Package org.biojava.nbio.core.sequence.template

Interface Sequence<C extends Compound>

Type Parameters:

C - Compound a Sequence holds

All Superinterfaces:

Accessioned, Iterable<C>

All Known Subinterfaces:

AlignedSequence<S,C>, MutableAlignedSequence<S,C>, ProxySequenceReader<C>, SequenceReader<C>, SequenceView<C>

All Known Implementing Classes:

AbstractSequence, ArrayListProxySequenceReader, ArrayListSequenceReader, BasicSequence, BitSequenceReader, CDSSequence, ChromosomeSequence, ComplementSequenceView, DNASequence, ExonSequence, FourBitSequenceReader, GenbankProxySequenceReader, GeneSequence, IntronSequence, JoiningSequenceReader, ProteinSequence, ReversedSequenceView, RNASequence, RnaSequenceView, SequenceFileProxyLoader, SequenceProxyView, SimpleAlignedSequence, SingleCompoundSequenceReader, StartCodonSequence, StopCodonSequence, StringProxySequenceReader, TranscriptSequence, TwoBitSequenceReader, UniprotProxySequenceReader

public interface Sequence<C extends Compound>
extends Iterable<C>, Accessioned

Main interface for defining a collection of Compounds and accessing them using biological indexes

Author:

Richard Holland, Andy Yates, Scooter Willis

Method Summary

Modifier and Type	Method	Description
int	countCompounds(C... compounds)	Returns the number of times we found a compound in the Sequence
List<C>	getAsList()	Returns the Sequence as a List of compounds
C	getCompoundAt(int position)	Returns the Compound at the given biological index
CompoundSet<C>	getCompoundSet()	Gets the compound set used to back this Sequence
int	getIndexOf(C compound)	Scans through the Sequence looking for the first occurrence of the given compound
SequenceView<C>	getInverse()	Does the right thing to get the inverse of the current Sequence.
int	getLastIndexOf(C compound)	Scans through the Sequence looking for the last occurrence of the given compound
int	getLength()	Returns the length of the Sequence
String	getSequenceAsString()	Returns the String representation of the Sequence
SequenceView<C>	getSubSequence(Integer start, Integer end)	Returns a portion of the sequence from the different positions.

Methods inherited from interface org.biojava.nbio.core.sequence.template.Accessioned

getAccession

Methods inherited from interface java.lang.Iterable

forEach, iterator, spliterator

Method Detail

getLength

int getLength()

Returns the length of the Sequence

getCompoundAt

C getCompoundAt(int position)

Returns the Compound at the given biological index

Parameters:

position - Biological index (1 to n)

Returns:

Compound at the specified position

getIndexOf

int getIndexOf(C compound)

Scans through the Sequence looking for the first occurrence of the given compound

Parameters:

compound - Compounds to look for

Returns:

Index of the first position of the compound in the sequence (1 to n)

getLastIndexOf

int getLastIndexOf(C compound)

Scans through the Sequence looking for the last occurrence of the given compound

Parameters:

compound - Compounds to look for

Returns:

Index of the last position of the compound in the sequence (1 to n)

getSequenceAsString

String getSequenceAsString()

Returns the String representation of the Sequence

getAsList

List<C> getAsList()

Returns the Sequence as a List of compounds

getSubSequence

SequenceView<C> getSubSequence(Integer start,
                               Integer end)

Returns a portion of the sequence from the different positions. This is indexed from 1

Parameters:

start - Biological index start; must be greater than 0

end - Biological end; must be less than length + 1

Returns:

A SequenceView of the offset

getCompoundSet

CompoundSet<C> getCompoundSet()

Gets the compound set used to back this Sequence

countCompounds

int countCompounds(C... compounds)

Returns the number of times we found a compound in the Sequence

Parameters:

compounds - Vargs of the compounds to count

Returns:

Number of times a compound was found

getInverse

SequenceView<C> getInverse()

Does the right thing to get the inverse of the current Sequence. This means either reversing the Sequence and optionally complementing the Sequence.