org.biojava.bio.program.phred
Class PhredFormat

java.lang.Object
  extended by org.biojava.bio.program.phred.PhredFormat
All Implemented Interfaces:
Serializable, EventListener, SequenceFormat, ParseErrorListener, ParseErrorSource

public class PhredFormat
extends Object
implements SequenceFormat, ParseErrorSource, ParseErrorListener, 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
static String DEFAULT
           
static String PROPERTY_DESCRIPTIONLINE
          Constant string which is the property key used to notify listeners of the description lines of Phred sequences.
 
Constructor Summary
PhredFormat()
           
 
Method Summary
 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  String describeSequence(Sequence seq)
          Return a suitable description line for a Sequence.
 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(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, PrintStream os)
          This method will print symbols to the line width followed by a new line etc.
 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
See Also:
Constant Field Values

PROPERTY_DESCRIPTIONLINE

public static final 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(BufferedReader reader,
                            SymbolTokenization symParser,
                            SeqIOListener siol)
                     throws IllegalSymbolException,
                            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.
IOException - if an error occurs while reading from the stream.
ParseException

describeSequence

protected 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,
                          PrintStream os)
                   throws 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:
IOException

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)
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.