Matrix Science header
Public Member Functions

ms_masses Class Reference
[Mascot configuration files module]

Reads and parses the masses file with residue and atom masses. More...

#include <ms_masses.hpp>

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List of all members.

Public Member Functions

 ms_masses ()
 Default constructor.
 ms_masses (const ms_masses &src)
 Copying constructor.
 ms_masses (const ms_umod_configfile &src, const ms_quant_component &quantComp)
 Constructor for prepared isotope-substituted version of masses.
 ms_masses (const char *filename, const matrix_science::ms_connection_settings *cs=0)
 Reads the file immediately after the construction.
 ms_masses (const ms_umod_configfile &src, bool addMissingResidueMasses=true)
 Copying constructor.
 ~ms_masses ()
 Destructor.
void appendErrors (const ms_errors &src)
 Copies all errors from another instance and appends them at the end of own list.
ms_modvector applyFixedMods (const ms_modvector *mods, ms_errs *err)
 Change residue masses according to the list of fixed modifications.
void applyIsotopes (const ms_umod_configfile *umodFile, const ms_quant_component *quantComp)
 Update masses of amino-acids with isotope substitution.
void clearAllErrors ()
 Remove all errors from the current list of errors.
void copyFrom (const ms_masses *right)
 Copies masses from another instance.
void copyFrom (const ms_umod_configfile *right, bool addMissingResidueMasses=true)
 Copies masses from a Unimod file.
void copyFrom (const ms_errors *right)
 Use this member to make a copy of another instance.
void defaultValues (bool useDefaultResidueMasses=true)
 Use this member to re-initialise internal members.
double getCarbonMass (const matrix_science::MASS_TYPE massType) const
 Returns a carbon(C) atom mass for a given mass type (MONO or AVE).
matrix_science::ms_connection_settings getConnectionSettings () const
 Returns the sessionID and proxy server for use with an HTTP transfer.
double getCtermDelta (const matrix_science::MASS_TYPE massType) const
 Returns C-term modification delta if there is a correspondent fixed modification applied.
double getCterminalMass (const matrix_science::MASS_TYPE massType) const
 Returns C-terminal group mass (i.e. fixed modification delta or OH-mass).
double getCtermNeutralLoss (const matrix_science::MASS_TYPE massType) const
 Returns C-term neutral loss value if there is a correspondent fixed modification applied.
double getElectronMass () const
 Returns an electron mass.
const ms_errsgetErrorHandler () const
 Retrive the error object using this function to get access to all errors and error parameters.
std::string getFileName () const
 Returns a file name set before or by default.
double getFragResidueMass (const matrix_science::MASS_TYPE massType, const char residue) const
 Returns a residue mass with neutral loss after applying fixed modifications.
double getHydrogenMass (const matrix_science::MASS_TYPE massType) const
 Returns a hydrogen (H) atom mass for a given mass type (MONO or AVE).
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.
double getNitrogenMass (const matrix_science::MASS_TYPE massType) const
 Returns a nitrogen (N) atom mass for a given mass type (MONO or AVE).
double getNtermDelta (const matrix_science::MASS_TYPE massType) const
 Returns N-term modification delta if there is a correspondent fixed modification applied.
double getNterminalMass (const matrix_science::MASS_TYPE massType) const
 Returns N-terminal group mass (i.e. fixed modification delta or H-mass).
double getNtermNeutralLoss (const matrix_science::MASS_TYPE massType) const
 Returns N-term neutral loss value if there is a correspondent fixed modification applied.
double getOxygenMass (const matrix_science::MASS_TYPE massType) const
 Returns a oxygen (O) atom mass for a given mass type (MONO or AVE).
double getResidueMass (const matrix_science::MASS_TYPE massType, const char residue) const
 Returns a mass for a given amino acid.
bool isResidueModified (const char residue) const
 Returns true for residues modified by fixed modifications.
bool isSame (const ms_masses &other, const MASS_TYPE massType) const
 Return true if other ms_masses is the same as this one.
bool isValid () const
 Call this function to determine if there have been any errors.
ms_massesoperator= (const ms_masses &right)
 C++ style assignment operator.
void read_file ()
 Reads the configuration file, parses it and fill the mass arrays.
void save_file ()
 Saves the information back to the file.
void setCarbonMass (const double massMono, const double massAve)
 Changes carbon mass values.
void setConnectionSettings (const matrix_science::ms_connection_settings &cs)
 Sets the sessionID and proxy server for use with an HTTP transfer.
void setCtermModification (const double monoDelta, const double aveDelta, const double monoNeutralLoss=0.0, const double aveNeutralLoss=0.0)
 Set C-term modification.
void setElectronMass (const double mass)
 Changes oxygen mass values.
void setFileName (const char *name)
 Set a custom file name instead of ../config/masses.
void setHydrogenMass (const double massMono, const double massAve)
 Changes hydrogen mass values.
void setNitrogenMass (const double massMono, const double massAve)
 Changes nitrogen mass values.
void setNtermModification (const double monoDelta, const double aveDelta, const double monoNeutralLoss=0.0, const double aveNeutralLoss=0.0)
 Set N-term modification.
void setOxygenMass (const double massMono, const double massAve)
 Changes oxygen mass values.
void setResidueMasses (const char residue, const double massMono, const double massAve)
 Changes mass values for a single residue.
void setResidueModification (const double monoDelta, const double aveDelta, const double monoNeutralLoss, const double aveNeutralLoss, const char *residues)
 Applies a single residue modification.

