org.biojava.bio.seq.io
Class GenbankFormat

java.lang.Object
  |
  +--org.biojava.bio.seq.io.GenbankFormat

public class GenbankFormat
extends java.lang.Object
implements SequenceFormat, java.io.Serializable

Format reader for EMBL files.

Author:
Thomas Down
See Also:
Serialized Form

Constructor Summary
GenbankFormat()
          Constuct a GENBANK format processor using a default FeatureBuilder object.
GenbankFormat(FeatureBuilder fb)
          Construct a GENBANK format processor using the specified FeatureBuilder object.
 
Method Summary
 Sequence readSequence(StreamReader.Context context, SymbolParser resParser, SequenceFactory sf)
          Read in a single sequence.
 void writeSequence(Sequence seq, java.io.PrintStream os)
          This is not implemented.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

GenbankFormat

public GenbankFormat()
Constuct a GENBANK format processor using a default FeatureBuilder object. (actually a SimpleFeatureBuilder).

GenbankFormat

public GenbankFormat(FeatureBuilder fb)
Construct a GENBANK format processor using the specified FeatureBuilder object.
Method Detail

readSequence

public Sequence readSequence(StreamReader.Context context,
                             SymbolParser resParser,
                             SequenceFactory sf)
                      throws IllegalSymbolException,
                             java.io.IOException,
                             BioException
Description copied from interface: SequenceFormat
Read in a single sequence.

The format is responsible for converting characters in a stream into a complete sequence. It should read from the stream contained in context, parse the symbol characters using resParser and generate a sequence from the resulting symbol list using sf. Any non-sequence information within the format should be read in either as features, or as annotation.

Specified by:
readSequence in interface SequenceFormat
Tags copied from interface: SequenceFormat
Parameters:
context - the context to parse from
resParser - the parser to parse chars to Symbol objects
sf - the sequence factory for generating a full sequence
Returns:
the resulting sequence

writeSequence

public void writeSequence(Sequence seq,
                          java.io.PrintStream os)
                   throws java.io.IOException
This is not implemented. It does not write anything to the stream.
Specified by:
writeSequence in interface SequenceFormat
Tags copied from interface: SequenceFormat
Parameters:
seq - the sequence to write out
os - the printstream to write to