This class encapsulates a single entry (an instrument) from a fragmentation_rules file. More...

#include <ms_fragmentationrules.hpp>

Inheritance diagram for ms_fragmentationrules:

Collaboration diagram for ms_fragmentationrules:

Public Types
enum	FRAG_SERIES_TYPE { FRAG_IMMONIUM = 4 , FRAG_A_SERIES = 5 , FRAG_A_MINUS_NH3 = 6 , FRAG_A_MINUS_H2O = 7 , FRAG_B_SERIES = 8 , FRAG_B_MINUS_NH3 = 9 , FRAG_B_MINUS_H2O = 10 , FRAG_C_SERIES = 11 , FRAG_X_SERIES = 12 , FRAG_Y_SERIES = 13 , FRAG_Y_MINUS_NH3 = 14 , FRAG_Y_MINUS_H2O = 15 , FRAG_Z_SERIES = 16 , FRAG_INTERNAL_YB = 17 , FRAG_INTERNAL_YA = 18 , FRAG_Z_PLUS_1 = 21 , FRAG_D_SERIES = 22 , FRAG_V_SERIES = 23 , FRAG_W_SERIES = 24 , FRAG_Z_PLUS_2 = 25 }
	Definitions for ID-constants for series used. More...

Public Member Functions
	ms_fragmentationrules ()
	Default constructor is used to create an empty object.

	ms_fragmentationrules (const ms_fragmentationrules &src)
	Copying constructor.

	~ms_fragmentationrules ()
	Destructor.

bool	anyNLseriesUsed (const int series) const
	Will return true if any 'neutral loss' series is specified for this series.

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.

void	clearSeries ()
	Deletes all series usage information.

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

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

void	defaultValues ()
	Initialises the instance with 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	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.

double	getMaxInternalMass () const
	Returns the maximum mass to be considered for internal fragments.

double	getMinInternalMass () const
	Returns the minimum mass to be considered for internal fragments.

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	getTitle () const
	Returns the title of the instrument.

bool	isCharged2Plus () const
	Returns true if the 'doubly charged 2+' fragmentation rule is specified.

bool	isCharged3Plus () const
	Returns true if the 'doubly charged 3+' fragmentation rule is specified.

bool	isSeriesUsed (const int series) const
	Returns true if a given series is specified for the instrument.

bool	isSinglyCharged () const
	Returns true if the 'singly charged' fragmentation rule is specified.

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

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

void	setCharged2Plus (const bool value)
	Change the availability the of 'doubly charged 2+' fragmentation rule.

void	setCharged3Plus (const bool value)
	Change the availability the of 'doubly charged 3+' fragmentation rule.

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

void	setMaxInternalMass (const double mass)
	Sets the maximum mass to be considered for internal fragments.

void	setMinInternalMass (const double mass)
	Set the minimum mass to be considered for internal fragments.

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	setSeriesUsed (const int series, const bool val)
	Sets availability on a given series.

void	setSinglyCharged (const bool value)
	Change the availability of the 'singly charged' fragmentation rule.

void	setTitle (const char *title)
	Assigns a new title to the rule.

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

bool	verifyRule (ms_errs *err_, const bool tryToFix)
	Tries to detect any inconsistencies in the instrument definition.

Static Public Member Functions
static int	getFirstSerie ()
	The lowest series number that can be used.

static int	getFirstSeries ()
	The lowest series number that can be used.

static int	getLastSerie ()
	The highest series number that can be used.

static int	getLastSeries ()
	The highest series number that can be used.

static std::string	getSeriesDescription (const int series)
	Returns a description string for a given series.

static std::string	getSeriesName (const int series)
	Returns a short series name.

static int	getTotalSeriesOutput ()
	Returns the length of the series string output in a Mascot results file.

static bool	isBackboneSeries (const int series)
	Returns true if the series is a 'backbone' fragment.

static bool	isNeutralLossSeries (const int series)
	Returns true if the series is a 'neutral loss' series.

Detailed Description

This class encapsulates a single entry (an instrument) from a fragmentation_rules file.

Objects of this class are normally created by loading a file using the ms_fragrulesfile class.

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_fragrules.cpp.

Member Enumeration Documentation

◆ FRAG_SERIES_TYPE

enum FRAG_SERIES_TYPE

Definitions for ID-constants for series used.

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

See http://www.matrixscience.com/help/fragmentation_help.html for details of ions types.

