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Public Member Functions

ms_inputquery Class Reference
[Mascot results file module]

This class encapsulates the input data in the mascot results file. More...

#include <ms_inputquery.hpp>

Collaboration diagram for ms_inputquery:
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List of all members.

Public Member Functions

 ms_inputquery (const ms_mascotresfile &resfile, const int q)
 Use this contructor to create an object to get the input data.
std::string getCharge () const
 Returns a string that represents the supplied charge for the query.
std::string getComp (int comp_no) const
 Returns a string that represents one of the sequence queries.
int getIndex () const
 Returns the zero based index of the peak list in an MGF, PKL or DTA file.
std::string getINSTRUMENT (const bool unescaped=true) const
 Returns an INSTRUMENT string if this has been specified at the query level.
double getIntMax () const
 Returns the maximum intensity of any ion.
double getIntMin () const
 Returns the minimum intensity of any ion.
std::string getIT_MODS (const bool unescaped=true) const
 Returns the names of variable modifications if such have been specified at the query level.
std::string getLocalVarModName (const int num) const
 Returns the query-level modification name by 1-based index.
std::string getLocus () const
 Returns the locus specified in the MGF file using the LOCUS= line.
double getMassMax () const
 Returns the maximum mass of any ion.
double getMassMin () const
 Returns the minimum mass of any ion.
double getMaxInternalMass () const
 Returns the maximum mass to be considered for internal fragments if an INSTRUMENT has been specified at the query level.
double getMinInternalMass () const
 Returns the minimum mass to be considered for internal fragemnts if an INSTRUMENT has been specified at the query level.
int getNumberOfLocalVarMods () const
 Returns the name of query-level variable modifications.
int getNumberOfPeaks (const int ions)
 Returns the number of ions peaks in an ms-ms spectrum.
int getNumUsed () const
 Returns the number of ions used for matching - value no longer available.
int getNumVals () const
 Returns the number of ions.
double getPeakIntensity (const int ions, const int peakNo)
 Returns the intensity of a particular ions peak.
std::vector< std::pair< double,
double > > 
getPeakList (const int ions)
 Returns a list of ions peaks for a query.
double getPeakMass (const int ions, const int peakNo)
 Returns the mass of a particular ions peak.
double getPepTol () const
 Returns the peptide tolerance for this query.
std::string getPepTolString () const
 Returns the peptol string .
std::string getPepTolUnits () const
 Returns the peptide tolerance units for this query.
std::string getRawfile () const
 Returns the rawfile specified in the MGF file using the RAWFILE= line.
std::string getRawScans (const int rawFileIdx=-1) const
 Returns the rawscan number(s) that were used to generate this peak list.
void getRawScans (std::vector< int > &index, std::vector< std::string > &rawscans) const
 Returns all rawscan numbers that were used to generate this peak list.
void getRetentionTimes (std::vector< int > &index, std::vector< std::string > &times) const
 Returns all retention times in seconds of the scans that were used to generate this peak list.
std::string getRetentionTimes (const int rawFileIdx=-1) const
 Returns the retention time(s) in seconds of the scans that were used to generate this peak list.
std::string getRULES () const
 Returns the instrument rules if this has been specified at the query level.
std::string getScanNumbers (const int rawFileIdx=-1) const
 Returns the scan number(s) that were used to generate this peak list.
void getScanNumbers (std::vector< int > &index, std::vector< std::string > &scans) const
 Returns all scan numbers that were used to generate this peak list.
std::string getSeq (int seq_no) const
 Returns a string that represents one of the sequence queries..
std::string getStringIons1 ()
 Returns the peak list for the ions as a string.
std::string getStringIons2 ()
 Returns the peak list for the ions as a string.
std::string getStringIons3 ()
 Returns the peak list for the ions as a string.
std::string getStringTitle (bool unescaped) const
 Returns the title for the ms-ms data (if any).
std::string getTag (int tag_no) const
 Returns a string that represents one of the sequence tag queries.
double getTotalIonsIntensity ()
 Returns the sum of all the ions intensities.

Detailed Description

This class encapsulates the input data in the mascot results file.

Although all these parameters could be obtained using the lower level functions such as ms_mascotresfile::getQuerySectionValue it is generally more convenient to use this object.

Examples:

resfile_input.cpp.


Constructor & Destructor Documentation

ms_inputquery ( const ms_mascotresfile resfile,
const int  q 
)

Use this contructor to create an object to get the input data.

