org.biojavax.bio.seq.io
Class FastaFormat

java.lang.Object
  org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
      org.biojavax.bio.seq.io.RichSequenceFormat.HeaderlessFormat
          org.biojavax.bio.seq.io.FastaFormat

All Implemented Interfaces:

SequenceFormat, RichSequenceFormat

public class FastaFormat
extends RichSequenceFormat.HeaderlessFormat

Format object representing FASTA files. These files are almost pure sequence data.

Since:

1.5

Author:

Thomas Down, Matthew Pocock, Greg Cox, Lukas Kall, Richard Holland, Mark Schreiber

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojavax.bio.seq.io.RichSequenceFormat

RichSequenceFormat.BasicFormat, RichSequenceFormat.HeaderlessFormat

Field Summary

protected static java.util.regex.Pattern	aminoAcids
protected static java.util.regex.Pattern	dp
static java.lang.String	FASTA_FORMAT The name of this format
protected static java.util.regex.Pattern	hp
protected static java.util.regex.Pattern	readableFiles

Constructor Summary

FastaFormat()

Method Summary

boolean	canRead(java.io.BufferedInputStream stream) Check to see if a given stream is in our format.
boolean	canRead(java.io.File file) Check to see if a given file is in our format.
java.lang.String	getDefaultFormat() getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.
FastaHeader	getHeader()
SymbolTokenization	guessSymbolTokenization(java.io.BufferedInputStream stream) On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
SymbolTokenization	guessSymbolTokenization(java.io.File file) On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.
void	processHeader(java.lang.String line, RichSeqIOListener rsiol, Namespace ns) Parse the Header information from the Fasta Description line
boolean	readRichSequence(java.io.BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rsiol, Namespace ns) Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
boolean	readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.
void	setHeader(FastaHeader header)
void	writeSequence(Sequence seq, Namespace ns) Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.
void	writeSequence(Sequence seq, java.io.PrintStream os) writeSequence writes a sequence to the specified PrintStream, using the default format.
void	writeSequence(Sequence seq, java.lang.String format, java.io.PrintStream os) writeSequence writes a sequence to the specified PrintStream, using the specified format.

Methods inherited from class org.biojavax.bio.seq.io.RichSequenceFormat.HeaderlessFormat

beginWriting, finishWriting

Methods inherited from class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat

getElideComments, getElideFeatures, getElideReferences, getElideSymbols, getLineWidth, getPrintStream, setElideComments, setElideFeatures, setElideReferences, setElideSymbols, setLineWidth, setPrintStream

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

FASTA_FORMAT

public static final java.lang.String FASTA_FORMAT

The name of this format

See Also:

Constant Field Values

hp

protected static final java.util.regex.Pattern hp

dp

protected static final java.util.regex.Pattern dp

readableFiles

protected static final java.util.regex.Pattern readableFiles

aminoAcids

protected static final java.util.regex.Pattern aminoAcids

Constructor Detail

FastaFormat

public FastaFormat()

Method Detail

canRead

public boolean canRead(java.io.File file)
                throws java.io.IOException

Check to see if a given file is in our format. Some formats may be able to determine this by filename, whilst others may have to open the file and read it to see what format it is in. A file is in FASTA format if the name ends with fa or fas, or the file starts with ">".

Specified by:

canRead in interface RichSequenceFormat

Overrides:

canRead in class RichSequenceFormat.BasicFormat

Parameters:

file - the File to check.

Returns:

true if the file is readable by this format, false if not.

Throws:

java.io.IOException - in case the file is inaccessible.

guessSymbolTokenization

public SymbolTokenization guessSymbolTokenization(java.io.File file)
                                           throws java.io.IOException

On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. For formats that only accept one tokenization, just return it without checking the file. For formats that accept multiple tokenizations, its up to you how you do it. Returns an protein parser if the first line of sequence contains any of F/L/I/P/Q/E, otherwise returns a DNA tokenizer.

Specified by:

guessSymbolTokenization in interface RichSequenceFormat

Overrides:

guessSymbolTokenization in class RichSequenceFormat.BasicFormat

Parameters:

file - the File object to guess the format of.

