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

Class FileProxyProteinSequenceCreator

java.lang.Object

org.biojava.nbio.core.sequence.io.FileProxyProteinSequenceCreator

All Implemented Interfaces:

SequenceCreatorInterface<AminoAcidCompound>

public class FileProxyProteinSequenceCreator
extends Object
implements SequenceCreatorInterface<AminoAcidCompound>

This class is a good example of using the SequenceCreatorInterface where during parsing of the stream the sequence and the offset index are passed to create a Protein sequence that will be loaded in lazily. This way you can load very large fasta files and store accession id and delay loading the sequence to save memory. The index is the file stream offset so when a ProteinSequence has a call to getSequence() the SequenceFileProxyLoader will open the file and offset to the index and retrieve the sequence. Same approach can be used for genome sequence data stored in a local fasta file, in a database or via http interface to a remote server

Author:

Scooter Willis <willishf at gmail dot com>

Constructor Summary

Constructors

Constructor	Description
FileProxyProteinSequenceCreator(File file, CompoundSet<AminoAcidCompound> compoundSet, SequenceParserInterface sequenceParser)	Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read

Method Summary

Modifier and Type	Method	Description
AbstractSequence<AminoAcidCompound>	getSequence(String sequence, long index)	Even though we are passing in the sequence we really only care about the length of the sequence and the offset index in the fasta file.
AbstractSequence<AminoAcidCompound>	getSequence(List<AminoAcidCompound> list)	Not sure of use case and currently not supported
AbstractSequence<AminoAcidCompound>	getSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, long index)	Should be able to extend the same concept to a remote URL call or database connection.

Methods inherited from class java.lang.Object

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

Constructor Detail

FileProxyProteinSequenceCreator

public FileProxyProteinSequenceCreator(File file,
                                       CompoundSet<AminoAcidCompound> compoundSet,
                                       SequenceParserInterface sequenceParser)

Need File so that we can store full path name in SequenceFileProxyLoader for Random File access as a quick read

Parameters:

fastaFile -

compoundSet -

Method Detail

getSequence

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

Even though we are passing in the sequence we really only care about the length of the sequence and the offset index in the fasta file.

Specified by:

getSequence in interface SequenceCreatorInterface<AminoAcidCompound>

Parameters:

sequence -

index -

Returns:

Throws:

CompoundNotFoundException

IOException

getSequence

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

Should be able to extend the same concept to a remote URL call or database connection. Not supported yet

Specified by:

getSequence in interface SequenceCreatorInterface<AminoAcidCompound>

Parameters:

proxyLoader -

index -

Returns:

getSequence

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

Not sure of use case and currently not supported

Specified by:

getSequence in interface SequenceCreatorInterface<AminoAcidCompound>

Parameters:

list -

Returns: