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bug fixes for UIS
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@jcharkow
jcharkow committed May 23, 2024
1 parent 56d456b commit d8b9151
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Showing 4 changed files with 18 additions and 5 deletions.
1 change: 1 addition & 0 deletions src/openms/include/OpenMS/ANALYSIS/OPENSWATH/OpenSwathScores.h
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Expand Up @@ -183,6 +183,7 @@ namespace OpenMS
std::vector<double> ind_total_area_intensity;
std::vector<double> ind_intensity_score;
std::vector<double> ind_apex_intensity;
std::vector<double> ind_apex_position;
std::vector<double> ind_fwhm;
std::vector<double> ind_total_mi;
std::vector<double> ind_log_intensity;
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5 changes: 5 additions & 0 deletions src/openms/source/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.cpp
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Expand Up @@ -350,6 +350,7 @@ namespace OpenMS
std::vector<double> ind_total_area_intensity;
std::vector<double> ind_intensity_score;
std::vector<double> ind_apex_intensity;
std::vector<double> ind_apex_position;
std::vector<double> ind_fwhm;
std::vector<double> ind_total_mi;
std::vector<double> ind_log_intensity;
Expand Down Expand Up @@ -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()));
Expand Down Expand Up @@ -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);
Expand Down Expand Up @@ -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;
Expand Down Expand Up @@ -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,
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16 changes: 11 additions & 5 deletions src/openms/source/ANALYSIS/OPENSWATH/OpenSwathOSWWriter.cpp
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Expand Up @@ -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");
Expand Down Expand Up @@ -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)
{
Expand All @@ -496,7 +496,7 @@ namespace OpenMS
<< points_across_baseline[i] << ", "
<< points_across_half_height[i];
}
sql_feature_ms2_transition << "); ";
sql_feature_uis_transition << "); ";

}
}
Expand All @@ -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");
Expand Down Expand Up @@ -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] << ", "
Expand All @@ -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)
{
Expand All @@ -585,6 +590,7 @@ namespace OpenMS
<< decoy_points_across_baseline[i] << ", "
<< decoy_points_across_half_height[i];
}
sql_feature_uis_transition << "); ";
}
}
}
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1 change: 1 addition & 0 deletions src/openms/source/KERNEL/MRMFeature.cpp
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Expand Up @@ -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);
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