From d8b915196b2561d4af1096f27bb56a028b4b4fc8 Mon Sep 17 00:00:00 2001 From: Joshua Charkow Date: Thu, 23 May 2024 12:25:18 -0400 Subject: [PATCH] bug fixes for UIS --- .../OpenMS/ANALYSIS/OPENSWATH/OpenSwathScores.h | 1 + .../OPENSWATH/MRMFeatureFinderScoring.cpp | 5 +++++ .../ANALYSIS/OPENSWATH/OpenSwathOSWWriter.cpp | 16 +++++++++++----- src/openms/source/KERNEL/MRMFeature.cpp | 1 + 4 files changed, 18 insertions(+), 5 deletions(-) diff --git a/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/OpenSwathScores.h b/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/OpenSwathScores.h index 5f9f45fb0e5..150db0a3d14 100644 --- a/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/OpenSwathScores.h +++ b/src/openms/include/OpenMS/ANALYSIS/OPENSWATH/OpenSwathScores.h @@ -183,6 +183,7 @@ namespace OpenMS std::vector ind_total_area_intensity; std::vector ind_intensity_score; std::vector ind_apex_intensity; + std::vector ind_apex_position; std::vector ind_fwhm; std::vector ind_total_mi; std::vector ind_log_intensity; diff --git a/src/openms/source/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.cpp b/src/openms/source/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.cpp index e25187c94ae..ddf2a1fccae 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.cpp @@ -350,6 +350,7 @@ namespace OpenMS std::vector ind_total_area_intensity; std::vector ind_intensity_score; std::vector ind_apex_intensity; + std::vector ind_apex_position; std::vector ind_fwhm; std::vector ind_total_mi; std::vector ind_log_intensity; @@ -405,6 +406,7 @@ namespace OpenMS ind_total_area_intensity.push_back(idmrmfeature.getFeature(native_ids_identification[i]).getMetaValue("total_xic")); ind_intensity_score.push_back(intensity_score); ind_apex_intensity.push_back(idmrmfeature.getFeature(native_ids_identification[i]).getMetaValue("peak_apex_int")); + ind_apex_position.push_back(idmrmfeature.getFeature(native_ids_identification[i]).getMetaValue("peak_apex_position")); ind_fwhm.push_back(idmrmfeature.getFeature(native_ids_identification[i]).getMetaValue("width_at_50")); ind_total_mi .push_back(total_mi); ind_log_intensity.push_back(std::log(idmrmfeature.getFeature(native_ids_identification[i]).getIntensity())); @@ -434,6 +436,7 @@ namespace OpenMS ind_total_area_intensity.push_back(0); ind_intensity_score.push_back(0); ind_apex_intensity.push_back(0); + ind_apex_position.push_back(0); ind_fwhm.push_back(0); ind_total_mi.push_back(0); ind_log_intensity.push_back(0); @@ -463,6 +466,7 @@ namespace OpenMS idscores.ind_total_area_intensity = ind_total_area_intensity; idscores.ind_intensity_score = ind_intensity_score; idscores.ind_apex_intensity = ind_apex_intensity; + idscores.ind_apex_position = ind_apex_position; idscores.ind_fwhm = ind_fwhm; idscores.ind_total_mi = ind_total_mi; idscores.ind_log_intensity = ind_log_intensity; @@ -1133,6 +1137,7 @@ namespace OpenMS su_.use_uis_scores = param_.getValue("Scores:use_uis_scores").toBool(); su_.use_ionseries_scores = param_.getValue("Scores:use_ionseries_scores").toBool(); su_.use_ms2_isotope_scores = param_.getValue("Scores:use_ms2_isotope_scores").toBool(); + su_.use_peak_shape_metrics = param_.getValue("Scores:use_peak_shape_metrics").toBool(); } void MRMFeatureFinderScoring::mapExperimentToTransitionList(const OpenSwath::SpectrumAccessPtr& input, diff --git a/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathOSWWriter.cpp b/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathOSWWriter.cpp index fbfba434faa..970cd25fa8b 100644 --- a/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathOSWWriter.cpp +++ b/src/openms/source/ANALYSIS/OPENSWATH/OpenSwathOSWWriter.cpp @@ -406,10 +406,10 @@ namespace OpenMS auto id_target_transition_names = getSeparateScore(feature_it, "id_target_transition_names"); auto