Constructor for ms_inputquery.

See Maintaining object references: two rules of thumb.

Parameters:
resfileMust be a valid ms_mascotresfile object.
qis the query number and must be in the range 1 to ms_mascotresfile::getNumQueries().

Member Function Documentation

std::string getCharge (  ) const

Returns a string that represents the supplied charge for the query.

This value will only be present if a charge was specified at the query level in the input (MGF, PKL, mzData, DTA) file. It will normally 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 for further information.

The default charge states are available from ms_searchparams::getCHARGE. Use ms_peptide::getCharge to return the actual charge state that was used for a peptide match.

Returns:
The charge(s) as a string.
std::string getComp ( int  comp_no ) const

Returns a string that represents one of the sequence queries.

Up to 20 sets of composition data can be entered for each peptide mass.

See also:
http://www.matrixscience.com/help/search_field_help.html#QUE for further information.
Parameters:
comp_nois an index for the comp() command. The input data is available as COMP1, COMP2 COMP3 etc. To get all composition data, call this function with numbers from 1 to 20.
Returns:
the comp() command as a string
int getIndex (  ) const

Returns the zero based index of the peak list in an MGF, PKL or DTA file.

In Mascot 2.3 and later, the index of each spectrum is saved as an index= value in each query section. This can be useful, because the query numbers are not the same as the index into the text file, and if there are non-unique titles, then it is hard to get back from the query to the original spectrum in the MGF, PKL or DTA file

The index is stored in mzIdentML files using the CV term:

   [Term]
   id: MS:1000774
   name: multiple peak list nativeID format
   def: "index=xsd:nonNegativeInteger" [PSI:MS]
   comment: Used for conversion of peak list files with multiple spectra, i.e. MGF, PKL, merged DTA files. Index is the spectrum number in the file, starting from 0.
   is_a: MS:1000767 ! native spectrum identifier format
   
Returns:
A zero based index, or -1 if the value is not available.
std::string getINSTRUMENT ( const bool  unescaped = true ) const

Returns an INSTRUMENT string if this has been specified at the query level.

This string will always be empty for versions of Mascot prior to 2.2.

A value is only returned when INSTRUMENT is specified in the MGF file. For example:

     BEGIN IONS
     PEPMASS=1234
     INSTRUMENT=ETD_TRAP
     50 1
     100 3
     400 5
     END IONS

The value is obtained from the INSTRUMENT= line in the relevant query section of the results file. If there is no instrument specified at the query level, then the INSTRUMENT specified in the search form is used. This can be retrieved using ms_searchparams::getINSTRUMENT().

See also ms_inputquery::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 instrument name.

See also:
http://www.matrixscience.com/help/search_field_help.html#INSTRUMENT for further information.
Parameters:
unescapedhas to be TRUE for human-readable instrument name and FALSE for generating input for a mascot search.
Returns:
The INSTRUMENT string, or an empty string if no instrument was specified at the query level.
double getIntMax (  ) const

Returns the maximum intensity of any ion.

Returns:
The maximum intensity. Even if ions are entered as ions(b- ...), ions(y-...) and ions(...), this function returns the maximum intensity of any ion.
double getIntMin (  ) const

Returns the minimum intensity of any ion.

Returns:
The minimum intensity. Even if ions are entered as ions(b- ...), ions(y-...) and ions(...), this function returns the minimum intensity of any ion.
std::string getIT_MODS ( const bool  unescaped = true ) const

Returns the names of variable modifications if such have been specified at the query level.

This string will always be empty for versions of Mascot prior to 2.2.

A value is only returned when variable modifications are specified in the MGF file. For example:

     BEGIN IONS
     PEPMASS=1234
     IT_MODS=Phospho (STY)
     50 1
     100 3
     400 5
     END IONS

The value is obtained from the IT_MODS= line in the relevant query section of the results file. If there are no modifications specified at the query level, then the IT_MODS specified in the search parameters are used. These can be retrieved using ms_searchparams::getIT_MODS().

See also:
http://www.matrixscience.com/help/search_field_help.html#MODS
Parameters:
unescapedhas to be TRUE for human readable modification names and FALSE for generating input for a mascot search.
Returns:
The IT_MODS string, or an empty string if no local modifications were specified.
std::string getLocalVarModName ( const int  num ) const

Returns the query-level modification name by 1-based index.

