org.biojava.bio.seq.io
Class GAMEFormat

java.lang.Object
  extended by 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
static String DEFAULT
           
 
Constructor Summary
GAMEFormat()
           
 
Method Summary
 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.