org.biojava.bio.seq.io
Class GAMEFormat
java.lang.Object
org.biojava.bio.seq.io.GAMEFormat
- All Implemented Interfaces:
- SequenceFormat
public class GAMEFormat
- extends java.lang.Object
- implements SequenceFormat
A rudimentary read-only GAME 1.2 Format object.
- Author:
- David Huen
Field Summary |
static java.lang.String |
DEFAULT
|
Method Summary |
java.lang.String |
getDefaultFormat()
Deprecated. |
boolean |
readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
this version only reads annotations (no symbols) |
void |
writeSequence(Sequence seq,
java.io.PrintStream os)
writeSequence writes a sequence to the specified
PrintStream, using the default format. |
void |
writeSequence(Sequence seq,
java.lang.String format,
java.io.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 |
DEFAULT
public static final java.lang.String DEFAULT
- See Also:
- Constant Field Values
GAMEFormat
public GAMEFormat()
readSequence
public boolean readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
throws java.io.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:
java.io.IOException
- if an error occurs while reading from the
stream.
writeSequence
public void writeSequence(Sequence seq,
java.io.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,
java.lang.String format,
java.io.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 java.lang.String getDefaultFormat()
- Deprecated.
getDefaultFormat
returns the String identifier for
the default format.
- Specified by:
getDefaultFormat
in interface SequenceFormat
- Returns:
- a
String
.