de.jstacs.data
Class Sequence

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

All Implemented Interfaces:

Comparable<Sequence>

Direct Known Subclasses:

ArbitrarySequence, DiscreteSequence, RecursiveSequence

public abstract class Sequence
extends Object
implements Comparable<Sequence>

This is the main class for all sequences. All sequences are immutable.

Author:

Jens Keilwagen

Nested Class Summary

protected static class	Sequence.CompositeSequence The class handles composite Sequences.
protected static class	Sequence.SubSequence This class handles subsequences.

Field Summary

protected AlphabetContainer	alphabetCon The underlying alphabets.
protected SequenceAnnotation[]	annotation The annotation of the Sequence.CompositeSequence.
protected Sequence	rc The pointer to the reverse complement of the Sequence.CompositeSequence.

Constructor Summary

protected

Sequence(AlphabetContainer container, SequenceAnnotation[] annotation) Creates a new Sequence.CompositeSequence with the given AlphabetContainer and the given annotation, but without the content.

Method Summary

Sequence	annotate(boolean add, SequenceAnnotation... annotation) This method allows to append annotation to a Sequence.CompositeSequence.
int	compareTo(Sequence s)
Sequence	complement() This method returns a new instance of Sequence.CompositeSequence containing the complementary current Sequence.CompositeSequence.
Sequence	complement(int start, int end) This method returns a new instance of Sequence.CompositeSequence containing a part of the complementary current Sequence.CompositeSequence.
abstract double	continuousVal(int pos) Returns the continuous value at position pos of the Sequence.CompositeSequence.
static Sequence	create(AlphabetContainer con, SequenceAnnotation[] annotation, String sequence, String delim) Creates a Sequence.CompositeSequence from a String based on the given AlphabetContainer using the given delimiter delim and some annotation for the Sequence.CompositeSequence.
static Sequence	create(AlphabetContainer con, String sequence) Creates a Sequence.CompositeSequence from a String based on the given AlphabetContainer using the standard delimiter for this AlphabetContainer.
static Sequence	create(AlphabetContainer con, String sequence, String delim) Creates a Sequence.CompositeSequence from a String based on the given AlphabetContainer using the given delimiter delim.
abstract int	discreteVal(int pos) Returns the discrete value at position pos of the Sequence.CompositeSequence.
boolean	equals(Object o)
protected abstract Sequence	flatCloneWithoutAnnotation() Works in analogy to Object.clone(), but does not clone the annotation.
AlphabetContainer	getAlphabetContainer() Return the alphabets, i.e. the AlphabetContainer, used in this Sequence.CompositeSequence.
SequenceAnnotation[]	getAnnotation() Returns the annotation of the Sequence.CompositeSequence.
Sequence	getCompositeSequence(AlphabetContainer abc, int[] starts, int[] lengths) This method should be used if one wants to create a Sample of Sequence.CompositeSequences.
Sequence	getCompositeSequence(int[] starts, int[] lengths) This is a very efficient way to create a Sequence.CompositeSequence for sequences with a simple AlphabetContainer.
abstract int	getLength() Returns the length of the Sequence.CompositeSequence.
Sequence	getSubSequence(AlphabetContainer abc, int start) This method should be used if one wants to create a Sample of subsequences of defined length.
Sequence	getSubSequence(AlphabetContainer abc, int start, int length) This method should be used if one wants to create a Sample of subsequences of defined length.
Sequence	getSubSequence(int start) This is a very efficient way to create a subsequence/suffix for Sequence.CompositeSequences with a simple AlphabetContainer.
Sequence	getSubSequence(int start, int length) This is a very efficient way to create a subsequence of defined length for Sequence.CompositeSequences with a simple AlphabetContainer.
int	hashCode()
Sequence	reverse() This method returns a new instance of Sequence.CompositeSequence containing the reverse current Sequence.CompositeSequence.
Sequence	reverse(int start, int end) This method returns a new instance of Sequence.CompositeSequence containing a part of the reverse current Sequence.CompositeSequence.
Sequence	reverseComplement() This method returns a new instance of Sequence.CompositeSequence containing the reverse complementary current Sequence.CompositeSequence.
Sequence	reverseComplement(int start, int end) This method returns a new instance of Sequence.CompositeSequence containing a reverse part of the complementary current Sequence.CompositeSequence.
protected int	toDiscrete(int pos, double content) This method converts a continuous value at position pos of the Sequence.CompositeSequence into a discrete one.
String	toString() Returns a String representation of the Sequence.CompositeSequence (normally the Sequence.CompositeSequence in its original Alphabet).
String	toString(int start) Returns a String representation of the Sequence.CompositeSequence (normally the Sequence.CompositeSequence in its original Alphabet) beginning at position start with a default delimiter as separator.
String	toString(int start, int end) Returns a String representation of the Sequence.CompositeSequence (normally the Sequence.CompositeSequence in its original Alphabet) between start and end with a default delimiter as separator.
String	toString(String delim, int start, int end) Returns a String representation of the Sequence.CompositeSequence (normally the Sequence.CompositeSequence in its original alphabet) between start and end with delim as separator.

