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Matrix Science Mascot Parser toolkit
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Matrix Science Mascot Parser toolkit
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A component within a match. More...
#include <ms_ms1quant_match_component.hpp>
Inherits ms_handle.
Public Member Functions | |
| ms_ms1quant_match_component () | |
| Default constructor. | |
| ms_ms1quant_match_component (const ms_ms1quant_match_component_body &body) | |
| Populated constructor. | |
| double | getAbsoluteValue (const int file_index=-1) const |
| Get the summed intensity values for this component across the XIC peak. Required for normalisation. | |
| std::string | getComponent () const |
| Get the component. | |
| int | getFileIndex (const int idx) const |
| Return the 1 based file_index. | |
| double | getMatchedFraction (const int file_index=-1) const |
| Get the matched fraction for the specified raw file. | |
| double | getMatchedRho (const int file_index=-1) const |
| Get the matched rho for the specified raw file. | |
| double | getMoverz () const |
| Get the calculated m/z value. | |
| int | getNumFileIndexesMatched () const |
| For replicate, using prefractionation, this can return a value greater than zero. | |
| int | getNumPeptides (const int file_index=ms_quant_file_index::file_index_value_not_set) const |
| Get the number of related peptides. | |
| int | getNumRanges (const int file_index=ms_quant_file_index::file_index_value_not_set) const |
| Get the number of ranges. | |
| void | getPeptideKey (const int file_index, int index, int &q, int &p) const |
| Get a related peptide's feature key by its index (1..n). | |
| void | getPeptideKey (int index, int &q, int &p) const |
| Get a related peptide's feature key by its index (1..n). | |
| ms_ms1quant_match_range | getRange (const int file_index, int index) const |
| Get a range value by its index (1..n). | |
| ms_ms1quant_match_range | getRange (int index) const |
| Get a range value by its index (1..n). | |
| double | getRelativeMass () const |
| Get the relative mass value. | |
| std::string | getSummedModsStr () const |
| Returns the string for any 'summed' modifications for this particular match. | |
| std::string | getVarModsStr () const |
| Returns the string for any 'variable' modifications for this particular match. | |
| ms_xic | getXic (const int file_index=ms_quant_file_index::file_index_value_not_set) const |
| Get the extracted ion chromatogram (XIC). | |
| bool | hasAbsoluteValue (const int file_index=-1) const |
| Check if the absolute value is available. | |
| bool | hasMatchedFraction (const int file_index=-1) const |
| Check if the matched fraction is available for the specified raw file. | |
| bool | hasMatchedRho (const int file_index=-1) const |
| Check if the matched rho is available for the specified raw file. | |
| bool | isComponentIdentified (const int file_index=-1) const |
| Check if the component has been identified. | |
Protected Member Functions | |
| std::size_t | getIdxFromFileIndex (const int file_index) const |
| Just used internally by inherited classes that need access to inherited XICs etc. | |
A component within a match.
This is stored in XML in "partner" and "absoluteValue" entities.
Default constructor.
Assigns reasonable default values to all internal members.
| ms_ms1quant_match_component | ( | const ms_ms1quant_match_component_body & | body | ) |
Populated constructor.
| body | The data loaded from the result file. |
| double getAbsoluteValue | ( | const int | file_index = -1 | ) | const |
Get the summed intensity values for this component across the XIC peak. Required for normalisation.
If ratio values not are absolute use total intensity as absolute value
| file_index | is used for replicate, where the samples have been prefractionated and there is a raw data file for each fraction, the method can be set up so that each component (i.e. sample) has a number of file_index values, one for each file. |
| std::string getComponent | ( | ) | const |
Get the component.
| int getFileIndex | ( | const int | idx | ) | const |
Return the 1 based file_index.
See getNumFileIndexesMatched()
| idx | must be in the range 0.. getNumFileIndexesMatched()-1 |
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protected |
Just used internally by inherited classes that need access to inherited XICs etc.
| file_index | is used for replicate, where the samples have been prefractionated and there is a raw data file for each fraction, the method can be set up so that each component (i.e. sample) has a number of file_index values, one for each file. |
| double getMatchedFraction | ( | const int | file_index = -1 | ) | const |
Get the matched fraction for the specified raw file.
This is only used for the replicate protocol where data sets have been merged. For the precursor protocol, use matrix_science::ms_ms1quant_charge_state::getMatchedFraction
| file_index | is used for replicate, where the samples have been prefractionated and there is a raw data file for each fraction, the method can be set up so that each component (i.e. sample) has a number of file_index values, one for each file. |
| double getMatchedRho | ( | const int | file_index = -1 | ) | const |
Get the matched rho for the specified raw file.
This is only used for the replicate protocol where data sets have been merged. For the precursor protocol, use matrix_science::ms_ms1quant_charge_state::getMatchedRho
| file_index | is used for replicate, where the samples have been prefractionated and there is a raw data file for each fraction, the method can be set up so that each component (i.e. sample) has a number of file_index values, one for each file. |
| double getMoverz | ( | ) | const |
Get the calculated m/z value.
| int getNumFileIndexesMatched | ( | ) | const |
For replicate, using prefractionation, this can return a value greater than zero.
