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

Class BlastXMLParser

  • All Implemented Interfaces:
    ResultFactory
    public class BlastXMLParser
extends java.lang.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

      All Methods Instance Methods Concrete 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.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • BlastXMLParser

        public BlastXMLParser()

    • Method Detail

      • setFile

        public void setFile​(java.io.File f)
        Specified by:
        setFile in interface ResultFactory

      • createObjects

        public java.util.List<Result> createObjects​(double maxEScore)
                                     throws java.io.IOException,
                                            java.text.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:
        java.io.IOException
        java.text.ParseException

      • getFileExtensions

        public java.util.List<java.lang.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​(java.util.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​(java.util.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​(java.util.List<Result> results)
                  throws java.io.IOException,
                         java.text.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:
        java.io.IOException
        java.text.ParseException