Equation instantiate_equation(Equation innerEq, Name variable, Real index, VarSymbolTable &symbolTable) {
VarSymbolTable v=symbolTable;
VarInfo vinfo = VarInfo(TypePrefixes(1,parameter), "Integer", Option<Comment>(), Modification(ModEq(Expression(index))));
v.insert(variable,vinfo);
if (is<Equality>(innerEq)) {
Equality eqeq = boost::get<Equality>(innerEq);
Expression l=eqeq.left(), r=eqeq.right();
//std::cout << "Left= " << l << " right " << r << std::endl;
return Equality(Visit(Modelica::PartEvalExp(v),l),Visit(Modelica::PartEvalExp(v),r));
} else {
ERROR("process_for_equations - instantiate_equation:\n"
"Incorrect equation type or not supported yet.\n");
}
return Equation();
}
PWIZ_API_DECL void addMIAPEExampleMetadata(TraData& td)
{
ContactPtr contactPtr(new Contact("JQP"));
contactPtr->set(MS_contact_name, "John Q. Public");
contactPtr->set(MS_contact_affiliation, "Department of Redundancy Department");
contactPtr->set(MS_contact_address, "1600 Pennsylvania Ave.");
td.contactPtrs.push_back(contactPtr);
Publication publication;
publication.id = "Al_et_al";
publication.set(MS_PubMed_identifier, 123456);
td.publications.push_back(publication);
InstrumentPtr lcqInstrumentPtr(new Instrument("LCQ"));
lcqInstrumentPtr->set(MS_LCQ_Deca);
lcqInstrumentPtr->set(MS_instrument_serial_number,"23433");
td.instrumentPtrs.push_back(lcqInstrumentPtr);
InstrumentPtr qtrapInstrumentPtr(new Instrument("QTRAP"));
qtrapInstrumentPtr->set(MS_4000_QTRAP);
td.instrumentPtrs.push_back(qtrapInstrumentPtr);
SoftwarePtr softwarePtr(new Software("Xcalibur"));
softwarePtr->set(MS_Xcalibur);
softwarePtr->version = "2.0.5";
SoftwarePtr softwareMaRiMba(new Software("MaRiMba"));
softwareMaRiMba->set(MS_MaRiMba);
softwareMaRiMba->version = "0.5";
SoftwarePtr softwarepwiz(new Software("pwiz"));
softwarepwiz->set(MS_pwiz);
softwarepwiz->version = "1.0";
td.softwarePtrs.push_back(softwareMaRiMba);
td.softwarePtrs.push_back(softwarepwiz);
td.softwarePtrs.push_back(softwarePtr);
ProteinPtr proteinPtr(new Protein("Q123"));
proteinPtr->set(MS_protein_accession, "Q123");
proteinPtr->sequence = "ABCD";
proteinPtr->set(MS_protein_name, "A short protein.");
proteinPtr->set(MS_molecular_mass, 12345, UO_dalton);
td.proteinPtrs.push_back(proteinPtr);
PeptidePtr peptide1Ptr(new Peptide("Pep1"));
peptide1Ptr->sequence = "AB";
peptide1Ptr->set(MS_theoretical_mass, 1234, UO_dalton);
peptide1Ptr->proteinPtrs.push_back(proteinPtr);
peptide1Ptr->modifications.push_back(Modification());
peptide1Ptr->modifications.back().set(UNIMOD_Methylmalonylation);
peptide1Ptr->modifications.back().location = 1;
peptide1Ptr->modifications.back().monoisotopicMassDelta = 123;
peptide1Ptr->retentionTimes.push_back(RetentionTime());
peptide1Ptr->retentionTimes.back().set(MS_predicted_retention_time, 42, UO_minute);
peptide1Ptr->retentionTimes.back().softwarePtr = softwareMaRiMba;
peptide1Ptr->evidence.set(MS_confident_peptide_sequence_number, 6);
td.peptidePtrs.push_back(peptide1Ptr);
CompoundPtr compound1Ptr(new Compound("Cmp1"));
compound1Ptr->set(MS_theoretical_mass, 1234, UO_dalton);
compound1Ptr->retentionTimes.push_back(RetentionTime());
