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Public Member Functions

ms_modification Class Reference
[Mascot configuration files module]

The class represents a single modification-entry in mod_file. More...

#include <ms_modfile.hpp>

Inheritance diagram for ms_modification:
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List of all members.

Public Member Functions

 ms_modification (const ms_masses *massFile=NULL)
 Default constructor.
 ms_modification (const ms_modification &src)
 Copying constructor.
 ~ms_modification ()
 Destructor.
void appendIgnoreMass (const double massMono, const double massAve)
 Appends a new ignore mass pair.
void appendModifiedResidue (const char residue, const double massMono, const double massAve)
 Adds one more residue that can be modified together with its new mass.
void clearIgnoreMasses ()
 Deletes all ignore-masses.
void clearModifiedResidues ()
 Deletes all residues modified together with their masses and deltas.
void copyFrom (const ms_modification *src)
 Copies modification configuration from another instance.
void copyMassFile (const ms_masses *massFile)
void defaultValues ()
 Re-initialises the object.
double getCTerminusMass (const MASS_TYPE massType) const
 Returns the mass of modified C-terminus.
double getDelta (const MASS_TYPE massType) const
 Returns delta (in Da) value for the given mass type.
bool getFromUnimod (const char *modName, const ms_umod_configfile *umod_file)
 Retrieves modification from the Unimod file object by its mod_file-style name.
double getIgnoreMass (const MASS_TYPE massType, const int idx) const
 Returns the value of the ith ignore mass. See getNumberOfIgnoreMasses() for more explanations.
const ms_massesgetMassFile () const
 Returns a pointer to ms_masses instance held internally.
int getModificationType () const
 Returns the type (or class) of modification.
char getModifiedResidue (const int n) const
 Traverse the modified residues list.
ms_vectorDouble getNeutralLoss (const MASS_TYPE massType) const
 Return neutral loss delta.
ms_vectorBool getNeutralLossRequired () const
 Returns a vector of boolean values (required/not required) for each neutral loss value.
double getNTerminusMass (const MASS_TYPE massType) const
 Returns the mass of modified N-terminus.
int getNumberOfIgnoreMasses () const
 Returns the number of masses to be ignored.
int getNumberOfModifiedResidues () const
 Returns a total number of modified residue for a residue-specific modification.
ms_vectorDouble getPepNeutralLoss (const MASS_TYPE massType) const
 Returns a vector of PepNeutralLoss-values.
std::string getPreceedingComments () const
 Returns any comments preceeding the section.
ms_vectorDouble getReqPepNeutralLoss (const MASS_TYPE massType) const
 Returns a vector of RepPepNeutralLoss-values.
double getResidueMass (const MASS_TYPE massType, const char residue) const
 Returns a mass of modified residue.
std::string getTitle () const
 Returns the modification title.
bool inErrorTolerant () const
 Returns whether this modification should be used in error tolerant searches.
bool inLongList () const
 Returns whether this modification is flagged to appear in the search form long list.
bool inShortList () const
 Returns whether this modification is flagged to appear in the search form short list.
bool isHidden () const
 Returns value of the Hidden parameter.
bool isResidueModified (const char residue) const
 Check a single residue.
bool isSubstitution () const
 Returns TRUE if the modification is derived from the substitutions file.
ms_modificationoperator= (const ms_modification &right)
 C++ style assignment operator.
void setCTerminusMass (const double massMono, const double massAve)
 Sets the mass of modified C-terminus.
void setDelta (const double massMono, const double massAve)
 Changes delta value for the given mass type.
void setHidden (const bool value)
 Sets the value of Hidden parameter.
void setInErrorTolerant (const bool value)
 Sets whether this modification should be used in error tolerant searches.
void setInLongList (const bool value)
 Sets whether this modification is flagged to appear in the search form long list.
void setInShortList (const bool value)
 Sets whether this modification is flagged to appear in the search form short list.
void setMassFile (const ms_masses *massFile)
 Stores pointer to the external ms_masses object to refer later.
void setModificationType (const int type)
 Sets the modification type parameter into the supplied value.
void setNeutralLoss (const ms_vectorDouble massMono, const ms_vectorDouble massAve, const ms_vectorBool required)
 Returns a vector of corresponding frequencies for each neutral loss value.
void setNTerminusMass (const double massMono, const double massAve)
 Sets the mass of modified N-terminus.
void setPepNeutralLoss (const ms_vectorDouble valuesMono, const ms_vectorDouble valuesAve)
 Set the vector of PepNeutralLoss-values.
void setPreceedingComments (const std::string &comments)
 Sets any comments preceeding the section.
void setReqPepNeutralLoss (const ms_vectorDouble valuesMono, const ms_vectorDouble valuesAve)
 Set the vector of RepPepNeutralLoss-values.
void setTitle (const char *value)
 Change the title for the modification.

