computes empirical formulas for given mass differences using a set of allowed elements More...
#include <OpenMS/DATASTRUCTURES/MassExplainer.h>
Public Types | |
| typedef Adduct::AdductsType | AdductsType |
| typedef std::vector< Compomer > ::const_iterator | CompomerIterator |
Public Member Functions | |
| void | compute () |
| fill map with possible mass-differences along with their explanation More... | |
| SignedSize | query (const Int net_charge, const float mass_to_explain, const float mass_delta, const float thresh_log_p, std::vector< Compomer >::const_iterator &firstExplanation, std::vector< Compomer >::const_iterator &lastExplanation) const |
| void | setAdductBase (AdductsType adduct_base) |
| Sets the set of possible adducts. More... | |
| AdductsType | getAdductBase () const |
| Returns the set of adducts. More... | |
| const Compomer & | getCompomerById (Size id) const |
| return a compomer by its Id (useful after a query() ). More... | |
Protected Member Functions | |
| bool | compomerValid_ (const Compomer &cmp) |
| check if the generated compomer is valid judged by its probability, charges etc More... | |
| Adduct | createAdduct_ (const String &formula, const Int charge, const DoubleReal p) const |
| create a proper adduct from formula and charge and probability More... | |
Protected Attributes | |
| std::vector< Compomer > | explanations_ |
| store possible explanations (as formula) for a certain ChargeDifference and MassDifference More... | |
| AdductsType | adduct_base_ |
| all allowed adducts, whose combination explains the mass difference More... | |
| Int | q_min_ |
| minimal expected charge More... | |
| Int | q_max_ |
| maximal expected charge More... | |
| Int | max_span_ |
| maximal span (in terms of charge) for co-features, e.g. a cluster with q={3,6} has span=4 More... | |
| DoubleReal | thresh_p_ |
| minimum required probability of a compound (all other compounds are discarded) More... | |
| Size | max_neutrals_ |
| Maximum number of neutral(q=0) adducts. More... | |
Constructors and destructor | |
| MassExplainer () | |
| Default constructor. More... | |
| MassExplainer (AdductsType adduct_base) | |
| Constructor. More... | |
| MassExplainer (Int q_min, Int q_max, Int max_span, DoubleReal thresh_logp) | |
| Constructor. More... | |
| MassExplainer (AdductsType adduct_base, Int q_min, Int q_max, Int max_span, DoubleReal thresh_logp, Size max_neutrals) | |
| Constructor. More... | |
| MassExplainer & | operator= (const MassExplainer &rhs) |
| Assignment operator. More... | |
| virtual | ~MassExplainer () |
| Destructor. More... | |
| void | init_ (bool init_thresh_p) |
computes empirical formulas for given mass differences using a set of allowed elements
| typedef Adduct::AdductsType AdductsType |
| typedef std::vector<Compomer>::const_iterator CompomerIterator |
| MassExplainer | ( | ) |
Default constructor.
| MassExplainer | ( | AdductsType | adduct_base | ) |
Constructor.
| MassExplainer | ( | Int | q_min, |
| Int | q_max, | ||
| Int | max_span, | ||
| DoubleReal | thresh_logp | ||
| ) |
Constructor.
| MassExplainer | ( | AdductsType | adduct_base, |
| Int | q_min, | ||
| Int | q_max, | ||
| Int | max_span, | ||
| DoubleReal | thresh_logp, | ||
| Size | max_neutrals | ||
| ) |
Constructor.
|
virtual |
Destructor.
|
protected |
check if the generated compomer is valid judged by its probability, charges etc
| void compute | ( | ) |
fill map with possible mass-differences along with their explanation
|
protected |
create a proper adduct from formula and charge and probability
| AdductsType getAdductBase | ( | ) | const |
Returns the set of adducts.
return a compomer by its Id (useful after a query() ).
|
private |
check consistency of input
| init_thresh_p | set default threshold (set to "false" to keep current value) |
| MassExplainer& operator= | ( | const MassExplainer & | rhs | ) |
Assignment operator.
| SignedSize query | ( | const Int | net_charge, |
| const float | mass_to_explain, | ||
| const float | mass_delta, | ||
| const float | thresh_log_p, | ||
| std::vector< Compomer >::const_iterator & | firstExplanation, | ||
| std::vector< Compomer >::const_iterator & | lastExplanation | ||
| ) | const |
search the mass database for explanations
| net_charge | net charge of compomer seeked |
| mass_to_explain | mass in Da that needs explanation |
| mass_delta | allowed deviation from exact mass |
| thresh_log_p | minimal log probability required |
| firstExplanation | begin range with candidates according to net_charge and mass |
| lastExplanation | end range |
| void setAdductBase | ( | AdductsType | adduct_base | ) |
Sets the set of possible adducts.
|
protected |
all allowed adducts, whose combination explains the mass difference
|
protected |
store possible explanations (as formula) for a certain ChargeDifference and MassDifference
|
protected |
Maximum number of neutral(q=0) adducts.
|
protected |
maximal span (in terms of charge) for co-features, e.g. a cluster with q={3,6} has span=4
|
protected |
maximal expected charge
|
protected |
minimal expected charge
|
protected |
minimum required probability of a compound (all other compounds are discarded)
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:29 using doxygen 1.8.5 |