UniProtXMLFormat (biojava-legacy 1.9.4 API)

java.lang.Object
- org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
- - org.biojavax.bio.seq.io.UniProtXMLFormat

All Implemented Interfaces:

SequenceFormat, RichSequenceFormat
```
public class UniProtXMLFormat
extends RichSequenceFormat.BasicFormat
```
Format reader for UniProtXML files. This version of UniProtXML 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.uniprot.org/support/docs/uniprot.xsd

Since:

1.5

Author:

Alan Li (code based on his work), Richard Holland

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class UniProtXMLFormat.Terms
Implements some UniProtXML-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`	`UniProtXMLFormat.Terms` Implements some UniProtXML-specific terms.

Field Summary

Fields
Modifier and Type	Field and Description
`protected static String`	`ACCESSION_TAG`
`protected static String`	`AUTHOR_LIST_TAG`
`protected static String`	`CITATION_TAG`
`protected static String`	`COMMENT_ABS_MAX_TAG`
`protected static String`	`COMMENT_ABSORPTION_TAG`
`protected static String`	`COMMENT_ERROR_ATTR`
`protected static String`	`COMMENT_EVENT_TAG`
`protected static String`	`COMMENT_EXPERIMENTS_TAG`
`protected static String`	`COMMENT_INTERACT_INTACT_ATTR`
`protected static String`	`COMMENT_INTERACT_LABEL_TAG`
`protected static String`	`COMMENT_INTERACTANT_TAG`
`protected static String`	`COMMENT_ISOFORM_TAG`
`protected static String`	`COMMENT_KIN_KM_TAG`
`protected static String`	`COMMENT_KIN_VMAX_TAG`
`protected static String`	`COMMENT_KINETICS_TAG`
`protected static String`	`COMMENT_LINK_TAG`
`protected static String`	`COMMENT_LINK_URI_ATTR`
`protected static String`	`COMMENT_LOCTYPE_ATTR`
`protected static String`	`COMMENT_MASS_ATTR`
`protected static String`	`COMMENT_METHOD_ATTR`
`protected static String`	`COMMENT_ORGANISMS_TAG`
`protected static String`	`COMMENT_PH_TAG`
`protected static String`	`COMMENT_REDOX_TAG`
`protected static String`	`COMMENT_TAG`
`protected static String`	`COMMENT_TEMPERATURE_TAG`
`protected static String`	`COMPONENT_TAG`
`protected static String`	`CONSORTIUM_TAG`
`protected static String`	`COPYRIGHT_TAG`
`protected static String`	`DBXREF_TAG`
`protected static String`	`DOMAIN_TAG`
`protected static String`	`EDITOR_LIST_TAG`
`protected static String`	`ENTRY_CREATED_ATTR`
`protected static String`	`ENTRY_GROUP_TAG`
`protected static String`	`ENTRY_NAMESPACE_ATTR`
`protected static String`	`ENTRY_TAG`
`protected static String`	`ENTRY_UPDATED_ATTR`
`protected static String`	`ENTRY_VERSION_ATTR`
`protected static String`	`EVIDENCE_ATTR`
`protected static String`	`EVIDENCE_ATTRIBUTE_ATTR`
`protected static String`	`EVIDENCE_CATEGORY_ATTR`
`protected static String`	`EVIDENCE_DATE_ATTR`
`protected static String`	`EVIDENCE_TAG`
`protected static String`	`FEATURE_DESC_ATTR`
`protected static String`	`FEATURE_ORIGINAL_TAG`
`protected static String`	`FEATURE_TAG`
`protected static String`	`FEATURE_VARIATION_TAG`
`protected static String`	`GENE_TAG`
`protected static String`	`GENELOCATION_NAME_TAG`
`protected static String`	`GENELOCATION_TAG`
`protected static String`	`ID_ATTR`
`protected static String`	`ID_TAG`
`protected static String`	`KEY_ATTR`
`protected static String`	`KEYWORD_TAG`
`protected static String`	`LINEAGE_TAG`
`protected static String`	`LOCATION_BEGIN_TAG`
`protected static String`	`LOCATION_END_TAG`
`protected static String`	`LOCATION_POSITION_ATTR`
`protected static String`	`LOCATION_POSITION_TAG`
`protected static String`	`LOCATION_SEQ_ATTR`
`protected static String`	`LOCATION_TAG`
`protected static String`	`LOCATOR_TAG`
`protected static String`	`NAME_ATTR`
`protected static String`	`NAME_TAG`
`protected static String`	`NOTE_TAG`
`protected static String`	`ORGANISM_TAG`
`protected static String`	`PERSON_TAG`
`protected static String`	`PROPERTY_TAG`
`protected static String`	`PROTEIN_EXISTS_TAG`
`protected static String`	`PROTEIN_TAG`
`protected static String`	`PROTEIN_TYPE_ATTR`
`protected static String`	`RC_LINE_TAG`
`protected static String`	`RC_PLASMID_TAG`
`protected static String`	`RC_SPECIES_TAG`
`protected static String`	`RC_STRAIN_TAG`
`protected static String`	`RC_TISSUE_TAG`
`protected static String`	`RC_TRANSP_TAG`
`protected static String`	`REF_ATTR`
`protected static String`	`REFERENCE_TAG`
`protected static String`	`RP_LINE_TAG`
`protected static Pattern`	`rppat`
`protected static String`	`SEQUENCE_CHECKSUM_ATTR`
`protected static String`	`SEQUENCE_LENGTH_ATTR`
`protected static String`	`SEQUENCE_MASS_ATTR`
`protected static String`	`SEQUENCE_MODIFIED_ATTR`
`protected static String`	`SEQUENCE_TAG`
`protected static String`	`SEQUENCE_VERSION_ATTR`
`protected static String`	`STATUS_ATTR`
`protected static String`	`TAXON_TAG`
`protected static String`	`TEXT_TAG`
`protected static String`	`TITLE_TAG`
`protected static String`	`TYPE_ATTR`
`static String`	`UNIPROTXML_FORMAT` The name of this format
`protected static String`	`VALUE_ATTR`
`protected static Pattern`	`xmlSchema`

