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

Class BlastTabularParser

java.lang.Object
org.biojava.nbio.core.search.io.blast.BlastTabularParser
All Implemented Interfaces:
ResultFactory
public class BlastTabularParser extends 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

  • Constructor Details

    • BlastTabularParser

      public BlastTabularParser()

  • Method Details

    • getFileExtensions

      public List<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(File f)
      Specified by:
      setFile in interface ResultFactory

    • createObjects

      public List<Result> createObjects(double maxEScore) throws IOException, 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:
      IOException
      ParseException

    • storeObjects

      public void storeObjects(List<Result> results) throws IOException, 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:
      IOException
      ParseException

    • setQueryReferences

      public void setQueryReferences(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(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)