Class BlastTabularParser

  • All Implemented Interfaces:
    ResultFactory

    public class BlastTabularParser
    extends java.lang.Object
    implements 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 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)
      Intended for use with run module.
      void setFile​(java.io.File f)  
      void setParsingConsistency​(org.biojava.nbio.core.search.io.blast.BlastTabularParser.PARSING_CONSISTENCY parsingConsistency)
      Tries to define a different level of consistency during parsing.
      void setQueryReferences​(java.util.List<Sequence> sequences)
      Intended for use with run module.
      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

      • BlastTabularParser

        public BlastTabularParser()
    • Method Detail

      • 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:
      • 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
      • 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
      • setQueryReferences

        public void setQueryReferences​(java.util.List<Sequence> sequences)
        Intended for use with run module. Although possible, does not make a lot of sense to have it with limited information such those in tabular report
        Specified by:
        setQueryReferences in interface ResultFactory
        Parameters:
        sequences -
      • setDatabaseReferences

        public void setDatabaseReferences​(java.util.List<Sequence> sequences)
        Intended for use with run module. Although possible, does not make a lot of sense to have it with limited information such those in tabular report
        Specified by:
        setDatabaseReferences in interface ResultFactory
        Parameters:
        sequences -
      • setParsingConsistency

        public void setParsingConsistency​(org.biojava.nbio.core.search.io.blast.BlastTabularParser.PARSING_CONSISTENCY parsingConsistency)
        Tries to define a different level of consistency during parsing. LITERAL is intended a strict parsing much tight to the report. IMPROVED consistency tries to import data much tight to the data model (I hope you got the idea, if not, have a look to the code. I suggest to use improved unless you have reasons to do not)