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<DoubleReal> & bb_init,
 
  121                                             std::vector<DoubleReal> & cr_init,
 
  122                                             std::vector<DoubleReal> & sc_init,
 
  124                                             const std::vector<DoubleReal> & bb_charges,
 
  125                                             const std::vector<DoubleReal> & 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:56
PILISNeutralLossModel b2_ion_losses_cr_
Definition: PILISModel.h:168
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:84
PILISNeutralLossModel y_ion_losses_cr_
Definition: PILISModel.h:171
const_iterator ConstIterator
Non-mutable iterator. 
Definition: StringList.h:67
int evaluate(const gsl_vector *x, void *params, gsl_vector *f, gsl_matrix *J)
Driver function for the evaluation of function and jacobian. 
Map< DoubleReal, std::vector< RichPeak1D > > peaks_
stores the peaks of a spectrum 
Definition: PILISModel.h:152
HiddenMarkovModel hmm_
base model used 
Definition: PILISModel.h:140
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:69
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:361
Hidden Markov Model implementation of PILIS. 
Definition: HiddenMarkovModel.h:134
A base class for all classes handling default parameters. 
Definition: DefaultParamHandler.h:90
bool valid_
true if the instance is valid 
Definition: PILISModel.h:149
Map class based on the STL map (containing serveral convenience functions) 
Definition: Map.h:50
PILISNeutralLossModel a_ion_losses_cd_
Definition: PILISModel.h:163
PILISNeutralLossModel a_ion_losses_cr_
Definition: PILISModel.h:162