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## 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 Pattern` | `aminoAcids`
`protected static Pattern` | `dp`
`static String` | `FASTA_FORMAT` The name of this format
`protected static Pattern` | `hp`
`protected static Pattern` | `readableFiles`

Constructor Summary
`FastaFormat()`

Method Summary
`boolean` | `canRead(BufferedInputStream stream)` Check to see if a given stream is in our format. A stream is in FASTA format if the stream starts with ">".
`boolean` | `canRead(File file)` 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 ">".
`String` | `getDefaultFormat()` `getDefaultFormat` returns the String identifier for the default sub-format written by a `SequenceFormat` implementation.
`FastaHeader` | `getHeader()`
`SymbolTokenization` | `guessSymbolTokenization(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. Returns an protein parser if the first line of sequence contains any of F/L/I/P/Q/E, otherwise returns a DNA tokenizer.
`SymbolTokenization` | `guessSymbolTokenization(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. 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.
`void` | `processHeader(String line, RichSeqIOListener rsiol, Namespace ns)` Parse the Header information from the Fasta Description line
`boolean` | `readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rsiol, Namespace ns)` Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols. If namespace is null, then the namespace of the sequence in the fasta is used.
`boolean` | `readSequence(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. If namespace is null, then the sequence's own namespace is used.
`void` | `writeSequence(Sequence seq, PrintStream os)` `writeSequence` writes a sequence to the specified PrintStream, using the default format.
`void` | `writeSequence(Sequence seq, String format, 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 String FASTA_FORMAT

  The name of this format

  See Also:
    Constant Field Values

### hp

    protected static final Pattern hp

### dp

    protected static final Pattern dp

### readableFiles

    protected static final Pattern readableFiles

### aminoAcids

    protected static final Pattern aminoAcids

Constructor Detail

### FastaFormat

    public FastaFormat()

Method Detail

### canRead

    public boolean canRead(File file)
                    throws 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:
    `IOException` - in case the file is inaccessible.

### guessSymbolTokenization

    public SymbolTokenization guessSymbolTokenization(File file)
                                               throws 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:
    `IOException` - if the file is unrecognisable or inaccessible.

### canRead

    public boolean canRead(BufferedInputStream stream)
                    throws 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:
    `IOException` - in case the stream is inaccessible.

### guessSymbolTokenization

    public SymbolTokenization guessSymbolTokenization(BufferedInputStream stream)
                                               throws 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:
    `IOException` - if the stream is unrecognisable or inaccessible.

### readSequence

    public boolean readSequence(BufferedReader reader,
                                SymbolTokenization symParser,
                                SeqIOListener listener)
                         throws IllegalSymbolException,
                                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.
    `IOException` - if an error occurs while reading from the stream.
    `ParseException`

### readRichSequence

    public boolean readRichSequence(BufferedReader reader,
                                    SymbolTokenization symParser,
                                    RichSeqIOListener rsiol,
                                    Namespace ns)
                             throws IllegalSymbolException,
                                    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.
    `IOException` - if there was a read error.
    `ParseException`

### processHeader

    public void processHeader(String line,
                              RichSeqIOListener rsiol,
                              Namespace ns)
                       throws IOException,
                              ParseException

  Parse the Header information from the Fasta Description line

  Parameters:
    `line` -
    `rsiol` -
    `ns` -
  Throws:
    `IOException`
    `ParseException`

### writeSequence

    public void writeSequence(Sequence seq,
                              PrintStream os)
                       throws 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:
    `IOException`

### writeSequence

    public void writeSequence(Sequence seq,
                              String format,
                              PrintStream os)
                       throws 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:
    `IOException` - if an error occurs.

### writeSequence

    public void writeSequence(Sequence seq,
                              Namespace ns)
                       throws 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:
    `IOException` - in case it couldn't write something

### getDefaultFormat

    public 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)

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