org.biojava.bio.program.gff3
Class GFF3Parser

java.lang.Object
  extended by org.biojava.bio.program.gff3.GFF3Parser

public class GFF3Parser
extends java.lang.Object

Parse a stream of GFF text into a stream of records and comments.

Developed from GFFParser.

Author:
Matthew Pocock

Constructor Summary
GFF3Parser()
           
 
Method Summary
protected  GFF3Record createRecord(GFF3DocumentHandler handler, java.util.List aList, java.lang.String rest, java.lang.String comment, Ontology ontology, Ontology fallBack)
          Actually turns a list of tokens, some value string and a comment into a GFF3Record and informs handler.
 GFFErrorHandler getErrorHandler()
          Find the error handler used by this parser.
 void parse(java.io.BufferedReader bReader, GFF3DocumentHandler handler, Ontology ontology)
          Informs handler of each line of gff read from bReader.
 void parse(java.io.BufferedReader bReader, GFF3DocumentHandler handler, Ontology ontology, java.lang.String locator)
          Informs handler of each line of GFF read from bReader
protected  void parseAttribute(java.lang.String attValList, Annotation anno, Ontology onto, Ontology fallBack)
          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

GFF3Parser

public GFF3Parser()
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,
                  GFF3DocumentHandler handler,
                  Ontology ontology)
           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 GFF3DocumentHandler that will listen for 'stuff'
ontology - an Ontology that all terms should come from
Throws:
- class="type">IOException if for any reason bReader throws one
- class="type">BioException if handler can not correct a parse error
java.io.IOException
BioException
ParserException

parse

public void parse(java.io.BufferedReader bReader,
                  GFF3DocumentHandler handler,
                  Ontology ontology,
                  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 GFF3DocumentHandler that will listen for 'stuff'
ontology - an Ontology that all terms should come from
Throws:
- class="type">IOException if for any reason bReader throws one
- class="type">BioException if handler can not correct a parse error
java.io.IOException
BioException
ParserException

createRecord

protected GFF3Record createRecord(GFF3DocumentHandler handler,
                                  java.util.List aList,
                                  java.lang.String rest,
                                  java.lang.String comment,
                                  Ontology ontology,
                                  Ontology fallBack)
                           throws BioException,
                                  ParserException,
                                  IgnoreRecordException
Actually turns a list of tokens, some value string and a comment into a GFF3Record and informs handler.

Parameters:
handler - a GFF3DocumentHandler to inform of any parse errors, and the completed GFF3Record
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.
ontology - the Ontology to resolve Terms in
Throws:
- class="type">BioException if handler could not correct a parse error
BioException
ParserException
IgnoreRecordException

parseAttribute

protected void parseAttribute(java.lang.String attValList,
                              Annotation anno,
                              Ontology onto,
                              Ontology fallBack)
                       throws ChangeVetoException
Parse attValList into a Map of attributes and value lists.

Populates an Annotation instance with Ontology Term keys and string/list values.

Parameters:
attValList - the String to parse
Throws:
ChangeVetoException