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 Details

  • Constructor Details

  • Method Details

    • 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.