PsmFromTsv Reader that also will work for RNA #737
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…r interface in Omics
Touched up PR
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| namespace Omics.SpectrumMatch | |||
| { | |||
| //for glcyo | |||
library spectrum is child class of mzspectrum spectrum match from tsv now abstract class
| @@ -86,6 +86,7 @@ static MzSpectrum() | |||
| } | |||
| } | |||
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| public MzSpectrum(){} | |||
| public MzSpectrum(double[,] mzintensities) | |||
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XArray and YArray can be removed from LibrarySpectrum as they are a member of MzSpectrum.
We can avoid the empty constructor in MzSpectrum by altering the LibrarySpectrum constructor as follows:
public LibrarySpectrum(string sequence, double precursorMz, int chargeState, List peaks, double? rt, bool isDecoy = false)
: base(peaks.Select(p => p.Mz).ToArray(), peaks.Select(p => p.Intensity).ToArray(), false)
{
Sequence = sequence;
PrecursorMz = precursorMz;
MatchedFragmentIons = peaks;
ChargeState = chargeState;
IsDecoy = isDecoy;
RetentionTime = rt;
Array.Sort(XArray, YArray);
}
| @@ -1,7 +1,7 @@ | |||
| using Chemistry; | |||
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I'm seeing three weird characters ("") at the start of this line
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Nevermind, the characters only show up on GitHub
| /// <summary> | ||
| /// All parsing should take place within the derived class constructurs | ||
| /// TODO: Reconsider this once osmtsv is added | ||
| /// </summary> |
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Should the TODO statement be left in?
If you don't have a constructor, shouldn't this be an abstract class?
We need to be able to load PSM data into multiple applications. Currently, it is MetaMorpheus. But that is highly limiting. Therefore, we are moving it to mzlib, to enable greater access.
In the process of making this PR it was decided that we should create an omics project that could house some classes appropriate to both RNA and protein.
To begin with we made a Fragmentation folder in Omics that has FragmentationTerminus, MatchedFragmentIon, Product, ProductType and TerminusSpecificProductType.
We also have a SpectrumMatch folder in Omics that contains LibrarySpectrum, SpectrumMatchFromTsv and SpectrumMatchFromTsvHeader
Note, we made several new header fields that get rid of reference to protein and peptide so that they could be used for RNA as well.