Represent a single entry in the enzymes file. More...

#include <ms_enzyme.hpp>

Inheritance diagram for ms_enzyme:

Collaboration diagram for ms_enzyme:

Public Types
enum	cuttertype { UNDEFINED_CUTTER = 0x0000 , NTERM_CUTTER = 0x0001 , CTERM_CUTTER = 0x0002 }
	Definitions for types of cutter. More...

Public Member Functions
	ms_enzyme ()
	Default constructor.

	ms_enzyme (const ms_enzyme &src)
	Copying constructor.

	~ms_enzyme ()
	Destructor.

void	addCutter (const cuttertype type, const char cleaveAtStr, const char restrictStr)
	Adds an cutter to the enzyme.

void	appendProperty (const char name, const char value, const char *delimiter, const bool bFirstPlace=false)
	Adds a new property with the given parameters.

void	appendText (const char *line, const bool bFirstPlace=false)
	Adds a new non-parsed property.

bool	canCleave (const int cutterNum, const char leftResidue, const char rightResidue) const
	Returns TRUE if the cutter can cut between the two residues.

void	clearAllCutters ()
	Deletes all cutters from the list.

void	copyFrom (const ms_customproperty *src)
	Copies all properties and comments from another instance.

void	copyFrom (const ms_enzyme *right)
	Can be used to create a clone.

void	defaultValues ()
	Use this member to re-initialise an instance to default values.

void	delNonEmpty ()
	Deletes all non-comment properties.

void	delProp (const char *name)
	Deletes all properties with the specified name.

void	delPropByNumber (const int index)
	Deletes a single property with the specified number only.

void	delPropStart (const char *nameBeginning)
	Deletes all properties whose names start with the given string.

int	findProperty (const char *name, const int startFrom=0) const
	Searches the list for a property with the given name.

int	findPropertyBeginning (const char *nameBeginning, const int startFrom=0) const
	Searches the list for a property with the partially matching name.

std::string	getCleave (const int cutterNum) const
	Returns the list of cleavage points for a cutter.

ms_enzyme::cuttertype	getCutterType (const int cutterNum) const
	Return the number of cutters that make up the enzyme definition.

std::string	getDefaultDelimiter () const
	Return current default delimiter string used for parsing/storing properties.

std::string	getDelimiterByNumber (const int index) const
	Returns a specific delimiter used for the property.

int	getNumberOfCutters () const
	Returns the number of cutters.

int	getNumberOfProperties () const
	Returns a total number of property/comment entries.

std::string	getPreceedingComments () const
	Returns any comments preceeding the section.

std::string	getPropertyName (const int index) const
	Returns a property name for a given index.

std::string	getPropValStringByName (const char *name) const
	Retrieves property value by name.

std::string	getPropValStringByNumber (const int index) const
	Retrieves property raw text values by number.

std::string	getRestrict (const int cutterNum) const
	Returns the list of restriction points for a cutter.

std::string	getTitle () const
	Returns a name of the enzyme as appears in the file.

bool	isIndependent () const
	Check whether multiple enzymes have been applied independently.

bool	isSemiSpecific () const
	Returns TRUE if the enzyme is semi-specific.

bool	isValid () const
	Use this method to do basic check on a newly created object.

ms_enzyme &	operator= (const ms_enzyme &right)
	C++ style operator= for copying.

void	setDefaultDelimiter (const char *delim)
	Allows to set a specific delimiter string to be used when no property-specific delimiter is supplied.

void	setIndependent (const bool bit)
	Sets the flag that specifies whether multiple enzymes have been applied independently.

void	setPreceedingComments (const std::string &comments)
	Sets any comments preceeding the section.

void	setPropertyName (const int index, const char *name)
	Changes name of the property with the given index.

void	setPropValBoolByName (const char *name, const bool value, const bool bFirstPlace=false)
	Changes a boolean value of the first entry with the given name or creates a new property if it is not found.

void	setPropValCharByName (const char *name, const char value, const bool bFirstPlace=false)
	Changes a single character value of the first entry with the given name or creates a new property if it is not found.