For protocols other than replicate, this will always return 1.
For replicate, where the samples have been prefractionated and there is a raw data file for each fraction, the method can be set up so that each component (i.e. sample) has a number of file_index values, one for each file.
| int getNumPeptides | ( | const int | file_index = ms_quant_file_index::file_index_value_not_set | ) | const |
Get the number of related peptides.
| file_index | is used for replicate, where the samples have been prefractionated and there is a raw data file for each fraction, the method can be set up so that each component (i.e. sample) has a number of file_index values, one for each file. |
| int getNumRanges | ( | const int | file_index = ms_quant_file_index::file_index_value_not_set | ) | const |
Get the number of ranges.
| file_index | is used for replicate, where the samples have been prefractionated and there is a raw data file for each fraction, the method can be set up so that each component (i.e. sample) has a number of file_index values, one for each file. |
| void getPeptideKey | ( | const int | file_index, |
| int | index, | ||
| int & | q, | ||
| int & | p | ||
| ) | const |
Get a related peptide's feature key by its index (1..n).
See Multiple return values in Perl, Java, Python and C#.
The returned keys can be used to get the ms_peptide using ms_mascotresults::getPeptide().
| file_index | is used for replicate, where the samples have been prefractionated and there is a raw data file for each fraction, the method can be set up so that each component (i.e. sample) has a number of file_index values, one for each file. |
| index | The index of the required peptide (1..getNumPeptides()). |
| q | The query number. |
| p | The rank. |
| void getPeptideKey | ( | int | index, |
| int & | q, | ||
| int & | p | ||
| ) | const |
Get a related peptide's feature key by its index (1..n).
See Multiple return values in Perl, Java, Python and C#.
The returned keys can be used to get the ms_peptide using ms_mascotresults::getPeptide().
| index | The index of the required peptide (1..getNumPeptides()). |
| q | The query number. |
| p | The rank. |
| matrix_science::ms_ms1quant_match_range getRange | ( | const int | file_index, |
| int | index | ||
| ) | const |
Get a range value by its index (1..n).
| file_index | is used for replicate, where the samples have been prefractionated and there is a raw data file for each fraction, the method can be set up so that each component (i.e. sample) has a number of file_index values, one for each file. |
| index | The index of the required range (1..getNumRanges()). |
| matrix_science::ms_ms1quant_match_range getRange | ( | int | index | ) | const |
Get a range value by its index (1..n).
| index | The index of the required range (1..getNumRanges()). |
| double getRelativeMass | ( | ) | const |
Get the relative mass value.
| std::string getSummedModsStr | ( | ) | const |
Returns the string for any 'summed' modifications for this particular match.
See ms_peptide::getSummedModsStr for details of the format
| std::string getVarModsStr | ( | ) | const |
Returns the string for any 'variable' modifications for this particular match.
See ms_peptide::getVarModsStr for details of the format
| matrix_science::ms_xic getXic | ( | const int | file_index = ms_quant_file_index::file_index_value_not_set | ) | const |
Get the extracted ion chromatogram (XIC).
| file_index | is used for replicate, where the samples have been prefractionated and there is a raw data file for each fraction, the method can be set up so that each component (i.e. sample) has a number of file_index values, one for each file. |
| bool hasAbsoluteValue | ( | const int | file_index = -1 | ) | const |
Check if the absolute value is available.
| file_index | is used for replicate, where the samples have been prefractionated and there is a raw data file for each fraction, the method can be set up so that each component (i.e. sample) has a number of file_index values, one for each file. |
| bool hasMatchedFraction | ( | const int | file_index = -1 | ) | const |
Check if the matched fraction is available for the specified raw file.
This is only used for the replicate protocol where data sets have been merged. For the precursor protocol, use matrix_science::ms_ms1quant_charge_state::getMatchedFraction
| file_index | is used for replicate, where the samples have been prefractionated and there is a raw data file for each fraction, the method can be set up so that each component (i.e. sample) has a number of file_index values, one for each file. |
| bool hasMatchedRho | ( | const int | file_index = -1 | ) | const |
Check if the matched rho is available for the specified raw file.
This is only used for the replicate protocol where data sets have been merged. For the precursor protocol, use matrix_science::ms_ms1quant_charge_state::getMatchedRho
| file_index | is used for replicate, where the samples have been prefractionated and there is a raw data file for each fraction, the method can be set up so that each component (i.e. sample) has a number of file_index values, one for each file. |
| bool isComponentIdentified | ( | const int | file_index = -1 | ) | const |
Check if the component has been identified.
| file_index | is used for replicate where a component comprises multiple raw data files, for example using prefractionation. This value defaults to ms_quant_file_index::file_index_value_not_set where the component match just originates from one data file |
1.9.6