OpenMS
2.5.0
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Generate the stream of configurations, ordered from most likely to least likely. More...
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsoSpecWrapper.h>
Public Member Functions | |
IsoSpecOrderedGeneratorWrapper (const std::vector< int > &isotopeNumbers, const std::vector< int > &atomCounts, const std::vector< std::vector< double > > &isotopeMasses, const std::vector< std::vector< double > > &isotopeProbabilities) | |
Constructor. More... | |
IsoSpecOrderedGeneratorWrapper (const EmpiricalFormula &formula) | |
Setup the algorithm to run on an EmpiricalFormula. More... | |
virtual bool | nextConf () override final |
Move the generator to a next isotopologue. More... | |
virtual Peak1D | getConf () override final |
Obtain the current isotopologue. More... | |
virtual double | getMass () override final |
Obtain the mass of the current isotopologue. More... | |
virtual double | getIntensity () override final |
Obtain the intensity (probability, relative peak height) of the current configuration. More... | |
virtual double | getLogIntensity () override final |
Obtain the natural logarithm of the intensity (probability, relative peak height) of the current configuration. More... | |
Public Member Functions inherited from IsoSpecGeneratorWrapper | |
virtual | ~IsoSpecGeneratorWrapper () |
Destructor. More... | |
Protected Attributes | |
IsoSpec::IsoOrderedGenerator | IOG |
Generate the stream of configurations, ordered from most likely to least likely.
This generator walks through the entire set of isotopologues of a given molecule, allowing the user to terminate the search on the fly. The returned isotopologues are guaranteed to be generated in order of descending probability (unlike the previous two generators which make no such guarantees).
This causes the algorithm to run in O(n*log(n)) and means that is it much slower than the previous two.
You should only use this generator if you don't know up-front when to stop the walk through the configuration space, and need to make the decision on the fly. If you know the threshold or the total probability needed, and only need the configurations sorted, it will be much faster to generate them using one of the previous algorithms and sort them afterwards.
IsoSpecOrderedGeneratorWrapper | ( | const std::vector< int > & | isotopeNumbers, |
const std::vector< int > & | atomCounts, | ||
const std::vector< std::vector< double > > & | isotopeMasses, | ||
const std::vector< std::vector< double > > & | isotopeProbabilities | ||
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Constructor.
isotopeNumbers | A vector of how many isotopes each element has, e.g. [2, 2, 3]) |
atomCounts | How many atoms of each we have [e.g. 12, 6, 6 for Glucose] |
isotopeMasses | Array with the individual elements isotopic masses |
isotopeProbabilities | Array with the individual elements isotopic probabilities |
IsoSpecOrderedGeneratorWrapper | ( | const EmpiricalFormula & | formula | ) |
Setup the algorithm to run on an EmpiricalFormula.
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inlinefinaloverridevirtual |
Obtain the current isotopologue.
Implements IsoSpecGeneratorWrapper.
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inlinefinaloverridevirtual |
Obtain the intensity (probability, relative peak height) of the current configuration.
Implements IsoSpecGeneratorWrapper.
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inlinefinaloverridevirtual |
Obtain the natural logarithm of the intensity (probability, relative peak height) of the current configuration.
This will be more precise (and faster) than just calling std::log(getIntensity()) - it will produce correct results even for configurations so unlikely that the double-precision floating point number returned from getIntensity() underflows to zero.
Implements IsoSpecGeneratorWrapper.
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inlinefinaloverridevirtual |
Obtain the mass of the current isotopologue.
Implements IsoSpecGeneratorWrapper.
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inlinefinaloverridevirtual |
Move the generator to a next isotopologue.
Advance the internal generator to the next isotopologue. The value returned determines whether the generator has been exhausted (that is, all eligible configurations have already been visited). It is invalid to call any other generator methods before the first call to nextConf(), as well as after this method returns false.
Implements IsoSpecGeneratorWrapper.
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protected |