public abstract class SimpleDiscreteSequence extends Sequence<int[]>
Sequence.CompositeSequence<T>, Sequence.RecursiveSequence<T>, Sequence.SubSequence<T>alphabetCon, annotation, rc| Constructor and Description |
|---|
SimpleDiscreteSequence(AlphabetContainer container,
SequenceAnnotation[] annotation)
This constructor creates a new
SimpleDiscreteSequence with the
AlphabetContainer container and the annotation
annotation but without the content. |
| Modifier and Type | Method and Description |
|---|---|
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 false. |
static SimpleDiscreteSequence |
shuffle(SimpleDiscreteSequence original,
int k)
This method implements the algorithm of D.
|
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, toStringpublic 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 sequenceWrongAlphabetException - if the AlphabetContainer is not discreteSequence.Sequence(AlphabetContainer, SequenceAnnotation[])public static SimpleDiscreteSequence shuffle(SimpleDiscreteSequence original, int k) throws Exception
original - the original sequencek - the value for the k-mers, k should be larger than (or equal to) 1Exception - if the shuffled sequence could not be createdpublic final double continuousVal(int pos)
Sequencepos of the
Sequence.continuousVal in class Sequence<int[]>pos - the position of the Sequencepos of the
Sequencepublic boolean isMultiDimensional()
Sequencetrue if the sequence is multidimensional, otherwise false.isMultiDimensional in class Sequence<int[]>true if the sequence is multidimensional, otherwise falsepublic int[] getEmptyContainer()
SequencegetEmptyContainer in class Sequence<int[]>Sequence.fillContainer(Object, int),
Sequence.isMultiDimensional()public void fillContainer(int[] container,
int pos)
SequencefillContainer in class Sequence<int[]>container - the container which is used for filling the content.pos - the positionSequence.getEmptyContainer(),
Sequence.isMultiDimensional()protected Object getEmptyRepresentation()
SequenceString 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)
SequenceaddToRepresentation 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)
SequencegetStringRepresentation 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)
SequenceSequence.hashCode() and the hash code for one specific position.hashCodeForPos in class Sequence<int[]>pos - the positionpublic int compareTo(int[] t1,
int[] t2)
SequenceSequence.compareTo(Sequence).compareTo in class Sequence<int[]>t1 - the first containert2 - the second containerSequence.getEmptyContainer(),
Sequence.fillContainer(Object, int),
Comparable.compareTo(java.lang.Object)