#include "RcppIdent.h"
RcppIdent::RcppIdent()
{
mzid = NULL;
}
void RcppIdent::open(const string& fileName)
{
filename = fileName;
mzid = new IdentDataFile(fileName);
}
Rcpp::List RcppIdent::getIDInfo( )
{
provider = (mzid->provider.contactRolePtr.get()!=0?mzid->provider.contactRolePtr.get()->name():"");
date = mzid->creationDate;
vector<AnalysisSoftwarePtr> as = mzid->analysisSoftwareList;
vector<SearchDatabasePtr> sdb = mzid->dataCollection.inputs.searchDatabase;
Rcpp::StringVector software(as.size());
for (size_t i = 0; i < as.size(); i++)
{
software[i] = as[i]->name + " " + as[i]->version + " " + (as[i]->contactRolePtr.get()!=0?as[i]->contactRolePtr->contactPtr->name:"") ;
}
vector<SpectrumIdentificationProtocolPtr> sip = mzid->analysisProtocolCollection.spectrumIdentificationProtocol;
string fragmentTolerance = "";
string parentTolerance = "";
if(!sip[0]->fragmentTolerance.empty())
{
fragmentTolerance = sip[0]->fragmentTolerance.cvParams[0].value + " " + sip[0]->fragmentTolerance.cvParam(MS_search_tolerance_plus_value).unitsName();
}
if(!sip[0]->parentTolerance.empty())
{
parentTolerance = sip[0]->parentTolerance.cvParams[0].value + " " + sip[0]->parentTolerance.cvParam(MS_search_tolerance_plus_value).unitsName();
}
vector<SearchModificationPtr> sm = sip[0]->modificationParams;
Rcpp::StringVector mod(sm.size());
for(size_t i = 0; i < sm.size(); i++)
{
mod[i] = cvTermInfo(sm[i]->cvParams[0].cvid).name;
}
vector<EnzymePtr> enz = sip[0]->enzymes.enzymes;
Rcpp::List enzymes;
Rcpp::StringVector name(enz.size());
Rcpp::StringVector nTermGain(enz.size());
Rcpp::StringVector cTermGain(enz.size());
Rcpp::StringVector minDistance(enz.size());
Rcpp::StringVector missedCleavages(enz.size());
for (size_t i = 0; i < enz.size(); i++)
{
name[i] = cvTermInfo(cleavageAgent(*enz[i].get())).name;
nTermGain[i] = enz[i]->nTermGain;
cTermGain[i] = enz[i]->cTermGain;
minDistance[i] = enz[i]->minDistance;
missedCleavages[i] = enz[i]->missedCleavages;
}
enzymes = Rcpp::List::create(
Rcpp::_["name"] = name,
Rcpp::_["nTermGain"] = nTermGain,
Rcpp::_["cTermGain"] = cTermGain,
Rcpp::_["minDistance"] = minDistance,
Rcpp::_["missedCleavages"] = missedCleavages
);
vector<SpectraDataPtr> sd = mzid->dataCollection.inputs.spectraData;
Rcpp::StringVector spectra(sd.size());
for (size_t i = 0; i < sd.size(); i++)
{
spectra[i] = sd[i]->location;
}
return Rcpp::List::create(
Rcpp::_["FileProvider"] = provider,
Rcpp::_["CreationDate"] = date,
Rcpp::_["software"] = software,
Rcpp::_["ModificationSearched"] = mod,
Rcpp::_["FragmentTolerance"] = fragmentTolerance,
Rcpp::_["ParentTolerance"] = parentTolerance,
Rcpp::_["enzymes"] = enzymes,
Rcpp::_["SpectraSource"] = spectra
);
}
Rcpp::DataFrame RcppIdent::getPsmInfo( )
{
vector<SpectrumIdentificationResultPtr> spectrumIdResult = mzid->analysisCollection.spectrumIdentification[0]->spectrumIdentificationListPtr->spectrumIdentificationResult;
std::vector<std::string> spectrumID;
std::vector<int> chargeState;
std::vector<int> rank;
std::vector<double> experimentalMassToCharge;
std::vector<double> calculatedMassToCharge;
std::vector<std::string> seq;
std::vector<std::string> peptideRef;
std::vector<int> modification;
std::vector<bool> isDecoy;
std::vector<bool> passThreshold;
std::vector<std::string> post;
std::vector<std::string> pre;
std::vector<int> start;
std::vector<int> end;
std::vector<std::string> DBSequenceID;
std::vector<std::string> DBseq;
std::vector<int> DBSequenceLen;
std::vector<std::string> DBdesc;
for (size_t i = 0; i < spectrumIdResult.size(); i++)
{
