[WIP] Deconvolution using UniDec #625
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Cool PR! The base directory was simplified to have as many files as possible in the |
acesnik
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Mar 31, 2022
mzLib.sln
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| {D2B8F696-1172-405B-B788-3251B27CC71A}.Release|x64.ActiveCfg = Release|x64 | ||
| {D2B8F696-1172-405B-B788-3251B27CC71A}.Release|x64.Build.0 = Release|x64 | ||
| {D2B8F696-1172-405B-B788-3251B27CC71A}.Release|x86.ActiveCfg = Release|x64 |
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Do you need these x86 and AnyCPU configurations? I think x64 is the only one that's used currently to allow > 2 GB RAM usage, so consider removing these x86 and AnyCPU ones.
…wisc#624) * fix median polish bug when proteins cannot be quantified * comment out protein quant intensity checks in some tests. add explainer comment
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Low-resolution, top-down mass spectra are difficult to deconvolute due to their lack of isotopically resolved peaks. UniDec is the current standard for the deconvolution of low-resolution protein mass spectra.
UniDec's primary algorithm is written in C, while mzLib is written in C#, requiring me to pass data back and forth between managed C# code and unmanaged C code. I created a dynamic library in C from which mzLib can call UniDec functions. I had to heavily rely on unsafe C# code (pointers and such) in order to efficiently pass data to the unmanaged C code functions.
There are significant issues with the initial commit which I will be working on in the coming weeks. The primary issues are 1) further optimizations of the UniDec algorithm and 2) memory management in both C and C#. There are several points in this code that risk int overflow issues, which the unmanaged C code will not tell you are occurring. I would also like to get rid of most of the unsafe C# code, but I'm not sure yet how viable that is.
Unit test coverage for the functions called from the C unmanaged code are forthcoming. Unit tests will also cover passing data structures back and forth between the managed and unmanaged code.