ms_searchparams Class Reference [Mascot results file module]

This class encapsulates the search parameters in the mascot results file. More...

#include <ms_mascotresparams.hpp>

List of all members.

Public Types
enum	MULTI_SITE_MODS {   MSM_NOT_PERMITTED = 0x0000,   MSM_EXCLUSIVE_PLUS_VARIABLE = 0x0001 }
	Possible values for MULTI_SITE_MODS. More...
Public Member Functions
	ms_searchparams (const ms_mascotresfile &resfile)
	Either explicitily create an object using this constructor or call ms_mascotresfile.params().
	~ms_searchparams ()
	Should never need to call this destructor directly.
std::string	getACCESSION ()
	This function returns a comma separated list of accession strings.
std::string	getAllUSERParams () const
	Returns all the 'user defined' parameters.
double	getCarbonMass () const
	Returns the mass of carbon as specified in the mascot/config/masses file.
std::string	getCHARGE ()
	Returns the charge state of the peptide masses entered.
std::string	getCLE ()
	Returns the name of the enzyme used for the search.
std::string	getCOM ()
	This is the comment or "Search title" entered by the user in the search form.
std::string	getCROSSLINKING () const
	Returns the name of the crosslinking method used.
double	getCTermMass ()
	Returns the C terminus mass.
std::string	getDATAURL ()
	Returns the URL of the uploaded file (if any).
std::string	getDB (int idx=1)
	Returns one of the database names used for the search.
int	getDECOY () const
	Returns a value showing if a decoy database has been searched.
double	getElectronMass () const
	Returns the mass of an electron as specified in the mascot/config/masses file.
bool	getERRORTOLERANT ()
	Returns 'true' for an error tolerant search.
std::string	getErrTolParentFilename ()
	Returns the filename of the 'parent' search for an error tolerant search.
std::string	getFILENAME ()
	Returns the name of the uploaded file (if any).
double	getFixedModsDelta (int num)
	Returns the delta mass for a fixed modification.
std::string	getFixedModsName (int num) const
double	getFixedModsNeutralLoss (int num)
	Returns the neutral loss value for the specified fixed modification.
std::string	getFixedModsResidues (int num) const
	Returns the residues modified for the specified fixed modification.
std::string	getFORMAT ()
	Returns the file format type selected by the user.
std::string	getFORMVER ()
	Returns the version of the form used to submit the search.
double	getHydrogenMass () const
	Returns the mass of nitrogen as specified in the mascot/config/masses file.
bool	getICAT ()
	Returns true if the user selected the ICAT button on the search form.
std::string	getINSTRUMENT ()
	Returns the instrument name that the user selected.
std::string	getINTERMEDIATE ()
	For a repeat search, it may be necessary to know the "parent" search.
std::string	getIT_MODS ()
	Returns a comma separated list of the variable modifications used in a search.
double	getITOL ()
	Returns the tolerance for msms ions.
std::string	getITOLU ()
	Returns the units that the ions tolerance is specified in.
int	getLIBRARY_SEARCH () const
	Returns a value showing if a spectral library has been searched.
double	getLibraryModDelta (int num) const
	Returns the delta mass of the specified spectral library modification.
std::string	getLibraryModName (int num) const
	Returns the name of the specified spectral library modification.
std::string	getLICENSE ()
	Returns the Mascot license string.
std::string	getMASS ()
	Returns whether monoisotopic or average masses have been specified.
MASS_TYPE	getMassType ()
	Returns either MASS_TYPE_MONO or MASS_TYPE_AVE.
double	getMaxInternalMass ()
	Returns the maximum mass to be considered for internal fragments.
double	getMinInternalMass ()
	Returns the minimum mass to be considered for internal fragments.
std::string	getMODS ()
	Returns a comma separated list of the fixed modifications used in a search.
unsigned int	getMULTI_SITE_MODS () const
	Returns a flag showing what MULTI_SITE_MODS options were selected.
double	getNitrogenMass () const
	Returns the mass of nitrogen as specified in the mascot/config/masses file.
double	getNTermMass ()
	Returns the N terminus mass.
int	getNumberOfDatabases ()
	Returns total number of databases used for the search.
int	getNumberOfLibraryMods () const
	Return the number of modifications in the spectral libraries searched.
bool	getOVERVIEW ()
	Returns true if the user selected the option to show the overview table.
double	getOxygenMass () const
	Returns the mass of oxygen as specified in the mascot/config/masses file.
int	getPEP_ISOTOPE_ERROR () const
	Returns a value showing how a peak detection error is handled.
int	getPFA ()
	Returns the number of missed cleavage points allowed for in a search.
double	getPRECURSOR ()
	Returns the precursor mass for an MS-MS query.
std::string	getQUANTITATION () const
	Returns the name of the quantitation method used.
std::string	getQUE ()
	Currently returns an empty string.
int	getREPORT ()
	Returns the number of results to show in the report.
std::string	getREPTYPE ()
	Returns the type of report requested by the user.
double	getResidueMass (char residue)
	Returns the mass of the specified residue (must be uppercase letter A-Z).
std::string	getRULES ()
	Returns as a comma separated list, the rules / ions series used for a search.
std::string	getSEARCH ()
	Returns the type of search -- this will be PMF, SQ, MIS.
int	getSEG ()
	Returns the segment or protein mass.
int	getSUBCLUSTER ()
	Returns the sub cluster number.
double	getTARGET_FDR_PERCENT () const
	Returns the target FDR specified as a search parameter.
std::string	getTAXONOMY ()
	Returns the name of the taxonomy selection.
double	getTOL ()
	Returns the peptide tolerance for the search.
std::string	getTOLU ()
	Returns the peptide tolerance units for the search.
std::string	getUSEREMAIL ()
	Returns the user's email address (if any) as entered in the search form.
std::string	getUSERField (int num)
	Returns the user fields USER00, USER01, USER02 ... USER12.
int	getUSERID ()
	Returns the user's USERID.
std::string	getUSERNAME ()
	Returns the user name (if any) as entered in the search form.
double	getVarModsDelta (int num)
	Returns the delta mass for a variable modification.
std::string	getVarModsName (int num) const
double	getVarModsNeutralLoss (int num)
	Returns the first neutral loss value for the specified variable modification.
std::vector< double >	getVarModsNeutralLosses (int num) const
	Returns all the neutral loss values for the specified variable modification.
std::vector< double >	getVarModsPepNeutralLoss (int num)
	Returns the peptide neutral loss value(s) for the specified variable modification.
std::vector< double >	getVarModsReqPepNeutralLoss (int num)
	Returns the required peptide neutral loss value(s) for the specified variable modification.

---

Detailed Description

This class encapsulates the search parameters in the mascot results file.

Although all these parameters could be obtained using the lower level functions in the ms_mascotresfile class, it is generally more convenient to use this object.

Examples:

resfile_params.cpp.

---

Member Enumeration Documentation

enum MULTI_SITE_MODS

Possible values for MULTI_SITE_MODS.

See Using enumerated values and static const ints in Perl, Java, Python and C#. The return value from getMULTI_SITE_MODS() is one or more of these values OR'd together.

Currently only has one permitted value, but could be extended in future.

Enumerator:

MSM_NOT_PERMITTED	The default value. Only one variable or exclusive mod per residue.
MSM_EXCLUSIVE_PLUS_VARIABLE	An exclusive mod and one or more variable mod may be specified for the same residue.

---

Constructor & Destructor Documentation

ms_searchparams

(

const ms_mascotresfile &

resfile )

Either explicitily create an object using this constructor or call ms_mascotresfile.params().

Search parameters can be obtained either by creating a search params object or by using the object created when the results file is created:

C++

   ms_mascotresfile resfile(filename);

   // Option 1:
   ms_searchparams *params = new ms_searchparams(resfile);
   // Option 2:
   ms_searchparams params = resfile.params();

Perl

   my $resfile = msparser::ms_mascotresfile->new($filename);

   # Option 1:
   my $params = msparser::ms_searchparams->new($resfile);
   # Option 2:
   my $params = $resfile->params();

Java

   ms_mascotresfile resfile = new ms_mascotresfile(filename);

   // Option 1:
   ms_searchparams params = new ms_searchparams(resfile);
   // Option 2:
   ms_searchparams params = resfile.params();

Python

   resfile = msparser.ms_mascotresfile(filename)

   # Option 1:
   params = msparser.ms_searchparams(resfile)
   # Option 2:
   params = resfile.params()

See Maintaining object references: two rules of thumb.

Parameters:

resfile

result file object

---

Member Function Documentation

std::string getACCESSION

(

)

This function returns a comma separated list of accession strings.

For an error tolerant search, the user typically specifies a list of accession "numbers" to be searched. This function returns a comma separated list of accession strings -- each will have double quotes around it. The string is obtained from the ACCESSION= line in the parameters section of the results file.

Returns:

comma separated list of accession strings

std::string getAllUSERParams

(

)

const

Returns all the 'user defined' parameters.

Returns a string of all the entries in the 'parameters' section that have a leading underscore. Each item is separated by a newline character. Note that if there are two user parameters with the same key (differing only by case), then the second one of these will be discarded.

Returns:

all the user defined parameters

double getCarbonMass

(

)

const

Returns the mass of carbon as specified in the mascot/config/masses file.

This is obtained from the carbon= line in the masses section of the results file.

The mass will also depend on whether monoisotopic or average masses were selected by the user. See getMASS().

Returns:

mass of carbon as specified in the mascot/config/masses file

std::string getCHARGE

(

)

Returns the charge state of the peptide masses entered.

This is obtained from the CHARGE= line in the parameters section of the results file. Use ms_peptide::getCharge to return the actual charge state that was used for a peptide match.

This is the default charge state that was used when running the search. It can be overridden by charge states in an uploaded file; see ms_inputquery::getCharge().

If the search was submitted from the standard Mascot search form, then it will be one of the following strings:

• '8-'
• '7-'
• '6-'
• '5-'
• '4-'
• '3-'
• '2- and 3-'
• '2-'
• '1-, 2- and 3-'
• '1-'
• 'Mr'
• '1+'
• '1+, 2+ and 3+'
• '2+'
• '2+ and 3+'
• '3+'
• '4+'
• '5+'
• '6+'
• '7+'
• '8+'

The charge can also be any comma separated list of charge states.

