UniProtXMLHandler Class Reference

SAX handler for UniProtKB XML <entry> documents. More...

#include <UniPEFF/include/UniProtXMLHandler.h>

Inheritance diagram for UniProtXMLHandler:

Public Types
enum class	CaptureTarget {   None , Accession , EntryName , FullName ,   PrimaryGene , TaxName , Sequence , FeatureOriginal ,   FeatureVariation , IsoformId , IsoformName }
using	EntryCallback = std::function< void(UniProtEntry &&)>
Public Types inherited from XMLHandler
enum	ActionMode { LOAD , STORE }
	Action to set the current mode (for error messages) More...
enum	LOADDETAIL { LD_ALLDATA , LD_RAWCOUNTS , LD_COUNTS_WITHOPTIONS }

Public Member Functions
	UniProtXMLHandler (const std::string &filename, EntryCallback callback)
	Build a handler that delivers each parsed UniProtEntry to callback.
	~UniProtXMLHandler () override
	Destructor.
void	onStartElement (const char16_t *qname, const XMLAttributes &attrs) override
	Parsing method for opening tags.
void	onEndElement (const char16_t *qname) override
	Parsing method for closing tags.
void	onCharacters (const char16_t *chars, Size length) override
	Parsing method for character data.
Public Member Functions inherited from XMLHandler
	XMLHandler (const std::string &filename, const std::string &version)
	Default constructor.
virtual	~XMLHandler ()
	Destructor.
void	reset ()
	Release internal memory used for parsing (call.
void	fatalError (ActionMode mode, const std::string &msg, UInt line=0, UInt column=0) const
	Fatal error handler. Throws a ParseError exception.
void	error (ActionMode mode, const std::string &msg, UInt line=0, UInt column=0) const
	Error handler for recoverable errors.
void	warning (ActionMode mode, const std::string &msg, UInt line=0, UInt column=0) const
	Warning handler.
virtual void	writeTo (std::ostream &)
	Writes the contents to a stream.
virtual LOADDETAIL	getLoadDetail () const
	handler which support partial loading, implement this method
virtual void	setLoadDetail (const LOADDETAIL d)
	handler which support partial loading, implement this method
DataValue	cvParamToValue (const ControlledVocabulary &cv, const std::string &parent_tag, const std::string &accession, const std::string &name, const std::string &value, const std::string &unit_accession) const
	Convert the value of a <cvParam value=.> (as commonly found in PSI schemata) to the DataValue with the correct type (e.g. int) according to the type stored in the CV (usually PSI-MS CV), as well as set its unit.
DataValue	cvParamToValue (const ControlledVocabulary &cv, const CVTerm &raw_term) const
	Convert the value of a <cvParam value=.> (as commonly found in PSI schemata) to the DataValue with the correct type (e.g. int) according to the type stored in the CV (usually PSI-MS CV), as well as set its unit.
void	checkUniqueIdentifiers_ (const std::vector< ProteinIdentification > &prot_ids) const

Private Member Functions
void	resetEntry_ ()
	Clear all per-entry state so the next <entry> starts fresh.
void	resetFeature_ ()
	Clear all per-feature state so the next <feature> starts fresh.

Static Private Member Functions
static int	parsePosition_ (const std::string &attr)

Private Attributes
EntryCallback	callback_
UniProtEntry	current_entry_
int	depth_ {0}
	Depth of the most recent element start, used to scope subtree handling.
int	entry_depth_ {0}
	<entry>
int	recommended_name_depth_ {0}
	<protein>/<recommendedName>
int	gene_depth_ {0}
	<gene>
int	organism_depth_ {0}
	<organism>
int	alt_products_depth_ {0}
	<comment type="alternative products"> (isoform definitions harvested, rest ignored)
int	isoform_depth_ {0}
	<isoform> inside the alternative-products comment
int	feature_depth_ {0}
	<feature>
int	sequence_depth_ {0}
	<sequence length="..."> (only the canonical sequence; isoform <sequence> elements have no content)
bool	full_name_captured_ {false}
std::string	char_buf_
	Buffer for character data; appended-to in characters(), consumed in endElement().
CaptureTarget	capture_ {CaptureTarget::None}
	Destination for the next buffered run of character data (None == not capturing).
UniProtFeature	current_feature_
	Per-feature working state (used between startElement("feature") and endElement("feature")).
UniProtIsoform	current_isoform_
	Per-isoform working state (used between startElement("isoform") and endElement("isoform")).

Additional Inherited Members
Static Public Member Functions inherited from XMLHandler
static std::string	writeXMLEscape (const std::string &to_escape)
	Escapes a string and returns the escaped string.
static DataValue	fromXSDString (const std::string &type, const std::string &value)
	Convert an XSD type (e.g. 'xsd:double') to a DataValue.
Protected Member Functions inherited from XMLHandler
void	writeUserParam_ (const std::string &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) const
	Writes the content of MetaInfoInterface to the file.
Int	asInt_ (const std::string &in) const
	Conversion of a std::string to an integer value.
Int	asInt_ (const char16_t *in) const
	Conversion of a Xerces string to an integer value.
UInt	asUInt_ (const std::string &in) const
	Conversion of a std::string to an unsigned integer value.
double	asDouble_ (const std::string &in) const
	Conversion of a std::string to a double value.
float	asFloat_ (const std::string &in) const
	Conversion of a std::string to a float value.
bool	asBool_ (const std::string &in) const
	Conversion of a string to a boolean value.
DateTime	asDateTime_ (std::string date_string) const
	Conversion of a xs:datetime string to a DateTime value.
bool	equal_ (const char16_t *a, const char16_t *b) const
	Returns if two Xerces strings are equal.
SignedSize	cvStringToEnum_ (const Size section, const std::string &term, const char *message, const SignedSize result_on_error=0)
std::string	attributeAsString_ (const XMLAttributes &a, const char *name) const
	Converts an attribute to a String.
Int	attributeAsInt_ (const XMLAttributes &a, const char *name) const
	Converts an attribute to a Int.
double	attributeAsDouble_ (const XMLAttributes &a, const char *name) const
	Converts an attribute to a double.
DoubleList	attributeAsDoubleList_ (const XMLAttributes &a, const char *name) const
	Converts an attribute to a DoubleList.
IntList	attributeAsIntList_ (const XMLAttributes &a, const char *name) const
	Converts an attribute to an IntList.
StringList	attributeAsStringList_ (const XMLAttributes &a, const char *name) const
	Converts an attribute to an StringList.
bool	optionalAttributeAsString_ (std::string &value, const XMLAttributes &a, const char *name) const
	Assigns the attribute content to the String value if the attribute is present.
bool	optionalAttributeAsInt_ (Int &value, const XMLAttributes &a, const char *name) const
	Assigns the attribute content to the Int value if the attribute is present.
bool	optionalAttributeAsUInt_ (UInt &value, const XMLAttributes &a, const char *name) const
	Assigns the attribute content to the UInt value if the attribute is present.
bool	optionalAttributeAsDouble_ (double &value, const XMLAttributes &a, const char *name) const
	Assigns the attribute content to the double value if the attribute is present.
bool	optionalAttributeAsDoubleList_ (DoubleList &value, const XMLAttributes &a, const char *name) const
	Assigns the attribute content to the DoubleList value if the attribute is present.
bool	optionalAttributeAsStringList_ (StringList &value, const XMLAttributes &a, const char *name) const
	Assigns the attribute content to the StringList value if the attribute is present.
bool	optionalAttributeAsIntList_ (IntList &value, const XMLAttributes &a, const char *name) const
	Assigns the attribute content to the IntList value if the attribute is present.
std::string	attributeAsString_ (const XMLAttributes &a, const char16_t *name) const
	Converts an attribute to a String.
Int	attributeAsInt_ (const XMLAttributes &a, const char16_t *name) const
	Converts an attribute to a Int.
double	attributeAsDouble_ (const XMLAttributes &a, const char16_t *name) const
	Converts an attribute to a double.
DoubleList	attributeAsDoubleList_ (const XMLAttributes &a, const char16_t *name) const
	Converts an attribute to a DoubleList.
IntList	attributeAsIntList_ (const XMLAttributes &a, const char16_t *name) const
	Converts an attribute to a IntList.
StringList	attributeAsStringList_ (const XMLAttributes &a, const char16_t *name) const
	Converts an attribute to a StringList.
bool	optionalAttributeAsString_ (std::string &value, const XMLAttributes &a, const char16_t *name) const
	Assigns the attribute content to the String value if the attribute is present.
bool	optionalAttributeAsInt_ (Int &value, const XMLAttributes &a, const char16_t *name) const
	Assigns the attribute content to the Int value if the attribute is present.
bool	optionalAttributeAsUInt_ (UInt &value, const XMLAttributes &a, const char16_t *name) const
	Assigns the attribute content to the UInt value if the attribute is present.
bool	optionalAttributeAsDouble_ (double &value, const XMLAttributes &a, const char16_t *name) const
	Assigns the attribute content to the double value if the attribute is present.
bool	optionalAttributeAsDoubleList_ (DoubleList &value, const XMLAttributes &a, const char16_t *name) const
	Assigns the attribute content to the DoubleList value if the attribute is present.
bool	optionalAttributeAsIntList_ (IntList &value, const XMLAttributes &a, const char16_t *name) const
	Assigns the attribute content to the IntList value if the attribute is present.
bool	optionalAttributeAsStringList_ (StringList &value, const XMLAttributes &a, const char16_t *name) const
	Assigns the attribute content to the StringList value if the attribute is present.
Protected Attributes inherited from XMLHandler
std::string	file_
	File name.
std::string	version_
	Schema version.
StringManager	sm_
	Helper class for string conversion.
std::vector< std::string >	open_tags_
	Stack of open XML tags.
LOADDETAIL	load_detail_
	parse only until total number of scans and chroms have been determined from attributes
std::vector< std::vector< std::string > >	cv_terms_
	Array of CV term lists (one sublist denotes one term and it's children)

Detailed Description

SAX handler for UniProtKB XML <entry> documents.

Streams individual <entry> elements into UniProtEntry POD instances and delivers each via a callback at </entry>. Implements the same scoping rules as the upstream C# UniPEFF tool: only the canonical <sequence> (carrying a "length" attribute) is captured, <gene> and <organism> are scanned via bounded depth tracking so their inner <name> elements never leak into the top-level "entry mnemonic" capture, and <feature> contents are buffered and classified at the closing tag rather than incrementally. The <comment type="alternative products"> subtree is parsed into UniProtIsoform records (id, name, sequence type and splice-variant refs); everything else inside it is ignored.

Member Typedef Documentation

EntryCallback

using EntryCallback = std::function<void(UniProtEntry&&)>

Callback invoked once per </entry>: receives ownership of the populated UniProtEntry. The handler resets its working state immediately after, so the callback is the only place the entry is reachable.

Member Enumeration Documentation

CaptureTarget

enum class CaptureTarget

strong

Where the next character-data run, if buffered, should be deposited at the closing tag of its enclosing element.

Enumerator
None
Accession
EntryName
FullName
PrimaryGene
TaxName
Sequence
FeatureOriginal
FeatureVariation
IsoformId
IsoformName

Constructor & Destructor Documentation

UniProtXMLHandler()

UniProtXMLHandler	(	const std::string &	filename,
		EntryCallback	callback
	)

Build a handler that delivers each parsed UniProtEntry to callback.

~UniProtXMLHandler()

~UniProtXMLHandler ( )

overridedefault

Destructor.

Member Function Documentation

onCharacters()

void onCharacters ( const char16_t *  chars, Size  length  )

overridevirtual

Parsing method for character data.

Reimplemented from XMLHandler.

References UniProtXMLHandler::capture_, UniProtXMLHandler::char_buf_, and UniProtXMLHandler::None.

onEndElement()

void onEndElement ( const char16_t *  qname )

overridevirtual

Parsing method for closing tags.

Reimplemented from XMLHandler.

References UniProtEntry::accession, UniProtXMLHandler::Accession, UniProtEntry::alt_accessions, UniProtXMLHandler::alt_products_depth_, UniProtXMLHandler::callback_, UniProtXMLHandler::capture_, UniProtXMLHandler::char_buf_, UniProtXMLHandler::current_entry_, UniProtXMLHandler::current_feature_, UniProtXMLHandler::current_isoform_, UniProtXMLHandler::depth_, UniProtXMLHandler::entry_depth_, UniProtXMLHandler::EntryName, UniProtXMLHandler::feature_depth_, UniProtXMLHandler::FeatureOriginal, UniProtEntry::features, UniProtXMLHandler::FeatureVariation, UniProtEntry::full_name, UniProtXMLHandler::full_name_captured_, UniProtXMLHandler::FullName, UniProtXMLHandler::gene_depth_, UniProtIsoform::id, UniProtXMLHandler::isoform_depth_, UniProtXMLHandler::IsoformId, UniProtXMLHandler::IsoformName, UniProtEntry::isoforms, UniProtIsoform::name, UniProtEntry::name, UniProtXMLHandler::None, UniProtXMLHandler::organism_depth_, UniProtFeature::original, UniProtEntry::primary_gene, UniProtXMLHandler::PrimaryGene, UniProtXMLHandler::recommended_name_depth_, UniProtXMLHandler::resetEntry_(), UniProtXMLHandler::resetFeature_(), UniProtEntry::sequence, UniProtXMLHandler::Sequence, UniProtXMLHandler::sequence_depth_, UniProtEntry::tax_name, UniProtXMLHandler::TaxName, and UniProtFeature::variation.

onStartElement()

void onStartElement ( const char16_t *  qname, const XMLAttributes &  attributes  )

overridevirtual

Parsing method for opening tags.

Reimplemented from XMLHandler.

References UniProtXMLHandler::Accession, UniProtXMLHandler::alt_products_depth_, UniProtFeature::begin, UniProtXMLHandler::capture_, UniProtXMLHandler::char_buf_, UniProtXMLHandler::current_entry_, UniProtXMLHandler::current_feature_, UniProtXMLHandler::current_isoform_, UniProtEntry::dataset, UniProtXMLHandler::depth_, UniProtFeature::description, UniProtFeature::end, UniProtXMLHandler::entry_depth_, UniProtEntry::entry_version, UniProtXMLHandler::EntryName, UniProtXMLHandler::feature_depth_, UniProtXMLHandler::FeatureOriginal, UniProtXMLHandler::FeatureVariation, UniProtXMLHandler::full_name_captured_, UniProtXMLHandler::FullName, UniProtXMLHandler::gene_depth_, UniProtFeature::has_position, UniProtFeature::has_range, UniProtFeature::id, UniProtIsoform::id, UniProtXMLHandler::isoform_depth_, UniProtXMLHandler::IsoformId, UniProtXMLHandler::IsoformName, UniProtFeature::location_sequence, UniProtIsoform::name, UniProtEntry::name, UniProtEntry::ncbi_tax_id, UniProtXMLHandler::None, UniProtXMLHandler::organism_depth_, UniProtXMLHandler::parsePosition_(), UniProtFeature::position, UniProtEntry::primary_gene, UniProtXMLHandler::PrimaryGene, UniProtEntry::protein_existence, UniProtXMLHandler::recommended_name_depth_, UniProtXMLHandler::resetEntry_(), UniProtXMLHandler::resetFeature_(), UniProtXMLHandler::Sequence, UniProtXMLHandler::sequence_depth_, UniProtIsoform::sequence_ref, UniProtIsoform::sequence_type, UniProtEntry::sequence_version, UniProtEntry::tax_name, UniProtXMLHandler::TaxName, UniProtFeature::type, and UniProtFeature::variation.

parsePosition_()

int parsePosition_ ( const std::string &  attr )

staticprivate

Parse a UniProt position attribute string; returns 0 when the attribute is absent or non-numeric (UniProt encodes "unknown" by omitting the attribute).

Referenced by UniProtXMLHandler::onStartElement().

resetEntry_()

void resetEntry_ ( )

private

Clear all per-entry state so the next <entry> starts fresh.

References UniProtXMLHandler::current_entry_, UniProtXMLHandler::current_isoform_, UniProtXMLHandler::feature_depth_, UniProtXMLHandler::full_name_captured_, UniProtXMLHandler::gene_depth_, UniProtXMLHandler::isoform_depth_, UniProtXMLHandler::organism_depth_, UniProtXMLHandler::recommended_name_depth_, and UniProtXMLHandler::sequence_depth_.

Referenced by UniProtXMLHandler::onEndElement(), and UniProtXMLHandler::onStartElement().

resetFeature_()

void resetFeature_ ( )

private

Clear all per-feature state so the next <feature> starts fresh.

