TMTTenPlexQuantitationMethod::TMTTenPlexQuantitationMethod()
{
setName("TMTTenPlexQuantitationMethod");
// // mass map outline - for further details please see #2427
// "126", 126.127726, x, x, 127C, 128C
// "127N", 127.124761, x, x, 128N, 129N
// "127C", 127.131081, x, 126, 128C, 129C
// "128N", 128.128116, x, 127N, 129N, 130N
// "128C", 128.134436, 126, 127C, 129C, 130C
// "129N", 129.131471, 127N, 128N, 130N, 131
// "129C", 129.137790, 127C, 128C, 130C, x
// "130N", 130.134825, 128N, 129N, 131, x
// "130C", 130.141145, 128C, 129C, x, x
// "131", 131.138180, 129N, 130N, x, x
// create the channel map //-2 -1 +1 +2
channels_.push_back(IsobaricChannelInformation("126", 0, "", 126.127726, -1, -1, 2, 4));
channels_.push_back(IsobaricChannelInformation("127N", 1, "", 127.124761, -1, -1, 3, 5));
channels_.push_back(IsobaricChannelInformation("127C", 2, "", 127.131081, -1, 0, 4, 6));
channels_.push_back(IsobaricChannelInformation("128N", 3, "", 128.128116, -1, 1, 5, 7));
channels_.push_back(IsobaricChannelInformation("128C", 4, "", 128.134436, 0, 2, 6, 8));
channels_.push_back(IsobaricChannelInformation("129N", 5, "", 129.131471, 1, 3, 7, 9));
channels_.push_back(IsobaricChannelInformation("129C", 6, "", 129.137790, 2, 4, 8, -1));
channels_.push_back(IsobaricChannelInformation("130N", 7, "", 130.134825, 3, 5, 9, -1));
channels_.push_back(IsobaricChannelInformation("130C", 8, "", 130.141145, 4, 6, -1, -1));
channels_.push_back(IsobaricChannelInformation("131", 9, "", 131.138180, 5, 7, -1, -1));
// we assume 126 to be the reference
reference_channel_ = 0;
setDefaultParams_();
}
/// Constructor with iTRAQ type (from enum ItraqConstants::ITRAQ_TYPES)
ItraqChannelExtractor::ItraqChannelExtractor(Int itraq_type) :
DefaultParamHandler("ItraqChannelExtractor"),
itraq_type_(itraq_type),
channel_map_()
{
init_();
setDefaultParams_();
}
/// Constructor (assuming 4plex)
ItraqChannelExtractor::ItraqChannelExtractor() :
DefaultParamHandler("ItraqChannelExtractor"),
itraq_type_(ItraqConstants::FOURPLEX),
channel_map_()
{
init_();
setDefaultParams_();
}
/// Constructor with iTRAQ type (from enum ItraqConstants::ITRAQ_TYPES) and param
ItraqChannelExtractor::ItraqChannelExtractor(Int itraq_type, const Param& param) :
DefaultParamHandler("ItraqChannelExtractor"),
itraq_type_(itraq_type),
channel_map_()
{
init_();
setDefaultParams_();
setParameters(param);
updateMembers_();
}
IsobaricChannelExtractor::IsobaricChannelExtractor(const IsobaricQuantitationMethod* const quant_method) :
DefaultParamHandler("IsobaricChannelExtractor"),
quant_method_(quant_method),
selected_activation_(""),
reporter_mass_shift_(0.1),
min_precursor_intensity_(1.0),
keep_unannotated_precursor_(true),
min_reporter_intensity_(0.0),
remove_low_intensity_quantifications_(false),
min_precursor_purity_(0.0),
max_precursor_isotope_deviation_(0.02)
{
setDefaultParams_();
}
ItraqFourPlexQuantitationMethod::ItraqFourPlexQuantitationMethod()
{
setName("ItraqFourPlexQuantitationMethod");
// create the channel map
channels_.push_back(IsobaricChannelInformation(114, 0, "", 114.1112));
channels_.push_back(IsobaricChannelInformation(115, 1, "", 115.1082));
channels_.push_back(IsobaricChannelInformation(116, 2, "", 116.1116));
channels_.push_back(IsobaricChannelInformation(117, 3, "", 117.1149));
// we assume 114 to be the reference
reference_channel_ = 0;
setDefaultParams_();
}
ItraqFourPlexQuantitationMethod::ItraqFourPlexQuantitationMethod()
{
setName("ItraqFourPlexQuantitationMethod");
// create the channel map
channels_.push_back(IsobaricChannelInformation("114", 0, "", 114.1112, -1, -1, 1, 2));
channels_.push_back(IsobaricChannelInformation("115", 1, "", 115.1082, -1, 0, 2, 3));
channels_.push_back(IsobaricChannelInformation("116", 2, "", 116.1116, 0, 1, 3, -1));
channels_.push_back(IsobaricChannelInformation("117", 3, "", 117.1149, 1, 2, -1, -1));
// we assume 114 to be the reference
reference_channel_ = 0;
