|
bool | add_a_ions_ |
|
bool | add_b_ions_ |
|
bool | add_c_ions_ |
|
bool | add_d_ions_ |
|
bool | add_w_ions_ |
|
bool | add_x_ions_ |
|
bool | add_y_ions_ |
|
bool | add_z_ions_ |
|
bool | add_aB_ions_ |
|
bool | add_first_prefix_ion_ |
|
bool | add_metainfo_ |
|
bool | add_precursor_peaks_ |
|
bool | add_all_precursor_charges_ |
|
double | a_intensity_ |
|
double | b_intensity_ |
|
double | c_intensity_ |
|
double | d_intensity_ |
|
double | w_intensity_ |
|
double | x_intensity_ |
|
double | y_intensity_ |
|
double | z_intensity_ |
|
double | aB_intensity_ |
|
double | precursor_intensity_ |
|
void | getSpectrum (MSSpectrum &spectrum, const NASequence &oligo, Int min_charge, Int max_charge) const |
| Generates a spectrum for an oligonucleotide sequence, with the ion types that are set in the tool parameters. More...
|
|
void | getMultipleSpectra (std::map< Int, MSSpectrum > &spectra, const NASequence &oligo, const std::set< Int > &charges, Int base_charge=1) const |
| Generates spectra in multiple charge states for an oligonucleotide sequence. More...
|
|
void | updateMembers_ () override |
| overwrite More...
|
|
void | addFragmentPeaks_ (MSSpectrum &spectrum, const std::vector< double > &fragment_masses, const String &ion_type, double offset, double intensity, Size start=0) const |
| Helper function to add (uncharged) fragment peaks to a spectrum. More...
|
|
void | addAMinusBPeaks_ (MSSpectrum &spectrum, const std::vector< double > &fragment_masses, const NASequence &oligo, Size start=0) const |
| Special version of addFragmentPeaks_() for a-B ions. More...
|
|
MSSpectrum | getUnchargedSpectrum_ (const NASequence &oligo) const |
| Generates a spectrum containing peaks for uncharged fragment masses. More...
|
|
void | addChargedSpectrum_ (MSSpectrum &spectrum, const MSSpectrum &uncharged_spectrum, Int charge, bool add_precursor) const |
| Adds a charged version of an uncharged spectrum to another spectrum. More...
|
|
Generates theoretical spectra for nucleic acid sequences.
Parameters of this class are:
Name | Type | Default | Restrictions | Description |
add_metainfo |
string | false |
true, false | Adds the type of peaks as meta information to the peaks, e.g. c1, y2, a3-B |
add_precursor_peaks |
string | false |
true, false | Adds peaks of the unfragmented precursor ion to the spectrum |
add_all_precursor_charges |
string | false |
true, false | Adds precursor peaks with all charges in the given range |
add_first_prefix_ion |
string | false |
true, false | If set to true a1, b1, ..., z1 ions are added |
add_a_ions |
string | false |
true, false | Add peaks of a-ions to the spectrum |
add_b_ions |
string | true |
true, false | Add peaks of b-ions to the spectrum |
add_c_ions |
string | false |
true, false | Add peaks of c-ions to the spectrum |
add_d_ions |
string | false |
true, false | Add peaks of d-ions to the spectrum |
add_w_ions |
string | false |
true, false | Add peaks of w-ions to the spectrum |
add_x_ions |
string | false |
true, false | Add peaks of x-ions to the spectrum |
add_y_ions |
string | true |
true, false | Add peaks of y-ions to the spectrum |
add_z_ions |
string | false |
true, false | Add peaks of z-ions to the spectrum |
add_a-B_ions |
string | false |
true, false | Add peaks of a-B-ions to the spectrum |
a_intensity |
float | 1.0 |
| Intensity of the a-ions |
b_intensity |
float | 1.0 |
| Intensity of the b-ions |
c_intensity |
float | 1.0 |
| Intensity of the c-ions |
d_intensity |
float | 1.0 |
| Intensity of the d-ions |
w_intensity |
float | 1.0 |
| Intensity of the w-ions |
x_intensity |
float | 1.0 |
| Intensity of the x-ions |
y_intensity |
float | 1.0 |
| Intensity of the y-ions |
z_intensity |
float | 1.0 |
| Intensity of the z-ions |
a-B_intensity |
float | 1.0 |
| Intensity of the a-B-ions |
precursor_intensity |
float | 1.0 |
| Intensity of the precursor peak |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
void getMultipleSpectra |
( |
std::map< Int, MSSpectrum > & |
spectra, |
|
|
const NASequence & |
oligo, |
|
|
const std::set< Int > & |
charges, |
|
|
Int |
base_charge = 1 |
|
) |
| const |
Generates spectra in multiple charge states for an oligonucleotide sequence.
- Parameters
-
spectra | Output spectra |
oligo | Target oligonucleotide sequence |
charges | Set of charge states to generate |
base_charge | Minimum charge for peaks in each spectrum |
One spectrum per element in charges
is generated in spectra
.
All values in charges
must be either positive or negative.
This function is more efficient than calling getSpectrum() multiple times, because spectra of lower charge states are reused.
Referenced by NucleicAcidSearchEngine::main_().