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

    java.lang.Object
      org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
          org.biojavax.bio.seq.io.EMBLxmlFormat

All Implemented Interfaces:
  SequenceFormat, RichSequenceFormat

    public class EMBLxmlFormat

extends RichSequenceFormat.BasicFormat

Format reader for EMBLxml files. This version of EMBLxml format will generate and write RichSequence objects. Loosely Based on code from the old, deprecated, org.biojava.bio.seq.io.GenbankXmlFormat object. Understands http://www.ebi.ac.uk/embl/dtd/EMBL_Services_V1.1.dtd

Since:
  1.5
Author:
  Alan Li (code based on his work), Richard Holland, Mark Schreiber

Nested Class Summary
`static class` | `EMBLxmlFormat.Terms` Implements some EMBLxml-specific terms.

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

Field Summary
`protected static String` | `AUTHOR_TAG`
`protected static String` | `BASEPOSITION_TAG`
`protected static String` | `BASEPOSITION_TYPE_ATTR`
`protected static String` | `CITATION_DATE_ATTR`
`protected static String` | `CITATION_FIRST_ATTR`
`protected static String` | `CITATION_ID_ATTR`
`protected static String` | `CITATION_INSTITUTE_ATTR`
`protected static String` | `CITATION_ISSUE_ATTR`
`protected static String` | `CITATION_LAST_ATTR`
`protected static String` | `CITATION_LOCATION_TAG`
`protected static String` | `CITATION_NAME_ATTR`
`protected static String` | `CITATION_PATENT_ATTR`
`protected static String` | `CITATION_PUB_ATTR`
`protected static String` | `CITATION_TAG`
`protected static String` | `CITATION_TYPE_ATTR`
`protected static String` | `CITATION_VOL_ATTR`
`protected static String` | `CITATION_YEAR_ATTR`
`protected static String` | `COMMENT_TAG`
`protected static String` | `COMNAME_TAG`
`protected static String` | `CONSORTIUM_TAG`
`protected static String` | `CONTIG_TAG`
`protected static String` | `DBREF_DB_ATTR`
`protected static String` | `DBREF_PRIMARY_ATTR`
`protected static String` | `DBREF_SEC_ATTR`
`protected static String` | `DBREFERENCE_TAG`
`protected static String` | `DESC_TAG`
`protected static String` | `EDITOR_TAG`
`static String` | `EMBLXML_FORMAT` The name of this format
`protected static String` | `ENTRY_ACCESSION_ATTR`
`protected static String` | `ENTRY_CREATED_ATTR`
`protected static String` | `ENTRY_DATACLASS_ATTR`
`protected static String` | `ENTRY_GROUP_TAG`
`protected static String` | `ENTRY_RELCREATED_ATTR`
`protected static String` | `ENTRY_RELUPDATED_ATTR`
`protected static String` | `ENTRY_STATUS_ATTR`
`protected static String` | `ENTRY_STATUS_DATE_ATTR`
`protected static String` | `ENTRY_SUBACC_ATTR`
`protected static String` | `ENTRY_SUBVER_ATTR`
`protected static String` | `ENTRY_SUBWGSVER_ATTR`
`protected static String` | `ENTRY_TAG`
`protected static String` | `ENTRY_TAX_DIVISION_ATTR`
`protected static String` | `ENTRY_UPDATED_ATTR`
`protected static String` | `ENTRY_VER_ATTR`
`protected static String` | `FEATURE_NAME_ATTR`
`protected static String` | `FEATURE_TAG`
`protected static String` | `KEYWORD_TAG`
`protected static String` | `LINEAGE_TAG`
`protected static String` | `LOC_ELEMENT_ACC_ATTR`
`protected static String` | `LOC_ELEMENT_COMPL_ATTR`
`protected static String` | `LOC_ELEMENT_TYPE_ATTR`
`protected static String` | `LOC_ELEMENT_VER_ATTR`
`protected static String` | `LOCATION_COMPL_ATTR`
`protected static String` | `LOCATION_ELEMENT_TAG`
`protected static String` | `LOCATION_TAG`
`protected static String` | `LOCATION_TYPE_ATTR`
`protected static String` | `LOCATOR_TAG`
`protected static String` | `ORGANELLE_TAG`
`protected static String` | `ORGANISM_TAG`
`protected static String` | `PATENT_TAG`
`protected static String` | `PROJ_ACC_TAG`
`protected static String` | `QUALIFIER_NAME_ATTR`
`protected static String` | `QUALIFIER_TAG`
`protected static String` | `REF_POS_BEGIN_ATTR`
`protected static String` | `REF_POS_END_ATTR`
`protected static String` | `REFERENCE_TAG`
`protected static String` | `SCINAME_TAG`
`protected static String` | `SEC_ACC_TAG`
`protected static String` | `SEQUENCE_LENGTH_ATTR`
`protected static String` | `SEQUENCE_TAG`
`protected static String` | `SEQUENCE_TOPOLOGY_ATTR`
`protected static String` | `SEQUENCE_TYPE_ATTR`
`protected static String` | `SEQUENCE_VER_ATTR`
`protected static String` | `TAXID_TAG`
`protected static String` | `TAXON_TAG`
`protected static String` | `TITLE_TAG`
`protected static Pattern` | `xmlSchema`