See also:

http://www.matrixscience.com/help/search_field_help.html#TWO

Returns:

The default charge(s) as a string.

std::string getCLE

(

)

Returns the name of the enzyme used for the search.

This is obtained from the CLE= line in the parameters section of the results file.

See also:

http://www.matrixscience.com/help/search_field_help.html#CLE

Returns:

name of the enzyme used for the search

std::string getCOM

(

)

This is the comment or "Search title" entered by the user in the search form.

This is obtained from the COM= line in the parameters section of the results file.

See also:

http://www.matrixscience.com/help/search_field_help.html#COM

Returns:

comment or "Search title" entered by the user in the search form

std::string getCROSSLINKING

(

)

const

Returns the name of the crosslinking method used.

Available in Mascot 2.7 and later.

See also:

http://www.matrixscience.com/help/search_field_help.html#CROSSLINKING

Returns:

If no crosslinking is specified, an empty string or "None". Otherwise return the name of the crosslinking method from the CROSSLINKING= value in the parameters section of the results file.

double getCTermMass

(

)

Returns the C terminus mass.

This is obtained from the C_term= line in the masses section of the results file.

The mass value will depend on whether monoisotopic or average masses were selected by the user (see getMASS()). Additionally, any fixed (but not variable) modifications are included in this mass. If no C terminus mods are specified, this value should be the same as getOxygenMass() + getHydrogenMass().

These values originate from the mascot/config/masses file, and are therefore user definable.

Returns:

C terminus mass

std::string getDATAURL

(

)

Returns the URL of the uploaded file (if any).

This is obtained from the DATAURL= line in the parameters section of the results file.

Returns:

URL of the uploaded file

std::string getDB

(

int

idx = 1 )

Returns one of the database names used for the search.

This is normally obtained from the DB= line in the parameters section of the results file.

It is not possible to find the database file name and path directly from its name. The get the path to the database file used in the search, use ms_mascotresfile::getFastaPath(), or you will need to manually parse the Databases section of mascot.dat and search for the line starting with the name returned by getDB(). Replace the last part of the path with the return value from the ms_mascotresfile::getFastaVer() function to complete the file name.

Mascot 2.6 and later support spectral libraries. Each spectral library must have a reference database into which found peptide sequences are mapped at the end of the search. The "effective" reference database could be one of the protein sequence databases searched, or it could be a separate database used only for lookup purposes. You can find the database number of the reference database with ms_mascotresfile::getReferenceDatabaseNumberOfSL(). If this is larger than getNumberOfDatabases(), the database name is obtained from the library_reference_DB line in the header section of the results file.

See also:

http://www.matrixscience.com/help/search_field_help.html#DB

Parameters:

idx	index of the database from 1 to getNumberOfDatabases() for databases or libraries searched, or an index returned by ms_mascotresfile::getReferenceDatabaseNumberOfSL().

Returns:

one of the database names used for the search

int getDECOY

(

)

const

Returns a value showing if a decoy database has been searched.

Available in Mascot 2.2 and later.

See also:

http://www.matrixscience.com/help/decoy_help.html#AUTO

The value is obtained from the DECOY= line in the parameters section of the results file. If there is no such line, this method returns -1. Otherwise, the method returns 0 if DECOY is off and 1 if DECOY is on.

Returns:

-1, 0 or 1.

double getElectronMass

(

)

const

Returns the mass of an electron as specified in the mascot/config/masses file.

This is obtained from the Electron= line in the masses section of the results file.

Results files produced by Mascot versions prior to 1.9 do not have this entry. For those files, the returned value will be zero.

Returns:

mass of an electron as specified in the mascot/config/masses file

bool getERRORTOLERANT

(

)

Returns 'true' for an error tolerant search.

This is obtained from the ERRORTOLERANT= line in the parameters section of the results file.

Use getACCESSION() to get the list of accession numbers that are used for an error tolerant search.

See also:

http://www.matrixscience.com/help/error_tolerant_help.html

Returns:

true if the search is error tolerant, false otherwise

std::string getErrTolParentFilename

(

)

Returns the filename of the 'parent' search for an error tolerant search.

Most programs should not need to call this function - it is used within the Mascot Parser.

An error tolerant search is normally performed as a repeat search. The filename for the 'parent' non error tolerant search is saved in the parameters section as _errortolerantsearchparent, and can be accessed using this function.

It is not possible to use getINTERMEDIATE(), because an error tolerant search can be performed as a repeat search from another error tolerant search.

See Error tolerant searches for further details.

Returns:

relative path to the parent error tolerant file

std::string getFILENAME

(

)

Returns the name of the uploaded file (if any).

This is obtained from the FILE= line in the parameters section of the results file.

Returns:

name of the uploaded file

double getFixedModsDelta

(

int

num )

Returns the delta mass for a fixed modification.

This value is obtained from the FixedMod[num]= line in the masses section of the results file.

Any number of fixed modifications can be applied during a search as long as multiple modifications don't affect the same residue/terminus. Information about fixed modifications can be found using these functions:

• getFixedModsName(int num)
• getFixedModsDelta(int num)
• getFixedModsNeutralLoss(int num)
• getFixedModsResidues(int num)

See the Mascot installation and setup manual (configuration and log files chapter) for more information about fixed modifications.

Parameters:

num	is the modification number. This number is not referenced elsewhere in the results file.