This method returns unescaped modification names as returned by getIT_MODS(), but accessible with a 1-based numerical index. You can produce the same vector of modification titles by splitting the return value of getIT_MODS(true) on comma ",".

Parameters:
numIndex of the query-level modification between 1 and getNumberOfLocalVarMods().
Returns:
The modification name, or the empty string if num is outside the index range.
std::string getLocus (  ) const

Returns the locus specified in the MGF file using the LOCUS= line.

LOCUS is an optional attribute for an MS-MS peak list in an MGF file.

LOCUS was introduced in Mascot 2.4

See also:
http://www.matrixscience.com/help/data_file_help.html#PARAMS
Returns:
The locus= value in the query section.
double getMassMax (  ) const

Returns the maximum mass of any ion.

Returns:
The maximum mass. Even if ions are entered as ions(b- ...), ions(y-...) and ions(...), this function returns the maximum mass of any ion.
double getMassMin (  ) const

Returns the minimum mass of any ion.

Returns:
The minimum mass. Even if ions are entered as ions(b- ...), ions(y-...) and ions(...), this function returns the minimum mass of any ion.
double getMaxInternalMass (  ) const

Returns the maximum mass to be considered for internal fragments if an INSTRUMENT has been specified at the query level.

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 MS-MS spectrum, in which case the values are returned using this function and ms_inputquery::getMinInternalMass

See also:
getMinInternalMass(), getRULES() and getINSTRUMENT()
Returns:
The maximum internal mass considered for this spectrum in this search If no instrument was specified at the query level, then this function will return -1.
double getMinInternalMass (  ) const

Returns the minimum mass to be considered for internal fragemnts if an INSTRUMENT has been specified at the query level.

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. A different instrument can be specified for each MS-MS spectrum, in which case the values are returned using this function and ms_inputquery::getMaxInternalMass.

See also:
ms_searchparams::getMinInternalMass(), ms_searchparams::getMaxInternalMass()
Returns:
The minimum internal mass considered for this spectrum in this search. If no instrument was specified at the query level, then this function will return -1.
int getNumberOfLocalVarMods (  ) const

Returns the name of query-level variable modifications.

Returns:
The number of unescaped modification names from getIT_MODS().
int getNumberOfPeaks ( const int  ions )

Returns the number of ions peaks in an ms-ms spectrum.

See also:
getPeakList(), getPeakMass() and getPeakIntensity()

The 'ions' value will normally be '1'. For ms-ms data entered via the sequence query, it is possible to specify that values are part of a b-series, y-series or either series -- see http://www.matrixscience.com/help/sq_help.html#IONS.

If all three types of ions are entered, then the separate values will be saved as ions1, ions2 and ions3 in the results file. For data uploaded from a file, only ions1 values will be found.

The ions1= value is read from file 'on demand', so execution of this function can take a while. The data is cached on the first call of one of the following functions:

Parameters:
ionswill be a value of 1..3.
Returns:
The number of peaks in the peak list.
int getNumUsed (  ) const

Returns the number of ions used for matching - value no longer available.

This value is always saved as '-1' in the results files, so this function always returns -1. To find the number of ions peaks used for scoring, see ms_peptide::getPeaksUsedFromIons1, ms_peptide::getPeaksUsedFromIons2 and ms_peptide::getPeaksUsedFromIons3.

Returns:
-1
int getNumVals (  ) const

Returns the number of ions.

This is retrieved from the num_vals= line of the query section.

Even if ions are entered as ions(b- ...), ions(y-...) and ions(...), this function returns the number of all ions.

Returns:
The number of ions.
double getPeakIntensity ( const int  ions,
const int  peakNo 
)

Returns the intensity of a particular ions peak.

See also:
getPeakList(), getNumberOfPeaks() and getPeakMass()

The 'ions' value will normally be '1'. For ms-ms data entered via the sequence query, it is possible to specify that values are part of a b-series, y-series or either series -- see http://www.matrixscience.com/help/sq_help.html#IONS.

If all three types of ions are entered, then the separate values will be saved as ions1, ions2 and ions3 in the results file. For data uploaded from a file, only ions1 values will be found.

The ions1= value is read from file 'on demand', so execution of this function can take a while. The data is cached on the first call of one of the following functions:

Parameters:
ionswill be a value of 1..3.
peakNoshould be in the range 1.. getNumberOfPeaks().
Returns:
If there is no peak information, then the return value will be 0.
std::vector< std::pair< double, double > > getPeakList ( const int  ions )

Returns a list of ions peaks for a query.

