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Fix: GetMetaValue for FIA-MS applications (#276)
* fix: prioritized the use of subordinate metadata when choosing between feature level and subordinate level * examples: updated FIAMS parameters and TraML templates * ci: bug in config.yml
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-16
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‎.circleci/config.yml

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Original file line numberDiff line numberDiff line change
@@ -172,7 +172,7 @@ jobs:
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cmake -G "Visual Studio 16 2019" -A x64 -DBUILD_TYPE=KISSFFT ~/OpenMS/contrib
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cmake -G "Visual Studio 16 2019" -A x64 -DBUILD_TYPE=HDF5 ~/OpenMS/contrib
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cd ~/OpenMS; mkdir openms_build; cd openms_build
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cmake -G "Visual Studio 16 2019" -A x64 -DCMAKE_CXX_STANDARD=14 -DCMAKE_CXX_EXTENSIONS=OFF -DCXX_STANDARD_REQUIRED=ON -DBoost_NO_SYSTEM_PATHS=ON -DBOOST_USE_STATIC=ON -DBOOST_ROOT="C:/local/boost_1_67_0" -DBOOST_INCLUDE_DIR="C:/local/boost_1_67_0" -DBOOST_LIBRARYDIR="C:/local/boost_1_67_0/lib64-msvc-14.2" -DOPENMS_CONTRIB_LIBS=~/OpenMS/contrib_build -DCMAKE_PREFIX_PATH="C:/lib/Qt/qt-5.12.9-dynamic-msvc2019-x86_64" -DHAS_XSERVER=OFF -DWITH_GUI=OFF -DENABLE_TUTORIALS=OFF -DENABLE_DOCS=OFF -DGIT_TRACKING=OFF -DENABLE_UPDATE_CHECK=OFF -DCMAKE_BUILD_TYPE=Release -DPYOPENMS=OFF -DOPENMS_COVERAGE=OFF ~/OpenMS
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cmake -G "Visual Studio 16 2019" -A x64 -DCMAKE_CXX_STANDARD=14 -DCMAKE_CXX_EXTENSIONS=OFF -DCXX_STANDARD_REQUIRED=ON -DBoost_NO_SYSTEM_PATHS=ON -DBOOST_USE_STATIC=ON -DBOOST_ROOT="C:/local/boost_1_67_0" -DBOOST_INCLUDE_DIR="C:/local/boost_1_67_0" -DBOOST_LIBRARYDIR="C:/local/boost_1_67_0/lib64-msvc-14.1" -DOPENMS_CONTRIB_LIBS=~/OpenMS/contrib_build -DCMAKE_PREFIX_PATH="C:/lib/Qt/qt-5.12.9-dynamic-msvc2019-x86_64" -DHAS_XSERVER=OFF -DWITH_GUI=OFF -DENABLE_TUTORIALS=OFF -DENABLE_DOCS=OFF -DGIT_TRACKING=OFF -DENABLE_UPDATE_CHECK=OFF -DCMAKE_BUILD_TYPE=Release -DPYOPENMS=OFF -DOPENMS_COVERAGE=OFF ~/OpenMS
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msbuild src\openswathalgo\OpenSWATHAlgo.sln /maxcpucount /p:Configuration=Release
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msbuild src\openms\OpenMS.sln /maxcpucount /p:Configuration=Release
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- run: |

