public interface SequenceFormat
Sequence formats are responsible for both reading and writing a sequence in a format, presumably in such a way as the written record can be read back in by the same formatter.
Where possible, the methods are parameterised so that they don't need any knowledge of the specific implementation of Sequence they are reading or writing. E.g. it should be possible to parameterise readSequence to read from a Genbank stream and construct Ensembl CORBA objects, just by specifying an Ensembl SequenceFactory.
More functionality is offered by
Use of this interface is prefered.
|Modifier and Type||Method and Description|
new implementations should only write a single format.
Read a sequence and pass data on to a SeqIOListener.
use writeSequence(Sequence seq, PrintStream os)
boolean readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) throws BioException, IllegalSymbolException, IOException
reader- The stream of data to parse.
symParser- A SymbolParser defining a mapping from character data to Symbols.
listener- A listener to notify when data is extracted from the stream.
IOException- if an error occurs while reading from the stream.
IllegalSymbolException- if it is not possible to translate character data from the stream into valid BioJava symbols.
BioException- if there is an error in the format of the stream.
void writeSequence(Sequence seq, PrintStream os) throws IOException
writeSequencewrites a sequence to the specified PrintStream, using the default format.
seq- the sequence to write out.
os- the printstream to write to.
void writeSequence(Sequence seq, String format, PrintStream os) throws IOException
writeSequencewrites a sequence to the specified
PrintStream, using the specified format.
Sequenceto write out.
Stringindicating which sub-format of those available from a particular
SequenceFormatimplemention to use when writing.
IOException- if an error occurs.
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