void	setPropValFloatByName (const char *name, const double value, const bool bFirstPlace=false)
	Changes an floating point value of the first entry with the given name or creates a new property if it is not found.

void	setPropValInt64ByName (const char *name, const INT64 value, const bool bFirstPlace=false)
	Changes a long 64-bit integer value of the first entry with the given name or creates a new property if it is not found.

void	setPropValIntByName (const char *name, const int value, const bool bFirstPlace=false)
	Changes an integer value of the first entry with the given name or creates a new property if it is not found.

void	setPropValStringByName (const char name, const char value, const bool bFirstPlace=false)
	Changes a string value of the first entry with the given name or creates a new property if it is not found.

void	setPropValStringByNumber (const int index, const char *value)
	Changes an string value of an existing property with the given index.

void	setSemiSpecific (const bool value)
	Sets a new value for the semi specific flag.

void	setTitle (const char *str)
	Sets a new title for the enzyme.

bool	uncommentProp (const int index, const char *delimeter=0)
	Uncomments a line in the configuration file.

bool	verifyEnzyme (ms_errs *errObj) const
	Tries to detect any inconsistencies in the enzyme definition.

Detailed Description

Represent a single entry in the enzymes file.

An instance of this class is normally be created by calling matrix_science::ms_enzymefile::getEnzymeByNumber() or matrix_science::ms_enzymefile::getEnzymeByName() and should then only be used in 'read-only' mode.

As well as 'simple' enzymes, the following cases are supported:

semi-specific enzymes (isSemiSpecific())
mixed cutters (C-term and N-term)
independent cutters (isIndependent())

In case of independent enzymes an instance contains several enzyme definitions that can be iterated through. Otherwise several enzymes with mixed-term cutting are combined together.

Also get yourselves acquainted with the base class ms_customproperty. It facilitates the following tasks:

Retrieving an unsupported property.
Retrieving a raw/text/XML property representation.
Checking for existence of a certain property rather than dealing with its default value.
Accessing commented lines in a section.

More functionality is described in the documentation for ms_customproperty.

Examples: config_enzymes.cpp, and tools_aahelper.cpp.

Member Enumeration Documentation

◆ cuttertype

enum cuttertype

Definitions for types of cutter.

See Using enumerated values and static const ints in Perl, Java, Python and C#.

Enumerator
UNDEFINED_CUTTER	Undefined - normally due to an invalid parameter when calling a function.
NTERM_CUTTER	N Terminus cutter - cuts before the specified residue(s).
CTERM_CUTTER	C Terminus cutter - cuts after the specified residue(s).

Constructor & Destructor Documentation

◆ ms_enzyme() [1/2]

ms_enzyme ( )

Default constructor.

An enzyme object should normally be created using matrix_science::ms_enzymefile::getEnzymeByNumber() or matrix_science::ms_enzymefile::getEnzymeByName().

◆ ms_enzyme() [2/2]

ms_enzyme ( const ms_enzyme & src )

Copying constructor.

Note: You cannot use this constructor in programming languages other than C++.

Parameters

src	is the enzyme to make a copy of.

◆ ~ms_enzyme()

~ms_enzyme ( )

Destructor.

Called automatically from C++ and other languages.

Member Function Documentation

◆ addCutter()

void addCutter	(	const cuttertype	type,
		const char *	cleaveAtStr,
		const char *	restrictStr
	)

Adds an cutter to the enzyme.

This function doesn't perform any checks for valid residues etc, so the verifyEnzyme() function should be called after adding a cutter.

Parameters

type	is either ms_enzyme::NTERM_CUTTER or ms_enzyme::CTERM_CUTTER.
cleaveAtStr	One or more residue letters which are the potential cleavage points.
restrictStr	Zero or more residue letters that are restriction points.

◆ appendProperty()

void appendProperty	(	const char *	name,
		const char *	value,
		const char *	delimiter,
		const bool	bFirstPlace = `false`
	)

inherited

Adds a new property with the given parameters.

Parameters

name	a property name to use.
value	a property value to use.
delimiter	a specific delimiter or an empty string for a default one to be used.
bFirstPlace	forces a new property to be put on top of the list.

