Package org.biojava.bio.seq.io

Class GAMEFormat

java.lang.Object

org.biojava.bio.seq.io.GAMEFormat

All Implemented Interfaces:

SequenceFormat

public class GAMEFormat
extends Object
implements SequenceFormat

A rudimentary read-only GAME 1.2 Format object.

Author:

David Huen

Field Summary

Fields

Modifier and Type	Field	Description
static String	DEFAULT

Constructor Summary

Constructors

Constructor	Description
GAMEFormat()

Method Summary

Modifier and Type	Method	Description
String	getDefaultFormat()	Deprecated.
boolean	readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)	this version only reads annotations (no symbols)
void	writeSequence(Sequence seq, PrintStream os)	writeSequence writes a sequence to the specified PrintStream, using the default format.
void	writeSequence(Sequence seq, String format, PrintStream os)	writeSequence writes a sequence to the specified PrintStream, using the specified format.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT

public static final String DEFAULT

See Also:

Constant Field Values

Constructor Detail

GAMEFormat

public GAMEFormat()

Method Detail

readSequence

public boolean readSequence(BufferedReader reader,
                            SymbolTokenization symParser,
                            SeqIOListener listener)
                     throws IOException

this version only reads annotations (no symbols)

Specified by:

readSequence in interface SequenceFormat

Parameters:

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.

Returns:

a boolean indicating whether or not the stream contains any more sequences.

Throws:

IOException - if an error occurs while reading from the stream.

writeSequence

public void writeSequence(Sequence seq,
                          PrintStream os)

Description copied from interface: SequenceFormat

writeSequence writes a sequence to the specified PrintStream, using the default format.

Specified by:

writeSequence in interface SequenceFormat

Parameters:

seq - the sequence to write out.

os - the printstream to write to.

writeSequence

public void writeSequence(Sequence seq,
                          String format,
                          PrintStream os)

Description copied from interface: SequenceFormat

writeSequence writes a sequence to the specified PrintStream, using the specified format.

Specified by:

writeSequence in interface SequenceFormat

Parameters:

seq - a Sequence to write out.

format - a String indicating which sub-format of those available from a particular SequenceFormat implemention to use when writing.

os - a PrintStream object.

getDefaultFormat

public String getDefaultFormat()

Deprecated.

getDefaultFormat returns the String identifier for the default format.

Specified by:

getDefaultFormat in interface SequenceFormat

Returns:

a String.