36 #ifndef OPENMS_ANALYSIS_ID_PILISMODEL_H
37 #define OPENMS_ANALYSIS_ID_PILISMODEL_H
97 void readFromFile(
const String & filename);
100 void writeGraphMLFile(
const String & filename);
105 void writeToFile(
const String & filename);
108 void init(
bool generate_models =
true);
120 bool getInitialTransitionProbabilities_(std::vector<double> & bb_init,
121 std::vector<double> & cr_init,
122 std::vector<double> & sc_init,
123 double & precursor_init,
124 const std::vector<double> & bb_charges,
125 const std::vector<double> & sc_charges,
137 void writeParameters_(std::ostream & os,
const Param & param);
174 void updateMembers_();
PILISNeutralLossModel b_ion_losses_cr_
Definition: PILISModel.h:165
A more convenient string class.
Definition: String.h:57
PILISNeutralLossModel b2_ion_losses_cr_
Definition: PILISModel.h:168
Map< double, std::vector< RichPeak1D > > peaks_
stores the peaks of a spectrum
Definition: PILISModel.h:152
This class implements the simulation of the spectra from PILIS.
Definition: PILISNeutralLossModel.h:62
PILISNeutralLossModel b_ion_losses_cd_
Definition: PILISModel.h:166
PILISNeutralLossModel b2_ion_losses_cd_
Definition: PILISModel.h:169
PILISNeutralLossModel y_ion_losses_cd_
Definition: PILISModel.h:172
A proton distribution model to calculate the proton distribution over charged peptides.
Definition: ProtonDistributionModel.h:71
Isotope distribution class.
Definition: IsotopeDistribution.h:61
Generates theoretical spectra with various options.
Definition: TheoreticalSpectrumGenerator.h:53
Representation of a peptide/protein sequence.
Definition: AASequence.h:70
PILISNeutralLossModel y_ion_losses_cr_
Definition: PILISModel.h:171
HiddenMarkovModel hmm_
base model used
Definition: PILISModel.h:140
std::vector< String >::const_iterator ConstIterator
Non-mutable iterator.
Definition: TextFile.h:57
This class implements the simulation of the spectra from PILIS.
Definition: PILISModel.h:67
Aligns the peaks of two spectra.
Definition: SpectrumAlignment.h:62
TheoreticalSpectrumGenerator tsg_
theoretical spectrum generator (needed for training/aligning and spectrum intensity extraction) ...
Definition: PILISModel.h:146
Management and storage of parameters / INI files.
Definition: Param.h:75
ProtonDistributionModel prot_dist_
proton distribution model
Definition: PILISModel.h:143
PILISNeutralLossModel precursor_model_cr_
precursor model used
Definition: PILISModel.h:158
SpectrumAlignment spectra_aligner_
the alignment algorithm used
Definition: PILISModel.h:155
PILISNeutralLossModel precursor_model_cd_
Definition: PILISModel.h:160
ResidueType
Definition: Residue.h:359
Hidden Markov Model implementation of PILIS.
Definition: HiddenMarkovModel.h:134
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
bool valid_
true if the instance is valid
Definition: PILISModel.h:149
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:51
PILISNeutralLossModel a_ion_losses_cd_
Definition: PILISModel.h:163
PILISNeutralLossModel a_ion_losses_cr_
Definition: PILISModel.h:162