Constructor Summary

Constructors
Constructor and Description

UniProtXMLFormat()

Constructors
Constructor and Description
`UniProtXMLFormat()`

Method Summary

All Methods Instance Methods Concrete 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
  - UNIPROTXML_FORMAT
```
public static final String UNIPROTXML_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_VERSION_ATTR
```
protected static final String ENTRY_VERSION_ATTR
```
    See Also:
    
    Constant Field Values
  - ENTRY_NAMESPACE_ATTR
```
protected static final String ENTRY_NAMESPACE_ATTR
```
    See Also:
    
    Constant Field Values
  - ENTRY_CREATED_ATTR
```
protected static final String ENTRY_CREATED_ATTR
```
    See Also:
    
    Constant Field Values
  - ENTRY_UPDATED_ATTR
```
protected static final String ENTRY_UPDATED_ATTR
```
    See Also:
    
    Constant Field Values
  - COPYRIGHT_TAG
```
protected static final String COPYRIGHT_TAG
```
    See Also:
    
    Constant Field Values
  - ACCESSION_TAG
```
protected static final String ACCESSION_TAG
```
    See Also:
    
    Constant Field Values
  - NAME_TAG
```
protected static final String NAME_TAG
```
    See Also:
    
    Constant Field Values
  - TEXT_TAG
```
protected static final String TEXT_TAG
```
    See Also:
    
    Constant Field Values
  - REF_ATTR
```
protected static final String REF_ATTR
```
    See Also:
    
    Constant Field Values
  - TYPE_ATTR
```
protected static final String TYPE_ATTR
```
    See Also:
    
    Constant Field Values
  - KEY_ATTR
```
protected static final String KEY_ATTR
```
    See Also:
    
    Constant Field Values
  - ID_ATTR
```
protected static final String ID_ATTR
```
    See Also:
    
    Constant Field Values
  - EVIDENCE_ATTR
```
protected static final String EVIDENCE_ATTR
```
    See Also:
    
    Constant Field Values
  - VALUE_ATTR
```
protected static final String VALUE_ATTR
```
    See Also:
    
    Constant Field Values
  - STATUS_ATTR
```
protected static final String STATUS_ATTR
```
    See Also:
    
    Constant Field Values
  - NAME_ATTR
```
protected static final String NAME_ATTR
```
    See Also:
    
    Constant Field Values
  - PROTEIN_TAG
```
protected static final String PROTEIN_TAG
```
    See Also:
    
    Constant Field Values
  - PROTEIN_TYPE_ATTR
```
protected static final String PROTEIN_TYPE_ATTR
```
    See Also:
    
    Constant Field Values
  - DOMAIN_TAG
```
protected static final String DOMAIN_TAG
```
    See Also:
    
    Constant Field Values
  - COMPONENT_TAG
```
protected static final String COMPONENT_TAG
```
    See Also:
    
    Constant Field Values
  - GENE_TAG
```
protected static final String GENE_TAG
```
    See Also:
    
    Constant Field Values
  - ORGANISM_TAG
```
protected static final String ORGANISM_TAG
```
    See Also:
    
    Constant Field Values
  - DBXREF_TAG
```
protected static final String DBXREF_TAG
```
    See Also:
    
    Constant Field Values
  - PROPERTY_TAG
```
protected static final String PROPERTY_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
  - GENELOCATION_TAG
```
protected static final String GENELOCATION_TAG
```
    See Also:
    