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

alphabetCon

protected AlphabetContainer alphabetCon

The underlying alphabets.

rc

protected Sequence rc

The pointer to the reverse complement of the Sequence.CompositeSequence.

annotation

protected SequenceAnnotation[] annotation

The annotation of the Sequence.CompositeSequence.

Constructor Detail

Sequence

protected Sequence(AlphabetContainer container,
                   SequenceAnnotation[] annotation)

Creates a new Sequence.CompositeSequence with the given AlphabetContainer and the given annotation, but without the content. The content has to be set by the constructor of the extending class.

Parameters:

container - the AlphabetContainer of the Sequence.CompositeSequence

annotation - the annotation of the Sequence.CompositeSequence

Method Detail

continuousVal

public abstract double continuousVal(int pos)

Returns the continuous value at position pos of the Sequence.CompositeSequence.

Parameters:

pos - the position of the Sequence.CompositeSequence

Returns:

the continuous value at position pos of the Sequence.CompositeSequence

discreteVal

public abstract int discreteVal(int pos)

Returns the discrete value at position pos of the Sequence.CompositeSequence.

Parameters:

pos - the position of the Sequence.CompositeSequence

Returns:

the discrete value at position pos of the Sequence.CompositeSequence

equals

public boolean equals(Object o)

Overrides:

equals in class Object

getAlphabetContainer

public final AlphabetContainer getAlphabetContainer()

Return the alphabets, i.e. the AlphabetContainer, used in this Sequence.CompositeSequence.

Returns:

the alphabets, i.e. the AlphabetContainer, used in this Sequence.CompositeSequence

getAnnotation

public final SequenceAnnotation[] getAnnotation()

Returns the annotation of the Sequence.CompositeSequence.

Returns:

the annotation of the Sequence.CompositeSequence (can be null)

getCompositeSequence

public Sequence getCompositeSequence(AlphabetContainer abc,
                                     int[] starts,
                                     int[] lengths)

This method should be used if one wants to create a Sample of Sequence.CompositeSequences. With this constructor you are enabled to create a Sample where every Sequence.CompositeSequence has the same AlphabetContainer instance.

Internally it is checked that the AlphabetContainer matches with the one of the Sequence.CompositeSequence.

Parameters:

abc - the new AlphabetContainer

starts - the start positions of the junks

lengths - the length of each junk

Returns:

the Sequence.CompositeSequence

See Also:

CompositeSequence#CompositeSequence(de.jstacs.data.AlphabetContainer, de.jstacs.data.Sequence, int[], int[])

getCompositeSequence

public Sequence getCompositeSequence(int[] starts,
                                     int[] lengths)

This is a very efficient way to create a Sequence.CompositeSequence for sequences with a simple AlphabetContainer.

Parameters:

starts - the start positions of the junks

lengths - the length of each junk

Returns:

the Sequence.CompositeSequence

See Also:

CompositeSequence#CompositeSequence(de.jstacs.data.Sequence, int[], int[])

getSubSequence

public final Sequence getSubSequence(AlphabetContainer abc,
                                     int start)

This method should be used if one wants to create a Sample of subsequences of defined length. With this constructor you are enabled to create a Sample where every Sequence.CompositeSequence has the same AlphabetContainer instance.

Internally it is checked that the AlphabetContainer matches with the one of the subsequence.

Parameters:

abc - the new AlphabetContainer

start - the index of the start position

Returns:

the subsequence

See Also:

getSubSequence(de.jstacs.data.AlphabetContainer, int, int)

getSubSequence

public Sequence getSubSequence(AlphabetContainer abc,
                               int start,
                               int length)

This method should be used if one wants to create a Sample of subsequences of defined length. With this constructor you are enabled to create a Sample where every Sequence.CompositeSequence has the same AlphabetContainer instance.

Internally it is checked that the AlphabetContainer matches with the one of the subsequence.