Detailed Description

The class represents a single modification-entry in mod_file.

Instances of this class are created in ms_modfile when parsing mod_file. It should be used in read-only mode. But if you really want to create a custom modification from scratch then specify modification type and supply the mass file object first and set residue masses or deltas second.

Modifications that only apply to a specific residue at a specific terminus need to be handled with care. An example is the conversion of Methionine to Homoserine lactone. This is defined in mod_file as follows:

   Title:Hse_lact (C-term M)
   ResiduesCterm:M -31.000631 -31.1002

These mods are always processed as variable mods, even if they were originally specified as fixed mods. Mascot Parser implicitly treats them as terminal group mods, so that the return values from Mascot Parser for this modification are as follows:

     ms_modification::getResidueMass(matrix_science::MASS_TYPE_MONO, "M") returns 0
     ms_modification::getDelta(matrix_science::MASS_TYPE_MONO) returns -48.003370665
     ms_modification::isResidueModified("M") returns TRUE
     ms_modification::getCTerminusMass(matrix_science::MASS_TYPE_MONO) returns -31.000631
     ms_masses::getResidueMass(matrix_science::MASS_TYPE_MONO, "M") returns 131.04048
     ms_masses::isResidueModified("M") returns FALSE
     ms_masses::getCtermDelta(matrix_science::MASS_TYPE_MONO) returns 0
     ms_masses::getCterminalMass(matrix_science::MASS_TYPE_MONO) returns 17.002739665

When writing code, you may wish to categorise such cases as residue mods. If so, in the case of Hse_lact, the mass of the modified residue would be the sum of the return values from ms_modification::getDelta() and ms_masses::getResidueMass().

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

More functionality is described in the documentation for ms_customproperty.

Examples:

config_modfile.cpp, and tools_aahelper.cpp.


Constructor & Destructor Documentation

ms_modification ( const ms_masses massFile = NULL )

Default constructor.

Not normally called from client applications.

Parameters:
massFileOptional parameter to specify the source file for this modification.
ms_modification ( const ms_modification src )

Copying constructor.

Not normally called from client applications.

Parameters:
srcreference to an ms_modification object

Member Function Documentation

void appendIgnoreMass ( const double  massMono,
const double  massAve 
)

Appends a new ignore mass pair.

See also:
getNumberOfIgnoreMasses(), getIgnoreMass(), clearIgnoreMasses()
Parameters:
massMonois the mono-isotopic mass of the fragment to be ignored.
massAveis the average mass of the fragment to be ignored.
void appendModifiedResidue ( const char  residue,
const double  massMono,
const double  massAve 
)

Adds one more residue that can be modified together with its new mass.

If you call this method for terminal residue modifications, the supplied masses are ignored, only the modified flag for the residue will be set and the total number of residues will be increased. However, if you need to set modified terminal masses for terminal modifications (residue-specific or not) use setNTerminusMass() and setCTerminusMass().

Parameters:
residueneeds to be a residue A-Z (or a-z).
massMonois the mono-isotopic mass of the modified residue.
massAveis the average mass of the modified residue.
void clearIgnoreMasses (  )

Deletes all ignore-masses.

See also:
getNumberOfIgnoreMasses(), getIgnoreMass(), appendIgnoreMass()
void clearModifiedResidues (  )

Deletes all residues modified together with their masses and deltas.

Values returned by getDelta() and getNeutralLoss() are not cleared.

void copyFrom ( const ms_modification src )

Copies modification configuration from another instance.

Parameters:
srcis the source modification to be copied.
void copyMassFile ( const ms_masses massFile )
Deprecated:
Do not use.
Parameters:
massFilepointer to a ms_masses object
void defaultValues (  )

Re-initialises the object.

Call this member if you want to re-use the instance by resetting all values to defaults.

Reimplemented from ms_customproperty.

double getCTerminusMass ( const MASS_TYPE  massType ) const

Returns the mass of modified C-terminus.

Call this method only for terminal modifications (irrespective of whether it is residue-specific or not). Residue modifications will always return zero.

Parameters:
massTypeshould be matrix_science::MASS_TYPE_MONO or matrix_science::MASS_TYPE_AVE.
Returns:
mass of C-Terminus
double getDelta ( const MASS_TYPE  massType ) const

Returns delta (in Da) value for the given mass type.

By default all values are equal to zero.

Parameters:
massTypeshould be matrix_science::MASS_TYPE_MONO or matrix_science::MASS_TYPE_AVE.
Returns:
difference between unmodified and modified mass.
bool getFromUnimod ( const char *  modName,
const ms_umod_configfile umod_file 
)

Retrieves modification from the Unimod file object by its mod_file-style name.

Parameters:
modNamemodification name in a mod_file style, such as "Acetyl (C)".
umod_filea pointer to a Unimod file object where the modification is retrieved from.
Returns:
TRUE if the modification is successfully retrieved and FALSE if it is not found in the the Unimod file.
double getIgnoreMass ( const MASS_TYPE  massType,
const int  idx 
) const

Returns the value of the ith ignore mass. See getNumberOfIgnoreMasses() for more explanations.

See also:
getNumberOfIgnoreMasses(), clearIgnoreMasses(), appendIgnoreMass()
Parameters:
massTypeshould be matrix_science::MASS_TYPE_MONO or matrix_science::MASS_TYPE_AVE.
idxindex of the mass to be ignored and can be one of 0..(getNumberOfIgnoreMasses()-1).
Returns:
The mass in Daltons.
const ms_masses * getMassFile (  ) const

Returns a pointer to ms_masses instance held internally.

See also:
setMassFile()
Returns:
A pointer to the ms_masses object used. See Maintaining object references: two rules of thumb.
int getModificationType (  ) const

Returns the type (or class) of modification.

By default this is a residue modification.

Returns:
One of the enumeration MOD_TYPES values.
char getModifiedResidue ( const int  n ) const

Traverse the modified residues list.

Parameters:
nresidue number that can be one of 0..(getNumberOfModifiedResidues()-1).
Returns:
a letter encoding an amino acid.
ms_vectorDouble getNeutralLoss ( const MASS_TYPE  massType ) const

Return neutral loss delta.

By default there is no neutral loss for the modification (zero).

Parameters:
massTypeshould be matrix_science::MASS_TYPE_MONO or matrix_science::MASS_TYPE_AVE.
Returns:
A vector of neutral loss values. For example, for phosphorylation three different netutral loss values may be specified.
ms_vectorBool getNeutralLossRequired (  ) const

Returns a vector of boolean values (required/not required) for each neutral loss value.

Returns:
The values in the vector have a one to one correspondence with the values returned by in getNeutralLoss().
double getNTerminusMass ( const MASS_TYPE  massType ) const

Returns the mass of modified N-terminus.

Call this method only for terminal modifications (irrespective of whether it is residue-specific or not). Residue modifications will always return zero.

Parameters:
massTypeshould be matrix_science::MASS_TYPE_MONO or matrix_science::MASS_TYPE_AVE.
Returns:
mass of N-Terminus
int getNumberOfIgnoreMasses (  ) const

Returns the number of masses to be ignored.

If a modification gives rise to intense, predictable non-sequence ion peaks, Mascot can be instructed to ignore these artefacts by means of "ignore masses". Initially, there is no ignore-masses in the list.

Returns:
The number of masses in the 'ignore' list.
int getNumberOfModifiedResidues (  ) const

Returns a total number of modified residue for a residue-specific modification.

By default the internal list of residues is empty.

Returns:
The number of modified residues.
ms_vectorDouble getPepNeutralLoss ( const MASS_TYPE  massType ) const

Returns a vector of PepNeutralLoss-values.

Parameters:
massTypeshould be matrix_science::MASS_TYPE_MONO or matrix_science::MASS_TYPE_AVE.
Returns:
vector of PepNeutralLoss values
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
ms_vectorDouble getReqPepNeutralLoss ( const MASS_TYPE  massType ) const

Returns a vector of RepPepNeutralLoss-values.

