org.biojava.bio.program.phred

Class PhredFormat

java.lang.Object

org.biojava.bio.program.phred.PhredFormat

All Implemented Interfaces:

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

public class PhredFormat
extends java.lang.Object
implements SequenceFormat, ParseErrorSource, ParseErrorListener, java.io.Serializable

Format object representing Phred Quality files. 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). Essentially a rework of FastaFormat to cope with the quirks of Phred Quality data.

Copyright (c) 2001

Company: AgResearch

Since:

1.1

Author:

Mark Schreiber, Greg Cox, Frans Verhoef

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	DEFAULT
static java.lang.String	PROPERTY_DESCRIPTIONLINE Constant string which is the property key used to notify listeners of the description lines of Phred sequences.

Constructor Summary

Constructors

Constructor and Description
PhredFormat()

Method Summary

Modifier and Type	Method and Description
void	addParseErrorListener(ParseErrorListener theListener) Adds a parse error listener to the list of listeners if it isn't already included.
void	BadLineParsed(ParseErrorEvent theEvent) This method determines the behaviour when a bad line is processed.
protected java.lang.String	describeSequence(Sequence seq) Return a suitable description line for a Sequence.
java.lang.String	getDefaultFormat() Deprecated.
int	getLineWidth() Retrive the current line width.
protected void	notifyParseErrorEvent(ParseErrorEvent theEvent) Passes the event on to all the listeners registered for ParseErrorEvents.
boolean	readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener siol) Read a sequence and pass data on to a SeqIOListener.
void	removeParseErrorListener(ParseErrorListener theListener) Removes a parse error listener from the list of listeners if it is included.
void	setLineWidth(int width) Set the line width.
void	writeSequence(Sequence seq, java.io.PrintStream os) This method will print symbols to the line width followed by a new line etc.
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

See Also:

Constant Field Values

PROPERTY_DESCRIPTIONLINE

public static final java.lang.String PROPERTY_DESCRIPTIONLINE

Constant string which is the property key used to notify listeners of the description lines of Phred sequences.

See Also:

Constant Field Values

Constructor Detail

PhredFormat

public PhredFormat()

Method Detail

getLineWidth

public int getLineWidth()

Retrive the current line width.

Returns:

the line width

setLineWidth

public void setLineWidth(int width)

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

Description copied from interface: SequenceFormat

Read a sequence and pass data on to a SeqIOListener.

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.

siol - 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:

IllegalSymbolException - if it is not possible to translate character data from the stream into valid BioJava symbols.

java.io.IOException - if an error occurs while reading from the stream.

ParseException

describeSequence

protected java.lang.String describeSequence(Sequence seq)

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

This method will print symbols to the line width followed by a new line etc. NOTE that an integer symbol does not always correspond to one character therefore a line width of sixty will print sixty characters followed by a new line. Not necessarily sixty integers.

Specified by:

writeSequence in interface SequenceFormat

Parameters:

seq - the sequence to write out.

os - the printstream to write to.

Throws:

java.io.IOException

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)

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)

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)

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)

Passes the event on to all the listeners registered for ParseErrorEvents.

Parameters:

theEvent - The event to be handed to the listeners.