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

Description

BlastXMLParser()
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.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- BlastXMLParser
  
  public BlastXMLParser()
Method Details
- 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

Class BlastXMLParser

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

BlastXMLParser

Method Details

setFile

createObjects

getFileExtensions

setQueryReferences

setDatabaseReferences

storeObjects