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small hackathon improvment #8

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small hackathon improvment #8

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608c4f7
Added Alignment Params (no logic)
FabianAicheler Oct 29, 2018
1daf2e6
small reorder of parameters
FabianAicheler Oct 29, 2018
bb53ae5
connect main body alignment Params to dialog
FabianAicheler Oct 29, 2018
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27 changes: 17 additions & 10 deletions src/utils/MetabolomicsLFQ.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -54,6 +54,8 @@

#include <OpenMS/ANALYSIS/ID/AccurateMassSearchEngine.h>

#include <OpenMS/ANALYSIS/MAPMATCHING/MapAlignmentAlgorithmPoseClustering.h>

#include <OpenMS/ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithmQT.h>
//#include "FeatureLinkerBase.cpp"

Expand Down Expand Up @@ -137,14 +139,10 @@ class UTILMetabolomicsLFQ :
//combined.insert("Linking:", fl_defaults);
//combined.insert("AccurateMassSearch", ams_defaults);

//AMS
//currently no adduct files as parameter, use hardwiring?
//do we want out_annotation as optional file, or hardwire?
registerOutputFile_("out_annotation", "<file>", "", "A copy of the input file, annotated with matching hits from the database.", false);
setValidFormats_("out_annotation", ListUtils::create<String>("featureXML,consensusXML"));
Param p_ams = AccurateMassSearchEngine().getDefaults();
combined.insert("Identification_ams:", p_ams);
combined.setSectionDescription("Identification_ams", "Accurate Mass Search parameters");
//MapAligner pose
Param p_align = MapAlignmentAlgorithmPoseClustering().getParameters();
combined.insert("Quantification_alignment:", p_align);
combined.setSectionDescription("Quantification_alignment", "Map Alignment parameters");

//FL
//do we set linking file explicitly?
Expand All @@ -157,6 +155,15 @@ class UTILMetabolomicsLFQ :
//Do we want to allow the keep_subelements' option or hardwire to false? (true returns ONLY the subelements I think, no consensus. Or something like that, have to evaluate use case.)
//registerFlag_("keep_subelements", "For consensusXML input only: If set, the sub-features of the inputs are transferred to the output.");

//AMS
//currently no adduct files as parameter, use hardwiring?
//do we want out_annotation as optional file, or hardwire?
registerOutputFile_("out_annotation", "<file>", "", "A copy of the input file, annotated with matching hits from the database.", false);
setValidFormats_("out_annotation", ListUtils::create<String>("featureXML,consensusXML"));
Param p_ams = AccurateMassSearchEngine().getDefaults();
combined.insert("Identification_ams:", p_ams);
combined.setSectionDescription("Identification_ams", "Accurate Mass Search parameters");


registerFullParam_(combined);
}
Expand Down Expand Up @@ -235,9 +242,9 @@ class UTILMetabolomicsLFQ :
writeDebug_("Parameters passed to FeatureFindingMetabo", ffm_param, 3);

// Parameter for MapAlignPoseClustering
Param ma_param = getParam_().copy("Quantification_alignment:", true);
writeDebug_("Parameters passed to MapAlignerPoseClustering", ma_param, 3);
/*
Param ma_param = getParam_().copy("Alignment:", true);
writeDebug_("Parameters passed to MapAlignmentPoseClustering algorithm", ma_param, 3);
MapAlignmentPoseClustering ma;
ma.setLogType(log_type_);
ma.setParameters(ff_param);
Expand Down