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

Class BlastTabularParser

java.lang.Object

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

All Implemented Interfaces:

ResultFactory

public class BlastTabularParser
extends Object
implements 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

Constructor Summary

Constructors

Constructor	Description
BlastTabularParser()

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)	Intended for use with run module.
void	setFile(File f)
void	setParsingConsistency(org.biojava.nbio.core.search.io.blast.BlastTabularParser.PARSING_CONSISTENCY parsingConsistency)	Tries to define a different level of consistency during parsing.
void	setQueryReferences(List<Sequence> sequences)	Intended for use with run module.
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 Details

BlastTabularParser

public BlastTabularParser()

Method Details

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:

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

Parameters:

maxEScore -

Returns:

Throws:

IOException

ParseException

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

Parameters:

results -

Throws:

IOException

ParseException

setQueryReferences

public void setQueryReferences(List<Sequence> sequences)

Intended for use with run module. Although possible, does not make a lot of sense to have it with limited information such those in tabular report

Specified by:

setQueryReferences in interface ResultFactory

Parameters:

sequences -

setDatabaseReferences

public void setDatabaseReferences(List<Sequence> sequences)

Intended for use with run module. Although possible, does not make a lot of sense to have it with limited information such those in tabular report

Specified by:

setDatabaseReferences in interface ResultFactory

Parameters:

sequences -

setParsingConsistency

public void setParsingConsistency(org.biojava.nbio.core.search.io.blast.BlastTabularParser.PARSING_CONSISTENCY parsingConsistency)

Tries to define a different level of consistency during parsing. LITERAL is intended a strict parsing much tight to the report. IMPROVED consistency tries to import data much tight to the data model (I hope you got the idea, if not, have a look to the code. I suggest to use improved unless you have reasons to do not)