Package org.biojava.nbio.core.search.io

Interface ResultFactory

All Known Implementing Classes:

BlastTabularParser, BlastXMLParser

public interface ResultFactory

Designed by Paolo Pavan. 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

Method Summary

Modifier and Type	Method	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.

Method Detail

getFileExtensions

List<String> getFileExtensions()

returns a list of file extensions associated to this ResultFactory

Returns:

setFile

void setFile(File f)

createObjects

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

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

Parameters:

maxEScore -

Returns:

Throws:

Exception

IOException

ParseException

storeObjects

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

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.

Parameters:

results -

Throws:

Exception

IOException

ParseException

setQueryReferences

void setQueryReferences(List<Sequence> sequences)

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.

Parameters:

sequences -

setDatabaseReferences

void setDatabaseReferences(List<Sequence> sequences)

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.

Parameters:

sequences -