for(size_t j = 0; j < spectrumIdResult[i]->spectrumIdentificationItem.size(); j++)
{
for(size_t k = 0; k < spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr.size(); k++)
{
spectrumID.push_back(spectrumIdResult[i]->spectrumID);
chargeState.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->chargeState);
rank.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->rank);
passThreshold.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->passThreshold);
experimentalMassToCharge.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->experimentalMassToCharge);
calculatedMassToCharge.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->calculatedMassToCharge);
seq.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptidePtr->peptideSequence);
peptideRef.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptidePtr->id);
modification.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptidePtr->modification.size());
isDecoy.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->isDecoy);
pre.push_back(string(1, spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->pre));
post.push_back(string(1, spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->post));
start.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->start);
end.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->end);
if(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->dbSequencePtr.get()!=0)
{
DBSequenceID.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->dbSequencePtr->accession);
DBSequenceLen.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->dbSequencePtr->length);
DBseq.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->dbSequencePtr->seq);
if(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->dbSequencePtr->cvParams.size() > 0)
{
DBdesc.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->dbSequencePtr->cvParams[0].value);
}
else
{
DBdesc.push_back("");
}
}
else
{
DBSequenceID.push_back("");
DBseq.push_back("");
DBdesc.push_back("");
}
}
}
}
return Rcpp::DataFrame::create(
Rcpp::_["spectrumID"] = spectrumID,
Rcpp::_["chargeState"] = chargeState,
Rcpp::_["rank"] = rank,
Rcpp::_["passThreshold"] = passThreshold,
Rcpp::_["experimentalMassToCharge"] = experimentalMassToCharge,
Rcpp::_["calculatedMassToCharge"] = calculatedMassToCharge,
Rcpp::_["sequence"] = seq,
Rcpp::_["peptideRef"] = peptideRef,
Rcpp::_["modNum"] = modification,
Rcpp::_["isDecoy"] = isDecoy,
Rcpp::_["post"] = post,
Rcpp::_["pre"] = pre,
Rcpp::_["start"] = start,
Rcpp::_["end"] = end,
Rcpp::_["DatabaseAccess"] = DBSequenceID,
Rcpp::_["DBseqLength"] = DBSequenceLen,
Rcpp::_["DatabaseSeq"] = DBseq,
Rcpp::_["DatabaseDescription"] = DBdesc
);
}
Rcpp::DataFrame RcppIdent::getModInfo( )
{
vector<SpectrumIdentificationResultPtr> spectrumIdResult = mzid->analysisCollection.spectrumIdentification[0]->spectrumIdentificationListPtr->spectrumIdentificationResult;
vector<string> spectrumID;
vector<string> seq;
vector<string> peptideRef;
vector<string> name;
vector<double> mass;
vector<int> loc;
for (size_t i = 0; i < spectrumIdResult.size(); i++)
{
for(size_t k = 0; k < spectrumIdResult[i]->spectrumIdentificationItem.size() ; k++)
{
if(spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->modification.size()>0)
{
for(size_t j = 0 ; j < spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->modification.size(); j++)
{
spectrumID.push_back(spectrumIdResult[i]->spectrumID);
seq.push_back(spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->peptideSequence);
peptideRef.push_back(spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->id);