◆ appendText()

void appendText	(	const char *	l,
		const bool	bFirstPlace = `false`
	)

inherited

Adds a new non-parsed property.

All property elements will be retrieved from the first parameter. Before calling this method, a specific default delimiter can be set using setDefaultDelimiter().

Parameters

l	raw text representation of the property to be parsed.
bFirstPlace	forces a new property to be put on top of the list.

◆ canCleave()

bool canCleave	(	const int	cutterNum,
		const char	leftResidue,
		const char	rightResidue
	)		const

Returns TRUE if the cutter can cut between the two residues.

Gives an answer for the question: Will the enzyme cut at the this position or not?

This function doesn't take into account the semi specific flag.

Parameters

cutterNum	must be in the range 0..getNumberOfCutters()-1.
leftResidue	amino acid letter representing a residue before the cutting point.
rightResidue	amino acid letter representing a residue after the cutting point.

Returns: True if the enzyme can cleave at this point.

◆ clearAllCutters()

void clearAllCutters ( )

Deletes all cutters from the list.

Only useful when defining enzymes 'on the fly'.

◆ copyFrom()

void copyFrom ( const ms_enzyme * right )

Can be used to create a clone.

Simply create an instance of the class using the default constructor and call this method.

Parameters

right pointer to another instance to copy from.

◆ defaultValues()

void defaultValues ( )

Use this member to re-initialise an instance to default values.

The default values are no cutters, no title, independent = false and semiSpecific = false.

◆ delProp()

void delProp ( const char * str )

inherited

Deletes all properties with the specified name.

Parameters

str	Property name to find a match and then delete.

◆ delPropStart()

void delPropStart ( const char * str )

inherited

Deletes all properties whose names start with the given string.

Parameters

str	Beginning a first part of the property name to delete.

◆ findProperty()

int findProperty	(	const char *	name,
		const int	startFrom = `0`
	)		const

inherited

Searches the list for a property with the given name.

If no property found with the given name -1 will be returned. There may be several property entries in the list with the same name.

Parameters

name	a property name to be found.
startFrom	a minimal property index to start search from.

Returns: a property index or -1 if no property found.

◆ findPropertyBeginning()

int findPropertyBeginning	(	const char *	nameBeginning,
		const int	startFrom = `0`
	)		const

inherited

Searches the list for a property with the partially matching name.

If no property found with the given name part -1 will be returned. There may be several property entries in the list whose names start with the given string.

Parameters

nameBeginning	first part of a property name to be found.
startFrom	a minimal property index to start search from.

Returns: a property index or -1 if no property found.

◆ getCleave()

std::string getCleave ( const int cutterNum ) const

Returns the list of cleavage points for a cutter.

Returns the residues after which an enzyme may cut (for a CTERM_CUTTER) or before which an enzyme may cut (for an NTERM_CUTTER).

See also: getRestrict()

Parameters

cutterNum must be in the range 0..getNumberOfCutters()-1.

Returns: A string of possible cleaveage points.

Examples: config_enzymes.cpp.

◆ getCutterType()

ms_enzyme::cuttertype getCutterType ( const int cutterNum ) const

Return the number of cutters that make up the enzyme definition.

Parameters

cutterNum must be in the range 0..getNumberOfCutters()-1.

Returns: ms_enzyme::NTERM_CUTTER, or ms_enzyme::CTERM_CUTTER or ms_enzyme::UNDEFINED_CUTTER if cutterNum is an invalid value.

Examples: config_enzymes.cpp.

◆ getDefaultDelimiter()

std::string getDefaultDelimiter ( ) const

inherited

Return current default delimiter string used for parsing/storing properties.

Returns: default delimiter

◆ getDelimiterByNumber()

std::string getDelimiterByNumber ( const int index ) const

inherited

Returns a specific delimiter used for the property.

Parameters

index Index for which to get a delimiter

Returns: corresponding delimiter

◆ getNumberOfCutters()

int getNumberOfCutters ( ) const

Returns the number of cutters.

For most enzymes, there will be just one cutter. See isIndependent() for details of multiple cutters in an enzyme.

The limit of 5 cutters per enzyme was raised to a limit of 20 cutters per enzyme in Parser 2.3.01.

