de.jstacs.data.sequences
Class PermutedSequence
java.lang.Object
de.jstacs.data.Sequence
de.jstacs.data.sequences.RecursiveSequence
de.jstacs.data.sequences.PermutedSequence
- All Implemented Interfaces:
- Comparable<Sequence>
public class PermutedSequence
- extends RecursiveSequence
This class is for permuted sequences.
- Author:
- Jan Grau
Methods inherited from class de.jstacs.data.Sequence |
annotate, compareTo, complement, complement, create, create, create, equals, getAlphabetContainer, getAnnotation, getCompositeSequence, getCompositeSequence, getSubSequence, getSubSequence, getSubSequence, getSubSequence, hashCode, reverse, reverse, reverseComplement, reverseComplement, toDiscrete, toString, toString, toString, toString |
PermutedSequence
public PermutedSequence(Sequence seq)
throws WrongAlphabetException
- Creates a new
PermutedSequence
by shuffling the symbols of a
given Sequence
.
- Parameters:
seq
- the initial sequence
- Throws:
WrongAlphabetException
- if the AlphabetContainer
is not simple- See Also:
RecursiveSequence.RecursiveSequence(de.jstacs.data.AlphabetContainer,
Sequence)
getIndex
protected int getIndex(int pos)
- Description copied from class:
RecursiveSequence
- Returns the index in the internal sequence.
- Specified by:
getIndex
in class RecursiveSequence
- Parameters:
pos
- the index in the external sequence
- Returns:
- the index in the internal sequence
getLength
public int getLength()
- Description copied from class:
Sequence
- Returns the length of the
Sequence.CompositeSequence
.
- Specified by:
getLength
in class Sequence
- Returns:
- the length of the
Sequence.CompositeSequence
flatCloneWithoutAnnotation
protected Sequence flatCloneWithoutAnnotation()
- Description copied from class:
Sequence
- Works in analogy to
Object.clone()
, but does not clone the
annotation. This method is used in
Sequence.annotate(boolean, SequenceAnnotation...)
.
- Specified by:
flatCloneWithoutAnnotation
in class Sequence
- Returns:
- the cloned
Sequence.CompositeSequence
without annotation