    Constant Field Values
  - GENELOCATION_NAME_TAG
```
protected static final String GENELOCATION_NAME_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
  - TITLE_TAG
```
protected static final String TITLE_TAG
```
    See Also:
    
    Constant Field Values
  - EDITOR_LIST_TAG
```
protected static final String EDITOR_LIST_TAG
```
    See Also:
    
    Constant Field Values
  - AUTHOR_LIST_TAG
```
protected static final String AUTHOR_LIST_TAG
```
    See Also:
    
    Constant Field Values
  - PERSON_TAG
```
protected static final String PERSON_TAG
```
    See Also:
    
    Constant Field Values
  - CONSORTIUM_TAG
```
protected static final String CONSORTIUM_TAG
```
    See Also:
    
    Constant Field Values
  - LOCATOR_TAG
```
protected static final String LOCATOR_TAG
```
    See Also:
    
    Constant Field Values
  - RP_LINE_TAG
```
protected static final String RP_LINE_TAG
```
    See Also:
    
    Constant Field Values
  - RC_LINE_TAG
```
protected static final String RC_LINE_TAG
```
    See Also:
    
    Constant Field Values
  - RC_SPECIES_TAG
```
protected static final String RC_SPECIES_TAG
```
    See Also:
    
    Constant Field Values
  - RC_TISSUE_TAG
```
protected static final String RC_TISSUE_TAG
```
    See Also:
    
    Constant Field Values
  - RC_TRANSP_TAG
```
protected static final String RC_TRANSP_TAG
```
    See Also:
    
    Constant Field Values
  - RC_STRAIN_TAG
```
protected static final String RC_STRAIN_TAG
```
    See Also:
    
    Constant Field Values
  - RC_PLASMID_TAG
```
protected static final String RC_PLASMID_TAG
```
    See Also:
    
    Constant Field Values
  - COMMENT_TAG
```
protected static final String COMMENT_TAG
```
    See Also:
    
    Constant Field Values
  - COMMENT_MASS_ATTR
```
protected static final String COMMENT_MASS_ATTR
```
    See Also:
    
    Constant Field Values
  - COMMENT_ERROR_ATTR
```
protected static final String COMMENT_ERROR_ATTR
```
    See Also:
    
    Constant Field Values
  - COMMENT_METHOD_ATTR
```
protected static final String COMMENT_METHOD_ATTR
```
    See Also:
    
    Constant Field Values
  - COMMENT_LOCTYPE_ATTR
```
protected static final String COMMENT_LOCTYPE_ATTR
```
    See Also:
    
    Constant Field Values
  - COMMENT_ABSORPTION_TAG
```
protected static final String COMMENT_ABSORPTION_TAG
```
    See Also:
    
    Constant Field Values
  - COMMENT_ABS_MAX_TAG
```
protected static final String COMMENT_ABS_MAX_TAG
```
    See Also:
    
    Constant Field Values
  - COMMENT_KINETICS_TAG
```
protected static final String COMMENT_KINETICS_TAG
```
    See Also:
    
    Constant Field Values
  - COMMENT_KIN_KM_TAG
```
protected static final String COMMENT_KIN_KM_TAG
```
    See Also:
    
    Constant Field Values
  - COMMENT_KIN_VMAX_TAG
```
protected static final String COMMENT_KIN_VMAX_TAG
```
    See Also:
    
    Constant Field Values
  - COMMENT_PH_TAG
```
protected static final String COMMENT_PH_TAG
```
    See Also:
    
    Constant Field Values
  - COMMENT_REDOX_TAG
```
protected static final String COMMENT_REDOX_TAG
```
    See Also:
    
    Constant Field Values
  - COMMENT_TEMPERATURE_TAG
```
