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java.lang.Objectde.jstacs.data.sequences.Sequence<int[]>
de.jstacs.data.sequences.SimpleDiscreteSequence
public abstract class SimpleDiscreteSequence
This is the main class for any discrete sequence.
Nested Class Summary |
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Nested classes/interfaces inherited from class de.jstacs.data.sequences.Sequence |
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Sequence.CompositeSequence<T>, Sequence.RecursiveSequence<T>, Sequence.SubSequence<T> |
Field Summary |
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Fields inherited from class de.jstacs.data.sequences.Sequence |
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alphabetCon, annotation, rc |
Constructor Summary | |
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SimpleDiscreteSequence(AlphabetContainer container,
SequenceAnnotation[] annotation)
This constructor creates a new SimpleDiscreteSequence with the
AlphabetContainer container and the annotation
annotation but without the content. |
Method Summary | |
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protected void |
addToRepresentation(Object representation,
int pos,
String delim)
This method adds the information of one position to the representation using the specified delimiter |
int |
compareTo(int[] t1,
int[] t2)
This method compares to container and is used in Sequence.compareTo(Sequence) . |
double |
continuousVal(int pos)
Returns the continuous value at position pos of the
Sequence . |
void |
fillContainer(int[] container,
int pos)
The method fills the content of a specific position in to the container. |
int[] |
getEmptyContainer()
The method returns a container that can be used for accessing the symbols for each position. |
protected Object |
getEmptyRepresentation()
Returns an empty representation which is used to create the String representation of this instance in the method Sequence.toString(String, int, int) . |
protected String |
getStringRepresentation(Object representation)
This method creates a String representation from the given representation. |
protected int |
hashCodeForPos(int pos)
This method is used in Sequence.hashCode() and the hash code for one specific position. |
boolean |
isMultiDimensional()
The method returns true if the sequence is multidimensional, otherwise . |
Methods inherited from class de.jstacs.data.sequences.Sequence |
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annotate, compareTo, complement, complement, create, create, create, discreteVal, equals, flatCloneWithoutAnnotation, getAlphabetContainer, getAnnotation, getCompositeSequence, getCompositeSequence, getHammingDistance, getLength, getNumberOfSequenceAnnotationsByType, getSequenceAnnotationByType, getSequenceAnnotationByTypeAndIdentifier, getSubSequence, getSubSequence, getSubSequence, getSubSequence, hashCode, matches, 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 |
Constructor Detail |
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public SimpleDiscreteSequence(AlphabetContainer container, SequenceAnnotation[] annotation) throws WrongAlphabetException
SimpleDiscreteSequence
with the
AlphabetContainer
container
and the annotation
annotation
but without the content. The content has to be
set by the constructor of the subclass.
container
- the AlphabetContainer
of the sequenceannotation
- the annotation of the sequence
WrongAlphabetException
- if the AlphabetContainer
is not discreteSequence.Sequence(AlphabetContainer, SequenceAnnotation[])
Method Detail |
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public final double continuousVal(int pos)
Sequence
pos
of the
Sequence
.
continuousVal
in class Sequence<int[]>
pos
- the position of the Sequence
pos
of the
Sequence
public boolean isMultiDimensional()
Sequence
true
if the sequence is multidimensional, otherwise .
isMultiDimensional
in class Sequence<int[]>
true
if the sequence is multidimensional, otherwise
public int[] getEmptyContainer()
Sequence
getEmptyContainer
in class Sequence<int[]>
Sequence.fillContainer(Object, int)
,
Sequence.isMultiDimensional()
public void fillContainer(int[] container, int pos)
Sequence
fillContainer
in class Sequence<int[]>
container
- the container which is used for filling the content.pos
- the positionSequence.getEmptyContainer()
,
Sequence.isMultiDimensional()
protected Object getEmptyRepresentation()
Sequence
String
representation of this instance in the method Sequence.toString(String, int, int)
.
getEmptyRepresentation
in class Sequence<int[]>
String
representationSequence.toString(String, int, int)
protected void addToRepresentation(Object representation, int pos, String delim)
Sequence
addToRepresentation
in class Sequence<int[]>
representation
- the representationpos
- the positiondelim
- the delimiter separating the information for different positionsSequence.getEmptyRepresentation()
,
Sequence.toString(String, int, int)
protected String getStringRepresentation(Object representation)
Sequence
getStringRepresentation
in class Sequence<int[]>
representation
- the representation instance (which should be created by Sequence.getEmptyContainer()
and filled by Sequence.addToRepresentation(Object, int, String)
)
Sequence.getEmptyRepresentation()
,
Sequence.addToRepresentation(Object, int, String)
,
Sequence.toString(String, int, int)
protected int hashCodeForPos(int pos)
Sequence
Sequence.hashCode()
and the hash code for one specific position.
hashCodeForPos
in class Sequence<int[]>
pos
- the position
public int compareTo(int[] t1, int[] t2)
Sequence
Sequence.compareTo(Sequence)
.
compareTo
in class Sequence<int[]>
t1
- the first containert2
- the second container
Sequence.getEmptyContainer()
,
Sequence.fillContainer(Object, int)
,
Comparable.compareTo(java.lang.Object)
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