org.biojava.bio.seq.io

Class FastaFormat

java.lang.Object

org.biojava.bio.seq.io.FastaFormat

All Implemented Interfaces:

java.io.Serializable, java.util.EventListener, SequenceFormat, ParseErrorListener, ParseErrorSource

Deprecated.

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

public class FastaFormat
extends java.lang.Object
implements SequenceFormat, java.io.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

Fields

Modifier and Type	Field and Description
static java.lang.String	DEFAULT Deprecated.
protected int	lineWidth Deprecated. The line width for output.
protected java.util.Vector	mListeners Deprecated.
static java.lang.String	PROPERTY_DESCRIPTIONLINE Deprecated. Constant string which is the property key used to notify listeners of the description lines of FASTA sequences.

Constructor Summary

Constructors

Constructor and Description
FastaFormat() Deprecated.

Method Summary

Methods

Modifier and Type	Method and Description
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 java.lang.String	describeSequence(Sequence seq) Deprecated. Return a suitable description line for a Sequence.
java.lang.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(java.io.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, java.io.PrintStream os) Deprecated. Writes a Sequence or RichSequence to a PrintStream in FASTA format.
void	writeSequence(Sequence seq, java.lang.String format, java.io.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 java.lang.String DEFAULT

Deprecated.

See Also:

Constant Field Values

PROPERTY_DESCRIPTIONLINE

public static final java.lang.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 java.util.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(java.io.BufferedReader reader,
                   SymbolTokenization symParser,
                   SeqIOListener siol)
                     throws IllegalSymbolException,
                            java.io.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

java.io.IOException - if there is a problem reading.

ParseException - if the source cannot be parsed.

describeSequence

protected java.lang.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,
                 java.io.PrintStream os)
                   throws java.io.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:

java.io.IOException - if data cannot be written to os

writeSequence

public void writeSequence(Sequence seq,
                 java.lang.String format,
                 java.io.PrintStream os)
                   throws java.io.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:

java.io.IOException - if an error occurs.

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.

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.