Detailed Description

Reads and parses the masses file with residue and atom masses.

After reading a file and before using the object, check its validity by calling isValid() and retrieve error descriptions with getLastErrorString() if not valid.

A class instance can be used even if the configuration file has been read with problems or not read at all. Default values will be given to all members in that case.

Examples:

config_masses.cpp, config_modfile.cpp, and tools_aahelper.cpp.


Constructor & Destructor Documentation

ms_masses (  )

Default constructor.

Sets default mass values for all residues

ms_masses ( const ms_masses src )

Copying constructor.

Parameters:
srcis the source object to copy masses from
ms_masses ( const ms_umod_configfile src,
bool  addMissingResidueMasses = true 
)

Copying constructor.

Implemented by calling copyFrom(const ms_umod_configfile *, bool)

Parameters:
srchas the residue and elemental masses that are used to initialise the masses
addMissingResidueMassesis used to specify whether residue masses missing from the src should be set to zero or set to the default masses. If true, then default masses are used and if false, then any missing masses are just set to zero.
ms_masses ( const ms_umod_configfile src,
const ms_quant_component quantComp 
)

Constructor for prepared isotope-substituted version of masses.

Masses of amino-acids are re-calculated with a different isotope applied (for example, 13C instead of C).

Parameters:
srca Unimod file object containing the composition of amino acids and original masses.
quantCompa quantitation component containing isotope substitutions used in the quantitation experiment. This object can be created from scratch without reading its content from a file, but normally it should be taken from the quantitation method selected by a user. An alternative way to apply isotope substition is to use applyIsotopes() method.
ms_masses ( const char *  filename,
const matrix_science::ms_connection_settings cs = 0 
)

Reads the file immediately after the construction.

Parameters:
filenamecan be either a local file path or a Mascot server URL, it cannot be an empty string or NULL pointer. If it is a URL it should be of the form http://your-server/mascot/cgi .
csis a pointer to the connection settings. This should contain a sessionID and optionally the proxy server settings.

Member Function Documentation

void appendErrors ( const ms_errors src ) [inherited]

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

Parameters:
srcThe object to copy the errors across from. See Maintaining object references: two rules of thumb.
ms_modvector applyFixedMods ( const ms_modvector mods,
ms_errs err 
)

Change residue masses according to the list of fixed modifications.

If you want to get the original (unmodified) masses of amino acids, load them from a file or obtain from another instance of the class.

Fixed modifications can also be applied separately using setNtermModification(), setCtermModification() and setResidueModification().

Parameters:
modsis the vector of modifications to apply
erris used to collect the errors. To add any errors to the ms_masses object, pass this->getErrorHandler()
Returns:
the new list of modifications
void applyIsotopes ( const ms_umod_configfile umodFile,
const ms_quant_component quantComp 
)

Update masses of amino-acids with isotope substitution.

Call this method explictly in order to re-calculate all amino acid masses according to a selected quantitation method. However, the quantitation component object can also be created on the fly with any custom isotope substitution. All applied fixed modifications are cancelled and should be re-applied if necessary with applyFixedMods() method.

Parameters:
umodFilea Unimod file object containing chemical composition of amino acids and element masses.
quantCompa quantitation component object with isotope substitution information. If the object doesn't have any isotope elements in it no action will be taken.
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 copyFrom ( const ms_errors right ) [inherited]

Use this member to make a copy of another instance.

Parameters:
rightis the source to initialise from
void copyFrom ( const ms_masses right )

Copies masses from another instance.

Parameters:
rightis the source masses object
void copyFrom ( const ms_umod_configfile right,
bool  addMissingResidueMasses = true 
)

Copies masses from a Unimod file.

Parameters:
righta pointer to unimod file object to copy the masses from.
addMissingResidueMassesis used to specify whether residue masses missing from right should be set to zero or set to the default masses. If true, then default masses are used and if false, then any missing masses are just set to zero.
void defaultValues ( bool  useDefaultResidueMasses = true )

Use this member to re-initialise internal members.

