[Feature] id filter on consensusXML #4798
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added 2 commits
June 25, 2020 21:22
By extracting IDs, saving their featureID and mapping back. I did not check if EVERY filter criterion makes sense for cXML but most of them (especially simple ones) should.
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nice! |
cbielow
reviewed
Jun 26, 2020
| for (auto&& p : f.getPeptideIdentifications()) | ||
| { | ||
| p.setMetaValue("feature_id", id); | ||
| peptides.emplace_back(p); |
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Requires std::move (or std::forward if you stick to auto&&).
Also emplace_back suggests emplacing a new type, but the type stays the same so push_back is enough.
| std::back_inserter(peptides)); | ||
| unassigned.clear(); | ||
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| std::swap(proteins, cmap.getProteinIdentifications()); |
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Move assignment is enough? No need to swap???
| @@ -705,7 +738,31 @@ class TOPPIDFilter : | |||
| << peptides.size() << " spectra identified with " | |||
| << IDFilter::countHits(peptides) << " spectrum matches." << endl; | |||
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| IdXMLFile().store(outputfile_name, proteins, peptides); | |||
| if (FileHandler::getTypeByFileName(inputfile_name) == FileTypes::IDXML) | |||
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Why not getType ? Would also cover content if suffix is ambiguous.
But query once to avoid duplicate work.
| { | ||
| UInt64 id = f.getUniqueId(); | ||
| id_to_featureref[id] = &f; | ||
| for (auto&& p : f.getPeptideIdentifications()) |
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I find this confusing, since there is no case where we use reference proxies in our code (that I'm aware of).
Use auto& p: ..?
| } | ||
| else if (FileHandler::getTypeByFileName(inputfile_name) == FileTypes::CONSENSUSXML) | ||
| { | ||
| for (auto&& p : peptides) |
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same with auto&& and emplace here
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