Package org.biojava.nbio.core.sequence.io

Class ProteinSequenceCreator

java.lang.Object

org.biojava.nbio.core.sequence.io.ProteinSequenceCreator

All Implemented Interfaces:

SequenceCreatorInterface<AminoAcidCompound>

Direct Known Subclasses:

CasePreservingProteinSequenceCreator

public class ProteinSequenceCreator
extends Object
implements SequenceCreatorInterface<AminoAcidCompound>

Used to create a ProteinSequence from a String to allow for details about the location of the sequence etc.

Author:

Scooter Willis

Constructor Summary

Constructors

Constructor	Description
ProteinSequenceCreator(CompoundSet<AminoAcidCompound> compoundSet)

Method Summary

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

Methods inherited from class java.lang.Object

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

Constructor Detail

ProteinSequenceCreator

public ProteinSequenceCreator(CompoundSet<AminoAcidCompound> compoundSet)

Parameters:

compoundSet -

Method Detail

getSequence

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

Specified by:

getSequence in interface SequenceCreatorInterface<AminoAcidCompound>

Parameters:

sequence -

index - not used in this implementation

Returns:

Throws:

CompoundNotFoundException

getSequence

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

Specified by:

getSequence in interface SequenceCreatorInterface<AminoAcidCompound>

Parameters:

list -

Returns:

getSequence

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

Specified by:

getSequence in interface SequenceCreatorInterface<AminoAcidCompound>

Parameters:

proxyLoader -

index - not used in this implementation

Returns: