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

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      java.util.List<Result> createObjects​(double maxEScore)
      Launch the parsing and get back a list of Result objects representing the search result in the specified file.
      java.util.List<java.lang.String> getFileExtensions()
      returns a list of file extensions associated to this ResultFactory
      void setDatabaseReferences​(java.util.List<Sequence> sequences)
      Specify the collection of sequences objects used as database in the Search run.
      void setFile​(java.io.File f)  
      void setQueryReferences​(java.util.List<Sequence> sequences)
      Specify the collection of sequences objects used as queries in the Search run.
      void storeObjects​(java.util.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

        java.util.List<java.lang.String> getFileExtensions()
        returns a list of file extensions associated to this ResultFactory
        Returns:
      • setFile

        void setFile​(java.io.File f)
      • createObjects

        java.util.List<Result> createObjects​(double maxEScore)
                                      throws java.io.IOException,
                                             java.text.ParseException
        Launch the parsing and get back a list of Result objects representing the search result in the specified file.
        Parameters:
        maxEScore -
        Returns:
        Throws:
        java.lang.Exception
        java.io.IOException
        java.text.ParseException
      • storeObjects

        void storeObjects​(java.util.List<Result> results)
                   throws java.io.IOException,
                          java.text.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:
        java.lang.Exception
        java.io.IOException
        java.text.ParseException
      • setQueryReferences

        void setQueryReferences​(java.util.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​(java.util.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 -