From c3cc8b67d6b24150f50f9fed7d128a9111a8dbd7 Mon Sep 17 00:00:00 2001 From: chen Date: Mon, 18 May 2020 12:29:40 +0200 Subject: [PATCH] prepareLine --- .../ANALYSIS/OPENSWATH/OpenSwathTSVWriter.cpp | 156 +++++++++--------- 1 file changed, 78 insertions(+), 78 deletions(-) diff --git a/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathTSVWriter.cpp b/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathTSVWriter.cpp index 2d7e9b3027e..b5f232e251c 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathTSVWriter.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathTSVWriter.cpp @@ -33,6 +33,7 @@ // -------------------------------------------------------------------------- #include +#include namespace OpenMS { @@ -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) { @@ -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& to_output)