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. |
Methods inherited from class java.lang.Object |
clone,
equals,
finalize,
getClass,
hashCode,
notify,
notifyAll,
toString,
wait,
wait,
wait |
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.
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 fromresParser
- the parser to parse chars to Symbol objectssf
- 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 outos
- the printstream to write to