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
The main class for any discrete sequence.
- Author:
- Jens Keilwagen
Method Summary |
double |
continuousVal(int pos)
Returns the continuous value of position pos . |
Methods inherited from class de.jstacs.data.Sequence |
annotate, compareTo, complement, complement, create, create, create, discreteVal, equals, flatCloneWithoutAnnotation, getAlphabetContainer, getAnnotation, getCompositeSequence, getCompositeSequence, getLength, 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 an instance with the AlphabetContainer and the annotation, but without the content.
The content has to be set by the constructor of the extending class.
- Parameters:
container
- the AlpahbetContainer of the sequenceannotation
- the annotation of the sequence
- Throws:
WrongAlphabetException
- if the AlphabetContainer is not discrete
continuousVal
public final double continuousVal(int pos)
- Description copied from class:
Sequence
- Returns the continuous value of position
pos
.
- Specified by:
continuousVal
in class Sequence
- Parameters:
pos
- the position
- Returns:
- the continuous value of position
pos