Called internally, but may also be used by other applications

Parameters:
useDefaultResidueMassesshould be set to true if the residue masses are to be initialised with default values. Otherwise they will all be set to mass zero.
double getCarbonMass ( const matrix_science::MASS_TYPE  massType ) const

Returns a carbon(C) atom mass for a given mass type (MONO or AVE).

Parameters:
massTypeone of two mass types (MASS_TYPE_MONO or MASS_TYPE_AVE).
Returns:
the mass of carbon
matrix_science::ms_connection_settings getConnectionSettings (  ) const

Returns the sessionID and proxy server for use with an HTTP transfer.

See also the constructor documentation and setConnectionSettings().

Returns:
The current connection settings.
double getCtermDelta ( const matrix_science::MASS_TYPE  massType ) const

Returns C-term modification delta if there is a correspondent fixed modification applied.

See also:
getCterminalMass()
Parameters:
massTypeone of two mass types (MASS_TYPE_MONO or MASS_TYPE_AVE).
Returns:
the delta compared to an unmodified C terminus mass
double getCterminalMass ( const matrix_science::MASS_TYPE  massType ) const

Returns C-terminal group mass (i.e. fixed modification delta or OH-mass).

See also:
getCtermDelta()
Parameters:
massTypeone of two mass types (MASS_TYPE_MONO or MASS_TYPE_AVE).
Returns:
the C terminus mass, including any applied modification
double getCtermNeutralLoss ( const matrix_science::MASS_TYPE  massType ) const

Returns C-term neutral loss value if there is a correspondent fixed modification applied.

See also:
getCterminalMass()
Parameters:
massTypeone of two mass types (MASS_TYPE_MONO or MASS_TYPE_AVE).
Returns:
the delta compared to an unmodified C terminus mass
double getElectronMass (  ) const

Returns an electron mass.

Returns:
the mass of an electron
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.
std::string getFileName (  ) const

Returns a file name set before or by default.

See also:
setFileName()
Returns:
the name of the masses file
double getFragResidueMass ( const matrix_science::MASS_TYPE  massType,
const char  residue 
) const

Returns a residue mass with neutral loss after applying fixed modifications.

Parameters:
massTypeone of two mass types (MASS_TYPE_MONO or MASS_TYPE_AVE).
residuea single letter encoding an amino acid in the range a..z or A..Z.
Returns:
an absolute fragment for the amino acid.
double getHydrogenMass ( const matrix_science::MASS_TYPE  massType ) const

Returns a hydrogen (H) atom mass for a given mass type (MONO or AVE).

Parameters:
massTypeone of two mass types (MASS_TYPE_MONO or MASS_TYPE_AVE).
Returns:
the mass of hydrogen
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.
double getNitrogenMass ( const matrix_science::MASS_TYPE  massType ) const

Returns a nitrogen (N) atom mass for a given mass type (MONO or AVE).

Parameters:
massTypeone of two mass types (MASS_TYPE_MONO or MASS_TYPE_AVE).
Returns:
the mass of nitrogen
double getNtermDelta ( const matrix_science::MASS_TYPE  massType ) const

Returns N-term modification delta if there is a correspondent fixed modification applied.

See also:
getNterminalMass()
Parameters:
massTypeone of two mass types (MASS_TYPE_MONO or MASS_TYPE_AVE).
Returns:
the delta compared to an unmodified N terminus mass
double getNterminalMass ( const matrix_science::MASS_TYPE  massType ) const

Returns N-terminal group mass (i.e. fixed modification delta or H-mass).

See also:
getNtermDelta()
Parameters:
massTypeone of two mass types (MASS_TYPE_MONO or MASS_TYPE_AVE).
Returns:
the N terminus mass, including any applied modification
double getNtermNeutralLoss ( const matrix_science::MASS_TYPE  massType ) const

Returns N-term neutral loss value if there is a correspondent fixed modification applied.

Parameters:
massTypeone of two mass types (MASS_TYPE_MONO or MASS_TYPE_AVE).
Returns:
any neutral loss on the N terminus
double getOxygenMass ( const matrix_science::MASS_TYPE  massType ) const

Returns a oxygen (O) atom mass for a given mass type (MONO or AVE).

Parameters:
massTypeone of two mass types (MASS_TYPE_MONO or MASS_TYPE_AVE).
Returns:
the mass of oxygen
double getResidueMass ( const matrix_science::MASS_TYPE  massType,
const char  residue 
) const

Returns a mass for a given amino acid.

Parameters:
massTypeone of two mass types (MASS_TYPE_MONO or MASS_TYPE_AVE).
residuea single letter encoding an amino acid in the range a..z or A..Z.
Returns:
an absolute mass for the amino acid.
Examples:
config_masses.cpp.
bool isResidueModified ( const char  residue ) const

Returns true for residues modified by fixed modifications.

