The class provides simplified access to ontology files in the .obo format. More...

#include <ms_obofile.hpp>

Inheritance diagram for ms_obofile:

Collaboration diagram for ms_obofile:

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Public Member Functions
	ms_obofile ()
	Default constructor - not generally useful.

	ms_obofile (const char *oboFileName)
	Constructor which loads the obo file from a local file.

	ms_obofile (const ms_obofile &right)
	Copying constructor.

	~ms_obofile ()
	Destructor.

void	appendErrors (const ms_errors &src)
	Copies all errors from another instance and appends them at the end of own list.

void	clearAllErrors ()
	Remove all errors from the current list of errors.

void	copyFrom (const ms_errors *right)
	Use this member to make a copy of another instance.

void	copyFrom (const ms_obofile *right)
	Copies all data from another instance of the class.

void	defaultValues ()
	Initialises the object.

std::string	findIDFromTagValue (const char tag, const char value) const
	Find the ontology term with an exact match to the passed tag/value pair.

const ms_errs *	getErrorHandler () const
	Retrive the error object using this function to get access to all errors and error parameters.

std::vector< std::string >	getItemFromId (const char *id) const
	Returns the vector of tag, value, comment strings for the specified ontology item.

int	getLastError () const
	Return the error description of the last error that occurred.

std::string	getLastErrorString () const
	Return the error description of the last error that occurred.

int	getNumberOfEntries () const
	Returns the number of entries .

bool	isValid () const
	Call this function to determine if there have been any errors.

ms_obofile &	operator= (const ms_obofile &right)
	Assignment operator.

void	parseLine (const std::string str, std::string &tag, std::string &value, std::string &comment) const
	Retrieves the tag, value and any comments from a line in the obo file.

Detailed Description

The class provides simplified access to ontology files in the .obo format.

The file format for the ontology files is described in http://www.geneontology.org/GO.format.obo-1_2.shtml .

This class provides limited read only access to OBO files. The aim of the class is to allow scripts using Mascot Parser to easily look up an ID for a given term in a local .obo file.

Constructor & Destructor Documentation

◆ ms_obofile() [1/3]

ms_obofile ( )

Default constructor - not generally useful.

Create a default empty ontology.

◆ ms_obofile() [2/3]

ms_obofile ( const char * oboFileName )

Constructor which loads the obo file from a local file.

Loads ontology from a local file. The file format will be:

[Term]
id: PI:00000
name: protein informatics cv
def: "Collection of terms for PSI Proteome Informatics standards." [PSI:PI]

[Term]
. . .

The ID of each term is indexed for fast access.

After loading, use the isValid() function to determine if there were any errors.

Parameters

oboFileName is the file name of the local file.

◆ ms_obofile() [3/3]

ms_obofile ( const ms_obofile & src )

Copying constructor.

Note: This constructor can only be used in C++.

Parameters

src	is the original OBO file.

◆ ~ms_obofile()

~ms_obofile ( )

Destructor.

No need to call this directly. Frees the complete ontology.

Member Function Documentation

◆ appendErrors()

void appendErrors ( const ms_errors & src )

inherited

Copies all errors from another instance and appends them at the end of own list.

Parameters

src	The object to copy the errors across from. See Maintaining object references: two rules of thumb.

◆ clearAllErrors()

void clearAllErrors ( )

inherited

Remove all errors from the current list of errors.

The list of 'errors' can include fatal errors, warning messages, information messages and different levels of debugging messages.

All messages are accumulated into a list in this object, until clearAllErrors() is called.

See Error Handling.

See also: isValid(), getLastError(), getLastErrorString(), getErrorHandler()

Examples: common_error.cpp, resfile_error.cpp, and resfile_summary.cpp.

◆ copyFrom() [1/2]

void copyFrom ( const ms_errors * right )

inherited

Use this member to make a copy of another instance.

Parameters

right is the source to initialise from

◆ copyFrom() [2/2]

void copyFrom ( const ms_obofile * right )

Copies all data from another instance of the class.

Parameters

right is the original object to copy to the new one.

◆ defaultValues()

void defaultValues ( )

Initialises the object.

Reset all values to their defaults.

◆ findIDFromTagValue()

std::string findIDFromTagValue	(	const char *	tag,
		const char *	value
	)		const

Find the ontology term with an exact match to the passed tag/value pair.