Returns:

The delta, or a value of zero if no delta is found.

std::string getFixedModsName

(

int

num )

const

This value is obtained from the FixedMod[num]= line in the masses section of the results file.

Any number of fixed modifications can be applied during a search as long as multiple modifications don't affect the same residue/terminus. Information about fixed modifications can be found using these functions:

• getFixedModsName(int num)
• getFixedModsDelta(int num)
• getFixedModsNeutralLoss(int num)
• getFixedModsResidues(int num)

See the Mascot installation and setup manual (configuration and log files chapter) for more information about fixed modifications.

Parameters:

num	is the modification number. This number is not referenced elsewhere in the results file.

Returns:

The modification name, or an empty string if no name is found.

double getFixedModsNeutralLoss

(

int

num )

Returns the neutral loss value for the specified fixed modification.

This value is obtained from the FixedModNeutralLoss[num]= line in the masses section of the results file.

Any number of fixed modifications can be applied during a search as long as multiple modifications don't affect the same residue/terminus. Information about fixed modifications can be found using these functions:

• getFixedModsName(int num)
• getFixedModsDelta(int num)
• getFixedModsNeutralLoss(int num)
• getFixedModsResidues(int num)

See the Mascot installation and setup manual (configuration and log files chapter) for more information about fixed modifications.

Parameters:

num	is the modification number. This number is not referenced elsewhere in the results file.

Returns:

The neutral loss delta, or zero if no neutral loss is found. Only a single neutral loss is permitted for a fixed modifcation.

std::string getFixedModsResidues

(

int

num )

const

Returns the residues modified for the specified fixed modification.

This value is obtained from the FixedModResidues[num]= line in the masses section of the results file.

Any number of fixed modifications can be applied during a search as long as multiple modifications don't affect the same residue/terminus. Information about fixed modifications can be found using these functions:

• getFixedModsName(int num)
• getFixedModsDelta(int num)
• getFixedModsNeutralLoss(int num)
• getFixedModsResidues(int num)

See the Mascot installation and setup manual (configuration and log files chapter) for more information about fixed modifications.

Parameters:

num	is the modification number. This number is not referenced elsewhere in the results file.

Returns:

The string representing which residues/terminus are modified. It will be of the form [A-Z]|C_term|N_term. Multiple residues will be listed as, for example, STY.

std::string getFORMAT

(

)

Returns the file format type selected by the user.

This is obtained from the FORMAT= line in the parameters section of the results file.

Currently supported formats:

• Mascot generic
• Sequest (.DTA)
• Finnigan (.ASC)
• Micromass (.PKL)
• PerSeptive (.PKS)
• Sciex API III
• Bruker (.XML)
• mzData (.XML)
• mzML (.XML)

See also:

http://www.matrixscience.com/help/data_file_help.html

Returns:

file format type selected by the user

std::string getFORMVER

(

)

Returns the version of the form used to submit the search.

This is obtained from the FORMVER= line in the parameters section of the results file.

This is currently 1.01.

Returns:

version of the form used to submit the search

double getHydrogenMass

(

)

const

Returns the mass of nitrogen as specified in the mascot/config/masses file.

This is obtained from the hydrogen= line in the masses section of the results file.

The mass will also depend on whether monoisotopic or average masses were selected by the user. See getMASS().

Returns:

mass of nitrogen as specified in the mascot/config/masses file

bool getICAT

(

)

Returns true if the user selected the ICAT button on the search form.

This is obtained from the ICAT= line in the parameters section of the results file.

See also:

http://www.matrixscience.com/help/search_field_help.html#ICAT

Returns:

If the value in the results file is (case insensitive) ON or 1, this will return true.

std::string getINSTRUMENT

(

)

Returns the instrument name that the user selected.

This is obtained from the INSTRUMENT= line in the parameters section of the results file.

This string will be NULL for versions of Mascot prior to 1.8.

See also getRULES(). It is preferable to use the rules rather than this name to determine which ions series were searched since the user can change the definition of the name.

See also:

http://www.matrixscience.com/help/search_field_help.html#INSTRUMENT

Returns:

instrument name that the user selected

std::string getINTERMEDIATE

(

)

For a repeat search, it may be necessary to know the "parent" search.

This is obtained from the INTERMEDIATE= line in the parameters section of the results file.

This function returns the file name for the results file of the 'parent' search.

Returns:

file name of the parent search result file

std::string getIT_MODS

(

)

Returns a comma separated list of the variable modifications used in a search.

This is obtained from the IT_MODS= line in the parameters section of the results file.

See also:

http://www.matrixscience.com/help/search_field_help.html#MODS

Returns:

comma separated list of the variable modifications used in a search

double getITOL

(

)

Returns the tolerance for msms ions.

This is obtained from the ITOL= line in the parameters section of the results file.

See also:

getITOLU()

http://www.matrixscience.com/help/search_field_help.html#ITOL

Returns:

tolerance for MS/MS ions

std::string getITOLU

(

)

Returns the units that the ions tolerance is specified in.

This is obtained from the ITOLU= line in the parameters section of the results file.

The units will be one of:

mmu

absolute milli-mass units, i.e. units of .001 Da

Da

absolute units of Da

See also:

getITOL()

http://www.matrixscience.com/help/search_field_help.html#ITOL

Returns:

unit that the ions tolerance is specified in

int getLIBRARY_SEARCH

(

)

const

Returns a value showing if a spectral library has been searched.