Constructor Summary
`EMBLxmlFormat()`

Method Summary
`void` | `beginWriting()` Informs the writer that we want to start writing.
`boolean` | `canRead(BufferedInputStream stream)` Check to see if a given stream is in our format. A stream is in EMBLxml format if the second XML line contains the phrase "http://www.ebi.ac.uk/schema/EMBL_schema.xsd".
`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 EMBLxml format if the second XML line contains the phrase "http://www.ebi.ac.uk/schema/EMBL_schema.xsd".
`void` | `finishWriting()` Informs the writer that are done writing.
`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 EMBLxml 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, PrintStream os)` `writeSequence` writes a sequence to the specified `PrintStream`, using the specified format.

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

### EMBLXML_FORMAT

    public static final String EMBLXML_FORMAT

  The name of this format

  See Also:
    Constant Field Values

### ENTRY_GROUP_TAG

    protected static final String ENTRY_GROUP_TAG

See Also:
  Constant Field Values

### ENTRY_TAG

    protected static final String ENTRY_TAG

See Also:
  Constant Field Values

### ENTRY_ACCESSION_ATTR

    protected static final String ENTRY_ACCESSION_ATTR

See Also:
  Constant Field Values

### ENTRY_TAX_DIVISION_ATTR

    protected static final String ENTRY_TAX_DIVISION_ATTR

See Also:
  Constant Field Values

### ENTRY_DATACLASS_ATTR

    protected static final String ENTRY_DATACLASS_ATTR

See Also:
  Constant Field Values

### ENTRY_CREATED_ATTR

    protected static final String ENTRY_CREATED_ATTR

See Also:
  Constant Field Values

### ENTRY_RELCREATED_ATTR

    protected static final String ENTRY_RELCREATED_ATTR

See Also:
  Constant Field Values

### ENTRY_UPDATED_ATTR

    protected static final String ENTRY_UPDATED_ATTR

See Also:
  Constant Field Values

### ENTRY_RELUPDATED_ATTR

    protected static final String ENTRY_RELUPDATED_ATTR

See Also:
  Constant Field Values

### ENTRY_VER_ATTR

    protected static final String ENTRY_VER_ATTR

See Also:
  Constant Field Values

### ENTRY_SUBACC_ATTR

    protected static final String ENTRY_SUBACC_ATTR

See Also:
  Constant Field Values

### ENTRY_SUBVER_ATTR

    protected static final String ENTRY_SUBVER_ATTR

See Also:
  Constant Field Values

### ENTRY_SUBWGSVER_ATTR

    protected static final String ENTRY_SUBWGSVER_ATTR

See Also:
  Constant Field Values

### ENTRY_STATUS_ATTR

    protected static final String ENTRY_STATUS_ATTR

See Also:
  Constant Field Values

### ENTRY_STATUS_DATE_ATTR

    protected static final String ENTRY_STATUS_DATE_ATTR

See Also:
  Constant Field Values

### SEC_ACC_TAG

    protected static final String SEC_ACC_TAG

See Also:
  Constant Field Values

### PROJ_ACC_TAG

    protected static final String PROJ_ACC_TAG

See Also:
  Constant Field Values

### DESC_TAG

    protected static final String DESC_TAG

See Also:
  Constant Field Values

### KEYWORD_TAG

    protected static final String KEYWORD_TAG

See Also:
  Constant Field Values

### REFERENCE_TAG

    protected static final String REFERENCE_TAG

See Also:
  Constant Field Values

### CITATION_TAG

    protected static final String CITATION_TAG

See Also:
  Constant Field Values

### CITATION_ID_ATTR

    protected static final String CITATION_ID_ATTR

See Also:
  Constant Field Values