This function is only useful for retrieving items where you expect the tag value to be unique – for example the "name" field.

Parameters

tag	is the name of the tag. For example, "name", "is_a", "property_value".
value	is the value to be found.

Returns: An empty string if there is no match, or the term ID if successful.

◆ getErrorHandler()

const ms_errs * getErrorHandler ( ) const

inherited

Retrive the error object using this function to get access to all errors and error parameters.

See Error Handling.

Returns: Constant pointer to the error handler

See also: isValid(), getLastError(), getLastErrorString(), clearAllErrors(), getErrorHandler()

Examples: common_error.cpp, and http_helper_getstring.cpp.

◆ getItemFromId()

std::vector< std::string > getItemFromId ( const char * id ) const

Returns the vector of tag, value, comment strings for the specified ontology item.

Returns all the lines in the [Term] for the specified ID.

Parameters

id	is the ID of the term. For example, "PI:00171".

Returns: vector of lines

◆ getLastError()

int getLastError ( ) const

inherited

Return the error description of the last error that occurred.

All errors are accumulated into a list in this object, until clearAllErrors() is called. This function returns the last error that occurred.

See Error Handling.

See also: isValid(), getLastErrorString(), clearAllErrors(), getErrorHandler()

Returns: the error number of the last error, or 0 if there have been no errors.

◆ getLastErrorString()

std::string getLastErrorString ( ) const

inherited

Return the error description of the last error that occurred.

All errors are accumulated into a list in this object, until clearAllErrors() is called. This function returns the last error that occurred.

Returns: Most recent error, warning, information or debug message

See Error Handling.

See also: isValid(), getLastError(), clearAllErrors(), getErrorHandler()

Examples: common_error.cpp, config_enzymes.cpp, config_fragrules.cpp, config_license.cpp, config_mascotdat.cpp, config_masses.cpp, config_modfile.cpp, config_procs.cpp, config_quantitation.cpp, config_taxonomy.cpp, http_helper_getstring.cpp, and tools_aahelper.cpp.

◆ getNumberOfEntries()

int getNumberOfEntries ( ) const

Returns the number of entries .

Each [Term] section is considered to be a single entry.

Returns: The number of terms in the ontology.

◆ isValid()

bool isValid ( ) const

inherited

Call this function to determine if there have been any errors.

This will return true unless there have been any fatal errors.

See Error Handling.

Returns: True if no fatal error occured

See also: getLastError(), getLastErrorString(), clearAllErrors(), getErrorHandler()

Examples: common_error.cpp, config_enzymes.cpp, config_fragrules.cpp, config_license.cpp, config_mascotdat.cpp, config_masses.cpp, config_modfile.cpp, config_procs.cpp, config_quantitation.cpp, config_taxonomy.cpp, http_helper_getstring.cpp, peptide_list.cpp, repeat_search.cpp, resfile_error.cpp, resfile_info.cpp, resfile_input.cpp, resfile_params.cpp, resfile_summary.cpp, and tools_aahelper.cpp.

◆ operator=()

ms_obofile & operator= ( const ms_obofile & right )

Assignment operator.

Parameters

right is the original object to copy to the new one.

Returns: reference to the current object

◆ parseLine()

void parseLine	(	const std::string	str,
		std::string &	tag,
		std::string &	value,
		std::string &	comment
	)		const

Retrieves the tag, value and any comments from a line in the obo file.

Note: This function can only be used from C++.

For example, for the following line, the tag would be "is_a", the value returned would be "PI:00153" and the comment would be "search engine specific score":

   is_a: PI:00153 ! search engine specific score

Parameters

str	is the input string.
tag	is the name of the tag in the input line.
value	is the value of the tag in the input line.
comment	is any comment (after the ! in the input line).

The documentation for this class was generated from the following files:

ms_obofile.hpp
ms_obofile.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ ms_obofile() [1/3]

◆ ms_obofile() [2/3]

◆ ms_obofile() [3/3]

◆ ~ms_obofile()

Member Function Documentation

◆ appendErrors()

◆ clearAllErrors()

◆ copyFrom() [1/2]

◆ copyFrom() [2/2]

◆ defaultValues()

◆ findIDFromTagValue()

◆ getErrorHandler()

◆ getItemFromId()

◆ getLastError()

◆ getLastErrorString()

◆ getNumberOfEntries()

◆ isValid()

◆ operator=()

◆ parseLine()