## org.biojavax.bio.seq.io
Class EMBLFormat

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

All Implemented Interfaces:
  SequenceFormat, RichSequenceFormat

    public class EMBLFormat

extends RichSequenceFormat.HeaderlessFormat

Format reader for EMBL files. This version of EMBL format will generate and write RichSequence objects. Loosely Based on code from the old, deprecated, org.biojava.bio.seq.io.EmblLikeFormat object.

This format will read both Pre-87 and 87+ versions of EMBL. It will also write them both. By default, it will write the most recent version. If you want an earlier one, you must specify the format by passing one of the constants defined in this class to `writeSequence(Sequence, String, Namespace)`.

Since:
  1.5
Author:
  Richard Holland, Jolyon Holdstock, Mark Schreiber

Nested Class Summary
`static class` `EMBLFormat.Terms` Implements some EMBL-specific terms.

Nested classes/interfaces inherited from interface org.biojavax.bio.seq.io.RichSequenceFormat
`RichSequenceFormat.BasicFormat, RichSequenceFormat.HeaderlessFormat`

Field Summary
`protected static String` `ACCESSION_TAG`
`protected static String` `AUTHORS_TAG`
`protected static String` `COMMENT_TAG`
`protected static String` `CONSORTIUM_TAG`
`protected static String` `CONTIG_TAG`
`protected static String` `DATABASE_XREF_TAG`
`protected static String` `DATE_TAG`
`protected static Pattern` `dbxp`
`protected static String` `DEFINITION_TAG`
`protected static String` `DELIMITER_TAG`
`protected static Pattern` `dp`
`static String` `EMBL_FORMAT` The name of the current format
`static String` `EMBL_PRE87_FORMAT` The name of the Pre-87 format
`protected static String` `END_SEQUENCE_TAG`
`protected static String` `FEATURE_HEADER_TAG`
`protected static String` `FEATURE_TAG`
`protected static Pattern` `headerLine`
`protected static String` `KEYWORDS_TAG`
`protected static String` `LOCATOR_TAG`
`protected static String` `LOCUS_TAG`
`protected static Pattern` `lp`
`protected static Pattern` `lpPre87`
`protected static String` `ORGANELLE_TAG`
`protected static String` `ORGANISM_TAG`
`protected static Pattern` `readableFileNames`
`protected static String` `REFERENCE_POSITION_TAG`
`protected static String` `REFERENCE_TAG`
`protected static String` `REFERENCE_XREF_TAG`
`protected static String` `REMARK_TAG`
`protected static Pattern` `rpp`
`protected static String` `SOURCE_TAG`
`protected static String` `START_SEQUENCE_TAG`
`protected static String` `TITLE_TAG`
`protected static String` `TPA_TAG`
`protected static String` `VERSION_TAG`
`protected static Pattern` `vp`

Constructor Summary
`EMBLFormat()`

Method Summary
`boolean` `canRead(BufferedInputStream stream)` Check to see if a given stream is in our format. A stream is in EMBL format if its first line matches the EMBL format for the ID line.
`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 EMBL format if its name contains the word eem or edat, or the first line matches the EMBL format for the ID line.
`String` `getDefaultFormat()` `getDefaultFormat` returns the String identifier for the default sub-format written by a `SequenceFormat` implementation.
`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. Always 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. Always returns a DNA tokenizer.
`boolean` `readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns)` Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
`boolean` `readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)` Read a sequence and pass data on to a SeqIOListener.
`void` `writeSequence(Sequence seq, Namespace ns)` Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. Namespace is ignored as EMBL has no concept of it.
`void` `writeSequence(Sequence seq, PrintStream os)` `writeSequence` writes a sequence to the specified PrintStream, using the default format.
`void` `writeSequence(Sequence seq, String format, Namespace ns)` As per `writeSequence(Sequence, Namespace)`, except that it also takes a format parameter.
`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