name.push_back(cvTermInfo(spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->modification[j]->cvParams[0].cvid).name);
mass.push_back(spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->modification[j]->monoisotopicMassDelta);
loc.push_back(spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->modification[j]->location);
}
}
}
}
return Rcpp::DataFrame::create(
Rcpp::_["spectrumID"] = spectrumID,
Rcpp::_["sequence"] = seq,
Rcpp::_["peptideRef"] = peptideRef,
Rcpp::_["name"] = name,
Rcpp::_["mass"] = mass,
Rcpp::_["location"] = loc);
}
Rcpp::DataFrame RcppIdent::getSubInfo( )
{
vector<SpectrumIdentificationResultPtr> spectrumIdResult = mzid->analysisCollection.spectrumIdentification[0]->spectrumIdentificationListPtr->spectrumIdentificationResult;
vector<string> spectrumID;
std::vector<std::string> seq;
std::vector<char> originalResidue;
std::vector<char> replacementResidue;
std::vector<int> loc;
for (size_t i = 0; i < spectrumIdResult.size(); i++)
{
if(spectrumIdResult[i]->spectrumIdentificationItem[0]->peptidePtr->substitutionModification.size() > 0)
{
for(size_t j = 0 ; j < spectrumIdResult[i]->spectrumIdentificationItem[0]->peptidePtr->substitutionModification.size(); j++)
{
spectrumID.push_back(spectrumIdResult[i]->spectrumID);
seq.push_back(spectrumIdResult[i]->spectrumIdentificationItem[0]->peptidePtr->peptideSequence);
originalResidue.push_back(spectrumIdResult[i]->spectrumIdentificationItem[0]->peptidePtr->substitutionModification[j]->originalResidue);
replacementResidue.push_back(spectrumIdResult[i]->spectrumIdentificationItem[0]->peptidePtr->substitutionModification[j]->replacementResidue);
loc.push_back(spectrumIdResult[i]->spectrumIdentificationItem[0]->peptidePtr->substitutionModification[j]->location);
}
}
}
return Rcpp::DataFrame::create(
Rcpp::_["spectrumID"] = spectrumID,
Rcpp::_["sequence"] = seq,
Rcpp::_["originalResidue"] = originalResidue,
Rcpp::_["replacementResidue"] = replacementResidue,
Rcpp::_["location"] = loc
);
}
Rcpp::DataFrame RcppIdent::getScore( ) {
vector<SpectrumIdentificationResultPtr> spectrumIdResult = mzid->analysisCollection.spectrumIdentification[0]->spectrumIdentificationListPtr->spectrumIdentificationResult;
vector<string> spectrumID;
vector<string> names;
int count = 0;
int nCvParams = 0;
for (size_t i = 0; i < spectrumIdResult[0]->spectrumIdentificationItem[0]->cvParams.size(); i++) {
if (!spectrumIdResult[0]->spectrumIdentificationItem[0]->cvParams[i].value.empty()) {
count++;
nCvParams++;
names.push_back(cvTermInfo(spectrumIdResult[0]->spectrumIdentificationItem[0]->cvParams[i].cvid).name);
}
}
if(count == 0) {
Rcpp::Rcout << "No scoring information available" << std::endl;
return Rcpp::DataFrame::create();
} else {
vector<vector<double> > score(count);
for (size_t i = 0; i < spectrumIdResult.size(); i++) {
for (size_t k = 0; k < spectrumIdResult[i]->spectrumIdentificationItem.size(); k++) {
for (size_t n = 0; n < spectrumIdResult[i]->spectrumIdentificationItem[k]->peptideEvidencePtr.size(); n++) {
spectrumID.push_back(spectrumIdResult[i]->spectrumID);
count = 0;
// The original loop iterated to j <
// spectrumIdResult[i]->spectrumIdentificationItem[k]->cvParams.size()
// which failed when some SpectrumIdentificationItem
// suddently have additional cvParams, such as in Mascot
// results - see https://github.com/sneumann/mzR/issues/136
for (size_t j = 0; j < nCvParams; j++) {
if (!spectrumIdResult[i]->spectrumIdentificationItem[k]->cvParams[j].value.empty()) {
score[count].push_back(lexical_cast<double>(spectrumIdResult[i]->spectrumIdentificationItem[k]->cvParams[j].value));
