EMBLxmlFormat (biojava-legacy 1.9.1 API)

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

Nested Classes
Modifier and Type Class and Description

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

Nested Classes
Modifier and Type	Class and Description
`static class`	`EMBLxmlFormat.Terms` Implements some EMBLxml-specific terms.

Field Summary

Fields
Modifier and Type	Field and Description
`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

Constructors
Constructor and Description

EMBLxmlFormat()

Constructors
Constructor and Description
`EMBLxmlFormat()`

Method Summary

Methods
Modifier and Type	Method and Description
`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.
`boolean`	`canRead(File file)` Check to see if a given file is in our format.
`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.
`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.
`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.
`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.

Class EMBLxmlFormat

Nested Class Summary

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

Field Summary

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Field Detail

EMBLXML_FORMAT

ENTRY_GROUP_TAG

ENTRY_TAG

ENTRY_ACCESSION_ATTR

ENTRY_TAX_DIVISION_ATTR

ENTRY_DATACLASS_ATTR

ENTRY_CREATED_ATTR

ENTRY_RELCREATED_ATTR

ENTRY_UPDATED_ATTR

ENTRY_RELUPDATED_ATTR

ENTRY_VER_ATTR

ENTRY_SUBACC_ATTR

ENTRY_SUBVER_ATTR

ENTRY_SUBWGSVER_ATTR

ENTRY_STATUS_ATTR

ENTRY_STATUS_DATE_ATTR

SEC_ACC_TAG

PROJ_ACC_TAG

DESC_TAG

KEYWORD_TAG

REFERENCE_TAG

CITATION_TAG

CITATION_ID_ATTR

CITATION_TYPE_ATTR

CITATION_DATE_ATTR

CITATION_NAME_ATTR

CITATION_VOL_ATTR

CITATION_ISSUE_ATTR

CITATION_FIRST_ATTR

CITATION_LAST_ATTR

CITATION_PUB_ATTR

CITATION_PATENT_ATTR

CITATION_INSTITUTE_ATTR

CITATION_YEAR_ATTR

DBREFERENCE_TAG

DBREF_DB_ATTR

DBREF_PRIMARY_ATTR

DBREF_SEC_ATTR

CONSORTIUM_TAG

TITLE_TAG

EDITOR_TAG

AUTHOR_TAG

PATENT_TAG

LOCATOR_TAG

CITATION_LOCATION_TAG

REF_POS_BEGIN_ATTR

REF_POS_END_ATTR

COMMENT_TAG

FEATURE_TAG

FEATURE_NAME_ATTR

ORGANISM_TAG

SCINAME_TAG

COMNAME_TAG

TAXID_TAG

LINEAGE_TAG

TAXON_TAG

ORGANELLE_TAG

QUALIFIER_TAG

QUALIFIER_NAME_ATTR

LOCATION_TAG

LOCATION_TYPE_ATTR

LOCATION_COMPL_ATTR

LOCATION_ELEMENT_TAG

LOC_ELEMENT_TYPE_ATTR

LOC_ELEMENT_ACC_ATTR

LOC_ELEMENT_VER_ATTR

LOC_ELEMENT_COMPL_ATTR

BASEPOSITION_TAG

BASEPOSITION_TYPE_ATTR

CONTIG_TAG

SEQUENCE_TAG