Available in Mascot 2.6 and later.

See also:

http://www.matrixscience.com/help/spectral_library.html

The value is obtained from the LIBRARY_SEARCH= line in the parameters section of the results file. If there is no such line, this method returns -1. Otherwise, the method returns 0 if LIBRARY_SEARCH is off and 1 if LIBRARY_SEARCH is on.

Returns:

-1, 0 or 1.

double getLibraryModDelta

(

int

num )

const

Returns the delta mass of the specified spectral library modification.

Library modifications are stored in the spectral_library section of the results file. These are all the modifications contained in the spectral libraries selected for searching. Individual spectral library matches, if they have modifications, refer to modification index numbers in this list.

The modification only has a delta mass if its name was in the Unimod configuration file at the time of the search. Otherwise only its name is recorded in the spectral_library section. It is better to look up the modification by name from the Unimod configuration file than rely on the delta mass being present.

Note that the list of modifications in actual matches in the search is different. See ms_peptidesummary::getNumDiscoveredLibraryMods().

Parameters:

num	is library modification index. See ms_peptidesummary::getLibraryModString(). The index should be between 1 and getNumberOfLibraryMods().

Returns:

modification delta mass, or 0.0 if not available.

std::string getLibraryModName

(

int

num )

const

Returns the name of the specified spectral library modification.

Library modifications are stored in the spectral_library section of the results file. These are all the modifications contained in the spectral libraries selected for searching. Individual spectral library matches, if they have modifications, refer to modification index numbers in this list.

Note that the list of modifications in actual matches in the search is different. See ms_peptidesummary::getNumDiscoveredLibraryMods().

Parameters:

num	is library modification index. See ms_peptidesummary::getLibraryModString(). The index should be between 1 and getNumberOfLibraryMods().

Returns:

modification name. The name may be a Unimod name, or it may be a free-text string; this depends on how the library was constructed.

std::string getLICENSE

(

)

Returns the Mascot license string.

This string is the one in the license file, and is printed out during a Mascot search. This is obtained from the LICENSE= line in the parameters section of the results file.

Returns:

Mascot license string

std::string getMASS

(

)

Returns whether monoisotopic or average masses have been specified.

This is obtained from the MASS= line in the parameters section of the results file. The returned text will be "Monoisotopic" or "Average" -- even if the text in the results file is, for example, all upper case.

See also:

getMassType() which may be a more useful function.

http://www.matrixscience.com/help/search_field_help.html#MASS

Returns:

"Monoisotopic" or "Average"

MASS_TYPE getMassType

(

)

Returns either MASS_TYPE_MONO or MASS_TYPE_AVE.

The value is obtained from the MASS= line in the parameters section of the results file.

See also:

getMASS()

Returns:

MASS_TYPE_MONO or MASS_TYPE_AVE

double getMaxInternalMass

(

)

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 

The value specified for the instrument is saved in the parameters section of the results file as INTERNALS=min,max. If there is no INTERNALS= line, the default value of 700.0 is returned.

A different instrument can be specified for each spectrum, in which case the values can be found using ms_inputquery::getMinInternalMass and ms_inputquery::getMaxInternalMass

See also:

getRULES(), getINSTRUMENT()

Returns:

The maximum internal mass considered in this search.

double getMinInternalMass

(

)

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 

The value specified for the instrument is saved in the parameters section of the results file as INTERNALS=min,max. If there is no INTERNALS= line, the default value of 0 is returned.

A different instrument can be specified for each spectrum, in which case the values can be found using ms_inputquery::getMinInternalMass and ms_inputquery::getMaxInternalMass.

See also:

getRULES() getINSTRUMENT()

Returns:

The minimum internal mass considered in this search.

std::string getMODS

(

)

Returns a comma separated list of the fixed modifications used in a search.

This is obtained from the MODS= line in the parameters section of the results file.

See also:

http://www.matrixscience.com/help/search_field_help.html#MODS

Returns:

comma separated list of the fixed modifications used in a search

unsigned int getMULTI_SITE_MODS

(

)

const

Returns a flag showing what MULTI_SITE_MODS options were selected.

Available in Mascot 2.4 and later.

See also:

ms_peptide::getSummedModsStr

Multiple modifications for the same site

Returns:

the value of MULTI_SITE_MODS in the paramters section of the results file. This will be one or more ms_searchparams::MULTI_SITE_MODS values OR'ed together. If there is no MULTI_SITE_MODS in the results file, then ms_searchparams::MSM_NOT_PERMITTED will be returned.

double getNitrogenMass

(

)

const

Returns the mass of nitrogen as specified in the mascot/config/masses file.

This is obtained from the nitrogen= line in the masses section of the results file.

The mass will also depend on whether monoisotopic or average masses were selected by the user. See getMASS().

Returns:

mass of nitrogen as specified in the mascot/config/masses file

double getNTermMass

(

)

Returns the N terminus mass.

This is obtained from the N_term= line in the masses section of the results file.

The mass value will depend on whether monoisotopic or average masses were selected by the user (see getMASS()). Additionally, any fixed (but not variable) modifications are included in this mass. If no N terminus mods are specified, this value should be the same as getHydrogenMass().

