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	clearSeries ()
	Deletes all series usage information.
void	copyFrom (const ms_fragmentationrules *right)
	Copies all information from another instance of the class.
void	defaultValues ()
	Initialises the instance with default values.
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.
std::string	getPreceedingComments () const
	Returns any comments preceeding the section.
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	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	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	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

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 ( )

Default constructor is used to create an empty object.

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

~ms_fragmentationrules ( )

Destructor.

Frees all memory allocated for the object.

Member Function Documentation

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.

void clearSeries ( )

Deletes all series usage information.

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

void copyFrom ( const ms_fragmentationrules * right )

Copies all information from another instance of the class.

Parameters:

right is the fragmentation rules to copy from.

void defaultValues ( )

Initialises the instance with default values.

Sets all series to be unused.

Reimplemented from ms_customproperty.

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.

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.

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'.

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'.

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.

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.

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

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

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

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.

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.

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.

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.

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.

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.

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

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.

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

ms_fragmentationrules & operator= ( const ms_fragmentationrules & right )

Assignment operator.

Parameters:

right is the fragmentation rules to copy from.

Returns:: reference to the current object

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.

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.

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.

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.

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

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.

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.

void setTitle ( const char * title )

Assigns a new title to the rule.

Parameters:

title is the new title.

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

ms_fragmentationrules Class Reference [Mascot configuration files module]

Public Types

Public Member Functions

Static Public Member Functions

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

ms_fragmentationrules Class Reference
[Mascot configuration files module]