Returns:

a SymbolTokenization to read the file with.

Throws:

java.io.IOException - if the file is unrecognisable or inaccessible.

canRead

public boolean canRead(java.io.BufferedInputStream stream)
                throws java.io.IOException

Check to see if a given stream is in our format. A stream is in FASTA format if the stream starts with ">".

Parameters:

stream - the BufferedInputStream to check.

Returns:

true if the stream is readable by this format, false if not.

Throws:

java.io.IOException - in case the stream is inaccessible.

guessSymbolTokenization

public SymbolTokenization guessSymbolTokenization(java.io.BufferedInputStream stream)
                                           throws java.io.IOException

On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. For formats that only accept one tokenization, just return it without checking the stream. For formats that accept multiple tokenizations, its up to you how you do it. Returns an protein parser if the first line of sequence contains any of F/L/I/P/Q/E, otherwise returns a DNA tokenizer.

Parameters:

stream - the BufferedInputStream object to guess the format of.

Returns:

a SymbolTokenization to read the stream with.

Throws:

java.io.IOException - if the stream is unrecognisable or inaccessible.

readSequence

public boolean readSequence(java.io.BufferedReader reader,
                            SymbolTokenization symParser,
                            SeqIOListener listener)
                     throws IllegalSymbolException,
                            java.io.IOException,
                            ParseException

Read a sequence and pass data on to a SeqIOListener.

Parameters:

reader - The stream of data to parse.

symParser - A SymbolParser defining a mapping from character data to Symbols.

listener - 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.

java.io.IOException - if an error occurs while reading from the stream.

ParseException

readRichSequence

public boolean readRichSequence(java.io.BufferedReader reader,
                                SymbolTokenization symParser,
                                RichSeqIOListener rsiol,
                                Namespace ns)
                         throws IllegalSymbolException,
                                java.io.IOException,
                                ParseException

Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols. Events are passed to the listener, and the namespace used for sequences read is the one given. If the namespace is null, then the default namespace for the parser is used, which may depend on individual implementations of this interface. If namespace is null, then the namespace of the sequence in the fasta is used. If the namespace is null and so is the namespace of the sequence in the fasta, then the default namespace is used.

Parameters:

reader - the input source

symParser - the tokenizer which understands the sequence being read

rsiol - the listener to send sequence events to

ns - the namespace to read sequences into.

Returns:

true if there is more to read after this, false otherwise.

Throws:

IllegalSymbolException - if the tokenizer couldn't understand one of the sequence symbols in the file.

java.io.IOException - if there was a read error.

ParseException

processHeader

public void processHeader(java.lang.String line,
                          RichSeqIOListener rsiol,
                          Namespace ns)
                   throws java.io.IOException,
                          ParseException

Parse the Header information from the Fasta Description line

Parameters:

line -

rsiol -

ns -

Throws:

java.io.IOException

ParseException

writeSequence

public void writeSequence(Sequence seq,
                          java.io.PrintStream os)
                   throws java.io.IOException

writeSequence writes a sequence to the specified PrintStream, using the default format.

Parameters:

seq - the sequence to write out.

os - the printstream to write to.

Throws:

java.io.IOException

writeSequence

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.

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:

java.io.IOException - if an error occurs.

writeSequence

public void writeSequence(Sequence seq,
                          Namespace ns)
                   throws java.io.IOException

Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. If namespace is given, sequences will be written with that namespace, otherwise they will be written with the default namespace of the implementing class (which is usually the namespace of the sequence itself). If you pass this method a sequence which is not a RichSequence, it will attempt to convert it using RichSequence.Tools.enrich(). Obviously this is not going to guarantee a perfect conversion, so it's better if you just use RichSequences to start with! If namespace is null, then the sequence's own namespace is used.

Parameters:

seq - the sequence to write

ns - the namespace to write it with

Throws:

java.io.IOException - in case it couldn't write something

getDefaultFormat

public java.lang.String getDefaultFormat()

getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.

Returns:

a String.

getHeader

public FastaHeader getHeader()

setHeader

public void setHeader(FastaHeader header)