These values originate from the mascot/config/masses file, and are therefore user definable.

Returns:

N terminus mass

int getNumberOfDatabases

(

)

Returns total number of databases used for the search.

This method is used in conjunction with getDB() to find out the total number of databases used in the search.

Mascot 2.6 and later support spectral libraries. The total number of databases searched includes the protein sequence and nucleic acid databases and spectral libraries, but does not include any reference databases of spectral libraries.

Returns:

The number of databases and libraries used in the search.

int getNumberOfLibraryMods

(

)

const

Return the number of modifications in the spectral libraries searched.

Library modifications are stored in the spectral_library section of the results file. These are all the modifications contained in the spectral libraries selected for searching. Individual spectral library matches, if they have modifications, refer to modification index numbers in this list.

Note that the list of modifications in actual matches in the search is different. See ms_peptidesummary::getNumDiscoveredLibraryMods().

Returns:

the number of entries in the spectral_library section, which equals the last non-empty index X in the ModX= lines.

bool getOVERVIEW

(

)

Returns true if the user selected the option to show the overview table.

This is obtained from the OVERVIEW= line in the parameters section of the results file.

See also:

http://www.matrixscience.com/help/search_field_help.html#OVERVIEW

Returns:

True if the value is (case insensitive) ON or 1.

double getOxygenMass

(

)

const

Returns the mass of oxygen as specified in the mascot/config/masses file.

This is obtained from the oxygen= line in the masses section of the results file.

The mass will also depend on whether monoisotopic or average masses were selected by the user. See getMASS().

Returns:

mass of oxygen as specified in the mascot/config/masses file

int getPEP_ISOTOPE_ERROR

(

)

const

Returns a value showing how a peak detection error is handled.

Available in Mascot 2.2 and later.

See also:

http://www.matrixscience.com/help/search_field_help.html#PEP_ISOTOPE_ERROR

Normal test for a peptide match is

exp > calc-tol  && exp < calc+tol 

If PEP_ISOTOPE_ERROR >= 1, also test for

exp > calc+1.003+tol && exp < calc+1.003-tol 

If PEP_ISOTOPE_ERROR >= 2, also test for

exp > calc+2.007+tol && exp < calc+2.007-tol 

Returns:

The value of PEP_ISOTOPE_ERROR in the parameters section of the results file. If there is no PEP_ISOTOPE_ERROR value in the results file, then -1 is returned.

int getPFA

(

)

Returns the number of missed cleavage points allowed for in a search.

This is obtained from the PFA= line in the parameters section of the results file

See also:

http://www.matrixscience.com/help/search_field_help.html#PFA

Returns:

number of missed cleavage points allowed for in a search

double getPRECURSOR

(

)

Returns the precursor mass for an MS-MS query.

This is obtained from the PRECURSOR= line in the parameters section of the results file.

Three data file formats, SCIEX API III and PerSeptive (.PKS) and Bruker (.XML), do not include m/z information for the precursor peptide. For these formats only, the Precursor field is used to specify the m/z value of the parent peptide.

See also:

http://www.matrixscience.com/help/search_field_help.html#PRECURSOR

Returns:

precursor mass for an MS-MS query

std::string getQUANTITATION

(

)

const

Returns the name of the quantitation method used.

Available in Mascot 2.2 and later.

See also:

http://www.matrixscience.com/help/search_field_help.html#QUANTITATION

Returns:

If no quantitation is specified, an empty string or "None". Otherwise return the name of the quantitation method from the QUANTITATION= value in the parameters section of the results file.

std::string getQUE

(

)

Currently returns an empty string.

This is obtained from the QUE= line in the parameters section of the results file.

Returns:

QUE

int getREPORT

(

)

Returns the number of results to show in the report.

This is obtained from the REPORT= line in the parameters section of the results file. For 'AUTO' a value of 0 is returned.

See also:

http://www.matrixscience.com/help/search_field_help.html#REPORT

Returns:

number of results to show in the report

std::string getREPTYPE

(

)

Returns the type of report requested by the user.

This is obtained from the REPTYPE= line in the parameters section of the results file

This will be one of:

• concise
• peptide
• protein

See also:

http://www.matrixscience.com/help/results_help.html

Returns:

type of report requested by the user

double getResidueMass

(

char

residue )

Returns the mass of the specified residue (must be uppercase letter A-Z).

This is obtained from the A=,B= etc. line in the masses section of the results file.

The mass value will depend on whether monoisotopic or average masses were selected by the user (see getMASS()). Additionally, any fixed (but not variable) modifications are included in this mass.

Parameters:

residue

uppercase letter A-Z

Returns:

mass of the specified residue

std::string getRULES

(

)

Returns as a comma separated list, the rules / ions series used for a search.

This is obtained from the RULES= line in the parameters section of the results file.