Returns: The number of cutters.

Examples: config_enzymes.cpp.

◆ getNumberOfProperties()

int getNumberOfProperties ( ) const

inherited

Returns a total number of property/comment entries.

Returns: Number of property/comment entries

◆ getPreceedingComments()

std::string getPreceedingComments ( ) const

inherited

Returns any comments preceeding the section.

Sections in the mascot.dat file may have comments preceeding them. In most cases, these comments need to stay 'attached' to the section.

Multiple line comments are supported by having a single string with newline characters

See also: setPreceedingComments()

Returns: any comments preceeding the section

◆ getPropertyName()

std::string getPropertyName ( const int index ) const

inherited

Returns a property name for a given index.

Parameters

index property number from 0 to (getNumberOfProperties()-1).

Returns: Rroperty name of an empty string for comments.

◆ getPropValStringByName()

std::string getPropValStringByName ( const char * name ) const

inherited

Retrieves property value by name.

Don't use this method for comments as they all have empty name. Also note that there might be several entries corresponding to the same name . – only the first value will be returned. If in doubt use findProperty() and getPropValStringByNumber() instead.

Parameters

name	Name for which to get a property value

Returns: corresponding property value

◆ getPropValStringByNumber()

std::string getPropValStringByNumber ( const int index ) const

inherited

Retrieves property raw text values by number.

Parameters

index Index for which to get a property value

Returns: corresponding property value

◆ getRestrict()

std::string getRestrict ( const int cutterNum ) const

Returns the list of restriction points for a cutter.

Returns the residues after which an enzyme may cut (for a CTERM_CUTTER) or before which an enzyme may cut (for an NTERM_CUTTER).

See also: getCleave()

Parameters

cutterNum must be in the range 0..getNumberOfCutters()-1.

Returns: A string of possible cleaveage points.

Examples: config_enzymes.cpp.

◆ isIndependent()

bool isIndependent ( ) const

Check whether multiple enzymes have been applied independently.

In cases where a single enzyme has been used, the 'independent' flag has no meaning and would normally be set to false. Where multiple enzymes are used on a single sample, these can have been applied in two different ways:

Independent = true indicates that the specificities should be treated as if independent digests had been performed on separate sample aliquots and the resulting peptide mixtures combined. Thus, any given peptide will conform to the specificity of one cleavage type only. In the case of CNBr+Trypsin, if Independent was true, you would not find any peptides resulting from cleavage after K or R at one end, and cleavage after M at the other.
Independent = false indicates that the specificities are combined, as if the reagents had been applied simultaneously or serially to a single sample aliquot.

See also: getNumberOfCutters()

Returns: True if the cutters are applied independently.

◆ isSemiSpecific()

bool isSemiSpecific ( ) const

Returns TRUE if the enzyme is semi-specific.

Enzymes don't function perfectly all the time. In most cases where they fail to cut at the specified cleavage point, this only affects one terminus. In Mascot, when a semi specific enzyme is defined, peptides only need to conform to the cleavage specificity at one end.

All enzymes represented by the entry have to be either semi-specific or not.

Returns: True if the enzyme is semi specific.

◆ isValid()

bool isValid ( ) const

Use this method to do basic check on a newly created object.

This function calls verifyEnzyme() and is merely provided to give a consistently available function interface to the object. To determine the cause of any inconsistencies or errors, call verifyEnzyme() with an error object.

Returns: False if there are any errors in the enzyme definition.

◆ operator=()

ms_enzyme & operator= ( const ms_enzyme & right )

C++ style operator= for copying.

Note: This operator is only available in C++.

Acts identically to copyFrom().

Parameters

right is the enzyme definition to copy from.

Returns: reference to the current object

◆ setDefaultDelimiter()

void setDefaultDelimiter ( const char * delim )

inherited

Allows to set a specific delimiter string to be used when no property-specific delimiter is supplied.

Parameters

delim String to set the default delimiter

◆ setIndependent()

void setIndependent ( const bool bit )

Sets the flag that specifies whether multiple enzymes have been applied independently.