protected static final String COMMENT_TEMPERATURE_TAG
```
    See Also:
    
    Constant Field Values
  - COMMENT_LINK_TAG
```
protected static final String COMMENT_LINK_TAG
```
    See Also:
    
    Constant Field Values
  - COMMENT_LINK_URI_ATTR
```
protected static final String COMMENT_LINK_URI_ATTR
```
    See Also:
    
    Constant Field Values
  - COMMENT_EVENT_TAG
```
protected static final String COMMENT_EVENT_TAG
```
    See Also:
    
    Constant Field Values
  - COMMENT_ISOFORM_TAG
```
protected static final String COMMENT_ISOFORM_TAG
```
    See Also:
    
    Constant Field Values
  - COMMENT_INTERACTANT_TAG
```
protected static final String COMMENT_INTERACTANT_TAG
```
    See Also:
    
    Constant Field Values
  - COMMENT_INTERACT_INTACT_ATTR
```
protected static final String COMMENT_INTERACT_INTACT_ATTR
```
    See Also:
    
    Constant Field Values
  - COMMENT_INTERACT_LABEL_TAG
```
protected static final String COMMENT_INTERACT_LABEL_TAG
```
    See Also:
    
    Constant Field Values
  - COMMENT_ORGANISMS_TAG
```
protected static final String COMMENT_ORGANISMS_TAG
```
    See Also:
    
    Constant Field Values
  - COMMENT_EXPERIMENTS_TAG
```
protected static final String COMMENT_EXPERIMENTS_TAG
```
    See Also:
    
    Constant Field Values
  - NOTE_TAG
```
protected static final String NOTE_TAG
```
    See Also:
    
    Constant Field Values
  - KEYWORD_TAG
```
protected static final String KEYWORD_TAG
```
    See Also:
    
    Constant Field Values
  - PROTEIN_EXISTS_TAG
```
protected static final String PROTEIN_EXISTS_TAG
```
    See Also:
    
    Constant Field Values
  - ID_TAG
```
protected static final String ID_TAG
```
    See Also:
    
    Constant Field Values
  - FEATURE_TAG
```
protected static final String FEATURE_TAG
```
    See Also:
    
    Constant Field Values
  - FEATURE_DESC_ATTR
```
protected static final String FEATURE_DESC_ATTR
```
    See Also:
    
    Constant Field Values
  - FEATURE_ORIGINAL_TAG
```
protected static final String FEATURE_ORIGINAL_TAG
```
    See Also:
    
    Constant Field Values
  - FEATURE_VARIATION_TAG
```
protected static final String FEATURE_VARIATION_TAG
```
    See Also:
    
    Constant Field Values
  - EVIDENCE_TAG
```
protected static final String EVIDENCE_TAG
```
    See Also:
    
    Constant Field Values
  - EVIDENCE_CATEGORY_ATTR
```
protected static final String EVIDENCE_CATEGORY_ATTR
```
    See Also:
    
    Constant Field Values
  - EVIDENCE_ATTRIBUTE_ATTR
```
protected static final String EVIDENCE_ATTRIBUTE_ATTR
```
    See Also:
    
    Constant Field Values
  - EVIDENCE_DATE_ATTR
```
protected static final String EVIDENCE_DATE_ATTR
```
    See Also:
    
    Constant Field Values
  - LOCATION_TAG
```
protected static final String LOCATION_TAG
```
    See Also:
    
    Constant Field Values
  - LOCATION_SEQ_ATTR
```
protected static final String LOCATION_SEQ_ATTR
```
    See Also:
    
    Constant Field Values
  - LOCATION_BEGIN_TAG
```
protected static final String LOCATION_BEGIN_TAG
```
    See Also:
    
    Constant Field Values
  - LOCATION_END_TAG
```
protected static final String LOCATION_END_TAG
```
    See Also:
    
