org.biojava.nbio.core.sequence.io

Class DNASequenceCreator

java.lang.Object

org.biojava.nbio.core.sequence.io.DNASequenceCreator

All Implemented Interfaces:

SequenceCreatorInterface<NucleotideCompound>

public class DNASequenceCreator
extends Object
implements SequenceCreatorInterface<NucleotideCompound>

A helper class that allows different ways to read a string and create a DNA sequence. Used in FastaReaderHelper and probably a layer that isn't needed

Author:

Scooter Willis

Constructor Summary

Constructors

Constructor and Description
DNASequenceCreator(CompoundSet<NucleotideCompound> compoundSet)

Method Summary

Modifier and Type	Method and Description
AbstractSequence<NucleotideCompound>	getSequence(List<NucleotideCompound> list)
AbstractSequence<NucleotideCompound>	getSequence(ProxySequenceReader<NucleotideCompound> proxyLoader, long index)
AbstractSequence<NucleotideCompound>	getSequence(String sequence, long index)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

DNASequenceCreator

public DNASequenceCreator(CompoundSet<NucleotideCompound> compoundSet)

Parameters:

compoundSet -

Method Detail

getSequence

public AbstractSequence<NucleotideCompound> getSequence(String sequence,
                                                        long index)
                                                 throws CompoundNotFoundException

Specified by:

getSequence in interface SequenceCreatorInterface<NucleotideCompound>

Parameters:

sequence - The Sequence from a String

index - Currently not used

Returns:

Throws:

CompoundNotFoundException

getSequence

public AbstractSequence<NucleotideCompound> getSequence(ProxySequenceReader<NucleotideCompound> proxyLoader,
                                                        long index)

Specified by:

getSequence in interface SequenceCreatorInterface<NucleotideCompound>

Parameters:

proxyLoader - The Sequence from a ProxySequenceReader

index - Currently not used

Returns:

getSequence

public AbstractSequence<NucleotideCompound> getSequence(List<NucleotideCompound> list)

Specified by:

getSequence in interface SequenceCreatorInterface<NucleotideCompound>

Parameters:

list -

Returns: