Used to load (storing not supported, yet) ProtXML files. More...

#include <OpenMS/FORMAT/ProtXMLFile.h>

Inheritance diagram for ProtXMLFile:

Collaboration diagram for ProtXMLFile:

Public Types
typedef ProteinIdentification::ProteinGroup	ProteinGroup
	A protein group (set of indices into ProteinIdentification)

Public Member Functions
	ProtXMLFile ()
	Constructor.

void	load (const std::string &filename, ProteinIdentification &protein_ids, PeptideIdentification &peptide_ids)
	Loads the identifications of an ProtXML file without identifier.

void	store (const std::string &filename, const ProteinIdentification &protein_ids, const PeptideIdentification &peptide_ids, const std::string &document_id="")
	[not implemented yet!] Stores the data in an ProtXML file

Public Member Functions inherited from XMLFile
	XMLFile ()
	Construct an XMLFile without schema info; `schema_location_` remains unset, so isValid cannot be used until derived-class logic initializes `schema_location_` before calling isValid.

	XMLFile (const std::string &schema_location, const std::string &version)
	Construct with a schema location for later isValid calls.

virtual	~XMLFile ()
	Virtual destructor — defaulted; allows safe deletion through a base-class pointer.

bool	isValid (const std::string &filename, std::ostream &os)
	Check if `filename` validates against the bound XML schema.

const std::string &	getVersion () const
	Return the schema version string passed to the parameterised constructor; empty for default-constructed instances.

Protected Member Functions
void	resetMembers_ ()
	reset members after reading/writing

void	onEndElement (const char16_t *qname) override
	Docu in base class.

void	onStartElement (const char16_t *qname, const Internal::XMLAttributes &attributes) override
	Docu in base class.

void	registerProtein_ (const std::string &protein_name)
	Creates a new protein entry (if not already present) and appends it to the current group.

void	matchModification_ (const double mass, const std::string &origin, std::string &modification_description)
	find modification name given a modified AA mass

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.

	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	onCharacters (const char16_t *chars, Size length)
	Parsing method for character data.

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

Protected Member Functions inherited from XMLFile
void	parse_ (const std::string &filename, XMLHandler *handler)
	Parse the XML file at `filename` through `handler`.

void	parseBuffer_ (const std::string &buffer, XMLHandler *handler)
	Parse an in-memory XML buffer through `handler`.

void	save_ (const std::string &filename, XMLHandler *handler) const
	Stores the contents of the XML handler given by `handler` in the file given by `filename`.

void	enforceEncoding_ (const std::string &encoding)
	Set or clear the XML-encoding override applied to subsequent parse_ / parseBuffer_ calls.

	XMLFile ()
	Construct an XMLFile without schema info; `schema_location_` remains unset, so isValid cannot be used until derived-class logic initializes `schema_location_` before calling isValid.

	XMLFile (const std::string &schema_location, const std::string &version)
	Construct with a schema location for later isValid calls.

virtual	~XMLFile ()
	Virtual destructor — defaulted; allows safe deletion through a base-class pointer.

bool	isValid (const std::string &filename, std::ostream &os)
	Check if `filename` validates against the bound XML schema.

const std::string &	getVersion () const
	Return the schema version string passed to the parameterised constructor; empty for default-constructed instances.

Protected Attributes
members for loading data
ProteinIdentification *	prot_id_
	Pointer to protein identification.

PeptideIdentification *	pep_id_
	Pointer to peptide identification.

PeptideHit *	pep_hit_
	Temporary peptide hit.

ProteinGroup	protein_group_
	protein group

bool	skip_protein_

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)

Protected Attributes inherited from XMLFile
std::string	schema_location_
	Path of the XML schema for validation; empty when the default constructor was used (isValid then throws `NotImplemented`).

std::string	schema_version_
	Schema version string returned by getVersion.

std::string	enforced_encoding_
	Optional XML encoding override applied to the `InputSource` in parse_ and parseBuffer_; empty disables the override. Used as a workaround for XTandem output XML which carries an encoding the parser otherwise stumbles on.

Additional Inherited Members
Protected 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 }

Static Protected 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.

Detailed Description

Used to load (storing not supported, yet) ProtXML files.

This class is used to load (storing not supported, yet) documents that implement the schema of ProtXML files.

A documented schema for this format comes with the TPP and can also be found at https://github.com/OpenMS/OpenMS/tree/develop/share/OpenMS/SCHEMAS

OpenMS can only read parts of the protein_summary subtree to extract protein-peptide associations. All other parts are silently ignored.

For protein groups, only the "group leader" carries its own probability and coverage in the protXML. Indistinguishable siblings (<indistinguishable_protein>) carry only a protein_name in the file (no probability or coverage of their own); on read they inherit the group leader's score (so that score-based filtering does not tear groups apart) and are left without a coverage value.

Note: ProteinProphet assigns probability=0 to "unneeded" (subsumable) proteins whose peptides are fully explained by higher-probability proteins in the same protein_group. These are distinct from truly indistinguishable proteins (which share 100% of their peptides and are represented as <indistinguishable_protein> elements in the protXML). During parsing, probability=0 <protein> elements are filtered out entirely: no ProteinHit, group entry, or peptide evidence is created for them. This prevents downstream tools like ProteinQuantifier from treating subsumable proteins as separate indistinguishable groups, which would incorrectly cause shared peptides to be discarded during quantification.

Data filled when reading a protXML:

ProteinHit: accession (from protein_name), score (ProteinProphet probability; indistinguishable siblings inherit the group leader's score), and coverage (from percent_coverage, group leader only). No meta values are set on ProteinHit.
PeptideHit: sequence (from peptide_sequence, including any modifications derived from <mod_aminoacid_mass>), score (from nsp_adjusted_probability), charge, and one PeptideEvidence per protein of the enclosing indistinguishable group. Meta values: is_unique (1/0 from is_nondegenerate_evidence) and is_contributing (1/0 from is_contributing_evidence).
The score type of both the ProteinIdentification and PeptideIdentification is set to "ProteinProphet probability" (higher is better).

Todo:
Writing of protXML is currently not supported

Member Typedef Documentation

◆ ProteinGroup

typedef ProteinIdentification::ProteinGroup ProteinGroup

A protein group (set of indices into ProteinIdentification)

Constructor & Destructor Documentation

◆ ProtXMLFile()

ProtXMLFile ( )

Constructor.

Member Function Documentation

◆ load()

void load	(	const std::string &	filename,
		ProteinIdentification &	protein_ids,
		PeptideIdentification &	peptide_ids
	)

Loads the identifications of an ProtXML file without identifier.

The information is read in and the information is stored in the corresponding variables

Exceptions

Exception::FileNotFound	is thrown if the file could not be opened
Exception::ParseError	is thrown if an error occurs during parsing

◆ matchModification_()

void matchModification_	(	const double	mass,
		const std::string &	origin,
		std::string &	modification_description
	)

protected

find modification name given a modified AA mass

Matches a mass of a modified AA to a mod in our modification db For ambiguous mods, the first (arbitrary) is returned If no mod is found an error is issued and the return string is empty

Note: A duplicate of this function is also used in PepXMLFile

Parameters

[in,out]	mass	Modified AA's mass
[in]	origin	AA one letter code
[in]	modification_description	[out] Name of the modification, e.g. 'Carboxymethyl (C)'

◆ onEndElement()

void onEndElement ( const char16_t * qname )

overrideprotectedvirtual

Docu in base class.

Reimplemented from XMLHandler.

◆ onStartElement()

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

overrideprotectedvirtual

Docu in base class.

Reimplemented from XMLHandler.

◆ registerProtein_()

void registerProtein_ ( const std::string & protein_name )

protected

Creates a new protein entry (if not already present) and appends it to the current group.

◆ resetMembers_()

void resetMembers_ ( )

protected

reset members after reading/writing

◆ store()

void store	(	const std::string &	filename,
		const ProteinIdentification &	protein_ids,
		const PeptideIdentification &	peptide_ids,
		const std::string &	document_id = `""`
	)

[not implemented yet!] Stores the data in an ProtXML file

[not implemented yet!] The data is stored in the file 'filename'.

Exceptions

Exception::UnableToCreateFile is thrown if the file could not be created

Member Data Documentation

◆ pep_hit_

PeptideHit* pep_hit_

protected

Temporary peptide hit.

◆ pep_id_

PeptideIdentification* pep_id_

protected

Pointer to peptide identification.

◆ prot_id_

ProteinIdentification* prot_id_

protected

Pointer to protein identification.

◆ protein_group_

ProteinGroup protein_group_

protected

protein group

◆ skip_protein_

bool skip_protein_

protected

true when inside a <protein> element with probability=0 (subsumable/"unneeded" protein); all child elements (peptides, indistinguishable_protein) are skipped during parsing

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ ProteinGroup

Constructor & Destructor Documentation

◆ ProtXMLFile()

Member Function Documentation

◆ load()

◆ matchModification_()

◆ onEndElement()

◆ onStartElement()

◆ registerProtein_()

◆ resetMembers_()

◆ store()

Member Data Documentation

◆ pep_hit_

◆ pep_id_

◆ prot_id_

◆ protein_group_

◆ skip_protein_