of the complementary current Sequence . |
int |
discreteVal(int pos)
Returns the discrete value at position pos of the
Sequence . |
protected SparseSequence |
flatCloneWithoutAnnotation()
Works in analogy to Object.clone() , but does not clone the
annotation. |
static DataSet |
getDataSet(AlphabetContainer con,
AbstractStringExtractor... se)
This method allows to create a DataSet containing SparseSequence s. |
static DataSet |
getDataSet(AlphabetContainer con,
String filename)
This method allows to create a DataSet containing SparseSequence s using
a file name. |
static DataSet |
getDataSet(AlphabetContainer con,
String filename,
SequenceAnnotationParser parser)
This method allows to create a DataSet containing SparseSequence s using
a file name. |
int |
getLength()
Returns the length of the Sequence . |
SparseSequence |
reverse(int start,
int end)
This method returns a new instance of Sequence containing a part
of the reverse current Sequence . |
SparseSequence |
reverseComplement(int start,
int end)
This method returns a new instance of Sequence containing a
reverse part of the complementary current Sequence . |
Methods inherited from class de.jstacs.data.sequences.SimpleDiscreteSequence |
---|
addToRepresentation, compareTo, continuousVal, fillContainer, getEmptyContainer, getEmptyRepresentation, getStringRepresentation, hashCodeForPos, isMultiDimensional |
Methods inherited from class de.jstacs.data.sequences.Sequence |
---|
annotate, compareTo, complement, create, create, create, equals, getAlphabetContainer, getAnnotation, getCompositeSequence, getCompositeSequence, getHammingDistance, getNumberOfSequenceAnnotationsByType, getSequenceAnnotationByType, getSequenceAnnotationByTypeAndIdentifier, getSubSequence, getSubSequence, getSubSequence, getSubSequence, hashCode, matches, reverse, reverseComplement, toDiscrete, toString, toString, toString, toString |
Methods inherited from class java.lang.Object |
---|
clone, finalize, getClass, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public SparseSequence(AlphabetContainer alphCon, String seq) throws WrongSequenceTypeException, WrongAlphabetException
SparseSequence
from a String
representation.
alphCon
- the AlphabetContainer
seq
- the sequence as String
WrongSequenceTypeException
- if the AlphabetContainer
is not simple or the
internal Alphabet
has more than 4
symbols
WrongAlphabetException
- if the AlphabetContainer
is not discreteSparseSequence(AlphabetContainer, SymbolExtractor)
public SparseSequence(AlphabetContainer alphCon, SymbolExtractor se) throws WrongSequenceTypeException, WrongAlphabetException
SparseSequence
from a SymbolExtractor
.
alphCon
- the AlphabetContainer
se
- the SymbolExtractor
WrongSequenceTypeException
- if the AlphabetContainer
is not simple or the
internal Alphabet
has more than 4
symbols
WrongAlphabetException
- if the AlphabetContainer
is not discreteSparseSequence(AlphabetContainer, int, SequenceAnnotation[])
Method Detail |
---|
public int discreteVal(int pos)
Sequence
pos
of the
Sequence
.
discreteVal
in class Sequence<int[]>
pos
- the position of the Sequence
pos
of the
Sequence
public int getLength()
Sequence
Sequence
.
getLength
in class Sequence<int[]>
Sequence
public SparseSequence complement(int start, int end) throws OperationNotSupportedException
Sequence
Sequence
containing a part
of the complementary current Sequence
.
AlphabetContainer
on
DNAAlphabet
returns "ATTAT".
complement
in class Sequence<int[]>
start
- the start position (inclusive) in the original
Sequence
end
- the end position (exclusive) in the original Sequence
Sequence
of the part
OperationNotSupportedException
- if the current Sequence
is not based on a
ComplementableDiscreteAlphabet
ComplementableDiscreteAlphabet
public SparseSequence reverse(int start, int end) throws OperationNotSupportedException
Sequence
Sequence
containing a part
of the reverse current Sequence
.
reverse
in class Sequence<int[]>
start
- the start position (inclusive) in the original
Sequence
end
- the end position (exclusive) in the original Sequence
Sequence
of the part
OperationNotSupportedException
- if the current Sequence
is based on an
AlphabetContainer
that is not simplepublic SparseSequence reverseComplement(int start, int end) throws OperationNotSupportedException
Sequence
Sequence
containing a
reverse part of the complementary current Sequence
. For more
details see the methods Sequence.reverse()
and Sequence.complement()
.
reverseComplement
in class Sequence<int[]>
start
- the start position (inclusive) in the original
Sequence
end
- the end position (exclusive) in the original Sequence
Sequence
of the part
OperationNotSupportedException
- if the current Sequence
is not discrete and simple
((not based on a ComplementableDiscreteAlphabet
)Sequence.reverse()
,
Sequence.complement()
,
ComplementableDiscreteAlphabet
protected SparseSequence flatCloneWithoutAnnotation()
Sequence
Object.clone()
, but does not clone the
annotation. This method is used in
Sequence.annotate(boolean, SequenceAnnotation...)
.
flatCloneWithoutAnnotation
in class Sequence<int[]>
Sequence
without annotationpublic static DataSet getDataSet(AlphabetContainer con, String filename, SequenceAnnotationParser parser) throws FileNotFoundException, WrongAlphabetException, WrongSequenceTypeException, EmptyDataSetException, IOException
DataSet
containing SparseSequence
s using
a file name. Annotations are parsed by the supplied SequenceAnnotationParser
. The file is
assumed to be in FastA format.
con
- the AlphabetContainer
for the DataSet
and SparseSequence
sfilename
- the file nameparser
- a parser for the annotations of the SparseSequence
s
DataSet
containing SparseSequence
s
FileNotFoundException
- if the file filename
could not be found
WrongAlphabetException
- if the alphabet does not fit the data
WrongSequenceTypeException
- if the data can not be represented as floats
EmptyDataSetException
- if not sequences exist in filename
IOException
- if the file could not be readpublic static DataSet getDataSet(AlphabetContainer con, String filename) throws FileNotFoundException, WrongAlphabetException, WrongSequenceTypeException, EmptyDataSetException, IOException
DataSet
containing SparseSequence
s using
a file name.
con
- the AlphabetContainer
for the DataSet
and SparseSequence
sfilename
- the file name
DataSet
containing SparseSequence
s
FileNotFoundException
- if the file filename
could not be found
WrongAlphabetException
- if the alphabet does not fit the data
WrongSequenceTypeException
- if the data can not be represented as floats
EmptyDataSetException
- if not sequences exist in filename
IOException
- if the file could not be readpublic static final DataSet getDataSet(AlphabetContainer con, AbstractStringExtractor... se) throws WrongSequenceTypeException, WrongAlphabetException, EmptyDataSetException
DataSet
containing SparseSequence
s.
con
- the AlphabetContainer
for the DataSet
and Sequence
sse
- the AbstractStringExtractor
s that handle the DataSet
as String
DataSet
containing SparseSequence
s
WrongSequenceTypeException
- if the AlphabetContainer
is not simple or the
internal Alphabet
has more than 4
symbols
WrongAlphabetException
- if the AlphabetContainer
is not discrete
EmptyDataSetException
- if a DataSet
with 0 (zero) Sequence
should be created
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