The numbers in the comma separated list have the following meanings:

   1 = singly charged
   2 = doubly charged if precursor 2+ or higher (not internal or immonium)
   3 = doubly charged if precursor 3+ or higher (not internal or immonium)
   4 = immonium
   5 = a series
   6 = a - NH3 if a significant and fragment includes RKNQ
   7 = a - H2O if a significant and fragment includes STED
   8 = b series
   9 = b - NH3 if b significant and fragment includes RKNQ
   10= b - H2O if b significant and fragment includes STED
   11= c series
   12= x series
   13= y series
   14= y - NH3 if y significant and fragment includes RKNQ
   15= y - H2O if y significant and fragment includes STED
   16= z series
   17= internal yb < 700 Da
   18= internal ya < 700 Da
   19= y or y++ must be significant
   20= y or y++ must be highest scoring series
   21= z+1 series
   22= d and d' series
   23= v series
   24= w and w' series
   25= z+2 series

See also:

getINSTRUMENT() to find the descriptive name of the selected instrument.

http://www.matrixscience.com/help/search_field_help.html#INSTRUMENT

Returns:

comma separated list, the rules / ions series used for a search

std::string getSEARCH

(

)

Returns the type of search -- this will be PMF, SQ, MIS.

This is obtained from the SEARCH= line in the parameters section of the results file.

Rather than using this value directly, it is generally easier to use the functions ms_mascotresfile::isMSMS(), ms_mascotresfile::isPMF() or ms_mascotresfile::isSQ(), and it is normally safer to use ms_mascotresfile::anyMSMS(), ms_mascotresfile::anyPMF() and ms_mascotresfile::anySQ().

Returns:

type of the search

int getSEG

(

)

Returns the segment or protein mass.

This is obtained from the SEG= line in the parameters section of the results file.

See also:

http://www.matrixscience.com/help/search_field_help.html#SEG

Returns:

segment or protein mass

int getSUBCLUSTER

(

)

Returns the sub cluster number.

This is obtained from the SUBCLUSTER= line in the parameters section of the results file.

For a large cluster, split up into multiple sub clusters, this returns the sub cluster number.

Returns:

The subcluster number.

double getTARGET_FDR_PERCENT

(

)

const

Returns the target FDR specified as a search parameter.

Available in Mascot 2.8 and later.

See also:

http://www.matrixscience.com/help/decoy_help.html#AUTO

The value is obtained from the TARGET_FDR_PERCENT= line in the parameters section of the results file. If there is no such line, or the value is not a floating point number, this method returns 0.0.

Returns:

0.0, or target FDR specified as a percentage.

std::string getTAXONOMY

(

)

Returns the name of the taxonomy selection.

This is obtained from the TAXONOMY= line in the parameters section of the results file.

To find out exactly which taxa were included and excluded from the search, the 'taxonomy' file in the mascot/config directory needs to be parsed.

See also:

http://www.matrixscience.com/help/search_field_help.html#TAXONOMY

Returns:

name of the taxonomy selection

double getTOL

(

)

Returns the peptide tolerance for the search.

This is obtained from the TOL= line in the parameters section of the results file.

See also:

http://www.matrixscience.com/help/search_field_help.html#TOL

Returns:

peptide tolerance for the search

std::string getTOLU

(

)

Returns the peptide tolerance units for the search.

This is obtained from the TOLU= line in the parameters section of the results file.

The units will be one of:

%%

fraction expressed as a percentage

mmu

absolute milli-mass units, i.e. units of .001 Da

Da

absolute units of Da

ppm

fraction expressed as parts per million

See also:

http://www.matrixscience.com/help/search_field_help.html#TOL

Returns:

peptide tolerance units for the search

std::string getUSEREMAIL

(

)

Returns the user's email address (if any) as entered in the search form.

This is obtained from the USERMAIL= line in the parameters section of the results file.

See also:

http://www.matrixscience.com/help/search_field_help.html#NAME

Returns:

user email

std::string getUSERField

(

int

num )

Returns the user fields USER00, USER01, USER02 ... USER12.

Parameters:

num	must be in the range 0..12.

Returns:

user fields

int getUSERID

(

)

Returns the user's USERID.

This is obtained from the USERID= line in the parameters section of the results file. This value is the users id if Mascot security is enabled.

Searches prior to version 2.1 will not have this parameter in which case it will return 0. For searches with Mascot 2.1 or later, where security is not enabled, this function will also return 0.

See Mascot security and authentication module

Returns:

user id

std::string getUSERNAME

(

)

Returns the user name (if any) as entered in the search form.

This is obtained from the USERNAME= line in the parameters section of the results file.

See also:

http://www.matrixscience.com/help/search_field_help.html#NAME

Returns:

user name as entered in the search form

double getVarModsDelta

(

int

num )

Returns the delta mass for a variable modification.

This value is obtained from the delta[num]= line in the masses section of the results file.

Each variable modification is assigned a number 1 to 32 (up to 32 variable modifications are allowed). In the results, a string is assigned for each matched peptide, and each character in the string will be 0..9A..W (0 for no modification). Information about the modification can be found using these functions:

• getVarModsName(int num)
• getVarModsDelta(int num)
• getVarModsNeutralLoss(int num)
• getVarModsNeutralLosses(int num)
• ms_mascotresults::getReadableVarMods()
• getVarModsPepNeutralLoss(int num)
• getVarModsReqPepNeutralLoss(int num)

See the Mascot installation and setup manual (configuration and log files chapter) for more information about variable modifications.

Parameters:

num	is the modification number. See ms_peptide::getVarModsStr for details of how to obtain this number.

Returns:

delta mass for a variable modification

std::string getVarModsName

(

int

num )

const

This value is obtained from the delta[num]= line in the masses section of the results file.