id_target_area_intensity = getSeparateScore(feature_it, "id_target_area_intensity"); auto id_target_total_area_intensity = getSeparateScore(feature_it, "id_target_total_area_intensity"); - auto id_target_apex_intensity = getSeparateScore(feature_it, "id_target_ind_apex_intensity"); + auto id_target_apex_intensity = getSeparateScore(feature_it, "id_target_apex_intensity"); auto id_target_peak_apex_position = getSeparateScore(feature_it, "id_target_peak_apex_position"); auto id_target_peak_fwhm = getSeparateScore(feature_it, "id_target_width_at_50"); - auto id_target_total_mi = getSeparateScore(feature_it, "id_target_apex_intensity"); + auto id_target_total_mi = getSeparateScore(feature_it, "id_target_total_mi"); auto id_target_intensity_score = getSeparateScore(feature_it, "id_target_intensity_score"); auto id_target_intensity_ratio_score = getSeparateScore(feature_it, "id_target_intensity_ratio_score"); auto id_target_log_intensity = getSeparateScore(feature_it, "id_target_ind_log_intensity"); @@ -477,7 +477,7 @@ namespace OpenMS << id_target_ind_mi_score[i] << ", " << id_target_ind_mi_ratio_score[i] << ", " << id_target_ind_isotope_correlation[i] << ", " - << id_target_ind_isotope_overlap[i] << "); "; + << id_target_ind_isotope_overlap[i]; if (enable_compute_peak_shape_metrics) { @@ -496,7 +496,7 @@ namespace OpenMS << points_across_baseline[i] << ", " << points_across_half_height[i]; } - sql_feature_ms2_transition << "); "; + sql_feature_uis_transition << "); "; } } @@ -505,6 +505,8 @@ namespace OpenMS auto id_decoy_area_intensity = getSeparateScore(feature_it, "id_decoy_area_intensity"); auto id_decoy_total_area_intensity = getSeparateScore(feature_it, "id_decoy_total_area_intensity"); auto id_decoy_apex_intensity = getSeparateScore(feature_it, "id_decoy_apex_intensity"); + auto id_decoy_peak_apex_position = getSeparateScore(feature_it, "id_decoy_peak_apex_position"); + auto id_decoy_peak_fwhm = getSeparateScore(feature_it, "id_decoy_width_at_50"); auto id_decoy_total_mi = getSeparateScore(feature_it, "id_decoy_total_mi"); auto id_decoy_intensity_score = getSeparateScore(feature_it, "id_decoy_intensity_score"); auto id_decoy_intensity_ratio_score = getSeparateScore(feature_it, "id_decoy_intensity_ratio_score"); @@ -555,6 +557,9 @@ namespace OpenMS << id_decoy_area_intensity[i] << ", " << id_decoy_total_area_intensity[i] << ", " << id_decoy_apex_intensity[i] << ", " + << id_decoy_peak_apex_position[i] << ", " + << id_decoy_peak_fwhm[i] << ", " + << id_decoy_ind_massdev_score[i] << ", " << id_decoy_total_mi[i] << ", " << id_decoy_intensity_score[i] << ", " << id_decoy_intensity_ratio_score[i] << ", " @@ -566,7 +571,7 @@ namespace OpenMS << id_decoy_ind_mi_score[i] << ", " << id_decoy_ind_mi_ratio_score[i] << ", " << id_decoy_ind_isotope_correlation[i] << ", " - << id_decoy_ind_isotope_overlap[i] << "); "; + << id_decoy_ind_isotope_overlap[i]; if (enable_compute_peak_shape_metrics) { @@ -585,6 +590,7 @@ namespace OpenMS << decoy_points_across_baseline[i] << ", " << decoy_points_across_half_height[i]; } + sql_feature_uis_transition << "); "; } } } diff --git a/src/openms/source/KERNEL/MRMFeature.cpp b/src/openms/source/KERNEL/MRMFeature.cpp index e5e13f1b07a..6192e4e4bed 100644 --- a/src/openms/source/KERNEL/MRMFeature.cpp +++ b/src/openms/source/KERNEL/MRMFeature.cpp @@ -146,6 +146,7 @@ namespace OpenMS setMetaValue(id + "intensity_score", idscores.ind_intensity_score); setMetaValue(id + "intensity_ratio_score", idscores.ind_intensity_ratio); setMetaValue(id + "apex_intensity", idscores.ind_apex_intensity); + setMetaValue(id + "peak_apex_position", idscores.ind_apex_position); setMetaValue(id + "width_at_50", idscores.ind_fwhm); setMetaValue(id + "total_mi", idscores.ind_total_mi); setMetaValue(id + "transition_names", idscores.ind_transition_names);