‎src/examples/data/FIAMS_FullScan_Unknowns/parameters.csv

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@@ -30,3 +30,10 @@ AccurateMassSearchEngine,use_feature_adducts,boolean,FALSE,FALSE,true; false,Whe
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AccurateMassSearchEngine,keep_unidentified_masses,boolean,FALSE,FALSE,true; false,Keep features that did not yield any DB hit.,FALSE,,
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AccurateMassSearchEngine,mzTab:exportIsotopeIntensities,boolean,FALSE,FALSE,true; false,[featureXML input only] Export column with available isotope trace intensities (opt_global_MTint),FALSE,,
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SequenceProcessor,n_thread,int,6,1,,Number of threads to use,TRUE,,
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MergeInjections,scan_polarity_merge_rule,string,WeightedMean,,,,TRUE,,
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MergeInjections,mass_range_merge_rule,string,Sum,,,,TRUE,,
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MergeInjections,dilution_series_merge_rule,string,Max,,,,TRUE,,
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MergeInjections,scan_polarity_merge_feature_name,string,peak_apex_int,,,,TRUE,,
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MergeInjections,mass_range_merge_feature_name,string,peak_apex_int,,,,TRUE,,
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MergeInjections,dilution_series_merge_feature_name,string,peak_apex_int,,,,TRUE,,
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MergeInjections,merge_subordinates,boolean,FALSE,TRUE,,,TRUE,,

‎src/examples/data/FIAMS_FullScan_Unknowns/traML_top10Serum.csv

Lines changed: 12 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -1,13 +1,13 @@
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ProteinName,FullPeptideName,transition_group_id,transition_name,RetentionTime,Annotation,PrecursorMz,MS1 Res,ProductMz,MS2 Res,Dwell,Fragmentor,Collision Energy,Cell Accelerator Voltage,LibraryIntensity,decoy,PeptideSequence,LabelType,PrecursorCharge,FragmentCharge,FragmentType,FragmentSeriesNumber,quantifying_transition,identifying_transition,detecting_transition
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HMDB:HMDB0000294,,HMDB:HMDB0000294,Urea,0,,0,5 ppm,0,5 ppm,,,,,1,0,,Light,1,1,,1,FALSE,FALSE,FALSE
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HMDB:HMDB0000190,,HMDB:HMDB0000190,Lactic acid,0,,0,5 ppm,0,5 ppm,,,,,1,0,,Light,1,1,,1,FALSE,FALSE,FALSE
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HMDB:HMDB0000289,,HMDB:HMDB0000289,Uric acid,0,,0,5 ppm,0,5 ppm,,,,,1,0,,Light,1,1,,1,FALSE,FALSE,FALSE
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HMDB:HMDB0004068,,HMDB:HMDB0004068,Melanin,0,,0,5 ppm,0,5 ppm,,,,,1,0,,Light,1,1,,1,FALSE,FALSE,FALSE
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HMDB:HMDB0002030,,HMDB:HMDB0002030,Fructosamine,0,,0,5 ppm,0,5 ppm,,,,,1,0,,Light,1,1,,1,FALSE,FALSE,FALSE
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HMDB:HMDB0001875,,HMDB:HMDB0001875,Methanol,0,,0,5 ppm,0,5 ppm,,,,,1,0,,Light,1,1,,1,FALSE,FALSE,FALSE
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HMDB:HMDB0000641,,HMDB:HMDB0000641,L-Glutamine,0,,0,5 ppm,0,5 ppm,,,,,1,0,,Light,1,1,,1,FALSE,FALSE,FALSE
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HMDB:HMDB0000067,,HMDB:HMDB0000067,Cholesterol,0,,0,5 ppm,0,5 ppm,,,,,1,0,,Light,1,1,,1,FALSE,FALSE,FALSE
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HMDB:HMDB0000182,,HMDB:HMDB0000182,L-Lysine,0,,0,5 ppm,0,5 ppm,,,,,1,0,,Light,1,1,,1,FALSE,FALSE,FALSE
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HMDB:HMDB0000122,,HMDB:HMDB0000122,D-Glucose,0,,0,5 ppm,0,5 ppm,,,,,1,0,,Light,1,1,,1,FALSE,FALSE,FALSE
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HMDB:HMDB0000161,,HMDB:HMDB0000161,L-Alanine,0,,0,5 ppm,0,5 ppm,,,,,1,0,,Light,1,1,,1,FALSE,FALSE,FALSE