    Constant Field Values
  - LOCATION_POSITION_ATTR
```
protected static final String LOCATION_POSITION_ATTR
```
    See Also:
    
    Constant Field Values
  - LOCATION_POSITION_TAG
```
protected static final String LOCATION_POSITION_TAG
```
    See Also:
    
    Constant Field Values
  - SEQUENCE_TAG
```
protected static final String SEQUENCE_TAG
```
    See Also:
    
    Constant Field Values
  - SEQUENCE_VERSION_ATTR
```
protected static final String SEQUENCE_VERSION_ATTR
```
    See Also:
    
    Constant Field Values
  - SEQUENCE_LENGTH_ATTR
```
protected static final String SEQUENCE_LENGTH_ATTR
```
    See Also:
    
    Constant Field Values
  - SEQUENCE_MASS_ATTR
```
protected static final String SEQUENCE_MASS_ATTR
```
    See Also:
    
    Constant Field Values
  - SEQUENCE_CHECKSUM_ATTR
```
protected static final String SEQUENCE_CHECKSUM_ATTR
```
    See Also:
    
    Constant Field Values
  - SEQUENCE_MODIFIED_ATTR
```
protected static final String SEQUENCE_MODIFIED_ATTR
```
    See Also:
    
    Constant Field Values
  - rppat
```
protected static final Pattern rppat
```
  - xmlSchema
```
protected static final Pattern xmlSchema
```
- Constructor Detail
  - UniProtXMLFormat
```
public UniProtXMLFormat()
```
- 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 UniProtXML format if the second XML line contains the phrase "http://www.uniprot.org/support/docs/uniprot.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 protein 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 UniProtXML format if the second XML line contains the phrase "http://www.uniprot.org/support/docs/uniprot.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 protein 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. 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
    
    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! 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.

Class UniProtXMLFormat

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

UNIPROTXML_FORMAT

ENTRY_GROUP_TAG

ENTRY_TAG

ENTRY_VERSION_ATTR

ENTRY_NAMESPACE_ATTR

ENTRY_CREATED_ATTR

ENTRY_UPDATED_ATTR

COPYRIGHT_TAG

ACCESSION_TAG

NAME_TAG

TEXT_TAG

REF_ATTR

TYPE_ATTR

KEY_ATTR

ID_ATTR

EVIDENCE_ATTR

VALUE_ATTR

STATUS_ATTR

NAME_ATTR

PROTEIN_TAG

PROTEIN_TYPE_ATTR

DOMAIN_TAG

COMPONENT_TAG

GENE_TAG

ORGANISM_TAG

DBXREF_TAG

PROPERTY_TAG

LINEAGE_TAG

TAXON_TAG

GENELOCATION_TAG

GENELOCATION_NAME_TAG

REFERENCE_TAG

CITATION_TAG

TITLE_TAG

EDITOR_LIST_TAG

AUTHOR_LIST_TAG

PERSON_TAG

CONSORTIUM_TAG

LOCATOR_TAG

RP_LINE_TAG

RC_LINE_TAG

RC_SPECIES_TAG

RC_TISSUE_TAG

RC_TRANSP_TAG

RC_STRAIN_TAG

RC_PLASMID_TAG

COMMENT_TAG

COMMENT_MASS_ATTR

COMMENT_ERROR_ATTR

COMMENT_METHOD_ATTR

COMMENT_LOCTYPE_ATTR

COMMENT_ABSORPTION_TAG

COMMENT_ABS_MAX_TAG

COMMENT_KINETICS_TAG

COMMENT_KIN_KM_TAG

COMMENT_KIN_VMAX_TAG

COMMENT_PH_TAG

COMMENT_REDOX_TAG

COMMENT_TEMPERATURE_TAG

COMMENT_LINK_TAG

COMMENT_LINK_URI_ATTR

COMMENT_EVENT_TAG

COMMENT_ISOFORM_TAG

COMMENT_INTERACTANT_TAG

COMMENT_INTERACT_INTACT_ATTR

COMMENT_INTERACT_LABEL_TAG

COMMENT_ORGANISMS_TAG

COMMENT_EXPERIMENTS_TAG

NOTE_TAG

KEYWORD_TAG

PROTEIN_EXISTS_TAG