Parameters:
residuea single letter encoding an amino acid in the range a..z or A..Z.
Returns:
true for residues modified by fixed modifications.
bool isSame ( const ms_masses right,
const MASS_TYPE  massType 
) const

Return true if other ms_masses is the same as this one.

Parameters:
rightis the object to test against
massTypespecifies whether to compare monoisotopic or average masses.
Returns:
true if all the masses are the same
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 is 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_masses & operator= ( const ms_masses right )

C++ style assignment operator.

Only available for C++

Parameters:
rightis the source object
Returns:
a reference to 'this'
void read_file (  )

Reads the configuration file, parses it and fill the mass arrays.

Called from the constructor: ms_masses(const char*, const ms_connection_settings*)

void save_file (  )

Saves the information back to the file.

See also:
setFileName() If the file cannot be opened for writing, an ms_errs::ERR_MSP_FAILED_TO_OPEN_FILE error is added.

Other errors in saving the file use ms_errs::ERR_MSP_FAILED_TO_WRITE_FILE

void setCarbonMass ( const double  massMono,
const double  massAve 
)

Changes carbon mass values.

Parameters:
massMonois the new monoisotopic mass of carbon
massAveis the new average mass of carbon
void setConnectionSettings ( const matrix_science::ms_connection_settings cs )

Sets the sessionID and proxy server for use with an HTTP transfer.

This value would normally be passed in the constructor.

Parameters:
csis the new connection settings.
void setCtermModification ( const double  monoDelta,
const double  aveDelta,
const double  monoNeutralLoss = 0.0,
const double  aveNeutralLoss = 0.0 
)

Set C-term modification.

Warning:
The name of this function and the name of the first two parameters are potentially misleading.
Parameters:
monoDeltais the mass of the CTerminus. If there is no fixed modification, the value passed should be the monoisotopic mass of hydrogen plus the monoisotopic mass of oxygen.
aveDeltais the mass of the CTerminus. If there is no fixed modification, the value passed should be the average mass of hydrogen plus the average mass of oxygen.
monoNeutralLossis the neutral loss of any fixed C terminus modification.
aveNeutralLossis the neutral loss of any fixed C terminusmodification.
void setElectronMass ( const double  mass )

Changes oxygen mass values.

Parameters:
massis the new monoisotopic mass of an electron
void setFileName ( const char *  name )

Set a custom file name instead of ../config/masses.

Does not re-read the file, just saves the new name

See also:
getFileName()
read_file()
Parameters:
nameis the new file name
void setHydrogenMass ( const double  massMono,
const double  massAve 
)

Changes hydrogen mass values.

Parameters:
massMonois the new monoisotopic mass of hydrogen
massAveis the new average mass of hydrogen
void setNitrogenMass ( const double  massMono,
const double  massAve 
)

Changes nitrogen mass values.

Parameters:
massMonois the new monoisotopic mass of nitrogen
massAveis the new average mass of nitrogen
void setNtermModification ( const double  monoDelta,
const double  aveDelta,
const double  monoNeutralLoss = 0.0,
const double  aveNeutralLoss = 0.0 
)

Set N-term modification.

Warning:
The name of this function and the name of the first two parameters are potentially misleading.
Parameters:
monoDeltais the mass of the NTerminus. If there is no fixed modification, the value passed should be the monoisotopic mass of hydrogen.
aveDeltais the mass of the NTerminus. If there is no fixed modification, the value passed should be the average mass of hydrogen.
monoNeutralLossis the neutral loss of any fixed N terminus modification.
aveNeutralLossis the neutral loss of any fixed N terminus modification.
void setOxygenMass ( const double  massMono,
const double  massAve 
)

Changes oxygen mass values.

Parameters:
massMonois the new monoisotopic mass of oxygen
massAveis the new average mass of oxygen
void setResidueMasses ( const char  residue,
const double  massMono,
const double  massAve 
)

Changes mass values for a single residue.

Parameters:
residuea single letter encoding an amino acid in the range a..z or A..Z.
massMonois the new monoisotopic mass for the residue
massAveis the new average mass for the residue
void setResidueModification ( const double  monoDelta,
const double  aveDelta,
const double  monoNeutralLoss,
const double  aveNeutralLoss,
const char *  residues 
)

Applies a single residue modification.

Parameters:
monoDeltais the delta in daltons for monoisotopic masses
aveDeltais the delta in daltons for average masses
monoNeutralLossis the neutral loss for monoisotopic masses (typically zero)
aveNeutralLossis the neutral loss for average masses (typically zero)
residuesis a null terminated string with one or more letters which encoding amino acids in the range a..z or A..Z.

The documentation for this class was generated from the following files:
Copyright © 2016 Matrix Science Ltd.  All Rights Reserved. Generated on Fri Jun 2 2017 01:44:53