|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectorg.biojava.bio.seq.io.FastaFormat
public class FastaFormat
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.
Field Summary | |
---|---|
static String |
DEFAULT
Deprecated. |
protected int |
lineWidth
Deprecated. The line width for output. |
protected Vector |
mListeners
Deprecated. |
static String |
PROPERTY_DESCRIPTIONLINE
Deprecated. Constant string which is the property key used to notify listeners of the description lines of FASTA sequences. |
Constructor Summary | |
---|---|
FastaFormat()
Deprecated. |
Method Summary | |
---|---|
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 String |
describeSequence(Sequence seq)
Deprecated. Return a suitable description line for a Sequence. |
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(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,
PrintStream os)
Deprecated. Writes a Sequence or RichSequence to a
PrintStream in FASTA format. |
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 |
---|
public static final String DEFAULT
public static final String PROPERTY_DESCRIPTIONLINE
protected Vector mListeners
protected int lineWidth
Constructor Detail |
---|
public FastaFormat()
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(BufferedReader reader, SymbolTokenization symParser, SeqIOListener siol) throws IllegalSymbolException, IOException, ParseException
SeqIOListener
using a SymbolTokenizer
to convert sequence strings
to Symbol
objects.
readSequence
in interface SequenceFormat
reader
- The reader that is the source of the informationsymParser
- converts text seqeunce to biojava objectssiol
- The listener that listens for event callbacks from this class.
The listener can be a RichSeqIOListener
.
IllegalSymbolException
- if symParser
doesn't know how to convert the text sequence into biojava Symbol
s
IOException
- if there is a problem reading.
ParseException
- if the source cannot be parsed.protected String describeSequence(Sequence seq)
public void writeSequence(Sequence seq, PrintStream os) throws IOException
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.
writeSequence
in interface SequenceFormat
seq
- the sequence to formatos
- the stream to write the sequence to. To print to screen use
System.out
IOException
- if data cannot be written to os
public void writeSequence(Sequence seq, String format, PrintStream os) throws 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.
IOException
- if an error occurs.public 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.
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |