Class GFFParser


  • public class GFFParser
    extends java.lang.Object
    Parse a stream of GFF text into a stream of records and comments.
    Author:
    Matthew Pocock, Thomas Down, Keith James (docs)
    • Constructor Summary

      Constructors 
      Constructor Description
      GFFParser()  
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      protected GFFRecord createRecord​(GFFDocumentHandler handler, java.util.List aList, java.lang.String rest, java.lang.String comment)
      Actually turns a list of tokens, some value string and a comment into a GFFRecord and informs handler.
      GFFErrorHandler getErrorHandler()
      Find the error handler used by this parser.
      void parse​(java.io.BufferedReader bReader, GFFDocumentHandler handler)
      Informs handler of each line of gff read from bReader.
      void parse​(java.io.BufferedReader bReader, GFFDocumentHandler handler, java.lang.String locator)
      Informs handler of each line of GFF read from bReader
      protected java.util.Map parseAttribute​(java.lang.String attValList)
      Parse attValList into a Map of attributes and value lists.
      void setErrorHandler​(GFFErrorHandler errors)
      Set the error handler used by this parser.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • GFFParser

        public GFFParser()
    • Method Detail

      • setErrorHandler

        public void setErrorHandler​(GFFErrorHandler errors)
        Set the error handler used by this parser.
      • getErrorHandler

        public GFFErrorHandler getErrorHandler()
        Find the error handler used by this parser.
      • parse

        public void parse​(java.io.BufferedReader bReader,
                          GFFDocumentHandler handler)
                   throws java.io.IOException,
                          BioException,
                          ParserException
        Informs handler of each line of gff read from bReader. This form of the method should only be used if no locator string is available for the resource being parsed.
        Parameters:
        bReader - the BufferedReader to parse
        handler - the GFFDocumentHandler that will listen for 'stuff'
        Throws:
        java.io.IOException
        BioException
        ParserException
      • parse

        public void parse​(java.io.BufferedReader bReader,
                          GFFDocumentHandler handler,
                          java.lang.String locator)
                   throws java.io.IOException,
                          BioException,
                          ParserException
        Informs handler of each line of GFF read from bReader
        Parameters:
        bReader - the BufferedReader to parse
        handler - the GFFDocumentHandler that will listen for 'stuff'
        Throws:
        java.io.IOException
        BioException
        ParserException
      • createRecord

        protected GFFRecord createRecord​(GFFDocumentHandler handler,
                                         java.util.List aList,
                                         java.lang.String rest,
                                         java.lang.String comment)
                                  throws BioException,
                                         ParserException,
                                         IgnoreRecordException
        Actually turns a list of tokens, some value string and a comment into a GFFRecord and informs handler.
        Parameters:
        handler - a GFFDocumentHandler to inform of any parse errors, and the completed GFFRecord
        aList - a List containing the 8 mandatory GFF columns
        rest - a String representing the unparsed attribute-value text, or null if there is none
        comment - a String containing the comment (without the leading '#' character.
        Throws:
        BioException
        ParserException
        IgnoreRecordException
      • parseAttribute

        protected java.util.Map parseAttribute​(java.lang.String attValList)
        Parse attValList into a Map of attributes and value lists.

        The resulting Map will have String keys, with List values. If there are no values associated with a key, then it will have an empty List, not null as its value.

        Parameters:
        attValList - the String to parse
        Returns:
        a Map of parsed attributes and value lists