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 Link icon

    Modifier and Type
    Method
    Description
    createObjects(double maxEScore)
    Launch the parsing and get back a list of Result objects representing the search result in the specified file.
    returns a list of file extensions associated to this ResultFactory
    void
    Specify the collection of sequences objects used as database in the Search run.
    void
     
    void
    Specify the collection of sequences objects used as queries in the Search run.
    void
    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 Link icon

    • getFileExtensions Link icon

      returns a list of file extensions associated to this ResultFactory
      Returns:
    • setFile Link icon

      void setFile(File f)
    • createObjects Link icon

      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:
      IOException
      ParseException
    • storeObjects Link icon

      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:
      IOException
      ParseException
    • setQueryReferences Link icon

      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 Link icon

      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 -