compound1Ptr->retentionTimes.back().set(MS_predicted_retention_time, 42, UO_minute);
compound1Ptr->retentionTimes.back().softwarePtr = softwareMaRiMba;
td.compoundPtrs.push_back(compound1Ptr);
Interpretation interpretation1;
interpretation1.set(MS_frag__y_ion);
interpretation1.set(MS_product_ion_series_ordinal, 8);
interpretation1.set(MS_product_ion_m_z_delta, 0.03);
Interpretation interpretation2;
interpretation2.set(MS_frag__b_ion___H2O);
interpretation2.set(MS_product_ion_series_ordinal, 9);
interpretation2.set(MS_product_ion_m_z_delta, -0.43);
Validation qtrapValidation;
qtrapValidation.set(MS_transition_optimized_on_specified_instrument);
qtrapValidation.set(MS_4000_QTRAP);
qtrapValidation.set(MS_peak_intensity, 4072, MS_percent_of_base_peak_times_100);
qtrapValidation.set(MS_peak_intensity_rank, 2);
qtrapValidation.set(MS_peak_targeting_suitability_rank, 1);
Configuration qtrapConfiguration;
qtrapConfiguration.instrumentPtr = qtrapInstrumentPtr;
qtrapConfiguration.contactPtr = contactPtr;
qtrapConfiguration.set(MS_dwell_time, 0.12, UO_second);
qtrapConfiguration.set(MS_collision_gas, "argon");
qtrapConfiguration.set(MS_collision_gas_pressure, 12, UO_pascal);
qtrapConfiguration.set(MS_collision_energy, 26, UO_electronvolt);
qtrapConfiguration.set(MS_cone_voltage, 1200, UO_volt);
qtrapConfiguration.set(MS_interchannel_delay, 0.1, UO_second);
qtrapConfiguration.set(MS_tube_lens_voltage, 23, UO_volt);
qtrapConfiguration.validations.push_back(qtrapValidation);
Transition& tra0 = td.transitions[0];
tra0.peptidePtr = peptide1Ptr;
tra0.precursor.set(MS_charge_state, 2);
tra0.product.set(MS_charge_state, 1);
tra0.prediction.softwarePtr = softwareMaRiMba;
tra0.prediction.set(MS_transition_purported_from_an_MS_MS_spectrum_on_a_different__specified_instrument);
tra0.prediction.set(MS_linear_ion_trap);
tra0.prediction.set(MS_peak_intensity, 10000, UO_electronvolt);
tra0.prediction.set(MS_peak_intensity_rank, 1);
tra0.prediction.set(MS_peak_targeting_suitability_rank, 1);
tra0.retentionTime.set(MS_local_retention_time, 40.02, UO_minute);
tra0.retentionTime.set(MS_retention_time_window_lower_offset, 3, UO_minute);
tra0.retentionTime.set(MS_retention_time_window_upper_offset, 3, UO_minute);
tra0.configurationList.push_back(qtrapConfiguration);
Transition& tra1 = td.transitions[1];
tra1.compoundPtr = compound1Ptr;
tra1.precursor.set(MS_charge_state, 2);
tra1.product.set(MS_charge_state, 1);
Configuration lcqConfiguration;
lcqConfiguration.instrumentPtr = lcqInstrumentPtr;
lcqConfiguration.contactPtr = contactPtr;
lcqConfiguration.set(MS_collision_energy, 42, UO_electronvolt);
Target& tar0 = td.targets.targetIncludeList[0];
tar0.compoundPtr = compound1Ptr;
tar0.precursor.set(MS_charge_state, 2);
tar0.retentionTime.set(MS_local_retention_time, 12.3, UO_minute);
tar0.retentionTime.set(MS_retention_time_window_lower_offset, 1, UO_minute);
tar0.retentionTime.set(MS_retention_time_window_upper_offset, 2, UO_minute);
tar0.configurationList.push_back(lcqConfiguration);
td.targets.targetExcludeList[0].peptidePtr = peptide1Ptr;
td.targets.targetExcludeList[0].precursor.set(MS_charge_state, 2);
} // addMIAPEExampleMetadata()