In cases where a single enzyme has been used, the 'independent' flag has no meaning and would normally be set to false. Where multiple enzymes are used on a single sample, these can have been applied in two different ways:

Independent = true indicates that the specificities should be treated as if independent digests had been performed on separate sample aliquots and the resulting peptide mixtures combined. Thus, any given peptide will conform to the specificity of one cleavage type only. In the case of CNBr+Trypsin, if Independent was true, you would not find any peptides resulting from cleavage after K or R at one end, and cleavage after M at the other.
Independent = false indicates that the specificities are combined, as if the reagents had been applied simultaneously or serially to a single sample aliquot.

See also: getNumberOfCutters()

Parameters

bit	is the new value.

◆ setPreceedingComments()

void setPreceedingComments ( const std::string & comments )

inherited

Sets any comments preceeding the section.

Sections in the mascot.dat file may have comments preceeding them. In most cases, these comments need to stay 'attached' to the section.

Multiple line comments are supported by having a single string with newline characters

See also: getPreceedingComments()

Parameters

comments any comments preceeding the section

◆ setPropertyName()

void setPropertyName	(	const int	index,
		const char *	name
	)

inherited

Changes name of the property with the given index.

Parameters

index	property number from 0 to (getNumberOfProperties()-1).
name	new name to be given to the property.

◆ setPropValBoolByName()

void setPropValBoolByName	(	const char *	name,
		const bool	value,
		const bool	bFirstPlace = `false`
	)

inherited

Changes a boolean value of the first entry with the given name or creates a new property if it is not found.

A new value will be converted into 1 (for TRUE) or 0 (for FALSE) character.

Parameters

name	a name of the property to find or add.
value	a new boolean value for the property.
bFirstPlace	if not found a new property can be put on top of the list.

◆ setPropValCharByName()

void setPropValCharByName	(	const char *	name,
		const char	value,
		const bool	bFirstPlace = `false`
	)

inherited

Changes a single character value of the first entry with the given name or creates a new property if it is not found.

Parameters

name	a name of the property to find or add.
value	a new single character value for the property.
bFirstPlace	if not found a new property can be put on top of the list.

◆ setPropValFloatByName()

void setPropValFloatByName	(	const char *	name,
		const double	value,
		const bool	bFirstPlace = `false`
	)

inherited

Changes an floating point value of the first entry with the given name or creates a new property if it is not found.

Parameters

name	a name of the property to find or add.
value	a new floating point value for the property.
bFirstPlace	if not found a new property can be put on top of the list.

◆ setPropValInt64ByName()

void setPropValInt64ByName	(	const char *	name,
		const INT64	value,
		const bool	bFirstPlace = `false`
	)

inherited

Changes a long 64-bit integer value of the first entry with the given name or creates a new property if it is not found.

Parameters

name	a name of the property to find or add.
value	a new long 64-bit integer value for the property.
bFirstPlace	if not found a new property can be put on top of the list.

◆ setPropValIntByName()

void setPropValIntByName	(	const char *	name,
		const int	value,
		const bool	bFirstPlace = `false`
	)

inherited

Changes an integer value of the first entry with the given name or creates a new property if it is not found.

Parameters

name	a name of the property to find or add.
value	a new integer value for the property.
bFirstPlace	if not found a new property can be put on top of the list.

◆ setPropValStringByName()

void setPropValStringByName	(	const char *	name,
		const char *	value,
		const bool	bFirstPlace = `false`
	)

inherited

Changes a string value of the first entry with the given name or creates a new property if it is not found.

Parameters

name	a name of the property to find or add.
value	a new string value for the property.
bFirstPlace	if not found a new property can be put on top of the list.

◆ setPropValStringByNumber()

void setPropValStringByNumber	(	const int	index,
		const char *	str
	)

inherited

Changes an string value of an existing property with the given index.

Parameters

index	an index of an existing property.
str	String value for the property.

◆ setSemiSpecific()

void setSemiSpecific ( const bool value )

Sets a new value for the semi specific flag.

C++ If you load an enzyme using matrix_science::ms_enzymefile::getEnzymeByNumber() or matrix_science::ms_enzymefile::getEnzymeByName(), you will not be able to call this member because those functions return a const pointer.