Enumerator
FRAG_IMMONIUM	Immonium ions.
FRAG_A_SERIES	A series ions.
FRAG_A_MINUS_NH3	Referred to as a* in Mascot reports.
FRAG_A_MINUS_H2O	Referred to as a^o in Mascot reports.
FRAG_B_SERIES	B series ions.
FRAG_B_MINUS_NH3	Referred to as b* in Mascot reports.
FRAG_B_MINUS_H2O	Referred to as b^o in Mascot reports.
FRAG_C_SERIES	C series ions.
FRAG_X_SERIES	X series ions.
FRAG_Y_SERIES	Y series ions.
FRAG_Y_MINUS_NH3	Referred to as y* in Mascot reports.
FRAG_Y_MINUS_H2O	Referred to as y^o in Mascot reports.
FRAG_Z_SERIES	Z series ions.
FRAG_INTERNAL_YB	Internal series, caused by double backbone cleavage. Combination of b type and y type cleavage.
FRAG_INTERNAL_YA	Internal series, caused by double backbone cleavage. Combination of a type and y type cleavage.
FRAG_Z_PLUS_1	Z+1 series.
FRAG_D_SERIES	D Satellite Ions. A series partial side chain. Collision induced dissociation of ions at keV energies.
FRAG_V_SERIES	V Satellite Ions. Y series partial side chain. Collision induced dissociation of ions at keV energies.
FRAG_W_SERIES	W Satellite Ions. Z series partial side chain. Collision induced dissociation of ions at keV energies.
FRAG_Z_PLUS_2	Z+2 series.

Constructor & Destructor Documentation

◆ ms_fragmentationrules()

ms_fragmentationrules ( )

Default constructor is used to create an empty object.

Use member functions to fill up the list of allowed series.

◆ ~ms_fragmentationrules()

~ms_fragmentationrules ( )

Destructor.

Frees all memory allocated for the object.

Member Function Documentation

◆ anyNLseriesUsed()

bool anyNLseriesUsed ( const int series ) const

Will return true if any 'neutral loss' series is specified for this series.

Parameters

series must be a number between getFirstSeries() and getLastSeries() inclusive.

Returns

true if the passed series

is A and A with loss of water or NH3 is also specified, or
is B and B with loss of water or NH3 is also specified, or
is Y and Y with loss of water or NH3 is also specified.

Otherwise returns false.

◆ 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.

◆ clearSeries()

void clearSeries ( )

Deletes all series usage information.

All series are set to be unused, but the instrument title is retained.

◆ copyFrom()

void copyFrom ( const ms_fragmentationrules * right )

Copies all information from another instance of the class.

Parameters

right is the fragmentation rules to copy from.

◆ defaultValues()

void defaultValues ( )

Initialises the instance with default values.

Sets all series to be unused.

◆ 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.

◆ 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

◆ getFirstSerie()

int getFirstSerie ( )

static

The lowest series number that can be used.

Deprecated:: Use getFirstSeries().

Returns: The first usable series number. Series numbers '1', '2' and '3' relate to allowed charge states rather than real series.

◆ getFirstSeries()

int getFirstSeries ( )

static

The lowest series number that can be used.

See also: ms_fragmentationrules::getLastSeries()

Returns: The first usable series number. Series numbers '1', '2' and '3' relate to allowed charge states rather than real series.

◆ getLastSerie()

int getLastSerie ( )

static

The highest series number that can be used.

Deprecated:: Use getLastSeries().

Returns: The last usable series number. More series may be added in later versions of Mascot, and using this function may allow code to be made 'future proof'.

◆ getLastSeries()

int getLastSeries ( )

static

The highest series number that can be used.

See also: ms_fragmentationrules::getFirstSeries()

Returns: The last usable series number. More series may be added in later versions of Mascot, and using this function may allow code to be made 'future proof'.

◆ getMaxInternalMass()

double getMaxInternalMass ( ) const

Returns the maximum mass to be considered for internal fragments.

Introduced in Mascot 2.2, the values for minimum and maximum internal masses are specified in the fragmentation_rules file as

   minInternalMass 0.0
   maxInternalMass 700.0

These are the masses used for the FRAG_INTERNAL_YB and FRAG_INTERNAL_YA series.

Returns: The maximum internal mass to be considered for this instrument.

◆ getMinInternalMass()

double getMinInternalMass ( ) const

Returns the minimum mass to be considered for internal fragments.

Introduced in Mascot 2.2, the values for minimum and maximum internal masses are specified in the fragmentation_rules file as

   minInternalMass 0.0
   maxInternalMass 700.0

These are the masses used for the FRAG_INTERNAL_YB and FRAG_INTERNAL_YA series.

