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java.lang.Objectorg.biojava.bio.program.phred.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 | |
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 | |
PhredFormat()
|
Method Summary | |
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. |
boolean |
readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener siol)
Read a sequence and pass data on to a SeqIOListener. |
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 |
public static final java.lang.String DEFAULT
public static final java.lang.String PROPERTY_DESCRIPTIONLINE
Constructor Detail |
public PhredFormat()
Method Detail |
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.
java.io.IOException
- if an error occurs while reading from the
stream.
IllegalSymbolException
- if it is not possible to
translate character data from the stream into valid BioJava
symbols.
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
.
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