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prepareLine
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chen committed May 18, 2020
1 parent f99300d commit c3cc8b6
Showing 1 changed file with 78 additions and 78 deletions.
156 changes: 78 additions & 78 deletions src/openms/source/ANALYSIS/OPENSWATH/OpenSwathTSVWriter.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@
// --------------------------------------------------------------------------

#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathTSVWriter.h>
#include <sstream>

namespace OpenMS
{
Expand Down Expand Up @@ -108,7 +109,7 @@ namespace OpenMS
const OpenSwath::LightTransition * transition,
const FeatureMap& output, const String id) const
{
String result = "";
std::stringstream fast_;
String decoy = "0"; // 0 = false
if (transition->decoy)
{
Expand Down Expand Up @@ -185,100 +186,99 @@ namespace OpenMS
main_var = (String)feature_it->getMetaValue("main_var_xx_lda_prelim_score");
}

String line =
id + "_run0"
+ "\t" + group_label
+ "\t" + "0"
+ "\t" + input_filename_
+ "\t" + (String)feature_it->getRT()
+ "\t" + "f_" + feature_it->getUniqueId() // TODO might not be unique!!!
+ "\t" + (String)pep.sequence
+ "\t" + (feature_it->metaValueExists("missedCleavages") ? (String)feature_it->getMetaValue("missedCleavages") : "")
+ "\t" + full_peptide_name
+ "\t" + (String)pep.charge
+ "\t" + (String)transition->precursor_mz
+ "\t" + (String)feature_it->getIntensity()
+ "\t" + protein_name
+ "\t" + gene_name
+ "\t" + decoy
fast_ <<
id << "_run0"
<< "\t" << group_label
<< "\t" << "0"
<< "\t" << input_filename_
<< "\t" << (String)feature_it->getRT()
<< "\t" << "f_" << feature_it->getUniqueId() // TODO might not be unique!!!
<< "\t" << (String)pep.sequence
<< "\t" << (feature_it->metaValueExists("missedCleavages") ? (String)feature_it->getMetaValue("missedCleavages") : "")
<< "\t" << full_peptide_name
<< "\t" << (String)pep.charge
<< "\t" << (String)transition->precursor_mz
<< "\t" << (String)feature_it->getIntensity()
<< "\t" << protein_name
<< "\t" << gene_name
<< "\t" << decoy
// Note: missing MetaValues will just produce a DataValue::EMPTY which lead to an empty column
+ "\t" + (String)feature_it->getMetaValue("assay_rt")
+ "\t" + (String)feature_it->getMetaValue("delta_rt")
+ "\t" + (String)feature_it->getMetaValue("leftWidth")
+ "\t" + main_var
+ "\t" + (String)feature_it->getMetaValue("norm_RT")
+ "\t" + (String)feature_it->getMetaValue("nr_peaks")
+ "\t" + (String)feature_it->getMetaValue("peak_apices_sum")
+ "\t" + (String)feature_it->getMetaValue("potentialOutlier")
+ "\t" + (String)feature_it->getMetaValue("initialPeakQuality")
+ "\t" + (String)feature_it->getMetaValue("rightWidth")
+ "\t" + (String)feature_it->getMetaValue("rt_score")
+ "\t" + (String)feature_it->getMetaValue("sn_ratio")
+ "\t" + (String)feature_it->getMetaValue("total_xic")
+ "\t" + (String)feature_it->getMetaValue("var_bseries_score")
+ "\t" + (String)feature_it->getMetaValue("var_dotprod_score")
+ "\t" + (String)feature_it->getMetaValue("var_intensity_score")
+ "\t" + (String)feature_it->getMetaValue("var_isotope_correlation_score")