References UniProtXMLHandler::current_feature_.

Referenced by UniProtXMLHandler::onEndElement(), and UniProtXMLHandler::onStartElement().

Member Data Documentation

alt_products_depth_

int alt_products_depth_ {0}

private

<comment type="alternative products"> (isoform definitions harvested, rest ignored)

Referenced by UniProtXMLHandler::onEndElement(), and UniProtXMLHandler::onStartElement().

callback_

EntryCallback callback_

private

Referenced by UniProtXMLHandler::onEndElement().

capture_

CaptureTarget capture_ {CaptureTarget::None}

private

Destination for the next buffered run of character data (None == not capturing).

Referenced by UniProtXMLHandler::onCharacters(), UniProtXMLHandler::onEndElement(), and UniProtXMLHandler::onStartElement().

char_buf_

std::string char_buf_

private

Buffer for character data; appended-to in characters(), consumed in endElement().

Referenced by UniProtXMLHandler::onCharacters(), UniProtXMLHandler::onEndElement(), and UniProtXMLHandler::onStartElement().

current_entry_

UniProtEntry current_entry_

private

Referenced by UniProtXMLHandler::onEndElement(), UniProtXMLHandler::onStartElement(), and UniProtXMLHandler::resetEntry_().

current_feature_

UniProtFeature current_feature_

private

Per-feature working state (used between startElement("feature") and endElement("feature")).

Referenced by UniProtXMLHandler::onEndElement(), UniProtXMLHandler::onStartElement(), and UniProtXMLHandler::resetFeature_().

current_isoform_

UniProtIsoform current_isoform_

private

Per-isoform working state (used between startElement("isoform") and endElement("isoform")).

Referenced by UniProtXMLHandler::onEndElement(), UniProtXMLHandler::onStartElement(), and UniProtXMLHandler::resetEntry_().

depth_

int depth_ {0}

private

Depth of the most recent element start, used to scope subtree handling.

Referenced by UniProtXMLHandler::onEndElement(), and UniProtXMLHandler::onStartElement().

entry_depth_

int entry_depth_ {0}

private

<entry>

Subtree gates. Each holds the depth at which the corresponding element opened so we know when its closing tag fires (depth_ == gate value during endElement). 0 means "not currently inside this subtree".

Referenced by UniProtXMLHandler::onEndElement(), and UniProtXMLHandler::onStartElement().

feature_depth_

int feature_depth_ {0}

private

<feature>

Referenced by UniProtXMLHandler::onEndElement(), UniProtXMLHandler::onStartElement(), and UniProtXMLHandler::resetEntry_().

full_name_captured_

bool full_name_captured_ {false}

private

Captures the <fullName> the first time we encounter it inside <protein>/<recommendedName>; later <fullName> elements (e.g. alternative names) are skipped.

Referenced by UniProtXMLHandler::onEndElement(), UniProtXMLHandler::onStartElement(), and UniProtXMLHandler::resetEntry_().

gene_depth_

int gene_depth_ {0}

private

<gene>

Referenced by UniProtXMLHandler::onEndElement(), UniProtXMLHandler::onStartElement(), and UniProtXMLHandler::resetEntry_().

isoform_depth_

int isoform_depth_ {0}

private

<isoform> inside the alternative-products comment

Referenced by UniProtXMLHandler::onEndElement(), UniProtXMLHandler::onStartElement(), and UniProtXMLHandler::resetEntry_().

organism_depth_

int organism_depth_ {0}

private

<organism>

Referenced by UniProtXMLHandler::onEndElement(), UniProtXMLHandler::onStartElement(), and UniProtXMLHandler::resetEntry_().

recommended_name_depth_

int recommended_name_depth_ {0}

private

<protein>/<recommendedName>

Referenced by UniProtXMLHandler::onEndElement(), UniProtXMLHandler::onStartElement(), and UniProtXMLHandler::resetEntry_().

sequence_depth_

int sequence_depth_ {0}

private

<sequence length="..."> (only the canonical sequence; isoform <sequence> elements have no content)

Referenced by UniProtXMLHandler::onEndElement(), UniProtXMLHandler::onStartElement(), and UniProtXMLHandler::resetEntry_().