Package org.biojava.bio.seq.io
Class FastaFormat
java.lang.Object
org.biojava.bio.seq.io.FastaFormat
- All Implemented Interfaces:
Serializable
,EventListener
,SequenceFormat
,ParseErrorListener
,ParseErrorSource
public class FastaFormat
extends Object
implements SequenceFormat, Serializable, ParseErrorListener, ParseErrorSource
Deprecated.
Use org.biojavax.bio.seq.io.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.
- Author:
- Thomas Down, Matthew Pocock, Greg Cox, Lukas Kall, Richard Holland, Mark Schreiber
- See Also:
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
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.Deprecated.int
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 aSeqIOListener
using aSymbolTokenizer
to convert sequence strings toSymbol
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 aSequence
orRichSequence
to aPrintStream
in FASTA format.void
writeSequence
(Sequence seq, String format, PrintStream os) Deprecated.use writeSequence(Sequence seq, PrintStream os)
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Field Details
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DEFAULT
Deprecated.- See Also:
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PROPERTY_DESCRIPTIONLINE
Deprecated.Constant string which is the property key used to notify listeners of the description lines of FASTA sequences.- See Also:
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mListeners
Deprecated. -
lineWidth
Deprecated.The line width for output.
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Constructor Details
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FastaFormat
public FastaFormat()Deprecated.
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Method Details
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getLineWidth
Deprecated.Retrive the current line width.- Returns:
- the line width
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setLineWidth
Deprecated.Set the line width.When writing, the lines of sequence will never be longer than the line width.
- Parameters:
width
- the new line width
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readSequence
public boolean readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener siol) throws IllegalSymbolException, IOException, ParseException Deprecated.Reads information from a flatfile to aSeqIOListener
using aSymbolTokenizer
to convert sequence strings toSymbol
objects.- Specified by:
readSequence
in interfaceSequenceFormat
- Parameters:
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 aRichSeqIOListener
.- Returns:
- true if there is another unread sequence in the source.
- Throws:
IllegalSymbolException
- ifsymParser
doesn't know how to convert the text sequence into biojavaSymbol
sIOException
- if there is a problem reading.ParseException
- if the source cannot be parsed.
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describeSequence
Deprecated.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
Deprecated.Writes aSequence
orRichSequence
to aPrintStream
in FASTA format. If the sequence is aRichSequence
the format of the header will be in line with the NCBI standard.- Specified by:
writeSequence
in interfaceSequenceFormat
- Parameters:
seq
- the sequence to formatos
- the stream to write the sequence to. To print to screen useSystem.out
- Throws:
IOException
- if data cannot be written toos
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writeSequence
Deprecated.use writeSequence(Sequence seq, PrintStream os)writeSequence
writes a sequence to the specifiedPrintStream
, using the specified format.- Specified by:
writeSequence
in interfaceSequenceFormat
- Parameters:
seq
- aSequence
to write out.format
- aString
indicating which sub-format of those available from a particularSequenceFormat
implemention to use when writing.os
- aPrintStream
object.- Throws:
IOException
- if an error occurs.
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getDefaultFormat
Deprecated.getDefaultFormat
returns the String identifier for the default format.- Specified by:
getDefaultFormat
in interfaceSequenceFormat
- Returns:
- a
String
.
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addParseErrorListener
Deprecated.Adds a parse error listener to the list of listeners if it isn't already included.- Specified by:
addParseErrorListener
in interfaceParseErrorSource
- Parameters:
theListener
- Listener to be added.
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removeParseErrorListener
Deprecated.Removes a parse error listener from the list of listeners if it is included.- Specified by:
removeParseErrorListener
in interfaceParseErrorSource
- Parameters:
theListener
- Listener to be removed.
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BadLineParsed
Deprecated.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 interfaceParseErrorListener
- Parameters:
theEvent
- The event that contains the bad line and token.
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notifyParseErrorEvent
Deprecated.Passes the event on to all the listeners registered for ParseErrorEvents.- Parameters:
theEvent
- The event to be handed to the listeners.
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