Library reader change to read pdeep and neutral loss #2056
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…//github.com/smith-chem-wisc/MetaMorpheus into LibraryReaderChangeToReadPdeepAndNeutralLoss
| double neutralLoss = 0; | ||
| if (split[2].Contains("-")) | ||
| { | ||
| String[] NL = split[2].Split(neutralLossSplit, StringSplitOptions.RemoveEmptyEntries).ToArray(); |
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NL should be lower case and more informative
…//github.com/smith-chem-wisc/MetaMorpheus into LibraryReaderChangeToReadPdeepAndNeutralLoss
| @@ -360,7 +495,15 @@ private void IndexSpectralLibrary(string path) | |||
| reader.DiscardBufferedData(); | |||
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| // parse the header | |||
| var libraryItem = ReadLibrarySpectrum(reader, onlyReadHeader: true); | |||
| LibrarySpectrum libraryItem; | |||
| if (path.Contains("pdeep")) | |||
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this seems a bit fragile. i can imagine users using a pdeep library but not having "pdeep" in the filename, and then getting a crash. but it would require a larger code rewrite to do it my preferred way (looking for "Spec=pDeep" in the comment field).
| double neutralLoss = 0; | ||
| if (split[2].Contains("-")) | ||
| { | ||
| String[] neutralLossInformation = split[2].Split(neutralLossSplit, StringSplitOptions.RemoveEmptyEntries).ToArray(); |
| char[] mwSplit = new char[] { ':' }; | ||
| char[] commentSplit = new char[] { ' ', ':', '=' }; | ||
| char[] modSplit = new char[] { '/', '(', ')' }; | ||
| char[] fragmentSplit = new char[] { '\t', '/' }; |
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these arrays should be static variables for the class. it will save you some time garbage collecting old arrays. same w/ arrays in ReadLibrarySpectrum
| return new LibrarySpectrum(sequence, precursorMz, z, matchedFragmentIons, rt); | ||
| } | ||
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| private LibrarySpectrum ReadLibrarySpectrum_pDeep(StreamReader reader, bool onlyReadHeader = false) |
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ideally you would not have a separate method that's a near duplicate of ReadLibrarySpectrum but i'll leave that up to you. maybe the pdeep library is too different to adapt ReadLibrarySpectrum. but it's not ideal to have this separate nearly-identical code
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