Represents a distribution of isotopes restricted to the first K elements. More...
#include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/IMS/IMSIsotopeDistribution.h>
Classes | |
| struct | Peak |
| Structure that represents an isotope peak - pair of mass and abundance. More... | |
Public Types | |
| typedef double | mass_type |
| Type of isotope mass. More... | |
| typedef double | abundance_type |
| Type of isotope abundance. More... | |
| typedef unsigned int | nominal_mass_type |
| Type of isotope nominal mass. More... | |
| typedef Peak | peak_type |
| Type of isotope peak. More... | |
| typedef std::vector< peak_type > | peaks_container |
| Type of container to store peaks. More... | |
| typedef peaks_container::iterator | peaks_iterator |
| Type of iterator over container with peaks. More... | |
| typedef peaks_container::const_iterator | const_peaks_iterator |
| Type of const iterator over container with peaks. More... | |
| typedef peaks_container::size_type | size_type |
| Type of peaks container's size. More... | |
| typedef std::vector< mass_type > | masses_container |
| Type of container with isotope masses. More... | |
| typedef masses_container::iterator | masses_iterator |
| Type of iterator over container with isotope masses. More... | |
| typedef masses_container::const_iterator | const_masses_iterator |
| Type of const iterator over container with isotope masses. More... | |
| typedef std::vector < abundance_type > | abundances_container |
| Type of container with isotope abundances. More... | |
| typedef abundances_container::iterator | abundances_iterator |
| Type of iterator over container with isotope abundances. More... | |
| typedef abundances_container::const_iterator | const_abundances_iterator |
| Type of const iterator over container with isotope abundances. More... | |
Static Public Attributes | |
| static abundance_type | ABUNDANCES_SUM_ERROR |
| Error to be allowed for isotope distribution. More... | |
| static size_type | SIZE |
| Length of isotope distribution. More... | |
Private Member Functions | |
| void | setMinimumSize_ () |
| Sets peaks/isotopes container minimum size. More... | |
Private Attributes | |
| peaks_container | peaks_ |
| Container for isotopes. More... | |
| nominal_mass_type | nominal_mass_ |
| Nominal mass of distribution. More... | |
Represents a distribution of isotopes restricted to the first K elements.
Represents a distribution of isotopes of chemical elements as a list of peaks each as a pair of mass and abundance. IsotopeDistribution unlike IsotopeSpecies has one abundance per a nominal mass. Here is an example in the format (mass; abundance %) for molecule H2O (values are taken randomly):
To the sake of faster computations distribution is restricted to the first K elements, where K can be set by adjusting size SIZE of distribution.
IsotopeDistribution implements folding with other distribution using an algorithm described in details in paper: Boecker et al. "Decomposing metabolic isotope patterns" WABI 2006.
Folding with itself is done using Russian Multiplication Scheme.
| typedef double abundance_type |
Type of isotope abundance.
| typedef std::vector<abundance_type> abundances_container |
Type of container with isotope abundances.
| typedef abundances_container::iterator abundances_iterator |
Type of iterator over container with isotope abundances.
| typedef abundances_container::const_iterator const_abundances_iterator |
Type of const iterator over container with isotope abundances.
| typedef masses_container::const_iterator const_masses_iterator |
Type of const iterator over container with isotope masses.
| typedef peaks_container::const_iterator const_peaks_iterator |
Type of const iterator over container with peaks.
| typedef std::vector<mass_type> masses_container |
Type of container with isotope masses.
| typedef masses_container::iterator masses_iterator |
Type of iterator over container with isotope masses.
| typedef unsigned int nominal_mass_type |
Type of isotope nominal mass.
| typedef std::vector<peak_type> peaks_container |
Type of container to store peaks.
| typedef peaks_container::iterator peaks_iterator |
Type of iterator over container with peaks.
| typedef peaks_container::size_type size_type |
Type of peaks container's size.
|
inlineexplicit |
Constructor with nominal mass.
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inlineexplicit |
Constructor with single isotope.
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inline |
Constructor with isotopes and nominal mass.
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inline |
Copy constructor.
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inline |
Destructor.
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inline |
Returns true if the distribution has no peaks, false - otherwise.
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inline |
Gets an abundance of isotope i.
| i | An index of isotope. |
i. | abundances_container getAbundances | ( | ) | const |
Gets abundances of isotopes.
| mass_type getAverageMass | ( | ) | const |
Gets an average mass of all isotopes.
Gets a mass of isotope i.
| i | An index of isotope. |
i. | masses_container getMasses | ( | ) | const |
Gets masses of isotopes.
|
inline |
Gets a nominal mass of distribution.
| void normalize | ( | ) |
Normalizes distribution, i.e. scaling abundances to be summed up to 1 with an error ABUNDANCES_SUM_ERROR allowed.
| bool operator!= | ( | const IMSIsotopeDistribution & | distribution | ) | const |
Inequality operator. Returns true, if a given distribution is unequal to this one, false - otherwise.
| IMSIsotopeDistribution& operator*= | ( | const IMSIsotopeDistribution & | distribution | ) |
Operator for folding this distributoin with a given distribution.
| distribution | Distribution to be folded with this one. |
| IMSIsotopeDistribution& operator*= | ( | unsigned int | pow | ) |
Operator for folding this distribution with itself pow times.
| pow | Number of times this distribution is to be folded with itself. |
| IMSIsotopeDistribution& operator= | ( | const IMSIsotopeDistribution & | distribution | ) |
Assignment operator.
| distribution | Isotope distribution to be assigned to this one. |
| bool operator== | ( | const IMSIsotopeDistribution & | distribution | ) | const |
Equality operator. Returns true, if a given distribution is equal to this one, false - otherwise.
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private |
Sets peaks/isotopes container minimum size.
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inline |
Sets a nominal mass for distribution.
| nominalMass | The new nominal mass for the distributoin. |
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inline |
Gets size of isotope distribution.
SIZE.
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static |
Error to be allowed for isotope distribution.
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private |
Nominal mass of distribution.
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private |
Container for isotopes.
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static |
Length of isotope distribution.
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:37 using doxygen 1.8.5 |