+ "\t" + (String)feature_it->getMetaValue("var_isotope_overlap_score")
+ "\t" + (String)feature_it->getMetaValue("var_library_corr")
+ "\t" + (String)feature_it->getMetaValue("var_library_dotprod")
+ "\t" + (String)feature_it->getMetaValue("var_library_manhattan")
+ "\t" + (String)feature_it->getMetaValue("var_library_rmsd")
+ "\t" + (String)feature_it->getMetaValue("var_library_rootmeansquare")
+ "\t" + (String)feature_it->getMetaValue("var_library_sangle")
+ "\t" + (String)feature_it->getMetaValue("var_log_sn_score")
+ "\t" + (String)feature_it->getMetaValue("var_manhatt_score")
+ "\t" + (String)feature_it->getMetaValue("var_massdev_score")
+ "\t" + (String)feature_it->getMetaValue("var_massdev_score_weighted")
+ "\t" + (String)feature_it->getMetaValue("var_norm_rt_score")
+ "\t" + (String)feature_it->getMetaValue("var_xcorr_coelution")
+ "\t" + (String)feature_it->getMetaValue("var_xcorr_coelution_weighted")
+ "\t" + (String)feature_it->getMetaValue("var_xcorr_shape")
+ "\t" + (String)feature_it->getMetaValue("var_xcorr_shape_weighted")
<< "\t" << (String)feature_it->getMetaValue("assay_rt")
<< "\t" << (String)feature_it->getMetaValue("delta_rt")
<< "\t" << (String)feature_it->getMetaValue("leftWidth")
<< "\t" << main_var
<< "\t" << (String)feature_it->getMetaValue("norm_RT")
<< "\t" << (String)feature_it->getMetaValue("nr_peaks")
<< "\t" << (String)feature_it->getMetaValue("peak_apices_sum")
<< "\t" << (String)feature_it->getMetaValue("potentialOutlier")
<< "\t" << (String)feature_it->getMetaValue("initialPeakQuality")
<< "\t" << (String)feature_it->getMetaValue("rightWidth")
<< "\t" << (String)feature_it->getMetaValue("rt_score")
<< "\t" << (String)feature_it->getMetaValue("sn_ratio")
<< "\t" << (String)feature_it->getMetaValue("total_xic")
<< "\t" << (String)feature_it->getMetaValue("var_bseries_score")
<< "\t" << (String)feature_it->getMetaValue("var_dotprod_score")
<< "\t" << (String)feature_it->getMetaValue("var_intensity_score")
<< "\t" << (String)feature_it->getMetaValue("var_isotope_correlation_score")
<< "\t" << (String)feature_it->getMetaValue("var_isotope_overlap_score")
<< "\t" << (String)feature_it->getMetaValue("var_library_corr")
<< "\t" << (String)feature_it->getMetaValue("var_library_dotprod")
<< "\t" << (String)feature_it->getMetaValue("var_library_manhattan")
<< "\t" << (String)feature_it->getMetaValue("var_library_rmsd")
<< "\t" << (String)feature_it->getMetaValue("var_library_rootmeansquare")
<< "\t" << (String)feature_it->getMetaValue("var_library_sangle")
<< "\t" << (String)feature_it->getMetaValue("var_log_sn_score")
<< "\t" << (String)feature_it->getMetaValue("var_manhatt_score")
<< "\t" << (String)feature_it->getMetaValue("var_massdev_score")
<< "\t" << (String)feature_it->getMetaValue("var_massdev_score_weighted")
<< "\t" << (String)feature_it->getMetaValue("var_norm_rt_score")
<< "\t" << (String)feature_it->getMetaValue("var_xcorr_coelution")
<< "\t" << (String)feature_it->getMetaValue("var_xcorr_coelution_weighted")
<< "\t" << (String)feature_it->getMetaValue("var_xcorr_shape")
<< "\t" << (String)feature_it->getMetaValue("var_xcorr_shape_weighted")