Each variable modification is assigned a number 1 to 32 (up to 32 variable modifications are allowed). In the results, a string is assigned for each matched peptide, and each character in the string will be 0..9A..W (0 for no modification). Information about the modification can be found using these functions:

• getVarModsName(int num)
• getVarModsDelta(int num)
• getVarModsNeutralLoss(int num)
• getVarModsNeutralLosses(int num)
• ms_mascotresults::getReadableVarMods()
• getVarModsPepNeutralLoss(int num)
• getVarModsReqPepNeutralLoss(int num)

See the Mascot installation and setup manual (configuration and log files chapter) for more information about variable modifications.

Parameters:

num	is the modification number. See ms_peptide::getVarModsStr for details of how to obtain this number.

Returns:

name of the specified variable modification selected by the user

double getVarModsNeutralLoss

(

int

num )

Returns the first neutral loss value for the specified variable modification.

Note:

This function is deprecated, since it only returns a single neutral loss value. This function has been replaced with getVarModsNeutralLosses() which returns multiple neutral losses

The value is obtained from the NeutralLoss[num]= line in the masses section of the results file.

Each variable modification is assigned a number 1 to 32 (up to 32 variable modifications are allowed). In the results, a string is assigned for each matched peptide, and each character in the string will be 0..9A..W (0 for no modification). Information about the modification can be found using these functions:

• getVarModsName(int num)
• getVarModsDelta(int num)
• getVarModsNeutralLoss(int num)
• getVarModsNeutralLosses(int num)
• ms_mascotresults::getReadableVarMods()
• getVarModsPepNeutralLoss(int num)
• getVarModsReqPepNeutralLoss(int num)

See the Mascot installation and setup manual (configuration and log files chapter) for more information about variable modifications.

Parameters:

num	is the modification number. See ms_peptide::getVarModsStr for details of how to obtain this number.

Returns:

first neutral loss value for the specified variable modification.

std::vector< double > getVarModsNeutralLosses

(

int

num )

const

Returns all the neutral loss values for the specified variable modification.

The first neutral loss is obtained from the NeutralLoss[num]= line in the masses section of the results file. Subsequent neutral losses considered (if any) are obtained from the NeutralLoss[num]_master= line; the first value on the comma separated line would be for neutralLossNum=2, the second for neutralLossNum=3 etc.

Each variable modification is assigned a number 1 to 32 (up to 32 variable modifications are allowed). In the results, a string is assigned for each matched peptide, and each character in the string will be 0..9A..W (0 for no modification). Information about the modification can be found using these functions:

• getVarModsName(int num)
• getVarModsDelta(int num)
• getVarModsNeutralLoss(int num)
• getVarModsNeutralLosses(int num)
• ms_mascotresults::getReadableVarMods()
• getVarModsPepNeutralLoss(int num)
• getVarModsReqPepNeutralLoss(int num)

See the Mascot installation and setup manual (configuration and log files chapter) for more information about variable modifications.

Parameters:

num	is the modification number. See ms_peptide::getVarModsStr for details of how to obtain this number.

Returns:

neutral loss values for the specified variable modification

std::vector< double > getVarModsPepNeutralLoss

(

int

num )

Returns the peptide neutral loss value(s) for the specified variable modification.

This value is obtained from the PepNeutralLoss[num]= line in the masses section of the results file.

Each variable modification is assigned a number 1 to 32 (up to 32 variable modifications are allowed). In the results, a string is assigned for each matched peptide, and each character in the string will be 0..9A..W (0 for no modification). Information about the modification can be found using these functions:

• getVarModsName(int num)
• getVarModsDelta(int num)
• getVarModsNeutralLoss(int num)
• getVarModsNeutralLosses(int num)
• ms_mascotresults::getReadableVarMods()
• getVarModsPepNeutralLoss(int num)
• getVarModsReqPepNeutralLoss(int num)

See the Mascot installation and setup manual (configuration and log files chapter) for more information about variable modifications.

Parameters:

num	is the modification number. See ms_peptide::getVarModsStr for details of how to obtain this number.

Returns:

peptide neutral loss value(s) for the specified variable modification

std::vector< double > getVarModsReqPepNeutralLoss

(

int

num )

Returns the required peptide neutral loss value(s) for the specified variable modification.

These value is obtained from the ReqPepNeutralLoss[num]= line in the masses section of the results file.

Each variable modification is assigned a number 1 to 32 (up to 32 variable modifications are allowed). In the results, a string is assigned for each matched peptide, and each character in the string will be 0..9A..W (0 for no modification). Information about the modification can be found using these functions:

• getVarModsName(int num)
• getVarModsDelta(int num)
• getVarModsNeutralLoss(int num)
• getVarModsNeutralLosses(int num)
• ms_mascotresults::getReadableVarMods()
• getVarModsPepNeutralLoss(int num)
• getVarModsReqPepNeutralLoss(int num)

See the Mascot installation and setup manual (configuration and log files chapter) for more information about variable modifications.

Parameters:

num	is the modification number. See ms_peptide::getVarModsStr for details of how to obtain this number.

Returns:

required peptide neutral loss value(s) for the specified variable modification

---

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

• ms_mascotresparams.hpp
• ms_mascotresparams.cpp