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java.lang.Objectde.jstacs.data.Sequence
de.jstacs.data.sequences.RecursiveSequence
public abstract class RecursiveSequence
This is the main class for subsequences, composite sequences, ... . All these sequences are defined on an existing sequence.
Nested Class Summary |
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Nested classes/interfaces inherited from class de.jstacs.data.Sequence |
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Sequence.CompositeSequence, Sequence.SubSequence |
Field Summary | |
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protected Sequence |
content
The internal sequence |
Fields inherited from class de.jstacs.data.Sequence |
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alphabetCon, annotation, rc |
Constructor Summary | |
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RecursiveSequence(AlphabetContainer alphabet,
Sequence seq)
This constructor creates a recursive sequence using the annotation of the given sequence. |
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RecursiveSequence(AlphabetContainer alphabet,
SequenceAnnotation[] annotation,
Sequence seq)
This constructor creates a recursive sequence. |
Method Summary | |
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double |
continuousVal(int pos)
Returns the continuous value of position pos . |
int |
discreteVal(int pos)
Returns the discrete value of position pos . |
protected abstract int |
getIndex(int pos)
Return the index in the internal sequence |
Methods inherited from class de.jstacs.data.Sequence |
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annotate, compareTo, complement, complement, create, create, create, equals, flatCloneWithoutAnnotation, getAlphabetContainer, getAnnotation, getCompositeSequence, getCompositeSequence, getLength, getSubSequence, getSubSequence, getSubSequence, getSubSequence, hashCode, reverse, reverse, reverseComplement, reverseComplement, toDiscrete, toString, toString, toString, toString |
Methods inherited from class java.lang.Object |
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clone, finalize, getClass, notify, notifyAll, wait, wait, wait |
Field Detail |
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protected Sequence content
Constructor Detail |
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public RecursiveSequence(AlphabetContainer alphabet, SequenceAnnotation[] annotation, Sequence seq)
alphabet
- the AlphabetContainerannotation
- the annotation of the recursive sequenceseq
- the sequencepublic RecursiveSequence(AlphabetContainer alphabet, Sequence seq)
alphabet
- the AlphabetContainerseq
- the sequenceMethod Detail |
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public final double continuousVal(int pos)
Sequence
pos
.
continuousVal
in class Sequence
pos
- the position
pos
public final int discreteVal(int pos)
Sequence
pos
.
discreteVal
in class Sequence
pos
- the position
pos
protected abstract int getIndex(int pos)
pos
- the index in the external sequence
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