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HMDB:HMDB0000123,,HMDB:HMDB0000123,Glycine,0,,0,5 ppm,0,5 ppm,,,,,1,0,,Light,1,1,,1,FALSE,FALSE,FALSE
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HMDB:HMDB0000294,Urea,HMDB:HMDB0000294,,0,,0,5 ppm,0,5 ppm,,,,,1,0,,Light,1,1,,1,FALSE,FALSE,FALSE
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HMDB:HMDB0000190,Lactic acid,HMDB:HMDB0000190,,0,,0,5 ppm,0,5 ppm,,,,,1,0,,Light,1,1,,1,FALSE,FALSE,FALSE
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HMDB:HMDB0000289,Uric acid,HMDB:HMDB0000289,,0,,0,5 ppm,0,5 ppm,,,,,1,0,,Light,1,1,,1,FALSE,FALSE,FALSE
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HMDB:HMDB0004068,Melanin,HMDB:HMDB0004068,,0,,0,5 ppm,0,5 ppm,,,,,1,0,,Light,1,1,,1,FALSE,FALSE,FALSE
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HMDB:HMDB0002030,Fructosamine,HMDB:HMDB0002030,,0,,0,5 ppm,0,5 ppm,,,,,1,0,,Light,1,1,,1,FALSE,FALSE,FALSE
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HMDB:HMDB0001875,Methanol,HMDB:HMDB0001875,,0,,0,5 ppm,0,5 ppm,,,,,1,0,,Light,1,1,,1,FALSE,FALSE,FALSE
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HMDB:HMDB0000641,L-Glutamine,HMDB:HMDB0000641,,0,,0,5 ppm,0,5 ppm,,,,,1,0,,Light,1,1,,1,FALSE,FALSE,FALSE
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HMDB:HMDB0000067,Cholesterol,HMDB:HMDB0000067,,0,,0,5 ppm,0,5 ppm,,,,,1,0,,Light,1,1,,1,FALSE,FALSE,FALSE
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HMDB:HMDB0000182,L-Lysine,HMDB:HMDB0000182,,0,,0,5 ppm,0,5 ppm,,,,,1,0,,Light,1,1,,1,FALSE,FALSE,FALSE
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HMDB:HMDB0000122,D-Glucose,HMDB:HMDB0000122,,0,,0,5 ppm,0,5 ppm,,,,,1,0,,Light,1,1,,1,FALSE,FALSE,FALSE
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HMDB:HMDB0000161,L-Alanine,HMDB:HMDB0000161,,0,,0,5 ppm,0,5 ppm,,,,,1,0,,Light,1,1,,1,FALSE,FALSE,FALSE
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HMDB:HMDB0000123,Glycine,HMDB:HMDB0000123,,0,,0,5 ppm,0,5 ppm,,,,,1,0,,Light,1,1,,1,FALSE,FALSE,FALSE

‎src/smartpeak/source/core/SequenceHandler.cpp

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -266,11 +266,11 @@ namespace SmartPeak
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} else if (meta_value == "peak_area") { // Subordinate intensity (also called "peak area)
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cast = static_cast<float>(subordinate.getIntensity());
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} else if (meta_value == "validation") { // The result of the validation
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cast = static_cast<std::string>(subordinate.getMetaValue(meta_value));
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} else if (feature.metaValueExists(meta_value) && !feature.getMetaValue(meta_value).isEmpty()) {
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cast = static_cast<float>(feature.getMetaValue(meta_value));
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cast = static_cast<std::string>(subordinate.getMetaValue(meta_value)); // Prioritize the subordinate over the feature
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} else if (subordinate.metaValueExists(meta_value) && !subordinate.getMetaValue(meta_value).isEmpty()) {
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cast = static_cast<float>(subordinate.getMetaValue(meta_value));
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} else if (feature.metaValueExists(meta_value) && !feature.getMetaValue(meta_value).isEmpty()) {
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cast = static_cast<float>(feature.getMetaValue(meta_value));
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} else {
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LOGV << "meta_value not found: " << meta_value;
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cast = "";

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