Parameters:

abc - the new AlphabetContainer

start - the index of the start position

length - the length of the new Sequence.CompositeSequence

Returns:

the subsequence

See Also:

SubSequence#SubSequence(de.jstacs.data.AlphabetContainer, de.jstacs.data.Sequence, int, int)

getSubSequence

public final Sequence getSubSequence(int start)

This is a very efficient way to create a subsequence/suffix for Sequence.CompositeSequences with a simple AlphabetContainer.

Parameters:

start - the index of the start position

Returns:

the subsequence

See Also:

getSubSequence(int, int)

getSubSequence

public Sequence getSubSequence(int start,
                               int length)

This is a very efficient way to create a subsequence of defined length for Sequence.CompositeSequences with a simple AlphabetContainer.

Parameters:

start - the index of the start position

length - the length of the new Sequence.CompositeSequence

Returns:

the subsequence

See Also:

SubSequence#SubSequence(Sequence, int, int)

annotate

public Sequence annotate(boolean add,
                         SequenceAnnotation... annotation)

This method allows to append annotation to a Sequence.CompositeSequence.

Parameters:

add - indicates whether to add the new annotation to the existing or not

annotation - the new annotation

Returns:

the new annotated Sequence.CompositeSequence

See Also:

Sequence.CompositeSequence.flatCloneWithoutAnnotation()

flatCloneWithoutAnnotation

protected abstract Sequence flatCloneWithoutAnnotation()

Works in analogy to Object.clone(), but does not clone the annotation. This method is used in annotate(boolean, SequenceAnnotation...).

Returns:

the cloned Sequence.CompositeSequence without annotation

getLength

public abstract int getLength()

Returns the length of the Sequence.CompositeSequence.

Returns:

the length of the Sequence.CompositeSequence

toString

public String toString()

Returns a String representation of the Sequence.CompositeSequence (normally the Sequence.CompositeSequence in its original Alphabet).

Overrides:

toString in class Object

Returns:

the Sequence.CompositeSequence as String

See Also:

toString(String, int, int)

toString

public String toString(int start)

Returns a String representation of the Sequence.CompositeSequence (normally the Sequence.CompositeSequence in its original Alphabet) beginning at position start with a default delimiter as separator.

Parameters:

start - the start index (inclusive)

Returns:

the Sequence.CompositeSequence as String

See Also:

toString(String, int, int)

toString

public String toString(int start,
                       int end)

Returns a String representation of the Sequence.CompositeSequence (normally the Sequence.CompositeSequence in its original Alphabet) between start and end with a default delimiter as separator.

Parameters:

start - the start index (inclusive)

end - the end index (exclusive)

Returns:

the Sequence.CompositeSequence as String

See Also:

toString(String, int, int)

compareTo

public int compareTo(Sequence s)

Specified by:

compareTo in interface Comparable<Sequence>

toDiscrete

protected int toDiscrete(int pos,
                         double content)

This method converts a continuous value at position pos of the Sequence.CompositeSequence into a discrete one.

Parameters:

pos - the position of the Sequence.CompositeSequence

content - the value at this position

Returns:

the discrete value for this position

See Also:

AlphabetContainer.toDiscrete(int, double)

toString

public String toString(String delim,
                       int start,
                       int end)

Returns a String representation of the Sequence.CompositeSequence (normally the Sequence.CompositeSequence in its original alphabet) between start and end with delim as separator.

Parameters:

delim - the delimiter/separator

start - the start index (inclusive)

end - the end index (exclusive)

Returns:

the Sequence.CompositeSequence as String

create

public static Sequence create(AlphabetContainer con,
                              String sequence)
                       throws WrongAlphabetException,
                              IllegalArgumentException

Creates a Sequence.CompositeSequence from a String based on the given AlphabetContainer using the standard delimiter for this AlphabetContainer.

Parameters:

con - the AlphabetContainer

sequence - the String containing the Sequence.CompositeSequence

Returns:

a new Sequence.CompositeSequence instance

Throws:

WrongAlphabetException - if sequence is not defined over con

IllegalArgumentException - if the delimiter is empty and the AlphabetContainer is not discrete

See Also:

create(AlphabetContainer, String, String)

create

public static Sequence create(AlphabetContainer con,
                              String sequence,
                              String delim)
                       throws WrongAlphabetException,
                              IllegalArgumentException

Creates a Sequence.CompositeSequence from a String based on the given AlphabetContainer using the given delimiter delim.

