FileProxyDNASequenceCreator

java.lang.Object
- org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator

All Implemented Interfaces:

SequenceCreatorInterface<NucleotideCompound>
```
public class FileProxyDNASequenceCreator
extends java.lang.Object
implements SequenceCreatorInterface<NucleotideCompound>
```
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 DNASequence 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

Constructor Summary

Constructors
Constructor	Description
`FileProxyDNASequenceCreator(java.io.File file, CompoundSet<NucleotideCompound> 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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`AbstractSequence<NucleotideCompound>`	`getSequence(java.lang.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<NucleotideCompound>`	`getSequence(java.util.List<NucleotideCompound> list)`	Not sure of use case and currently not supported
`AbstractSequence<NucleotideCompound>`	`getSequence(ProxySequenceReader<NucleotideCompound> 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
  - FileProxyDNASequenceCreator
```
public FileProxyDNASequenceCreator(java.io.File file,
                                   CompoundSet<NucleotideCompound> 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<NucleotideCompound> getSequence(java.lang.String sequence,
                                                        long index)
                                                 throws CompoundNotFoundException,
                                                        java.io.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<NucleotideCompound>
    
    Parameters:
    
    sequence -
    
    index -
    
    Returns:
    
    Throws:
    
    CompoundNotFoundException
    
    java.io.IOException
  - getSequence
```
public AbstractSequence<NucleotideCompound> getSequence(ProxySequenceReader<NucleotideCompound> 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<NucleotideCompound>
    
    Parameters:
    
    proxyLoader -
    
    index -
    
    Returns:
  - getSequence
```
public AbstractSequence<NucleotideCompound> getSequence(java.util.List<NucleotideCompound> list)
```
    Not sure of use case and currently not supported
    
    Specified by:
    
    getSequence in interface SequenceCreatorInterface<NucleotideCompound>
    
    Parameters:
    
    list -
    
    Returns:

Class FileProxyDNASequenceCreator

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

FileProxyDNASequenceCreator

Method Detail

getSequence

getSequence

getSequence