de.jstacs.data.sequences
Class DiscreteSequence
java.lang.Object
de.jstacs.data.Sequence
de.jstacs.data.sequences.DiscreteSequence
- All Implemented Interfaces:
- Comparable<Sequence>
- Direct Known Subclasses:
- ByteSequence, IntSequence, ShortSequence, SparseSequence
public abstract class DiscreteSequence
- extends Sequence
This is the main class for any discrete sequence.
- Author:
- Jens Keilwagen
Methods inherited from class de.jstacs.data.Sequence |
annotate, compareTo, complement, complement, create, create, create, discreteVal, equals, flatCloneWithoutAnnotation, getAlphabetContainer, getAnnotation, getCompositeSequence, getCompositeSequence, getHammingDistance, getLength, getNumberOfSequenceAnnotationsByType, getSequenceAnnotationByType, getSubSequence, getSubSequence, getSubSequence, getSubSequence, hashCode, reverse, reverse, reverseComplement, reverseComplement, toDiscrete, toString, toString, toString, toString |
DiscreteSequence
public DiscreteSequence(AlphabetContainer container,
SequenceAnnotation[] annotation)
throws WrongAlphabetException
- This constructor creates a new
DiscreteSequence
with the
AlphabetContainer
container
and the annotation
annotation
but without the content. The content has to be
set by the constructor of the extending class.
- Parameters:
container
- the AlphabetContainer
of the sequenceannotation
- the annotation of the sequence
- Throws:
WrongAlphabetException
- if the AlphabetContainer
is not discrete- See Also:
Sequence.Sequence(AlphabetContainer, SequenceAnnotation[])
continuousVal
public final double continuousVal(int pos)
- Description copied from class:
Sequence
- Returns the continuous value at position
pos
of the
Sequence.CompositeSequence
.
- Specified by:
continuousVal
in class Sequence
- Parameters:
pos
- the position of the Sequence.CompositeSequence
- Returns:
- the continuous value at position
pos
of the
Sequence.CompositeSequence