Returns: The minimum internal mass to be considered for this instrument.

◆ 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

◆ getSeriesDescription()

std::string getSeriesDescription ( const int series )

static

Returns a description string for a given series.

Parameters

series must be a number between getFirstSeries() and getLastSeries() inclusive.

Returns: series description

◆ getSeriesName()

std::string getSeriesName ( const int series )

static

Returns a short series name.

Parameters

series must be a number between getFirstSeries() and getLastSeries() inclusive.

Returns: series name

◆ getTitle()

std::string getTitle ( ) const

Returns the title of the instrument.

This is obtained from the

title:

line in the fragmentation_rules file.

Returns: The title.

◆ getTotalSeriesOutput()

int getTotalSeriesOutput ( )

static

Returns the length of the series string output in a Mascot results file.

See also: ms_peptide::getVarModsStr()

Returns: the number of series that output for each peptide in the Mascot results file.

◆ isBackboneSeries()

bool isBackboneSeries ( const int series )

static

Returns true if the series is a 'backbone' fragment.

Parameters

series must be a number between getFirstSeries() and getLastSeries() inclusive.

Returns: true if the series is A, B, Y, C, X, Z, Z+1, Z+2 or loss of water or NH3 from A,B or Y.

◆ isCharged2Plus()

bool isCharged2Plus ( ) const

Returns true if the 'doubly charged 2+' fragmentation rule is specified.

Returns: true if rule 2, doubly charged if precursor 2+ or higher is specified and therefore 2+ ions, for the specified series (not internal or immonium) are to be considered.

◆ isCharged3Plus()

bool isCharged3Plus ( ) const

Returns true if the 'doubly charged 3+' fragmentation rule is specified.

Returns: true if rule 3, doubly charged if precursor 3+ or higher is specified and therefore 2+ ions, for the specified series (not internal or immonium) are to be considered.

◆ isNeutralLossSeries()

bool isNeutralLossSeries ( const int series )

static

Returns true if the series is a 'neutral loss' series.

Parameters

series must be a number between getFirstSeries() and getLastSeries() inclusive.

Returns: true if the series is loss of water or NH3 from A,B or Y.

◆ isSeriesUsed()

bool isSeriesUsed ( const int series ) const

Returns true if a given series is specified for the instrument.

Currently supported series are (FRAG_SERIES_TYPE):

4 - immonium ions
5 - 'a' ions
6 - 'a-NH3' or 'a*' ions
7 - 'a-H2O' or 'a0' ions
8 - 'b' ions
9 - 'b-NH3' or 'b*' ions
10 - 'b-H2O' or 'b0' ions
11 - 'c' ions
12 - 'x' ions
13 - 'y' ions
14 - 'y-NH3' or 'y*' ions
15 - 'y-H2O' or 'y0' ions
16 - 'z' ions
17 - internal fragments 'yb'
18 - internal fragments 'ya'
21 - 'z+1' ions
22 - high-energy 'd' ions
23 - high-energy 'v' ions
24 - high-energy 'w' ions
25 - 'z+2' ions

In addition, two more rules may be specified:

19 - 'y' or 'y++' series presense must be significant
20 - 'y' or 'y++' must be highest scoring series

Parameters

series must be a number between getFirstSeries() and getLastSeries() inclusive.

Returns: true if the series if used, false otherwise

◆ isSinglyCharged()

bool isSinglyCharged ( ) const

Returns true if the 'singly charged' fragmentation rule is specified.

Returns: true if rule 1 singly charged ions is specified and therefore 1+ ions, for the specified series are to be considered.

◆ isValid()

bool isValid ( ) const

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

The verifyRule() function will generally be more useful.

Returns: true if the series and masses are consistent, false otherwise

◆ operator=()

ms_fragmentationrules & operator= ( const ms_fragmentationrules & right )

Assignment operator.

Parameters

right is the fragmentation rules to copy from.

Returns: reference to the current object

◆ setCharged2Plus()

void setCharged2Plus ( const bool value )

Change the availability the of 'doubly charged 2+' fragmentation rule.

Parameters

value should be set to true if rule 2, doubly charged if precursor 2+ or higher is to be specified and therefore 2+ ions, for the specified series (not internal or immonium) are to be considered.

◆ setCharged3Plus()

void setCharged3Plus ( const bool value )

Change the availability the of 'doubly charged 3+' fragmentation rule.

Parameters

value should be set to true if rule 3, doubly charged if precursor 3+ or higher is to be specified and therefore 2+ ions, for the specified series (not internal or immonium) are to be considered.