Do not use this function from programming languages other than C++. Use getNumberOfPeaks(), getPeakMass() and getPeakIntensity() instead.

The 'ions' value will normally be '1'. For MS-MS data entered via the sequence query, it is possible to specify that values are part of a b-series, y-series or either series -- see http://www.matrixscience.com/help/sq_help.html#IONS.

If all three types of ions are entered, then the separate values will be saved as ions1, ions2 and ions3 in the results file. For data uploaded from a file, only ions1 values will be found.

The ions1= value is read from file 'on demand', so execution of this function can take a while. The data is cached on the first call of one of the following functions:

Parameters:
ionsions value, can be 1, 2 or 3
Returns:
The peak list.
double getPeakMass ( const int  ions,
const int  peakNo 
)

Returns the mass of a particular ions peak.

See also:
getPeakList(), getNumberOfPeaks() and getPeakIntensity()

The 'ions' value will normally be '1'. For ms-ms data entered via the sequence query, it is possible to specify that values are part of b-series, y-series or either series -- see http://www.matrixscience.com/help/sq_help.html#IONS.

If all three types of ions are entered, then the separate values will be saved as ions1, ions2 and ions3 in the results file. For data uploaded from a file, only ions1 values will be found.

The ions1= value is read from file 'on demand', so execution of this function can take a while. The data is cached on the first call of one of the following functions:

Parameters:
ionswill be a value of 1..3.
peakNoshould be in the range 1.. getNumberOfPeaks().
Returns:
If there is no peak information, then the return value will be 0.
double getPepTol (  ) const

Returns the peptide tolerance for this query.

peptol(tolerance,unit) may be used to specify a mass tolerance for an individual query, over-riding the search form default. For example, peptol(10,%) or peptol(2,Da).

Returns:
Will return 0 if there is no peptide tolerance override for this query.
std::string getPepTolString (  ) const

Returns the peptol string .

Returns, for example, peptol(2.01,Da). The number is always returned in 'fixed' notation. Trailing zeros apart from the one (if any) after the decimal are removed.

This function is intended to be used to create a sequence query string rather than for use to display in a report.

See also:
getPepTolUnits(), getPepTol()
Returns:
Will return an empty string if there is no peptide tolerance override for this query.
std::string getPepTolUnits (  ) const

Returns the peptide tolerance units for this query.

In the search form, the command peptol(tolerance,unit) may be used override the default mass tolerance for an individual query. For example, peptol(10,%) or peptol(2,Da).

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
Da
absolute units of Da
Returns:
Will return an empty string if there is no peptide tolerance override for this query.
std::string getRawfile (  ) const

Returns the rawfile specified in the MGF file using the RAWFILE= line.

RAWFILE is an optional attribute for an MS-MS peak list in an MGF file.

RAWFILE was introduced in Mascot 2.4.

See also:
http://www.matrixscience.com/help/data_file_help.html#PARAMS
Returns:
The rawfile= value in the query section.
std::string getRawScans ( const int  rawFileIdx = -1 ) const

Returns the rawscan number(s) that were used to generate this peak list.

RAWSCANS is an optional attribute for an MS-MS peak list in an MGF file.

Separate values for multiple raw files were introduced in Mascot 2.3. The results file may contain "rawscans" with no brackets or zero or more "rawscans[i]" lines.

If rawFileIdx is -1, this method returns the unbracketed value. Otherwise, an individual bracketed line is retrieved.

To retrieve all unbracketed and bracketed values, use ms_inputquery::getRawScans(std::vector<int>&, std::vector<std::string>&).

See also:
http://www.matrixscience.com/help/data_file_help.html#PARAMS
Parameters:
rawFileIdxis the raw file index for MGF files that were created from multiple raw files.
Returns:
The scan number(s) in the form a[[-b][,c[-d]]]
void getRawScans ( std::vector< int > &  index,
std::vector< std::string > &  rawscans 
) const

Returns all rawscan numbers that were used to generate this peak list.

RAWSCANS is an optional attribute for an MS-MS peak list in an MGF file.

Separate values for multiple raw files were introduced in Mascot 2.3. The results file may contain "rawscans" with no brackets or zero or more "rawscans[i]" lines.

