org.biojavax.bio.seq.io

Class RichSequenceFormat.HeaderlessFormat

java.lang.Object

org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat

org.biojavax.bio.seq.io.RichSequenceFormat.HeaderlessFormat

All Implemented Interfaces:

SequenceFormat, RichSequenceFormat

Direct Known Subclasses:

EMBLFormat, FastaFormat, GenbankFormat, UniProtFormat

Enclosing interface:

RichSequenceFormat

public abstract static class RichSequenceFormat.HeaderlessFormat
extends RichSequenceFormat.BasicFormat

Provides the basic implementation required for simple header/footer-less files such as Genbank.

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojavax.bio.seq.io.RichSequenceFormat

RichSequenceFormat.BasicFormat, RichSequenceFormat.HeaderlessFormat

Constructor Summary

Constructors

Constructor and Description
RichSequenceFormat.HeaderlessFormat()

Method Summary

Methods

Modifier and Type	Method and Description
void	beginWriting() Informs the writer that we want to start writing.
void	finishWriting() Informs the writer that are done writing.

Methods inherited from class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat

canRead, getElideComments, getElideFeatures, getElideReferences, getElideSymbols, getLineWidth, getPrintStream, guessSymbolTokenization, setElideComments, setElideFeatures, setElideReferences, setElideSymbols, setLineWidth, setPrintStream

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.biojavax.bio.seq.io.RichSequenceFormat

canRead, guessSymbolTokenization, readRichSequence, writeSequence

Methods inherited from interface org.biojava.bio.seq.io.SequenceFormat

getDefaultFormat, readSequence, writeSequence, writeSequence

Constructor Detail

RichSequenceFormat.HeaderlessFormat

public RichSequenceFormat.HeaderlessFormat()

Method Detail

beginWriting

public void beginWriting()
                  throws IOException

Informs the writer that we want to start writing. This will do any initialisation required, such as writing the opening tags of an XML file that groups sequences together.

Throws:

IOException - if writing fails.

finishWriting

public void finishWriting()
                   throws IOException

Informs the writer that are done writing. This will do any finalisation required, such as writing the closing tags of an XML file that groups sequences together.

Throws:

IOException - if writing fails.