org.biojava.nbio.core.search.io.blast

Class BlastXMLParser

java.lang.Object

org.biojava.nbio.core.search.io.blast.BlastXMLParser

All Implemented Interfaces:

ResultFactory

public class BlastXMLParser
extends Object
implements ResultFactory

Re-designed by Paolo Pavan on the footprint of: org.biojava.nbio.genome.query.BlastXMLQuery by Scooter Willis You may want to find my contacts on Github and LinkedIn for code info or discuss major changes. https://github.com/paolopavan

Author:

Paolo Pavan

Constructor Summary

Constructors

Constructor and Description
BlastXMLParser()

Method Summary

Modifier and Type	Method and Description
List<Result>	createObjects(double maxEScore) Launch the parsing and get back a list of Result objects representing the search result in the specified file.
List<String>	getFileExtensions() returns a list of file extensions associated to this ResultFactory
void	setDatabaseReferences(List<Sequence> sequences) Specify the collection of sequences objects used as database in the Search run.
void	setFile(File f)
void	setQueryReferences(List<Sequence> sequences) Specify the collection of sequences objects used as queries in the Search run.
void	storeObjects(List<Result> results) The factory that implements this method will be able to save the Search results to a file in the same format that it is able to read.

Methods inherited from class java.lang.Object

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

Constructor Detail

BlastXMLParser

public BlastXMLParser()

Method Detail

setFile

public void setFile(File f)

Specified by:

setFile in interface ResultFactory

createObjects

public List<Result> createObjects(double maxEScore)
                           throws IOException,
                                  ParseException

Description copied from interface: ResultFactory

Launch the parsing and get back a list of Result objects representing the search result in the specified file.

Specified by:

createObjects in interface ResultFactory

Returns:

Throws:

IOException

ParseException

getFileExtensions

public List<String> getFileExtensions()

Description copied from interface: ResultFactory

returns a list of file extensions associated to this ResultFactory

Specified by:

getFileExtensions in interface ResultFactory

Returns:

setQueryReferences

public void setQueryReferences(List<Sequence> sequences)

Description copied from interface: ResultFactory

Specify the collection of sequences objects used as queries in the Search run. They will be associated back to the query during the construction of the Result object.

Specified by:

setQueryReferences in interface ResultFactory

setDatabaseReferences

public void setDatabaseReferences(List<Sequence> sequences)

Description copied from interface: ResultFactory

Specify the collection of sequences objects used as database in the Search run. They will be associated back to the Hit during the construction of the Hit object.

Specified by:

setDatabaseReferences in interface ResultFactory

storeObjects

public void storeObjects(List<Result> results)
                  throws IOException,
                         ParseException

Description copied from interface: ResultFactory

The factory that implements this method will be able to save the Search results to a file in the same format that it is able to read.

Specified by:

storeObjects in interface ResultFactory

Throws:

IOException

ParseException