### CITATION_TYPE_ATTR

    protected static final String CITATION_TYPE_ATTR

See Also:
  Constant Field Values

### CITATION_DATE_ATTR

    protected static final String CITATION_DATE_ATTR

See Also:
  Constant Field Values

### CITATION_NAME_ATTR

    protected static final String CITATION_NAME_ATTR

See Also:
  Constant Field Values

### CITATION_VOL_ATTR

    protected static final String CITATION_VOL_ATTR

See Also:
  Constant Field Values

### CITATION_ISSUE_ATTR

    protected static final String CITATION_ISSUE_ATTR

See Also:
  Constant Field Values

### CITATION_FIRST_ATTR

    protected static final String CITATION_FIRST_ATTR

See Also:
  Constant Field Values

### CITATION_LAST_ATTR

    protected static final String CITATION_LAST_ATTR

See Also:
  Constant Field Values

### CITATION_PUB_ATTR

    protected static final String CITATION_PUB_ATTR

See Also:
  Constant Field Values

### CITATION_PATENT_ATTR

    protected static final String CITATION_PATENT_ATTR

See Also:
  Constant Field Values

### CITATION_INSTITUTE_ATTR

    protected static final String CITATION_INSTITUTE_ATTR

See Also:
  Constant Field Values

### CITATION_YEAR_ATTR

    protected static final String CITATION_YEAR_ATTR

See Also:
  Constant Field Values

### DBREFERENCE_TAG

    protected static final String DBREFERENCE_TAG

See Also:
  Constant Field Values

### DBREF_DB_ATTR

    protected static final String DBREF_DB_ATTR

See Also:
  Constant Field Values

### DBREF_PRIMARY_ATTR

    protected static final String DBREF_PRIMARY_ATTR

See Also:
  Constant Field Values

### DBREF_SEC_ATTR

    protected static final String DBREF_SEC_ATTR

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

### EDITOR_TAG

    protected static final String EDITOR_TAG

See Also:
  Constant Field Values

### AUTHOR_TAG

    protected static final String AUTHOR_TAG

See Also:
  Constant Field Values

### PATENT_TAG

    protected static final String PATENT_TAG

See Also:
  Constant Field Values

### LOCATOR_TAG

    protected static final String LOCATOR_TAG

See Also:
  Constant Field Values

### CITATION_LOCATION_TAG

    protected static final String CITATION_LOCATION_TAG

See Also:
  Constant Field Values

### REF_POS_BEGIN_ATTR

    protected static final String REF_POS_BEGIN_ATTR

See Also:
  Constant Field Values

### REF_POS_END_ATTR

    protected static final String REF_POS_END_ATTR

See Also:
  Constant Field Values

### COMMENT_TAG

    protected static final String COMMENT_TAG

See Also:
  Constant Field Values

### FEATURE_TAG

    protected static final String FEATURE_TAG

See Also:
  Constant Field Values

### FEATURE_NAME_ATTR

    protected static final String FEATURE_NAME_ATTR

See Also:
  Constant Field Values

### ORGANISM_TAG

    protected static final String ORGANISM_TAG

See Also:
  Constant Field Values

### SCINAME_TAG

    protected static final String SCINAME_TAG

See Also:
  Constant Field Values

### COMNAME_TAG

    protected static final String COMNAME_TAG

See Also:
  Constant Field Values

### TAXID_TAG

    protected static final String TAXID_TAG

See Also:
  Constant Field Values

### LINEAGE_TAG

    protected static final String LINEAGE_TAG

See Also:
  Constant Field Values

### TAXON_TAG

    protected static final String TAXON_TAG

See Also:
  Constant Field Values

### ORGANELLE_TAG

    protected static final String ORGANELLE_TAG

See Also:
  Constant Field Values

### QUALIFIER_TAG

    protected static final String QUALIFIER_TAG