Calling this function will not affect the enzymes file. See ms_enzymefile::updateByNumber() and ms_enzymefile::updateByName().

Enzymes don't function perfectly all the time. In most cases where they fail to cut at the specified cleavage point, this only affects one terminus. In Mascot, when a semi specific enzyme is defined, peptides only need to conform to the cleavage specificity at one end.

All enzymes represented by the entry have to be either semi-specific or not.

Parameters

value is the new flag to specify if the enzyme is semi specific.

Examples: config_enzymes.cpp.

◆ setTitle()

void setTitle ( const char * str )

Sets a new title for the enzyme.

C++: If you load an enzyme using matrix_science::ms_enzymefile::getEnzymeByNumber() or matrix_science::ms_enzymefile::getEnzymeByName(), you will not be able to call this member because those functions return a const pointer.

Calling this will not affect the enzymes file. See ms_enzymefile::updateByNumber() and ms_enzymefile::updateByName().

Parameters

str	is the new name for the enzyme.

◆ uncommentProp()

bool uncommentProp	(	const int	index,
		const char *	delimeter = `0`
	)

inherited

Uncomments a line in the configuration file.

Removes a # and any white space. Finds the delimeter and extracts the property name and value.

Parameters

index	must be a value between 0 and getNumberOfProperties().
delimeter	will often be a space. If not supplied, the default delimeter will be used.

Returns: true if the delimiter was found, false otherwise

◆ verifyEnzyme()

bool verifyEnzyme ( ms_errs * errObj ) const

Tries to detect any inconsistencies in the enzyme definition.

If errors are found in the enzyme definition, the ms_errs::ERR_MSP_ENZYME_DEFINITION_PROBLEM error will be set, once for each error. Each error message will also include one of following additional text strings.

The reason or method required to 'fix' the error are the following:

"empty title" - Need to call setTitle().
"no cutting rules" - Need to call addCutter() at least once.
"more restrict than cleave rules for C-term" - probably an internal parser error.
"more restrict than cleave rules for N-term" - probably an internal parser error.
"no cleavage residues for a cutter" - addCutter() has been called with an empty or invalid cleaveAtStr().
"too many cleavage residues specified" - all residues have been specified for cleaving at.
"too many restricting residues specified" - all residues have been specified as restriction, meaning that the enzyme won't cut anywhere.
"cleavage residues must be uppercase A-Z" - a lower case letter or a non alphabetic character has been specified.
"restrict residues must be uppercase A-Z" - a lower case letter or a non alphabetic character has been specified.

Parameters

errObj passed error-object to store error messages.

Returns: true if the enzyme definition is valid.

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

ms_enzyme.hpp
ms_enzyme.cpp

Public Types

Public Member Functions

Detailed Description

Member Enumeration Documentation

◆ cuttertype

Constructor & Destructor Documentation

◆ ms_enzyme() [1/2]

◆ ms_enzyme() [2/2]

◆ ~ms_enzyme()

Member Function Documentation

◆ addCutter()

◆ appendProperty()

◆ appendText()

◆ canCleave()

◆ clearAllCutters()

◆ copyFrom()

◆ defaultValues()

◆ delProp()

◆ delPropStart()

◆ findProperty()

◆ findPropertyBeginning()

◆ getCleave()

◆ getCutterType()

◆ getDefaultDelimiter()

◆ getDelimiterByNumber()

◆ getNumberOfCutters()

◆ getNumberOfProperties()

◆ getPreceedingComments()

◆ getPropertyName()

◆ getPropValStringByName()

◆ getPropValStringByNumber()

◆ getRestrict()

◆ isIndependent()

◆ isSemiSpecific()

◆ isValid()

◆ operator=()

◆ setDefaultDelimiter()

◆ setIndependent()

◆ setPreceedingComments()

◆ setPropertyName()

◆ setPropValBoolByName()

◆ setPropValCharByName()

◆ setPropValFloatByName()

◆ setPropValInt64ByName()

◆ setPropValIntByName()

◆ setPropValStringByName()

◆ setPropValStringByNumber()

◆ setSemiSpecific()

◆ setTitle()

◆ uncommentProp()

◆ verifyEnzyme()