setDefaultParams_();
}
TMTSixPlexQuantitationMethod::TMTSixPlexQuantitationMethod()
{
setName("TMTSixPlexQuantitationMethod");
// create the channel map
channels_.push_back(IsobaricChannelInformation("126", 0, "", 126.127725, -1, -1, 1, 2));
channels_.push_back(IsobaricChannelInformation("127", 1, "", 127.124760, -1, 0, 2, 3));
channels_.push_back(IsobaricChannelInformation("128", 2, "", 128.134433, 0, 1, 3, 4));
channels_.push_back(IsobaricChannelInformation("129", 3, "", 129.131468, 1, 2, 4, 5));
channels_.push_back(IsobaricChannelInformation("130", 4, "", 130.141141, 2, 3, 5, -1));
channels_.push_back(IsobaricChannelInformation("131", 5, "", 131.138176, 3, 4, -1, -1));
// we assume 126 to be the reference
reference_channel_ = 0;
setDefaultParams_();
}
TMTSixPlexQuantitationMethod::TMTSixPlexQuantitationMethod()
{
setName("TMTSixPlexQuantitationMethod");
// create the channel map
channels_.push_back(IsobaricChannelInformation(126, 0, "", 126.127725));
channels_.push_back(IsobaricChannelInformation(127, 1, "", 127.124760));
channels_.push_back(IsobaricChannelInformation(128, 2, "", 128.134433));
channels_.push_back(IsobaricChannelInformation(129, 3, "", 129.131468));
channels_.push_back(IsobaricChannelInformation(130, 4, "", 130.141141));
channels_.push_back(IsobaricChannelInformation(131, 5, "", 131.138176));
// we assume 126 to be the reference
reference_channel_ = 0;
setDefaultParams_();
}
ItraqEightPlexQuantitationMethod::ItraqEightPlexQuantitationMethod()
{
setName("ItraqFourPlexQuantitationMethod");
// create the channel map
channels_.push_back(IsobaricChannelInformation(113, 0, "", 113.1078));
channels_.push_back(IsobaricChannelInformation(114, 1, "", 114.1112));
channels_.push_back(IsobaricChannelInformation(115, 2, "", 115.1082));
channels_.push_back(IsobaricChannelInformation(116, 3, "", 116.1116));
channels_.push_back(IsobaricChannelInformation(117, 4, "", 117.1149));
channels_.push_back(IsobaricChannelInformation(118, 5, "", 118.1120));
channels_.push_back(IsobaricChannelInformation(119, 6, "", 119.1153));
channels_.push_back(IsobaricChannelInformation(121, 7, "", 121.1220));
// we assume 114 to be the reference
reference_channel_ = 0;
setDefaultParams_();
}
TMTTenPlexQuantitationMethod::TMTTenPlexQuantitationMethod()
{
setName("TMTTenPlexQuantitationMethod");
// create the channel map
channels_.push_back(IsobaricChannelInformation("126", 0, "", 126.127725, -1, -1, 2, 3));
channels_.push_back(IsobaricChannelInformation("127N", 1, "", 127.124760, -1, -1, 3, 4));
channels_.push_back(IsobaricChannelInformation("127C", 2, "", 127.131079, -1, 0, 4, 5));
channels_.push_back(IsobaricChannelInformation("128N", 3, "", 128.128114, -1, 1, 5, 6));
channels_.push_back(IsobaricChannelInformation("128C", 4, "", 128.134433, 0, 2, 6, 7));
channels_.push_back(IsobaricChannelInformation("129N", 5, "", 129.131468, 1, 3, 7, 8));
channels_.push_back(IsobaricChannelInformation("129C", 6, "", 129.137787, 2, 4, 8, 9));
channels_.push_back(IsobaricChannelInformation("130N", 7, "", 130.134822, 3, 6, 9, -1));
channels_.push_back(IsobaricChannelInformation("130C", 8, "", 130.141141, 4, 6, -1, -1));
channels_.push_back(IsobaricChannelInformation("131", 9, "", 131.138176, 5, 7, -1, -1));
// we assume 126 to be the reference
reference_channel_ = 0;
setDefaultParams_();
}
DigestSimulation::DigestSimulation() :
DefaultParamHandler("DigestSimulation")
{
setDefaultParams_();
}
IsobaricQuantifier::IsobaricQuantifier(const IsobaricQuantitationMethod* const quant_method) :
DefaultParamHandler("IsobaricQuantifier"),
quant_method_(quant_method)
{
setDefaultParams_();
}
DetectabilitySimulation::DetectabilitySimulation() :
DefaultParamHandler("DetectabilitySimulation")
{
setDefaultParams_();
}
RTSimulation::RTSimulation(const SimRandomNumberGenerator& random_generator) :
DefaultParamHandler("RTSimulation"), rnd_gen_(&random_generator)
{
setDefaultParams_();
updateMembers_();
}