Parameters:
massTypeshould be matrix_science::MASS_TYPE_MONO or matrix_science::MASS_TYPE_AVE.
Returns:
vector of RepPepNeutralLoss values
double getResidueMass ( const MASS_TYPE  massType,
const char  residue 
) const

Returns a mass of modified residue.

Only modified residues will have non-zero mass. So, the default value returned by this function is zero.

Parameters:
massTypeshould be matrix_science::MASS_TYPE_MONO or matrix_science::MASS_TYPE_AVE.
residuea letter encoding an amino acid.
Returns:
modification delta + absolute mass of the residue, in Daltons, or 0 if the residue is not modified.
std::string getTitle (  ) const

Returns the modification title.

A text string that is used to identify the modification in forms and reports. By default this is empty.

Returns:
The title.
Examples:
config_modfile.cpp, and tools_aahelper.cpp.
bool isHidden (  ) const

Returns value of the Hidden parameter.

If you wish to include modifications in mod_file without having them appear in a search form, the property Hidden should be set to TRUE.

By default this is not hidden.

Returns:
TRUE is the modification is hidden.
bool isResidueModified ( const char  residue ) const

Check a single residue.

By default FALSE is returned for each residue, meaning "residue not modified".

Parameters:
residuea letter encoding an amino acid.
Returns:
TRUE if the residue is modified.
bool isSubstitution (  ) const

Returns TRUE if the modification is derived from the substitutions file.

If the modification is AA-substitution then this method will return TRUE.

Returns:
true if the modification is from substitution
ms_modification & operator= ( const ms_modification right )

C++ style assignment operator.

Parameters:
rightis the source modification to be copied.
Returns:
reference to the current object
void setCTerminusMass ( const double  massMono,
const double  massAve 
)

Sets the mass of modified C-terminus.

The method only has an effect for c-terminus modifications. This method will also override the delta value depending on the terminus mass supplied with the mass file object. However, if the mass file object has some fixed modifications applied, the delta will reflect this fact (not the terminus mass itself).

Parameters:
massMonomass mono-isotopic
massAveaverage mass
void setDelta ( const double  massMono,
const double  massAve 
)

Changes delta value for the given mass type.

By default all values are equal to zero.

Parameters:
massMonois the delta using 12C monoisotopic masses.
massAveis the delta using average masses.
void setHidden ( const bool  value )

Sets the value of Hidden parameter.

If you wish to include modifications in mod_file without having them appear in a search form, the property Hidden should be set to TRUE.

By default this is not hidden.

Parameters:
valueshould be set to TRUE if the modification is to be hidden.
Examples:
config_modfile.cpp.
void setMassFile ( const ms_masses massFile )

Stores pointer to the external ms_masses object to refer later.

If no external ms_masses instance is supplied, then the modification object will create an internal ms_masses instance filled with default values. Create an instance of ms_masses class, call its ms_masses::read_file() member and then call this function to supply the instance as a parameter. Alternatively, you can use copyMassFile() for content copying instead of pointer-copying.

Remember to keep massFile in memory for as long as you use this class object. See Memory management conventions.

Parameters:
massFilemust be a valid pointer to an ms_masses object. See Maintaining object references: two rules of thumb.
void setModificationType ( const int  type )

Sets the modification type parameter into the supplied value.

Parameters:
typeshould be one of the MOD_TYPES values.
void setNeutralLoss ( const ms_vectorDouble  massMono,
const ms_vectorDouble  massAve,
const ms_vectorBool  required 
)

Returns a vector of corresponding frequencies for each neutral loss value.

Change neutral loss delta.

All three arrays must be the same length or the function will fail.

Parameters:
massMonois an array of mono-isotopic mass neutral losses.
massAveis an array of average mass neutral losses.
requiredis an array of booleans to specify if fragments with the loss must be seen for the series to be scored.
void setNTerminusMass ( const double  massMono,
const double  massAve 
)

Sets the mass of modified N-terminus.

The method only has an effect for n-terminus modifications. This method will also override the delta value depending on the terminus mass supplied with the mass file object. However, if the mass file object has some fixed modifications applied, the delta will reflect this fact (not the terminus mass itself).

Parameters:
massMonomass mono-isotopic
massAveaverage mass
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:
commentsany comments preceeding the section
void setTitle ( const char *  value )

Change the title for the modification.

See getTitle() for more information.

Parameters:
valueis a string value for the new title.

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