Extension of bruker precursor information (2nd attempt) #3191
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@@ -52,13 +52,13 @@ class Serializer_MGF::Impl | |
| void read(shared_ptr<istream> is, MSData& msd) const; | ||
| }; | ||
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| template <typename T> | ||
| struct nosci10_policy : boost::spirit::karma::real_policies<T> | ||
| { | ||
| // we want to generate up to 10 fractional digits | ||
| static unsigned int precision(T) { return 10; } | ||
| // we want the numbers always to be in fixed format | ||
| static int floatfield(T) { return boost::spirit::karma::real_policies<T>::fmtflags::fixed; } | ||
| }; | ||
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@@ -78,25 +78,25 @@ void Serializer_MGF::Impl::write(ostream& os, const MSData& msd, | |
| SpectrumList& sl = *msd.run.spectrumListPtr; | ||
| SpectrumWorkerThreads spectrumWorkers(sl, useWorkerThreads, continueOnError); | ||
| for (size_t i=0, end=sl.size(); i < end; ++i) | ||
| { | ||
| SpectrumPtr s; | ||
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There was a problem hiding this comment. I'm still seeing whitespace changes here. You know how to review the diff in GitHub? You can also review it locally if you set your diff engine to show whitespace changes. There was a problem hiding this comment. yes, sorry, but unfortunately it's not finished yet. Yes, It's easy to see whitespace changes, but undoing them without removing other important things is a bit difficult for me. But I´m on it. Thank you. There was a problem hiding this comment. Whitespaces should now be removed. |
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| try | ||
| { | ||
| // s = sl->spectrum(i, true); | ||
| s = spectrumWorkers.processBatch(i); | ||
| } | ||
| catch (std::exception& e) | ||
| { | ||
| if (continueOnError) | ||
| { | ||
| cerr << "Skipping spectrum " << i << " \"" << (s ? s->id : sl.spectrumIdentity(i).id) << "\": " << e.what() << endl; | ||
| continue; | ||
| } | ||
| else | ||
| throw; | ||
| } | ||
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| const Scan& scan = !s->scanList.empty() ? s->scanList.scans[0] : Scan(); | ||
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| if (s->cvParam(MS_ms_level).valueAs<int>() > 1 && | ||
| !s->precursors.empty() && | ||
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@@ -105,16 +105,16 @@ void Serializer_MGF::Impl::write(ostream& os, const MSData& msd, | |
| os << "BEGIN IONS\n"; | ||
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| const SelectedIon& si = s->precursors[0].selectedIons[0]; | ||
| CVParam scanTimeParam = scan.cvParam(MS_scan_start_time); | ||
| CVParam chargeParam = si.cvParam(MS_charge_state); | ||
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| CVParam spectrumTitle = s->cvParam(MS_spectrum_title); | ||
| if (!spectrumTitle.empty()) | ||
| os << "TITLE=" << spectrumTitle.value << '\n'; | ||
| else if (titleIsThermoDTA) | ||
| { | ||
| string scan_string = id::value(s->id, "scan"); | ||
| os << "TITLE=" << thermoBasename << '.' << scan_string << '.' << scan_string << '.' << chargeParam.value << '\n'; | ||
| } | ||
| else | ||
| os << "TITLE=" << s->id << '\n'; | ||
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@@ -132,6 +132,16 @@ void Serializer_MGF::Impl::write(ostream& os, const MSData& msd, | |
| os << " " << intensityParam.valueFixedNotation(); | ||
| os << '\n'; | ||
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| CVParam inverseReduceIonMobility = scan.cvParam(MS_inverse_reduced_ion_mobility); | ||
| if (!inverseReduceIonMobility.empty()) | ||
| os << "INVREION=" << inverseReduceIonMobility.valueFixedNotation(); | ||
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There was a problem hiding this comment. Did you check whether some official product already writes it this way? Because according to the official MGF spec this is not a valid parameter. https://www.matrixscience.com/help/data_file_help.html There was a problem hiding this comment. okay, I´ll check this. There was a problem hiding this comment. I hope it´s done now. :-) |
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| os << '\n'; | ||
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| CVParam collisionalCrossSectionalArea = scan.cvParam(MS_collisional_cross_sectional_area); | ||
| if (!collisionalCrossSectionalArea.empty()) | ||
| os << "COLLCROSSSA=" << collisionalCrossSectionalArea.valueFixedNotation(); | ||
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There was a problem hiding this comment. There is no official MGF parameter for this. I would be more comfortable with this in the TITLE string, unless a Bruker product is already writing MGFs this way. There was a problem hiding this comment. okay, Is there an example of adding some parameters to the title string? There was a problem hiding this comment. There's a titleMaker filter that allows for easy customization of the MGF title string with a user-defined format. Although it doesn't support CCS currently, only instrument-level ion mobility metrics. If you don't want to use that, you can add "ccs=" to the title string above this, before the line: There was a problem hiding this comment. Okay, that sounds good, I'll implement it that way. |
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| os << '\n'; | ||
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| if (chargeParam.empty()) | ||
| { | ||
| vector<string> charges; | ||
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@@ -148,9 +158,9 @@ void Serializer_MGF::Impl::write(ostream& os, const MSData& msd, | |
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| const BinaryDataArray& mzArray = *s->getMZArray(); | ||
| const BinaryDataArray& intensityArray = *s->getIntensityArray(); | ||
| using namespace boost::spirit::karma; | ||
| typedef real_generator<double, nosci10_policy<double> > nosci10_type; | ||
| static const nosci10_type nosci10 = nosci10_type(); | ||
| char buffer[256]; | ||
| for (size_t p=0; p < s->defaultArrayLength; ++p) | ||
| { | ||
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Revert whitespace only change.
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sure, I´ll fix this.
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Should be removed.