Browse code

add peptide_ref to modification and psm info

Michael Nestor authored on 28/07/2020 19:55:10
Showing1 changed files

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@@ -101,6 +101,7 @@ Rcpp::DataFrame RcppIdent::getPsmInfo(  )
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     std::vector<double> experimentalMassToCharge;
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     std::vector<double> calculatedMassToCharge;
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     std::vector<std::string> seq;
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+    std::vector<std::string> peptide_ref;
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     std::vector<int> modification;
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     std::vector<bool> isDecoy;
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     std::vector<bool> passThreshold;
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@@ -127,6 +128,7 @@ Rcpp::DataFrame RcppIdent::getPsmInfo(  )
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 		experimentalMassToCharge.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->experimentalMassToCharge);
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 		calculatedMassToCharge.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->calculatedMassToCharge);
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 		seq.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptidePtr->peptideSequence);
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+		peptide_ref.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptidePtr->id);
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 		modification.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptidePtr->modification.size());
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 		isDecoy.push_back(spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->isDecoy);
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 		pre.push_back(string(1, spectrumIdResult[i]->spectrumIdentificationItem[j]->peptideEvidencePtr[k]->pre));
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@@ -168,6 +170,7 @@ Rcpp::DataFrame RcppIdent::getPsmInfo(  )
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 	       Rcpp::_["experimentalMassToCharge"]	= experimentalMassToCharge,
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 	       Rcpp::_["calculatedMassToCharge"]	= calculatedMassToCharge,
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 	       Rcpp::_["sequence"]	= seq,
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+	       Rcpp::_["peptide_ref"]	= peptide_ref,
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 	       Rcpp::_["modNum"]	= modification,
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 	       Rcpp::_["isDecoy"]	= isDecoy,
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 	       Rcpp::_["post"]	= post,
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@@ -187,6 +190,7 @@ Rcpp::DataFrame RcppIdent::getModInfo(  )
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     vector<SpectrumIdentificationResultPtr> spectrumIdResult = mzid->analysisCollection.spectrumIdentification[0]->spectrumIdentificationListPtr->spectrumIdentificationResult;
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     vector<string> spectrumID;
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     vector<string> seq;
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+    vector<string> peptide_ref;
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     vector<string> name;
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     vector<double> mass;
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     vector<int> loc;
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@@ -201,6 +205,7 @@ Rcpp::DataFrame RcppIdent::getModInfo(  )
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 		{
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 		    spectrumID.push_back(spectrumIdResult[i]->spectrumID);
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 		    seq.push_back(spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->peptideSequence);
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+		    peptide_ref.push_back(spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->id);
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 		    name.push_back(cvTermInfo(spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->modification[j]->cvParams[0].cvid).name);
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 		    mass.push_back(spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->modification[j]->monoisotopicMassDelta);
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 		    loc.push_back(spectrumIdResult[i]->spectrumIdentificationItem[k]->peptidePtr->modification[j]->location);
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@@ -212,6 +217,7 @@ Rcpp::DataFrame RcppIdent::getModInfo(  )
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     return Rcpp::DataFrame::create(
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 	       Rcpp::_["spectrumID"]	= spectrumID,
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 	       Rcpp::_["sequence"]	= seq,
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+	       Rcpp::_["peptide_ref"]	= peptide_ref,
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 	       Rcpp::_["name"]	= name,
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 	       Rcpp::_["mass"]	= mass,
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 	       Rcpp::_["location"]	= loc);
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@@ -347,16 +353,16 @@ Rcpp::DataFrame RcppIdent::getSpecParams(  )
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         }
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         Rcpp::List res(score.size() + 1);
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-        
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+
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         names.insert(names.begin(), "spectrumID");
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-        
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+
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         res[0] = Rcpp::wrap(spectrumID);
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-        
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+
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         for(size_t i = 0; i < score.size(); i++)
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         {
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             res[i + 1] = Rcpp::wrap(score[i]);
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         }
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-        
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+
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         res.attr("names") = names;
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         Rcpp::DataFrame out(res);
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