public class MultiDimensionalArbitrarySequence extends MultiDimensionalSequence<double[]>
Sequence.CompositeSequence<T>, Sequence.RecursiveSequence<T>, Sequence.SubSequence<T>
content
alphabetCon, annotation, rc
Constructor and Description |
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MultiDimensionalArbitrarySequence(SequenceAnnotation[] seqAn,
ArbitrarySequence... sequence)
This constructor creates an
MultiDimensionalDiscreteSequence from a set of individual Sequence s. |
Modifier and Type | Method and Description |
---|---|
int |
compareTo(double[] t1,
double[] t2)
This method compares to container and is used in
Sequence.compareTo(Sequence) . |
void |
fillContainer(double[] container,
int pos)
The method fills the content of a specific position in to the container.
|
double[] |
getEmptyContainer()
The method returns a container that can be used for accessing the symbols for each position.
|
protected MultiDimensionalArbitrarySequence |
getInstance(SequenceAnnotation[] seqAn,
Sequence... seqs)
Returns a new instance of a
MultiDimensionalSequence with given SequenceAnnotation s and given Sequence s. |
addToRepresentation, complement, continuousVal, discreteVal, flatCloneWithoutAnnotation, getAnnotations, getEmptyRepresentation, getLength, getNumberOfSequences, getSequence, getStringRepresentation, hashCodeForPos, isMultiDimensional, reverseComplement
annotate, compareTo, complement, create, create, create, equals, getAlphabetContainer, getAnnotation, getCompositeSequence, getCompositeSequence, getHammingDistance, getNumberOfSequenceAnnotationsByType, getSequenceAnnotationByType, getSequenceAnnotationByTypeAndIdentifier, getSubSequence, getSubSequence, getSubSequence, getSubSequence, hashCode, matches, reverse, reverse, reverseComplement, toDiscrete, toString, toString, toString, toString
public MultiDimensionalArbitrarySequence(SequenceAnnotation[] seqAn, ArbitrarySequence... sequence) throws WrongLengthException, WrongAlphabetException
MultiDimensionalDiscreteSequence
from a set of individual Sequence
s.seqAn
- the annotations for the aligned sequencessequence
- the individual sequences that have been alignedWrongLengthException
- if the sequences have different lengthsWrongAlphabetException
- if the sequences have different AlphabetContainer
spublic void fillContainer(double[] container, int pos)
Sequence
fillContainer
in class Sequence<double[]>
container
- the container which is used for filling the content.pos
- the positionSequence.getEmptyContainer()
,
Sequence.isMultiDimensional()
public double[] getEmptyContainer()
Sequence
getEmptyContainer
in class Sequence<double[]>
Sequence.fillContainer(Object, int)
,
Sequence.isMultiDimensional()
protected MultiDimensionalArbitrarySequence getInstance(SequenceAnnotation[] seqAn, Sequence... seqs) throws WrongLengthException, WrongAlphabetException
MultiDimensionalSequence
MultiDimensionalSequence
with given SequenceAnnotation
s and given Sequence
s.getInstance
in class MultiDimensionalSequence<double[]>
seqAn
- the sequence annotationsseqs
- the sequence buidl9ing the new MultiDimensionalSequence
MultiDimensionalSequence
with given SequenceAnnotation
s and given Sequence
sWrongLengthException
- if the sequences have different lengthsWrongAlphabetException
- if the sequences have different AlphabetContainer
sMultiDimensionalSequence.flatCloneWithoutAnnotation()
,
Sequence.complement()
,
Sequence.reverseComplement()
public int compareTo(double[] t1, double[] t2)
Sequence
Sequence.compareTo(Sequence)
.compareTo
in class Sequence<double[]>
t1
- the first containert2
- the second containerSequence.getEmptyContainer()
,
Sequence.fillContainer(Object, int)
,
Comparable.compareTo(java.lang.Object)