### EMBL_PRE87_FORMAT

    public static final String EMBL_PRE87_FORMAT

  The name of the Pre-87 format

  See Also:
    Constant Field Values

### EMBL_FORMAT

    public static final String EMBL_FORMAT

  The name of the current format

  See Also:
    Constant Field Values

### LOCUS_TAG

    protected static final String LOCUS_TAG

See Also:
  Constant Field Values

### ACCESSION_TAG

    protected static final String ACCESSION_TAG

See Also:
  Constant Field Values

### VERSION_TAG

    protected static final String VERSION_TAG

See Also:
  Constant Field Values

### DEFINITION_TAG

    protected static final String DEFINITION_TAG

See Also:
  Constant Field Values

### DATE_TAG

    protected static final String DATE_TAG

See Also:
  Constant Field Values

### DATABASE_XREF_TAG

    protected static final String DATABASE_XREF_TAG

See Also:
  Constant Field Values

### SOURCE_TAG

    protected static final String SOURCE_TAG

See Also:
  Constant Field Values

### ORGANISM_TAG

    protected static final String ORGANISM_TAG

See Also:
  Constant Field Values

### ORGANELLE_TAG

    protected static final String ORGANELLE_TAG

See Also:
  Constant Field Values

### REFERENCE_TAG

    protected static final String REFERENCE_TAG

See Also:
  Constant Field Values

### REFERENCE_POSITION_TAG

    protected static final String REFERENCE_POSITION_TAG

See Also:
  Constant Field Values

### REFERENCE_XREF_TAG

    protected static final String REFERENCE_XREF_TAG

See Also:
  Constant Field Values

### AUTHORS_TAG

    protected static final String AUTHORS_TAG

See Also:
  Constant Field Values

### CONSORTIUM_TAG

    protected static final String CONSORTIUM_TAG

See Also:
  Constant Field Values

### TITLE_TAG

    protected static final String TITLE_TAG

See Also:
  Constant Field Values

### LOCATOR_TAG

    protected static final String LOCATOR_TAG

See Also:
  Constant Field Values

### REMARK_TAG

    protected static final String REMARK_TAG

See Also:
  Constant Field Values

### KEYWORDS_TAG

    protected static final String KEYWORDS_TAG

See Also:
  Constant Field Values

### COMMENT_TAG

    protected static final String COMMENT_TAG

See Also:
  Constant Field Values

### FEATURE_HEADER_TAG

    protected static final String FEATURE_HEADER_TAG

See Also:
  Constant Field Values

### FEATURE_TAG

    protected static final String FEATURE_TAG

See Also:
  Constant Field Values

### CONTIG_TAG

    protected static final String CONTIG_TAG

See Also:
  Constant Field Values

### TPA_TAG

    protected static final String TPA_TAG

See Also:
  Constant Field Values

### START_SEQUENCE_TAG

    protected static final String START_SEQUENCE_TAG

See Also:
  Constant Field Values

### DELIMITER_TAG

    protected static final String DELIMITER_TAG

See Also:
  Constant Field Values

### END_SEQUENCE_TAG

    protected static final String END_SEQUENCE_TAG

See Also:
  Constant Field Values

### dp

    protected static final Pattern dp

### lp

    protected static final Pattern lp

### lpPre87

    protected static final Pattern lpPre87

### vp

    protected static final Pattern vp

### rpp

    protected static final Pattern rpp

### dbxp

    protected static final Pattern dbxp

### readableFileNames

    protected static final Pattern readableFileNames

### headerLine

    protected static final Pattern headerLine

Constructor Detail

### EMBLFormat

    public EMBLFormat()

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 EMBL format if its name contains the word eem or edat, or the first line matches the EMBL format for the ID line.

  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. Always 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 EMBL format if its first line matches the EMBL format for the ID line.

  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. Always 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 rlistener,
                                    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.

  Parameters:
    `reader` - the input source
    `symParser` - the tokenizer which understands the sequence being read
    `rlistener` - 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`

### 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! Namespace is ignored as EMBL has no concept of it.

  Parameters:
    `seq` - the sequence to write
    `ns` - the namespace to write it with
  Throws:
    `IOException` - in case it couldn't write something

### writeSequence

    public void writeSequence(Sequence seq,
                              String format,
                              Namespace ns)
                       throws IOException

  As per `writeSequence(Sequence, Namespace)`, except that it also takes a format parameter. This can be any of the formats defined as constants in this class.

  Parameters:
    `seq` - see `writeSequence(Sequence, Namespace)`
    `format` - the format to use.
    `ns` - see `writeSequence(Sequence, Namespace)`
  Throws:
    `IOException` - see `writeSequence(Sequence, Namespace)`

### getDefaultFormat

    public String getDefaultFormat()

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

  Returns:
    a `String`.