◆ 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

◆ setMaxInternalMass()

void setMaxInternalMass ( const double mass )

Sets the maximum mass to be considered for internal fragments.

Introduced in Mascot 2.2, the values for minimum and maximum internal masses are specified in the fragmentation_rules file as

   minInternalMass 0.0
   maxInternalMass 700.0

These are the masses used for the FRAG_INTERNAL_YB and FRAG_INTERNAL_YA series.

Parameters

mass	The new maximum internal mass to be considered for this instrument.

◆ setMinInternalMass()

void setMinInternalMass ( const double mass )

Set the minimum mass to be considered for internal fragments.

Introduced in Mascot 2.2, the values for minimum and maximum internal masses are specified in the fragmentation_rules file as

   minInternalMass 0.0
   maxInternalMass 700.0

These are the masses used for the FRAG_INTERNAL_YB and FRAG_INTERNAL_YA series.

Parameters

mass	The new minimum internal mass to be considered for this instrument.

◆ 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.

◆ setSeriesUsed()

void setSeriesUsed	(	const int	series,
		const bool	val
	)

Sets availability on a given series.

See isSeriesUsed() for a list of available series.

Parameters

series	must be a number between getFirstSeries() and getLastSeries() inclusive.
val	is a boolean value to specify whether the series should be considered.

Examples: config_fragrules.cpp.

◆ setSinglyCharged()

void setSinglyCharged ( const bool value )

Change the availability of the 'singly charged' fragmentation rule.

Parameters

value should be set to true if rule 1 (singly charged ions) are to be considered.

◆ setTitle()

void setTitle ( const char * title )

Assigns a new title to the rule.

Parameters

title is the new title.

◆ 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

◆ verifyRule()

bool verifyRule	(	ms_errs *	errObj,
		const bool	tryToFix
	)

Tries to detect any inconsistencies in the instrument definition.

This method tries to detect any inconsistencies and to fix some of them.

When tryToFix is set to true will force the method to try and fix the instrument definition and return a success code. In this case, error descriptions for the problems detected (and fixed) will be accumulated in errObj.

For example, if the FRAG_A_MINUS_NH3 series is specified, and FRAG_A_SERIES isn't specified, then, if tryToFix is specified, FRAG_A_SERIES will be added, and the ms_errs::ERR_MSP_FRAGMENTATION_RULES error will be added to the errObj list.

Parameters

errObj	error-object to store error messages.
tryToFix	if true, try to fix any problems encountered.

Returns: always true, errors are set if something is wrong

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

ms_fragmentationrules.hpp
ms_fragmentationrules.cpp

Public Types

Public Member Functions

Static Public Member Functions

Detailed Description

Member Enumeration Documentation

◆ FRAG_SERIES_TYPE

Constructor & Destructor Documentation

◆ ms_fragmentationrules()

◆ ~ms_fragmentationrules()

Member Function Documentation

◆ anyNLseriesUsed()

◆ appendProperty()

◆ appendText()

◆ clearSeries()

◆ copyFrom()

◆ defaultValues()

◆ delProp()

◆ delPropStart()

◆ findProperty()

◆ findPropertyBeginning()

◆ getDefaultDelimiter()

◆ getDelimiterByNumber()

◆ getFirstSerie()

◆ getFirstSeries()

◆ getLastSerie()

◆ getLastSeries()

◆ getMaxInternalMass()

◆ getMinInternalMass()

◆ getNumberOfProperties()

◆ getPreceedingComments()

◆ getPropertyName()

◆ getPropValStringByName()

◆ getPropValStringByNumber()

◆ getSeriesDescription()

◆ getSeriesName()

◆ getTitle()

◆ getTotalSeriesOutput()

◆ isBackboneSeries()

◆ isCharged2Plus()

◆ isCharged3Plus()

◆ isNeutralLossSeries()

◆ isSeriesUsed()

◆ isSinglyCharged()

◆ isValid()

◆ operator=()

◆ setCharged2Plus()

◆ setCharged3Plus()

◆ setDefaultDelimiter()

◆ setMaxInternalMass()

◆ setMinInternalMass()

◆ setPreceedingComments()

◆ setPropertyName()

◆ setPropValBoolByName()

◆ setPropValCharByName()

◆ setPropValFloatByName()

◆ setPropValInt64ByName()

◆ setPropValIntByName()

◆ setPropValStringByName()

◆ setPropValStringByNumber()

◆ setSeriesUsed()

◆ setSinglyCharged()

◆ setTitle()

◆ uncommentProp()

◆ verifyRule()