ms_spectral_lib_peak_list Class Reference [Mascot utilities and tools module]

This class is used to encapsulate a peak list from a single spectrum in a NIST .msp or a SpectraST .sptxt file. More...

#include <ms_spectral_lib_peak_list.hpp>

Inheritance diagram for ms_spectral_lib_peak_list:

Collaboration diagram for ms_spectral_lib_peak_list:

List of all members.

Public Types
enum	PEAK_ANNOTATION_LEVEL {   ANNOT_LVL_NONE,   ANNOT_LVL_QUESTION_MARKS,   ANNOT_LVL_SOME_PEAKS,   ANNOT_LVL_CANNOT_ANNOTATE }
	Amount of annotation as returned by getAnnotationLevel() More...
Public Member Functions
	ms_spectral_lib_peak_list ()
	Constructor.
	ms_spectral_lib_peak_list (const ms_spectral_lib_peak_list &src)
	Copying constructor.
	ms_spectral_lib_peak_list (std::vector< std::string > input, ms_spectral_lib::FILE_FORMAT format)
	Constructor from a peak list in NIST format.
	~ms_spectral_lib_peak_list ()
	Destructor.
void	addPeaks (const std::vector< double > &vecMz, const std::vector< double > &vecIntensity)
	add peaks from masses and intensities
void	annotatePeaks (const ms_fragmentvector *fragments, const double fragmentToleranceValue, const std::string fragmentToleranceUnit, double precursorMz)
	annotate peaks for the given tolerance.
void	annotatePeaks (const std::vector< ms_fragment > *fragments, const double fragmentToleranceValue, const std::string fragmentToleranceUnit, double precursorMz)
	annotate peaks for the given tolerance, from a C++ vector.
void	appendErrors (const ms_errors &src)
	Copies all errors from another instance and appends them at the end of own list.
std::vector< std::string >	asText (ms_spectral_lib::FILE_FORMAT format) const
	Return the whole peak list as an array of strings.
void	clearAllErrors ()
	Remove all errors from the current list of errors.
void	clearAnnotation ()
	Removes all annotation from all peaks.
void	copyFrom (const ms_errors *right)
	Use this member to make a copy of another instance.
void	copyFrom (const ms_spectral_lib_peak_list *right)
	Use this member to make a copy of another instance.
std::string	getChecksum () const
	Return the 'checksum' for the original peak list before any calls to annotatePeaks.
const ms_errs *	getErrorHandler () const
	Retrive the error object using this function to get access to all errors and error parameters.
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	getNumPeaks () const
	Returns the number of peaks in the peak list.
const ms_spectral_lib_peak *	getPeak (const int pkNum) const
	Return a single peak.
PEAK_ANNOTATION_LEVEL	getPeakAnnotationLevel () const
	Return information about the amount of peak annotation - i.e. what experimental peaks matched to calculated peaks.
bool	isValid () const
	Call this function to determine if there have been any errors.
ms_spectral_lib_peak_list &	operator= (const ms_spectral_lib_peak_list &right)
	C++ style assignment operator.
void	setAnnotationLevel (PEAK_ANNOTATION_LEVEL level)

---

Detailed Description

This class is used to encapsulate a peak list from a single spectrum in a NIST .msp or a SpectraST .sptxt file.

---

Member Enumeration Documentation

enum PEAK_ANNOTATION_LEVEL

Amount of annotation as returned by getAnnotationLevel()

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

See ms_spectral_lib_peak::getAnnotation for a description of the annotation format.

Most files supplied by NIST have annotation, but PRIDE files don't have any annotation.

Enumerator:

ANNOT_LVL_NONE	None of the peaks have any annotation.
ANNOT_LVL_QUESTION_MARKS	In Parser 2.6.0, when calling ms_spectral_lib_file::saveAs(), the resulting file adds "?" to each peak without annotation. At least one peak has a question mark, and none have any 'matching' annotation.
ANNOT_LVL_SOME_PEAKS	One or more peaks have annotation that is not just a "?".
ANNOT_LVL_CANNOT_ANNOTATE	A call to ms_spectral_lib_entry::annotatePeaks() or ms_spectral_lib_peak_list::annotatePeaks() failed to annotate the peak list.

---

Constructor & Destructor Documentation

ms_spectral_lib_peak_list	(	std::vector< std::string >	input,
		ms_spectral_lib::FILE_FORMAT	format
	)

Constructor from a peak list in NIST format.

An ms_spectral_lib_peak_list object is nomally created by calling ms_spectral_lib_entry::getPeakListObject rather than calling this constructor which simply creates the ms_spectral_lib_peak objects using this constructor.