+ "\t" + (String)feature_it->getMetaValue("var_im_xcorr_shape")
+ "\t" + (String)feature_it->getMetaValue("var_im_xcorr_coelution")
+ "\t" + (String)feature_it->getMetaValue("var_im_delta_score")
+ "\t" + (String)feature_it->getMetaValue("var_im_ms1_delta_score")
+ "\t" + (String)feature_it->getMetaValue("im_drift")
+ "\t" + (String)feature_it->getMetaValue("im_drift_weighted")
<< "\t" << (String)feature_it->getMetaValue("var_im_xcorr_shape")
<< "\t" << (String)feature_it->getMetaValue("var_im_xcorr_coelution")
<< "\t" << (String)feature_it->getMetaValue("var_im_delta_score")
<< "\t" << (String)feature_it->getMetaValue("var_im_ms1_delta_score")
<< "\t" << (String)feature_it->getMetaValue("im_drift")
<< "\t" << (String)feature_it->getMetaValue("im_drift_weighted")

+ "\t" + (String)feature_it->getMetaValue("var_yseries_score")
+ "\t" + (String)feature_it->getMetaValue("var_elution_model_fit_score");
<< "\t" << (String)feature_it->getMetaValue("var_yseries_score")
<< "\t" << (String)feature_it->getMetaValue("var_elution_model_fit_score");

if (use_ms1_traces_)
{
line += "\t" + (String)feature_it->getMetaValue("var_ms1_ppm_diff")
+ "\t" + (String)feature_it->getMetaValue("var_ms1_isotope_correlation")
+ "\t" + (String)feature_it->getMetaValue("var_ms1_isotope_overlap")
+ "\t" + (String)feature_it->getMetaValue("var_ms1_xcorr_coelution")
+ "\t" + (String)feature_it->getMetaValue("var_ms1_xcorr_shape");
fast_ << "\t" << (String)feature_it->getMetaValue("var_ms1_ppm_diff")
<< "\t" << (String)feature_it->getMetaValue("var_ms1_isotope_correlation")
<< "\t" << (String)feature_it->getMetaValue("var_ms1_isotope_overlap")
<< "\t" << (String)feature_it->getMetaValue("var_ms1_xcorr_coelution")
<< "\t" << (String)feature_it->getMetaValue("var_ms1_xcorr_shape");
}

line += "\t" + (String)feature_it->getMetaValue("xx_lda_prelim_score")
+ "\t" + (String)feature_it->getMetaValue("xx_swath_prelim_score");
fast_ << "\t" << (String)feature_it->getMetaValue("xx_lda_prelim_score")
<< "\t" << (String)feature_it->getMetaValue("xx_swath_prelim_score");
if (sonar_)
{
line += "\t" + (String)feature_it->getMetaValue("var_sonar_lag")
+ "\t" + (String)feature_it->getMetaValue("var_sonar_shape")
+ "\t" + (String)feature_it->getMetaValue("var_sonar_log_sn")
+ "\t" + (String)feature_it->getMetaValue("var_sonar_log_diff")
+ "\t" + (String)feature_it->getMetaValue("var_sonar_log_trend")
+ "\t" + (String)feature_it->getMetaValue("var_sonar_rsq");
fast_ << "\t" << (String)feature_it->getMetaValue("var_sonar_lag")
<< "\t" << (String)feature_it->getMetaValue("var_sonar_shape")
<< "\t" << (String)feature_it->getMetaValue("var_sonar_log_sn")
<< "\t" << (String)feature_it->getMetaValue("var_sonar_log_diff")
<< "\t" << (String)feature_it->getMetaValue("var_sonar_log_trend")
<< "\t" << (String)feature_it->getMetaValue("var_sonar_rsq");

}
if (use_ms1_traces_)
{
line += "\t" + ListUtils::concatenate(aggr_prec_Peak_Area, ";") + "\t" + ListUtils::concatenate(aggr_prec_Peak_Apex, ";") + "\t" + ListUtils::concatenate(aggr_prec_Fragment_Annotation, ";");
fast_ << "\t" << ListUtils::concatenate(aggr_prec_Peak_Area, ";") << "\t" << ListUtils::concatenate(aggr_prec_Peak_Apex, ";") << "\t" << ListUtils::concatenate(aggr_prec_Fragment_Annotation, ";");
}
line += "\t" + ListUtils::concatenate(aggr_Peak_Area, ";") + "\t" + ListUtils::concatenate(aggr_Peak_Apex, ";") + "\t" + ListUtils::concatenate(aggr_Fragment_Annotation, ";");
line += "\t" + ListUtils::concatenate(rt_fwhm, ";");
line += "\t" + (feature_it->metaValueExists("masserror_ppm") ? ListUtils::concatenate(feature_it->getMetaValue("masserror_ppm").toDoubleList(), ";") : "");
fast_ << "\t" << ListUtils::concatenate(aggr_Peak_Area, ";") << "\t" << ListUtils::concatenate(aggr_Peak_Apex, ";") << "\t" << ListUtils::concatenate(aggr_Fragment_Annotation, ";");
fast_ << "\t" << ListUtils::concatenate(rt_fwhm, ";");
fast_ << "\t" << (feature_it->metaValueExists("masserror_ppm") ? ListUtils::concatenate(feature_it->getMetaValue("masserror_ppm").toDoubleList(), ";") : "");

line += "\n";
result += line;
fast_ << "\n";
} // end of iteration
return result;
return fast_.str();
}

void OpenSwathTSVWriter::writeLines(const std::vector<String>& to_output)
Expand Down

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