org.biojava.bio.seq.io
Class FastaFormat

java.lang.Object
  extended by org.biojava.bio.seq.io.FastaFormat
All Implemented Interfaces:
Serializable, EventListener, SequenceFormat, ParseErrorListener, ParseErrorSource

Deprecated. Use org.biojavax.bio.seq.io.FastaFormat

public class FastaFormat
extends Object
implements SequenceFormat, Serializable, ParseErrorListener, ParseErrorSource

Format object representing FASTA files. These files are almost pure sequence data. The only `sequence property' reported by this parser is PROPERTY_DESCRIPTIONLINE, which is the contents of the sequence's description line (the line starting with a '>' character). Normally, the first word of this is a sequence ID. If you wish it to be interpreted as such, you should use FastaDescriptionLineParser as a SeqIO filter. If you pass it a RichSeqIOListener, you'll get RichSequence objects in return. Likewise, if you write RichSequence objects, you'll get absolutely correct FASTA formatted output.

Author:
Thomas Down, Matthew Pocock, Greg Cox, Lukas Kall, Richard Holland, Mark Schreiber
See Also:
Serialized Form

Field Summary
static String DEFAULT
          Deprecated.  
protected  int lineWidth
          Deprecated. The line width for output.
protected  Vector mListeners
          Deprecated.  
static String PROPERTY_DESCRIPTIONLINE
          Deprecated. Constant string which is the property key used to notify listeners of the description lines of FASTA sequences.
 
Constructor Summary
FastaFormat()
          Deprecated.  
 
Method Summary
 void addParseErrorListener(ParseErrorListener theListener)
          Deprecated. Adds a parse error listener to the list of listeners if it isn't already included.
 void BadLineParsed(ParseErrorEvent theEvent)
          Deprecated. This method determines the behaviour when a bad line is processed.
protected  String describeSequence(Sequence seq)
          Deprecated. Return a suitable description line for a Sequence.
 String getDefaultFormat()
          Deprecated.  
 int getLineWidth()
          Deprecated. Retrive the current line width.
protected  void notifyParseErrorEvent(ParseErrorEvent theEvent)
          Deprecated. Passes the event on to all the listeners registered for ParseErrorEvents.
 boolean readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener siol)
          Deprecated. Reads information from a flatfile to a SeqIOListener using a SymbolTokenizer to convert sequence strings to Symbol objects.
 void removeParseErrorListener(ParseErrorListener theListener)
          Deprecated. Removes a parse error listener from the list of listeners if it is included.
 void setLineWidth(int width)
          Deprecated. Set the line width.
 void writeSequence(Sequence seq, PrintStream os)
          Deprecated. Writes a Sequence or RichSequence to a PrintStream in FASTA format.
 void writeSequence(Sequence seq, String format, PrintStream os)
          Deprecated. use writeSequence(Sequence seq, PrintStream os)
 
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
Deprecated. 
See Also:
Constant Field Values

PROPERTY_DESCRIPTIONLINE

public static final String PROPERTY_DESCRIPTIONLINE
Deprecated. 
Constant string which is the property key used to notify listeners of the description lines of FASTA sequences.

See Also:
Constant Field Values

mListeners

protected Vector mListeners
Deprecated. 

lineWidth

protected int lineWidth
Deprecated. 
The line width for output.

Constructor Detail

FastaFormat

public FastaFormat()
Deprecated. 
Method Detail

getLineWidth

public int getLineWidth()
Deprecated. 
Retrive the current line width.

Returns:
the line width

setLineWidth

public void setLineWidth(int width)
Deprecated. 
Set the line width.

When writing, the lines of sequence will never be longer than the line width.

Parameters:
width - the new line width

readSequence

public boolean readSequence(BufferedReader reader,
                            SymbolTokenization symParser,
                            SeqIOListener siol)
                     throws IllegalSymbolException,
                            IOException,
                            ParseException
Deprecated. 
Reads information from a flatfile to a SeqIOListener using a SymbolTokenizer to convert sequence strings to Symbol objects.

Specified by:
readSequence in interface SequenceFormat
Parameters:
reader - The reader that is the source of the information
symParser - converts text seqeunce to biojava objects
siol - The listener that listens for event callbacks from this class. The listener can be a RichSeqIOListener.
Returns:
true if there is another unread sequence in the source.
Throws:
IllegalSymbolException - if symParser doesn't know how to convert the text sequence into biojava Symbols
IOException - if there is a problem reading.
ParseException - if the source cannot be parsed.

describeSequence

protected String describeSequence(Sequence seq)
Deprecated. 
Return a suitable description line for a Sequence. If the sequence's annotation bundle contains PROPERTY_DESCRIPTIONLINE, this is used verbatim. Otherwise, the sequence's name is used.


writeSequence

public void writeSequence(Sequence seq,
                          PrintStream os)
                   throws IOException
Deprecated. 
Writes a Sequence or RichSequence to a PrintStream in FASTA format. If the sequence is a RichSequence the format of the header will be in line with the NCBI standard.

Specified by:
writeSequence in interface SequenceFormat
Parameters:
seq - the sequence to format
os - the stream to write the sequence to. To print to screen use System.out
Throws:
IOException - if data cannot be written to os

writeSequence

public void writeSequence(Sequence seq,
                          String format,
                          PrintStream os)
                   throws IOException
Deprecated. use writeSequence(Sequence seq, PrintStream os)

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.
Throws:
IOException - if an error occurs.

getDefaultFormat

public String getDefaultFormat()
Deprecated. 

getDefaultFormat returns the String identifier for the default format.

Specified by:
getDefaultFormat in interface SequenceFormat
Returns:
a String.

addParseErrorListener

public void addParseErrorListener(ParseErrorListener theListener)
Deprecated. 
Adds a parse error listener to the list of listeners if it isn't already included.

Specified by:
addParseErrorListener in interface ParseErrorSource
Parameters:
theListener - Listener to be added.

removeParseErrorListener

public void removeParseErrorListener(ParseErrorListener theListener)
Deprecated. 
Removes a parse error listener from the list of listeners if it is included.

Specified by:
removeParseErrorListener in interface ParseErrorSource
Parameters:
theListener - Listener to be removed.

BadLineParsed

public void BadLineParsed(ParseErrorEvent theEvent)
Deprecated. 
This method determines the behaviour when a bad line is processed. Some options are to log the error, throw an exception, ignore it completely, or pass the event through.

This method should be overwritten when different behavior is desired.

Specified by:
BadLineParsed in interface ParseErrorListener
Parameters:
theEvent - The event that contains the bad line and token.

notifyParseErrorEvent

protected void notifyParseErrorEvent(ParseErrorEvent theEvent)
Deprecated. 
Passes the event on to all the listeners registered for ParseErrorEvents.

Parameters:
theEvent - The event to be handed to the listeners.


Copyright © 2012 BioJava. All Rights Reserved.