count++;
}
}
}
}
}
Rcpp::List res(score.size() + 1);
names.insert(names.begin(), "spectrumID");
res[0] = Rcpp::wrap(spectrumID);
for(size_t i = 0; i < score.size(); i++) {
res[i + 1] = Rcpp::wrap(score[i]);
}
res.attr("names") = names;
Rcpp::DataFrame out(res);
return out;
}
}
Rcpp::DataFrame RcppIdent::getSpecParams( )
{
vector<SpectrumIdentificationResultPtr> spectrumIdResult = mzid->analysisCollection.spectrumIdentification[0]->spectrumIdentificationListPtr->spectrumIdentificationResult;
vector<string> spectrumID;
vector<string> names;
int count = 0;
for(size_t i = 0; i < spectrumIdResult[0]->cvParams.size(); i++)
{
if(!spectrumIdResult[0]->cvParams[i].value.empty())
{
count++;
names.push_back(cvTermInfo(spectrumIdResult[0]->cvParams[i].cvid).name);
}
}
if(count == 0)
{
Rcpp::Rcout << "No spectrum cvParams available" << std::endl;
return Rcpp::DataFrame::create();
}
else
{
vector<vector<string> > score(count);
for (size_t i = 0; i < spectrumIdResult.size(); i++)
{
spectrumID.push_back(spectrumIdResult[i]->spectrumID);
count = 0;
for(size_t j = 0; j < spectrumIdResult[i]->cvParams.size(); j++)
{
if(!spectrumIdResult[i]->cvParams[j].value.empty())
{
score[count].push_back(lexical_cast<string>(spectrumIdResult[i]->cvParams[j].value));
count++;
}
}
}
Rcpp::List res(score.size() + 1);
names.insert(names.begin(), "spectrumID");
res[0] = Rcpp::wrap(spectrumID);
for(size_t i = 0; i < score.size(); i++)
{
res[i + 1] = Rcpp::wrap(score[i]);
}
res.attr("names") = names;
Rcpp::DataFrame out(res);
return out;
}
}
Rcpp::List RcppIdent::getPara( )
{
std::vector<SpectrumIdentificationProtocolPtr> sip = mzid->analysisProtocolCollection.spectrumIdentificationProtocol;
std::vector<std::string> names, values;
names.push_back("searchType");
values.push_back(underscore(cvTermInfo(sip[0]->searchType.cvid).name));
for(int i = 0 ; i < sip[0]->additionalSearchParams.cvParams.size(); i++)
{
names.push_back(underscore(cvTermInfo(sip[0]->additionalSearchParams.cvParams[i].cvid).name));
values.push_back("true");
}
for(int i = 0; i < sip[0]->additionalSearchParams.userParams.size(); i++)
{
names.push_back(underscore(sip[0]->additionalSearchParams.userParams[i].name));
if(sip[0]->additionalSearchParams.userParams[i].value.empty())
{
values.push_back("true");
}
else
{
values.push_back(sip[0]->additionalSearchParams.userParams[i].value);
}
}
Rcpp::List res(names.size());
for (size_t i = 0; i < names.size(); i++)
{
if (isNumber(values[i]))
{
res[i] = Rcpp::wrap(lexical_cast<double>(values[i]));
}
else if (isBool(values[i]))
{
res[i] = Rcpp::wrap(toBool(values[i]));
}
else
{
res[i] = Rcpp::wrap(values[i]);
}
}
res.attr("names") = names;
return res;
}
Rcpp::DataFrame RcppIdent::getDB( )
{
vector<SearchDatabasePtr> sdb = mzid->dataCollection.inputs.searchDatabase;
std::vector<std::string> dbLocation;
std::vector<std::string> dbID;
std::vector<std::string> dbName;
std::vector<std::string> dbVersion;
std::vector<long> numDatabaseSequences;
std::vector<long> numResidues;
for (size_t i = 0; i < sdb.size(); i++)
{
dbLocation.push_back(sdb[i]->location);
dbID.push_back(sdb[i]->id);
dbName.push_back(sdb[i]->name);
dbVersion.push_back(sdb[i]->version);
numDatabaseSequences.push_back(sdb[i]->numDatabaseSequences);
numResidues.push_back(sdb[i]->numResidues);
}
Rcpp::DataFrame database = Rcpp::List::create(
Rcpp::_["location"] = dbLocation,
Rcpp::_["id"] = dbID,
Rcpp::_["name"] = dbName,
Rcpp::_["numDatabaseSequences"] = numDatabaseSequences,
Rcpp::_["numResidues"] = numResidues,
Rcpp::_["version"] = dbVersion
);
return database;
}
