TextWriter& operator()(const UserParam& userParam)
{
os_ << indent_ << "userParam: " << userParam.name;
if (!userParam.value.empty()) os_ << ", " << userParam.value;
if (!userParam.type.empty()) os_ << ", " << userParam.type;
if (userParam.units != CVID_Unknown) os_ << ", " << cvTermInfo(userParam.units).name;
os_ << std::endl;
return *this;
}
TextWriter& operator()(const CVParam& cvParam)
{
os_ << indent_ << "cvParam: " << cvTermInfo(cvParam.cvid).name;
if (!cvParam.value.empty())
os_ << ", " << cvParam.value;
if (cvParam.units != CVID_Unknown)
os_ << ", " << cvParam.unitsName();
os_ << std::endl;
return *this;
}
ostream& operator<<(ostream& os, const CVMap& cm)
{
string id = typeid(cm).name();
os << cm.getTag() << "\t" << cm.keyword
<< "\t" << cvTermInfo(cm.cvid).id
<< "\t" << cm.path
<< "\n";
return os;
}
InstrumentInfo(const MSData& msd)
{
if (!msd.instrumentConfigurationPtrs.empty() &&
msd.instrumentConfigurationPtrs[0]->hasCVParamChild(MS_instrument_model))
{
CVTermInfo model = cvTermInfo(msd.instrumentConfigurationPtrs[0]->cvParamChild(MS_instrument_model).cvid);
CVTermInfo vendor = model;
while (!vendor.parentsIsA.empty() &&
find(vendor.parentsIsA.begin(), vendor.parentsIsA.end(), MS_instrument_model) == vendor.parentsIsA.end())
vendor = cvTermInfo(vendor.parentsIsA[0]);
vendorName = vendor.shortName();
bal::replace_all(vendorName, " instrument model", "");
if (vendor.cvid != model.cvid)
modelName = model.shortName();
serialNumber = msd.instrumentConfigurationPtrs[0]->cvParam(MS_instrument_serial_number).value;
}
if (vendorName.empty()) vendorName = "unknown";
if (modelName.empty()) modelName = "unknown";
if (serialNumber.empty()) serialNumber = "unknown";
}
const std::string& getCleavageAgentRegex(CVID agentCvid) const
{
if (!pwiz::cv::cvIsA(agentCvid, MS_cleavage_agent_name))
throw invalid_argument("[getCleavageAgentRegex] CVID is not a cleavage agent.");
map<CVID, const CVTermInfo*>::const_iterator regexTermItr =
cleavageAgentToRegexMap_.find(agentCvid);
if (regexTermItr == cleavageAgentToRegexMap_.end())
throw runtime_error("[getCleavageAgentRegex] No regex relation for cleavage agent " + cvTermInfo(agentCvid).name);
return regexTermItr->second->name;
}
