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 Details

    • 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 -