Leading and trailing white space is removed from each line.

Any format errors will be set in this object and isValid() will then return false.

Parameters:

input	is a vector or raw strings from the .msp file.
format	is one of the ms_spectral_lib::FILE_FORMAT values.

ms_spectral_lib_peak_list

(

const ms_spectral_lib_peak_list &

src )

Copying constructor.

Parameters:

src	is the source to initialise from

---

Member Function Documentation

void addPeaks	(	const std::vector< double > &	vecMz,
		const std::vector< double > &	vecIntensity
	)

add peaks from masses and intensities

Note that both vectors MUST have the same size.

Existing peaks are not removed.

Parameters:

vecMz	vector of m/z values
vecIntensity	vector of intensity values

void annotatePeaks	(	const ms_fragmentvector *	fragments,
		const double	fragmentToleranceValue,
		const std::string	fragmentToleranceUnit,
		double	precursorMz
	)

annotate peaks for the given tolerance.

See also:

annotatePeaks(const std::vector<ms_fragment> *fragments, const double fragmentToleranceValue, const std::string fragmentToleranceUnit, double precursorMz)

Parameters:

fragments	to a vector of fragments to be used for annotation
fragmentToleranceValue	fragment tolerance as a double
fragmentToleranceUnit	fragment tolerance unit (ppm, %, mmu or Da)
precursorMz	m/z value of the precursor, used to annotate a peak with a p class (p for precursor)

void annotatePeaks	(	const std::vector< ms_fragment > *	fragments,
		const double	fragmentToleranceValue,
		const std::string	fragmentToleranceUnit,
		double	precursorMz
	)

annotate peaks for the given tolerance, from a C++ vector.

Annotate the peaks stored in the object according to the NIST format, if the provided format is different, the NIST format will still be used. The existing annotation on peaks is overriden. All annotations are between double quotes.

Note that default values are used for the mass of Nitrogen, Helium, Oxygen and Carbon, the mono-isotopic type of these values are used. If a peak cannot be encoded in MSP format (for example for w ion series), or if there is no matching fragment, the annotation of the peak will be "?". Ion series c, x and z are not accepted in the MSP format; ion series b, y and y are respectively used instead with a differential neutral loss.

Parameters:

fragments	to a vector of fragments to be used for annotation, it doesn't have to be sorted
fragmentToleranceValue	fragment tolerance as a double
fragmentToleranceUnit	fragment tolerance unit (ppm, %, mmu or Da)
precursorMz	m/z value of the precursor, used to annotate a peak with a p class (p for precursor)

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.

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.

void clearAnnotation

(

)

Removes all annotation from all peaks.

Does not change the file format associated with each peak.

See also ms_spectral_lib_peak::clearAnnotation

void copyFrom

(

const ms_spectral_lib_peak_list *

right )

Use this member to make a copy of another instance.

Parameters:

right

is the source to initialise from

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

std::string getChecksum

(

)

const

Return the 'checksum' for the original peak list before any calls to annotatePeaks.

All spaces, tabs, newlines, carriage returns and quotation marks are removed before calculating the checksum

This is the checksum of the original 'file' entry before any annotations have been added, or format changes made.

For example: aj5r7ovt6b6q4wr7btazzd4s6i

Returns:

the checksum as a string

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.

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.

Reimplemented in ms_mascotresfile.

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()

Reimplemented in ms_mascotresfile.

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.

int getNumPeaks

(

)

const

Returns the number of peaks in the peak list.

Returns:

the number of peaks in the list

const ms_spectral_lib_peak * getPeak

(

const int

pkNum )

const

Return a single peak.

Parameters:

pkNum

must be in the range 1..getNumPeaks()

Returns:

a pointer to the peak object, or 0 if pkNum is out of range

ms_spectral_lib_peak_list::PEAK_ANNOTATION_LEVEL getPeakAnnotationLevel

(

)

const

Return information about the amount of peak annotation - i.e. what experimental peaks matched to calculated peaks.

Returns:

one of the ms_spectral_lib_peak_list::PEAK_ANNOTATION_LEVEL values

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, resfile_summary.cpp, and tools_aahelper.cpp.

ms_spectral_lib_peak_list & operator=

(

const ms_spectral_lib_peak_list &

right )

C++ style assignment operator.

Parameters:

right

is the source to initialise from

Returns:

reference to the current object

void setAnnotationLevel

(

PEAK_ANNOTATION_LEVEL

level )

Parameters:

level

is the new annotation level

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

• ms_spectral_lib_peak_list.hpp
• ms_spectral_lib_peak_list.cpp