public class UniProtXMLFormat extends RichSequenceFormat.BasicFormat
Modifier and Type | Class and Description |
---|---|
static class |
UniProtXMLFormat.Terms
Implements some UniProtXML-specific terms.
|
RichSequenceFormat.BasicFormat, RichSequenceFormat.HeaderlessFormat
Modifier and Type | Field and Description |
---|---|
protected static java.lang.String |
ACCESSION_TAG |
protected static java.lang.String |
AUTHOR_LIST_TAG |
protected static java.lang.String |
CITATION_TAG |
protected static java.lang.String |
COMMENT_ABS_MAX_TAG |
protected static java.lang.String |
COMMENT_ABSORPTION_TAG |
protected static java.lang.String |
COMMENT_ERROR_ATTR |
protected static java.lang.String |
COMMENT_EVENT_TAG |
protected static java.lang.String |
COMMENT_EXPERIMENTS_TAG |
protected static java.lang.String |
COMMENT_INTERACT_INTACT_ATTR |
protected static java.lang.String |
COMMENT_INTERACT_LABEL_TAG |
protected static java.lang.String |
COMMENT_INTERACTANT_TAG |
protected static java.lang.String |
COMMENT_ISOFORM_TAG |
protected static java.lang.String |
COMMENT_KIN_KM_TAG |
protected static java.lang.String |
COMMENT_KIN_VMAX_TAG |
protected static java.lang.String |
COMMENT_KINETICS_TAG |
protected static java.lang.String |
COMMENT_LINK_TAG |
protected static java.lang.String |
COMMENT_LINK_URI_ATTR |
protected static java.lang.String |
COMMENT_LOCTYPE_ATTR |
protected static java.lang.String |
COMMENT_MASS_ATTR |
protected static java.lang.String |
COMMENT_METHOD_ATTR |
protected static java.lang.String |
COMMENT_ORGANISMS_TAG |
protected static java.lang.String |
COMMENT_PH_TAG |
protected static java.lang.String |
COMMENT_REDOX_TAG |
protected static java.lang.String |
COMMENT_TAG |
protected static java.lang.String |
COMMENT_TEMPERATURE_TAG |
protected static java.lang.String |
COMPONENT_TAG |
protected static java.lang.String |
CONSORTIUM_TAG |
protected static java.lang.String |
COPYRIGHT_TAG |
protected static java.lang.String |
DBXREF_TAG |
protected static java.lang.String |
DOMAIN_TAG |
protected static java.lang.String |
EDITOR_LIST_TAG |
protected static java.lang.String |
ENTRY_CREATED_ATTR |
protected static java.lang.String |
ENTRY_GROUP_TAG |
protected static java.lang.String |
ENTRY_NAMESPACE_ATTR |
protected static java.lang.String |
ENTRY_TAG |
protected static java.lang.String |
ENTRY_UPDATED_ATTR |
protected static java.lang.String |
ENTRY_VERSION_ATTR |
protected static java.lang.String |
EVIDENCE_ATTR |
protected static java.lang.String |
EVIDENCE_ATTRIBUTE_ATTR |
protected static java.lang.String |
EVIDENCE_CATEGORY_ATTR |
protected static java.lang.String |
EVIDENCE_DATE_ATTR |
protected static java.lang.String |
EVIDENCE_TAG |
protected static java.lang.String |
FEATURE_DESC_ATTR |
protected static java.lang.String |
FEATURE_ORIGINAL_TAG |
protected static java.lang.String |
FEATURE_TAG |
protected static java.lang.String |
FEATURE_VARIATION_TAG |
protected static java.lang.String |
GENE_TAG |
protected static java.lang.String |
GENELOCATION_NAME_TAG |
protected static java.lang.String |
GENELOCATION_TAG |
protected static java.lang.String |
ID_ATTR |
protected static java.lang.String |
ID_TAG |
protected static java.lang.String |
KEY_ATTR |
protected static java.lang.String |
KEYWORD_TAG |
protected static java.lang.String |
LINEAGE_TAG |
protected static java.lang.String |
LOCATION_BEGIN_TAG |
protected static java.lang.String |
LOCATION_END_TAG |
protected static java.lang.String |
LOCATION_POSITION_ATTR |
protected static java.lang.String |
LOCATION_POSITION_TAG |
protected static java.lang.String |
LOCATION_SEQ_ATTR |
protected static java.lang.String |
LOCATION_TAG |
protected static java.lang.String |
LOCATOR_TAG |
protected static java.lang.String |
NAME_ATTR |
protected static java.lang.String |
NAME_TAG |
protected static java.lang.String |
NOTE_TAG |
protected static java.lang.String |
ORGANISM_TAG |
protected static java.lang.String |
PERSON_TAG |
protected static java.lang.String |
PROPERTY_TAG |
protected static java.lang.String |
PROTEIN_EXISTS_TAG |
protected static java.lang.String |
PROTEIN_TAG |
protected static java.lang.String |
PROTEIN_TYPE_ATTR |
protected static java.lang.String |
RC_LINE_TAG |
protected static java.lang.String |
RC_PLASMID_TAG |
protected static java.lang.String |
RC_SPECIES_TAG |
protected static java.lang.String |
RC_STRAIN_TAG |
protected static java.lang.String |
RC_TISSUE_TAG |
protected static java.lang.String |
RC_TRANSP_TAG |
protected static java.lang.String |
REF_ATTR |
protected static java.lang.String |
REFERENCE_TAG |
protected static java.lang.String |
RP_LINE_TAG |
protected static java.util.regex.Pattern |
rppat |
protected static java.lang.String |
SEQUENCE_CHECKSUM_ATTR |
protected static java.lang.String |
SEQUENCE_LENGTH_ATTR |
protected static java.lang.String |
SEQUENCE_MASS_ATTR |
protected static java.lang.String |
SEQUENCE_MODIFIED_ATTR |
protected static java.lang.String |
SEQUENCE_TAG |
protected static java.lang.String |
SEQUENCE_VERSION_ATTR |
protected static java.lang.String |
STATUS_ATTR |
protected static java.lang.String |
TAXON_TAG |
protected static java.lang.String |
TEXT_TAG |
protected static java.lang.String |
TITLE_TAG |
protected static java.lang.String |
TYPE_ATTR |
static java.lang.String |
UNIPROTXML_FORMAT
The name of this format
|
protected static java.lang.String |
VALUE_ATTR |
protected static java.util.regex.Pattern |
xmlSchema |
Constructor and Description |
---|
UniProtXMLFormat() |
Modifier and Type | Method and Description |
---|---|
void |
beginWriting()
Informs the writer that we want to start writing.
|
boolean |
canRead(java.io.BufferedInputStream stream)
Check to see if a given stream is in our format.
|
boolean |
canRead(java.io.File file)
Check to see if a given file is in our format.
|
void |
finishWriting()
Informs the writer that are done writing.
|
java.lang.String |
getDefaultFormat()
getDefaultFormat returns the String identifier for
the default sub-format written by a SequenceFormat
implementation. |
SymbolTokenization |
guessSymbolTokenization(java.io.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(java.io.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(java.io.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(java.io.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,
java.io.PrintStream os)
writeSequence writes a sequence to the specified
PrintStream, using the default format. |
void |
writeSequence(Sequence seq,
java.lang.String format,
java.io.PrintStream os)
writeSequence writes a sequence to the specified
PrintStream , using the specified format. |
getElideComments, getElideFeatures, getElideReferences, getElideSymbols, getLineWidth, getPrintStream, setElideComments, setElideFeatures, setElideReferences, setElideSymbols, setLineWidth, setPrintStream
public static final java.lang.String UNIPROTXML_FORMAT
protected static final java.lang.String ENTRY_GROUP_TAG
protected static final java.lang.String ENTRY_TAG
protected static final java.lang.String ENTRY_VERSION_ATTR
protected static final java.lang.String ENTRY_NAMESPACE_ATTR
protected static final java.lang.String ENTRY_CREATED_ATTR
protected static final java.lang.String ENTRY_UPDATED_ATTR
protected static final java.lang.String COPYRIGHT_TAG
protected static final java.lang.String ACCESSION_TAG
protected static final java.lang.String NAME_TAG
protected static final java.lang.String TEXT_TAG
protected static final java.lang.String REF_ATTR
protected static final java.lang.String TYPE_ATTR
protected static final java.lang.String KEY_ATTR
protected static final java.lang.String ID_ATTR
protected static final java.lang.String EVIDENCE_ATTR
protected static final java.lang.String VALUE_ATTR
protected static final java.lang.String STATUS_ATTR
protected static final java.lang.String NAME_ATTR
protected static final java.lang.String PROTEIN_TAG
protected static final java.lang.String PROTEIN_TYPE_ATTR
protected static final java.lang.String DOMAIN_TAG
protected static final java.lang.String COMPONENT_TAG
protected static final java.lang.String GENE_TAG
protected static final java.lang.String ORGANISM_TAG
protected static final java.lang.String DBXREF_TAG
protected static final java.lang.String PROPERTY_TAG
protected static final java.lang.String LINEAGE_TAG
protected static final java.lang.String TAXON_TAG
protected static final java.lang.String GENELOCATION_TAG
protected static final java.lang.String GENELOCATION_NAME_TAG
protected static final java.lang.String REFERENCE_TAG
protected static final java.lang.String CITATION_TAG
protected static final java.lang.String TITLE_TAG
protected static final java.lang.String EDITOR_LIST_TAG
protected static final java.lang.String AUTHOR_LIST_TAG
protected static final java.lang.String PERSON_TAG
protected static final java.lang.String CONSORTIUM_TAG
protected static final java.lang.String LOCATOR_TAG
protected static final java.lang.String RP_LINE_TAG
protected static final java.lang.String RC_LINE_TAG
protected static final java.lang.String RC_SPECIES_TAG
protected static final java.lang.String RC_TISSUE_TAG
protected static final java.lang.String RC_TRANSP_TAG
protected static final java.lang.String RC_STRAIN_TAG
protected static final java.lang.String RC_PLASMID_TAG
protected static final java.lang.String COMMENT_TAG
protected static final java.lang.String COMMENT_MASS_ATTR
protected static final java.lang.String COMMENT_ERROR_ATTR
protected static final java.lang.String COMMENT_METHOD_ATTR
protected static final java.lang.String COMMENT_LOCTYPE_ATTR
protected static final java.lang.String COMMENT_ABSORPTION_TAG
protected static final java.lang.String COMMENT_ABS_MAX_TAG
protected static final java.lang.String COMMENT_KINETICS_TAG
protected static final java.lang.String COMMENT_KIN_KM_TAG
protected static final java.lang.String COMMENT_KIN_VMAX_TAG
protected static final java.lang.String COMMENT_PH_TAG
protected static final java.lang.String COMMENT_REDOX_TAG
protected static final java.lang.String COMMENT_TEMPERATURE_TAG
protected static final java.lang.String COMMENT_LINK_TAG
protected static final java.lang.String COMMENT_LINK_URI_ATTR
protected static final java.lang.String COMMENT_EVENT_TAG
protected static final java.lang.String COMMENT_ISOFORM_TAG
protected static final java.lang.String COMMENT_INTERACTANT_TAG
protected static final java.lang.String COMMENT_INTERACT_INTACT_ATTR
protected static final java.lang.String COMMENT_INTERACT_LABEL_TAG
protected static final java.lang.String COMMENT_ORGANISMS_TAG
protected static final java.lang.String COMMENT_EXPERIMENTS_TAG
protected static final java.lang.String NOTE_TAG
protected static final java.lang.String KEYWORD_TAG
protected static final java.lang.String PROTEIN_EXISTS_TAG
protected static final java.lang.String ID_TAG
protected static final java.lang.String FEATURE_TAG
protected static final java.lang.String FEATURE_DESC_ATTR
protected static final java.lang.String FEATURE_ORIGINAL_TAG
protected static final java.lang.String FEATURE_VARIATION_TAG
protected static final java.lang.String EVIDENCE_TAG
protected static final java.lang.String EVIDENCE_CATEGORY_ATTR
protected static final java.lang.String EVIDENCE_ATTRIBUTE_ATTR
protected static final java.lang.String EVIDENCE_DATE_ATTR
protected static final java.lang.String LOCATION_TAG
protected static final java.lang.String LOCATION_SEQ_ATTR
protected static final java.lang.String LOCATION_BEGIN_TAG
protected static final java.lang.String LOCATION_END_TAG
protected static final java.lang.String LOCATION_POSITION_ATTR
protected static final java.lang.String LOCATION_POSITION_TAG
protected static final java.lang.String SEQUENCE_TAG
protected static final java.lang.String SEQUENCE_VERSION_ATTR
protected static final java.lang.String SEQUENCE_LENGTH_ATTR
protected static final java.lang.String SEQUENCE_MASS_ATTR
protected static final java.lang.String SEQUENCE_CHECKSUM_ATTR
protected static final java.lang.String SEQUENCE_MODIFIED_ATTR
protected static final java.util.regex.Pattern rppat
protected static final java.util.regex.Pattern xmlSchema
public boolean canRead(java.io.File file) throws java.io.IOException
canRead
in interface RichSequenceFormat
canRead
in class RichSequenceFormat.BasicFormat
file
- the File
to check.java.io.IOException
- in case the file is inaccessible.public SymbolTokenization guessSymbolTokenization(java.io.File file) throws java.io.IOException
guessSymbolTokenization
in interface RichSequenceFormat
guessSymbolTokenization
in class RichSequenceFormat.BasicFormat
file
- the File
object to guess the format of.SymbolTokenization
to read the file with.java.io.IOException
- if the file is unrecognisable or inaccessible.public boolean canRead(java.io.BufferedInputStream stream) throws java.io.IOException
stream
- the BufferedInputStream
to check.java.io.IOException
- in case the stream is inaccessible.public SymbolTokenization guessSymbolTokenization(java.io.BufferedInputStream stream) throws java.io.IOException
stream
- the BufferedInputStream
object to guess the format of.SymbolTokenization
to read the stream with.java.io.IOException
- if the stream is unrecognisable or inaccessible.public boolean readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) throws IllegalSymbolException, java.io.IOException, ParseException
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.IllegalSymbolException
- if it is not possible to
translate character data from the stream into valid BioJava
symbols.java.io.IOException
- if an error occurs while reading from the
stream.ParseException
public boolean readRichSequence(java.io.BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) throws IllegalSymbolException, java.io.IOException, ParseException
reader
- the input sourcesymParser
- the tokenizer which understands the sequence being readrlistener
- the listener to send sequence events tons
- the namespace to read sequences into.IllegalSymbolException
- if the tokenizer couldn't understand one of the
sequence symbols in the file.java.io.IOException
- if there was a read error.ParseException
public void beginWriting() throws java.io.IOException
java.io.IOException
- if writing fails.public void finishWriting() throws java.io.IOException
java.io.IOException
- if writing fails.public void writeSequence(Sequence seq, java.io.PrintStream os) throws java.io.IOException
writeSequence
writes a sequence to the specified
PrintStream, using the default format.seq
- the sequence to write out.os
- the printstream to write to.java.io.IOException
public void writeSequence(Sequence seq, java.lang.String format, java.io.PrintStream os) throws java.io.IOException
writeSequence
writes a sequence to the specified
PrintStream
, using the specified format.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.java.io.IOException
- if an error occurs.public void writeSequence(Sequence seq, Namespace ns) throws java.io.IOException
seq
- the sequence to writens
- the namespace to write it withjava.io.IOException
- in case it couldn't write somethingpublic java.lang.String getDefaultFormat()
getDefaultFormat
returns the String identifier for
the default sub-format written by a SequenceFormat
implementation.String
.