de.jstacs.data.sequences
Class DiscreteSequence

java.lang.Object
  extended by de.jstacs.data.Sequence
      extended by 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

Nested Class Summary
 
Nested classes/interfaces inherited from class de.jstacs.data.Sequence
Sequence.CompositeSequence, Sequence.SubSequence
 
Field Summary
 
Fields inherited from class de.jstacs.data.Sequence
alphabetCon, annotation, rc
 
Constructor Summary
DiscreteSequence(AlphabetContainer container, SequenceAnnotation[] annotation)
          This constructor creates an instance with the AlphabetContainer and the annotation, but without the content.
 
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
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
 

Constructor Detail

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 sequence
annotation - the annotation of the sequence
Throws:
WrongAlphabetException - if the AlphabetContainer is not discrete
Method Detail

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