This method returns all rawscans lines, bracketed or not. The elements returned in index are the indices, and the corresponding elements in scans are the values. For example, if the query section has

 rawscans=sn13
 

then both index and times will have one element. index[0] will be -1 (unbracketed) and rawscans[0] will be sn13. If the query section instead has

 rawscans[3]=sn13
 rawscans[5]=sn24
 

then index[0] == 3, index[1] == 5 and rawscans[0] == "sn13", rawscans[1] == "sn24".

If you already know which lines are present in the query section, you can use ms_inputquery::getRawScans(const int) to access the individual lines.

See also:
http://www.matrixscience.com/help/data_file_help.html#PARAMS
Parameters:
[out]indexVector of index numbers for corresponding "rawscans" lines. Unbracketed line has index -1, and the other indices start from 0.
[out]rawscansVector of values from the "rawscans" lines in the same order as the index vector.
void getRetentionTimes ( std::vector< int > &  index,
std::vector< std::string > &  times 
) const

Returns all retention times in seconds of the scans that were used to generate this peak list.

RTINSECONDS is an optional attribute for an MS-MS peak list in an MGF file.

Separate values for multiple raw files were introduced in Mascot 2.3. The results file may contain "rtinseconds" with no brackets or zero or more "rtinseconds[i]" lines.

This method returns all rtinseconds lines, bracketed or not. The elements returned in index are the indices, and the corresponding elements in scans are the values. For example, if the query section has

 rtinseconds=1234.0
 

then both index and times will have one element. index[0] will be -1 (unbracketed) and times[0] will be 1234.0. If the query section instead has

 rtinseconds[3]=1234.0
 rtinseconds[5]=1244.0
 

then index[0] == 3, index[1] == 5 and times[0] == 1234.0, times[1] == 1244.0.

If you already know which lines are present in the query section, you can use ms_inputquery::getRetentionTimes(const int) to access the individual lines.

See also:
http://www.matrixscience.com/help/data_file_help.html#PARAMS
Parameters:
[out]indexVector of index numbers for corresponding "rtinseconds" lines. Unbracketed line has index -1, and the other indices start from 0.
[out]timesVector of values from the "rtinseconds" lines in the same order as the index vector.
std::string getRetentionTimes ( const int  rawFileIdx = -1 ) const

Returns the retention time(s) in seconds of the scans that were used to generate this peak list.

RTINSECONDS is an optional attribute for an MS-MS peak list in an MGF file.

Separate values for multiple raw files were introduced in Mascot 2.3. The results file may contain "rtinseconds" with no brackets or zero or more "rtinseconds[i]" lines.

If rawFileIdx is -1, this method returns the unbracketed value. Otherwise, an individual bracketed line is retrieved.

To retrieve all unbracketed and bracketed values, use ms_inputquery::getRetentionTimes(std::vector<int>&, std::vector<std::string>&).

See also:
http://www.matrixscience.com/help/data_file_help.html#PARAMS
Parameters:
rawFileIdxis the raw file index for MGF files that were created from multiple raw files.
Returns:
The retention time(s) in the form v[[-w][,x[-y]]].
std::string getRULES (  ) const

Returns the instrument rules if this has been specified at the query level.

This string will always be empty for versions of Mascot prior to 2.2.

A value is only returned when INSTRUMENT is specified in the MGF file. For example:

     BEGIN IONS
     PEPMASS=1234
     INSTRUMENT=ETD_TRAP
     50 1
     100 3
     400 5
     END IONS

The value is obtained from the RULES= line in the relevant query section of the results file. If there is no instrument specified at the query level, then RULES specified in the search form, and the rules for this query are the global rules which can be retrieved using ms_searchparams::getRULES().

It is preferable to use the rules rather than the instrument name to determine which ions series were searched since the user can change the definition of the instrument name.

See also:
getINSTRUMENT()
Returns:
The RULES string, or an empty string if no instrument was specified. See ms_searchparams::getRULES() for a full definition of the rules.
std::string getScanNumbers ( const int  rawFileIdx = -1 ) const

Returns the scan number(s) that were used to generate this peak list.

SCANS is an optional attribute for an MS-MS peak list in an MGF file.

Separate values for multiple raw files were introduced in Mascot 2.3. The results file may contain "scans" with no brackets or zero or more "scans[i]" lines.

If rawFileIdx is -1, this method returns the unbracketed value. Otherwise, an individual bracketed line is retrieved.

To retrieve all unbracketed and bracketed values, use ms_inputquery::getScanNumbers(std::vector<int>&, std::vector<std::string>&).

