Package org.biojava.bio.seq.io
Class GAMEFormat
java.lang.Object
org.biojava.bio.seq.io.GAMEFormat
- All Implemented Interfaces:
SequenceFormat
A rudimentary read-only GAME 1.2 Format object.
- Author:
- David Huen
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionDeprecated.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 specifiedPrintStream
, using the specified format.
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Field Details
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DEFAULT
- See Also:
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Constructor Details
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GAMEFormat
public GAMEFormat()
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Method Details
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readSequence
public boolean readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) throws IOException this version only reads annotations (no symbols)- Specified by:
readSequence
in interfaceSequenceFormat
- 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.
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writeSequence
Description copied from interface:SequenceFormat
writeSequence
writes a sequence to the specified PrintStream, using the default format.- Specified by:
writeSequence
in interfaceSequenceFormat
- Parameters:
seq
- the sequence to write out.os
- the printstream to write to.
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writeSequence
Description copied from interface:SequenceFormat
writeSequence
writes a sequence to the specifiedPrintStream
, using the specified format.- Specified by:
writeSequence
in interfaceSequenceFormat
- Parameters:
seq
- aSequence
to write out.format
- aString
indicating which sub-format of those available from a particularSequenceFormat
implemention to use when writing.os
- aPrintStream
object.
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getDefaultFormat
Deprecated.getDefaultFormat
returns the String identifier for the default format.- Specified by:
getDefaultFormat
in interfaceSequenceFormat
- Returns:
- a
String
.
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