See Also:
  Constant Field Values

### QUALIFIER_NAME_ATTR

    protected static final String QUALIFIER_NAME_ATTR

See Also:
  Constant Field Values

### LOCATION_TAG

    protected static final String LOCATION_TAG

See Also:
  Constant Field Values

### LOCATION_TYPE_ATTR

    protected static final String LOCATION_TYPE_ATTR

See Also:
  Constant Field Values

### LOCATION_COMPL_ATTR

    protected static final String LOCATION_COMPL_ATTR

See Also:
  Constant Field Values

### LOCATION_ELEMENT_TAG

    protected static final String LOCATION_ELEMENT_TAG

See Also:
  Constant Field Values

### LOC_ELEMENT_TYPE_ATTR

    protected static final String LOC_ELEMENT_TYPE_ATTR

See Also:
  Constant Field Values

### LOC_ELEMENT_ACC_ATTR

    protected static final String LOC_ELEMENT_ACC_ATTR

See Also:
  Constant Field Values

### LOC_ELEMENT_VER_ATTR

    protected static final String LOC_ELEMENT_VER_ATTR

See Also:
  Constant Field Values

### LOC_ELEMENT_COMPL_ATTR

    protected static final String LOC_ELEMENT_COMPL_ATTR

See Also:
  Constant Field Values

### BASEPOSITION_TAG

    protected static final String BASEPOSITION_TAG

See Also:
  Constant Field Values

### BASEPOSITION_TYPE_ATTR

    protected static final String BASEPOSITION_TYPE_ATTR

See Also:
  Constant Field Values

### CONTIG_TAG

    protected static final String CONTIG_TAG

See Also:
  Constant Field Values

### SEQUENCE_TAG

    protected static final String SEQUENCE_TAG

See Also:
  Constant Field Values

### SEQUENCE_TYPE_ATTR

    protected static final String SEQUENCE_TYPE_ATTR

See Also:
  Constant Field Values

### SEQUENCE_LENGTH_ATTR

    protected static final String SEQUENCE_LENGTH_ATTR

See Also:
  Constant Field Values

### SEQUENCE_TOPOLOGY_ATTR

    protected static final String SEQUENCE_TOPOLOGY_ATTR

See Also:
  Constant Field Values

### SEQUENCE_VER_ATTR

    protected static final String SEQUENCE_VER_ATTR

See Also:
  Constant Field Values

### xmlSchema

    protected static final Pattern xmlSchema

Constructor Detail

### EMBLxmlFormat

    public EMBLxmlFormat()

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 EMBLxml format if the second XML line contains the phrase "http://www.ebi.ac.uk/schema/EMBL_schema.xsd".

  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 EMBLxml format if the second XML line contains the phrase "http://www.ebi.ac.uk/schema/EMBL_schema.xsd".

  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`

### beginWriting

    public void beginWriting()
                      throws IOException

  Informs the writer that we want to start writing. This will do any initialisation required, such as writing the opening tags of an XML file that groups sequences together.

  Throws:
    `IOException` - if writing fails.

### finishWriting

    public void finishWriting()
                       throws IOException

  Informs the writer that are done writing. This will do any finalisation required, such as writing the closing tags of an XML file that groups sequences together.

  Throws:
    `IOException` - if writing fails.

### 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 EMBLxml 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

### getDefaultFormat

    public String getDefaultFormat()

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

  Returns:
    a `String`.

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