See also:
http://www.matrixscience.com/help/data_file_help.html#PARAMS
Parameters:
rawFileIdxis the raw file index for MGF files that were created from multiple raw files.
Returns:
The scan number(s) in the form a[[-b][,c[-d]]].
void getScanNumbers ( std::vector< int > &  index,
std::vector< std::string > &  scans 
) const

Returns all scan numbers that were used to generate this peak list.

SCANS is an optional attribute for an MS-MS peak list in an MGF file.

Separate values for multiple raw files were introduced in Mascot 2.3. The results file may contain "scans" with no brackets or zero or more "scans[i]" lines.

This method returns all scans lines, bracketed or not. The elements returned in index are the indices, and the corresponding elements in scans are the values. For example, if the query section has

 scans=1
 

then both index and scans will have one element. index[0] will be -1 (unbracketed) and scans[0] will be 1. If the query section instead has

 scans[3]=13
 scans[5]=26
 

then index[0] == 3, index[1] == 5 and scans[0] == 13, scans[1] == 26.

If you already know which lines are present in the query section, you can use ms_inputquery::getScanNumbers(const int) to access the individual lines.

See also:
http://www.matrixscience.com/help/data_file_help.html#PARAMS
Parameters:
[out]indexVector of index numbers for corresponding "scans" lines. Unbracketed line has index -1, and the other indices start from 0.
[out]scansVector of values from the "scans" lines in the same order as the index vector.
std::string getSeq ( int  seq_no ) const

Returns a string that represents one of the sequence queries..

Up to 20 sets of sequence information can be entered for each peptide mass.

See also:
http://www.matrixscience.com/help/search_field_help.html#QUE for further information.
Parameters:
seq_nois an index for the seq() command. The input data is available as SEQ1, SEQ2 SEQ3 etc. To get all sequence data, call this function with numbers from 1 to 20.
Returns:
the seq() command as a string.
std::string getStringIons1 (  )

Returns the peak list for the ions as a string.

The ions1= value is read from file 'on demand', so execution of this function can take a while. The data is cached on the first call of one of the following functions:

Returns:
The ions1= value in the form: 136.070000:42.95,175.110000:133.1,299.060000:710.1,415.030000:144.6 . . .
std::string getStringIons2 (  )

Returns the peak list for the ions as a string.

The ions2= value is read from file 'on demand', so execution of this function can take a while. The data is cached on the first call of one of the following functions:

Returns:
The ions2= value in the form: 136.070000:42.95,175.110000:133.1,299.060000:710.1,415.030000:144.6 . . .
std::string getStringIons3 (  )

Returns the peak list for the ions as a string.

The ions3= value is read from file 'on demand', so execution of this function can take a while. The data is cached on the first call of one of the following functions:

Returns:
The ions3= value in the form: 136.070000:42.95,175.110000:133.1,299.060000:710.1,415.030000:144.6 . . .
std::string getStringTitle ( bool  unescaped ) const

Returns the title for the ms-ms data (if any).

The string will have a maximum length of 30k characters. It might for example be:

1: Scan 2443 (rt=1651.36) [P:\\service\\on_campus\\Nunari\\Laura\\ft20061020.RAW] 
Parameters:
unescaped- If this is false, then any non alpha-numeric characters in the string will be converted to %xx where the xx are the hex representation of the character.
Returns:
The title string.
std::string getTag ( int  tag_no ) const

Returns a string that represents one of the sequence tag queries.

Up to 20 tag/etag commands can be entered for each peptide mass.

See also:
http://www.matrixscience.com/help/search_field_help.html#QUE for further information.
Parameters:
tag_nois an index for the tag() command. The input data is available as TAG1, TAG2 TAG3 etc. To get all tags, call this function with numbers from 1 to 20.
Returns:
the tag() command as a string in the format e,977.4,[Q|K][Q|K][Q|K]EE,1619.7 where the first character will be 'e' for etag and 't' for tag.
double getTotalIonsIntensity (  )

Returns the sum of all the ions intensities.

See also ms_mascotresfile::getObservedIntensity. If the precursor intensity wasn't supplied in the input file, this function can be called instead. Processing this function for a large number of spectra may take some time since it will need to load the ions1= values from disk and sum all the intensities.

See also ms_peptide::getIonsIntensity which just calls this function.

The ions1= value is read from file 'on demand', so execution of this function can take a while. The data is cached on the first call of one of the following functions:

Returns:
Will return 0 if there is no MS-MS data.

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 01:44:52