IMSAlphabet#
- class pyopenms.IMSAlphabet#
Bases:
object
Cython implementation of _IMSAlphabet
Original C++ documentation is available here
Holds an indexed list of bio-chemical elements.
Presents an indexed list of bio-chemical elements of type (or derived from type) ‘Element’. Due to indexed structure ‘Alphabet’ can be used similar to std::vector, for example to add a new element to ‘Alphabet’ function push_back(element_type) can be used. Elements or their properties (such as element’s mass) can be accessed by index in a constant time. On the other hand accessing elements by their names takes linear time. Due to this and also the fact that ‘Alphabet’ is ‘heavy-weighted’ (consisting of ‘Element’ -s or their derivatives where the depth of derivation as well is undefined resulting in possibly ‘heavy’ access operations) it is recommended not use ‘Alphabet’ directly in operations where fast access to ‘Element’ ‘s properties is required. Instead consider to use ‘light-weighted’ equivalents, such as ‘Weights’
- Parameters:
map – MSExperiment to receive the identifications
fmap – FeatureMap with PeptideIdentifications for the MSExperiment
clear_ids – Reset peptide and protein identifications of each scan before annotating
map_ms1 – Attach Ids to MS1 spectra using RT mapping only (without precursor, without m/z)
- __init__()#
Overload:
- __init__(self) None
Overload:
- __init__(self, in_0: IMSAlphabet) None
Overload:
- __init__(self, elements: List[IMSElement]) None
Methods
Overload:
clear
(self)Clears the alphabet data
erase
(self, name)Removes the element with 'name' from the alphabet
getAverageMasses
(self)Gets average masses of elements
Overload:
Overload:
getMasses
(self, isotope_index)Gets masses of elements isotopes given by 'isotope_index'
getName
(self, index)Gets the symbol of the element with an 'index' in alphabet
hasName
(self, name)Returns true if there is an element with symbol 'name' in the alphabet, false - otherwise
load
(self, fname)Loads the alphabet data from the file 'fname' using the default parser.
Overload:
setElement
(self, name, mass, forced)Overwrites an element in the alphabet with the 'name' with a new element constructed from the given 'name' and 'mass'
size
(self)sortByNames
(self)Sorts the alphabet by names
sortByValues
(self)Sorts the alphabet by mass values
- clear(self) None #
Clears the alphabet data
- erase(self, name: bytes) bool #
Removes the element with ‘name’ from the alphabet
- getAverageMasses(self) List[float] #
Gets average masses of elements
- getElement()#
Overload:
- getElement(self, name: bytes) IMSElement
Gets the element with ‘index’ and returns element with the given index in alphabet
Overload:
- getElement(self, index: int) IMSElement
Gets the element with ‘index’
- getMass()#
Overload:
- getMass(self, name: bytes) float
Gets mono isotopic mass of the element with the symbol ‘name’
Overload:
- getMass(self, index: int) float
Gets mass of the element with an ‘index’ in alphabet
- getMasses(self, isotope_index: int) List[float] #
Gets masses of elements isotopes given by ‘isotope_index’
- getName(self, index: int) bytes #
Gets the symbol of the element with an ‘index’ in alphabet
- hasName(self, name: bytes) bool #
Returns true if there is an element with symbol ‘name’ in the alphabet, false - otherwise
- load(self, fname: String) None #
Loads the alphabet data from the file ‘fname’ using the default parser. If there is no file ‘fname’, throws an ‘IOException’
- push_back()#
Overload:
- push_back(self, name: bytes, value: float) None
Adds a new element with ‘name’ and mass ‘value’
Overload:
- push_back(self, element: IMSElement) None
Adds a new ‘element’ to the alphabet
- setElement(self, name: bytes, mass: float, forced: bool) None #
Overwrites an element in the alphabet with the ‘name’ with a new element constructed from the given ‘name’ and ‘mass’
- size(self) int #
- sortByNames(self) None #
Sorts the alphabet by names
- sortByValues(self) None #
Sorts the alphabet by mass values