Parameters:

con - the AlphabetContainer

sequence - the String containing the Sequence.CompositeSequence

delim - the given delimiter

Returns:

a new Sequence.CompositeSequence instance

Throws:

WrongAlphabetException - if sequence is not defined over con

IllegalArgumentException - if the delimiter is empty and the AlphabetContainer is not discrete

See Also:

create(AlphabetContainer, SequenceAnnotation[], String, String)

create

public static Sequence create(AlphabetContainer con,
                              SequenceAnnotation[] annotation,
                              String sequence,
                              String delim)
                       throws WrongAlphabetException,
                              IllegalArgumentException

Creates a Sequence.CompositeSequence from a String based on the given AlphabetContainer using the given delimiter delim and some annotation for the Sequence.CompositeSequence.

Parameters:

con - the AlphabetContainer

annotation - the annotation for the Sequence.CompositeSequence

sequence - the String containing the Sequence.CompositeSequence

delim - the given delimiter

Returns:

a new Sequence.CompositeSequence instance

Throws:

WrongAlphabetException - if sequence is not defined over con

IllegalArgumentException - if the delimiter is empty and the AlphabetContainer is not discrete

reverse

public final Sequence reverse()
                       throws OperationNotSupportedException

This method returns a new instance of Sequence.CompositeSequence containing the reverse current Sequence.CompositeSequence.
So invoking this method, for instance, on the sequence "TAATA" returns "ATAAT".

Returns:

the reverse Sequence.CompositeSequence

Throws:

OperationNotSupportedException - if the current Sequence.CompositeSequence is based on an AlphabetContainer that is not simple

See Also:

reverse(int, int)

reverse

public Sequence reverse(int start,
                        int end)
                 throws OperationNotSupportedException

This method returns a new instance of Sequence.CompositeSequence containing a part of the reverse current Sequence.CompositeSequence.

Parameters:

start - the start position (inclusive) in the original Sequence.CompositeSequence

end - the end position (exclusive) in the original Sequence.CompositeSequence

Returns:

the reverse Sequence.CompositeSequence of the part

Throws:

OperationNotSupportedException - if the current Sequence.CompositeSequence is based on an AlphabetContainer that is not simple

complement

public Sequence complement()
                    throws OperationNotSupportedException

This method returns a new instance of Sequence.CompositeSequence containing the complementary current Sequence.CompositeSequence.
So invoking this method, for instance, on the sequence "TAATA" with an AlphabetContainer on DNAAlphabet returns "ATTAT".

Returns:

the complementary Sequence.CompositeSequence

Throws:

OperationNotSupportedException - if the current Sequence.CompositeSequence is not based on a ComplementableDiscreteAlphabet

See Also:

ComplementableDiscreteAlphabet, complement(int, int)

complement

public Sequence complement(int start,
                           int end)
                    throws OperationNotSupportedException

This method returns a new instance of Sequence.CompositeSequence containing a part of the complementary current Sequence.CompositeSequence.
So invoking this method, for instance, on the sequence "TAATA" with an AlphabetContainer on DNAAlphabet returns "ATTAT".

Parameters:

start - the start position (inclusive) in the original Sequence.CompositeSequence

end - the end position (exclusive) in the original Sequence.CompositeSequence

Returns:

the complementary Sequence.CompositeSequence of the part

Throws:

OperationNotSupportedException - if the current Sequence.CompositeSequence is not based on a ComplementableDiscreteAlphabet

See Also:

ComplementableDiscreteAlphabet

reverseComplement

public Sequence reverseComplement()
                           throws OperationNotSupportedException

This method returns a new instance of Sequence.CompositeSequence containing the reverse complementary current Sequence.CompositeSequence. For more details see the methods reverse() and complement().

Returns:

the reverse complementary Sequence.CompositeSequence

Throws:

OperationNotSupportedException - if the current Sequence.CompositeSequence is not discrete and simple (not based on a ComplementableDiscreteAlphabet)

See Also:

reverse(), complement(), reverseComplement(int, int), ComplementableDiscreteAlphabet

reverseComplement

public Sequence reverseComplement(int start,
                                  int end)
                           throws OperationNotSupportedException

This method returns a new instance of Sequence.CompositeSequence containing a reverse part of the complementary current Sequence.CompositeSequence. For more details see the methods reverse() and complement().

Parameters:

start - the start position (inclusive) in the original Sequence.CompositeSequence

end - the end position (exclusive) in the original Sequence.CompositeSequence

Returns:

the reverse complementary Sequence.CompositeSequence of the part

Throws:

OperationNotSupportedException - if the current Sequence.CompositeSequence is not discrete and simple ((not based on a ComplementableDiscreteAlphabet)

See Also:

reverse(), complement(), ComplementableDiscreteAlphabet

hashCode

public int hashCode()

Overrides:

hashCode in class Object