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java.lang.Objectorg.biojava.bio.program.phred.PhredFormat
public class PhredFormat
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
Field Summary | |
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static java.lang.String |
DEFAULT
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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 | |
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PhredFormat()
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Method Summary | |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final java.lang.String DEFAULT
public static final java.lang.String PROPERTY_DESCRIPTIONLINE
Constructor Detail |
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public PhredFormat()
Method Detail |
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public int getLineWidth()
public void setLineWidth(int width)
When writing, the lines of sequence will never be longer than the line width.
width
- the new line widthpublic boolean readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener siol) throws IllegalSymbolException, java.io.IOException, ParseException
SequenceFormat
readSequence
in interface SequenceFormat
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.
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
protected java.lang.String describeSequence(Sequence seq)
public void writeSequence(Sequence seq, java.io.PrintStream os) throws java.io.IOException
writeSequence
in interface SequenceFormat
seq
- the sequence to write out.os
- the printstream to write to.
java.io.IOException
public void writeSequence(Sequence seq, java.lang.String format, java.io.PrintStream os) throws java.io.IOException
writeSequence
writes a sequence to the specified
PrintStream
, using the specified format.
writeSequence
in interface SequenceFormat
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.
java.io.IOException
- if an error occurs.public java.lang.String getDefaultFormat()
getDefaultFormat
returns the String identifier for
the default format.
getDefaultFormat
in interface SequenceFormat
String
.public void addParseErrorListener(ParseErrorListener theListener)
addParseErrorListener
in interface ParseErrorSource
theListener
- Listener to be added.public void removeParseErrorListener(ParseErrorListener theListener)
removeParseErrorListener
in interface ParseErrorSource
theListener
- Listener to be removed.public void BadLineParsed(ParseErrorEvent theEvent)
This method should be overwritten when different behavior is desired.
BadLineParsed
in interface ParseErrorListener
theEvent
- The event that contains the bad line and token.protected void notifyParseErrorEvent(ParseErrorEvent theEvent)
theEvent
- The event to be handed to the listeners.
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