Update instrumentControl branch#4
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avcarr2 wants to merge 251 commits intoavcarr2:InstrumentControlOldfrom
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Update instrumentControl branch#4avcarr2 wants to merge 251 commits intoavcarr2:InstrumentControlOldfrom
avcarr2 wants to merge 251 commits intoavcarr2:InstrumentControlOldfrom
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* change directory before restore * try coverlet.collector * update nuget badge to have downloads * codecov file location
* use nuget pack not dotnet pack
… etc.) (#609) * correct Within calculation * update unit tests * join products and cleave once products * unit tests for single cleavage products * remove unused test * fix broken unit tests * fix failing unit tests * add biomarkers during protein db load and revert add during digest * auto add biomarkers during protein database load if checked and revert biomarkers during digest * do not write biomarkers to xml database * default to retain methionine in biomarker generation * unit testage * increase unit test coverge * even more unit test coverage * more unit tests * codemaid * addressedReviewerComments Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu> Co-authored-by: acesnik <anthony.cesnik@gmail.com>
… for tests (#620) * use nuget pack not dotnet pack * name * setup nuget separately * change release name back * readme * image before releases * use multiline * use line concatenation for a couple places * no slash * use && * break up steps more
* correct Within calculation * update unit tests * first correct top-down biomarker test * remove unused test code * quotable protease * unquotable * add full length proteoform proteolysis products for biomarker search with unit tests * new strategy for adding proteolysis products * more complete biomarker addition * works for protein.xml databases * add unit test biomarkers with xml database * clean up * more clean up * fix unit test * adjust biomarker generation for three initiator methionine behaviors (cleave, retain, variable) * make sure decoy biomarkers for standard xml proteolysis products are generated * deal appropriately w/ n-terminal methionine cleavage * last litle unit test tweaks * delete unused code * add biomarkers during protein database load * greater clarity for biomarker proteolysis product entries * change digest for top-down biomarker search to resolve issues in MM * bro. shouldn't have been that hard * cleanup * add unit test * don't need to cover unit tests with unit tests * increase unit test coverage of protein.cs * codemaid * biomarkers on protein with no methionine * unit test booster * ACs comments * more summary statemsn * deleted mzlib.sln scarry Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu>
* fix median polish bug when proteins cannot be quantified * comment out protein quant intensity checks in some tests. add explainer comment
* correct Within calculation * update unit tests * first correct top-down biomarker test * remove unused test code * quotable protease * unquotable * add full length proteoform proteolysis products for biomarker search with unit tests * new strategy for adding proteolysis products * more complete biomarker addition * works for protein.xml databases * add unit test biomarkers with xml database * clean up * more clean up * fix unit test * adjust biomarker generation for three initiator methionine behaviors (cleave, retain, variable) * make sure decoy biomarkers for standard xml proteolysis products are generated * deal appropriately w/ n-terminal methionine cleavage * last litle unit test tweaks * delete unused code * add biomarkers during protein database load * greater clarity for biomarker proteolysis product entries * change digest for top-down biomarker search to resolve issues in MM * bro. shouldn't have been that hard * cleanup * add unit test * don't need to cover unit tests with unit tests * increase unit test coverage of protein.cs * codemaid * biomarkers on protein with no methionine * unit test booster * ACs comments * more summary statemsn * deleted mzlib.sln scarry * delete empty line * c-terminal products w/ and w/o methionine * delete remaining initiator meth behavior dependances * remove reference to meth behavior in biomarker test functions * fix effected unit tests * fix more unit tests * Biomarkers changed to Truncations * Biomarker to truncation * added method summaries * MsDataScan tests to boost coverage * more MsDataScan tests * more MsDataFile tests * delete unused comment Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu>
* net6.0 * merge upstream and update workflows * use nuget pack not dotnet pack * name * setup nuget separately * change release name back * readme * image before releases * replace webclient with httpclient * use multiline * use line concatenation for a couple places * no slash * use && * break up steps more * fix xml writer errors and such * more fixes * fix httpclient * code cleanup * add back comments Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu>
* correct Within calculation * update unit tests * first correct top-down biomarker test * remove unused test code * quotable protease * unquotable * add full length proteoform proteolysis products for biomarker search with unit tests * new strategy for adding proteolysis products * more complete biomarker addition * works for protein.xml databases * add unit test biomarkers with xml database * clean up * more clean up * fix unit test * adjust biomarker generation for three initiator methionine behaviors (cleave, retain, variable) * make sure decoy biomarkers for standard xml proteolysis products are generated * deal appropriately w/ n-terminal methionine cleavage * last litle unit test tweaks * delete unused code * add biomarkers during protein database load * greater clarity for biomarker proteolysis product entries * change digest for top-down biomarker search to resolve issues in MM * bro. shouldn't have been that hard * cleanup * add unit test * don't need to cover unit tests with unit tests * increase unit test coverage of protein.cs * codemaid * biomarkers on protein with no methionine * unit test booster * ACs comments * more summary statemsn * deleted mzlib.sln scarry * delete empty line * c-terminal products w/ and w/o methionine * delete remaining initiator meth behavior dependances * remove reference to meth behavior in biomarker test functions * fix effected unit tests * fix more unit tests * Biomarkers changed to Truncations * Biomarker to truncation * added method summaries * MsDataScan tests to boost coverage * more MsDataScan tests * more MsDataFile tests * delete unused comment * deleting the last vestiges of the term biomarker Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu>
* correct Within calculation * update unit tests * this is the spot * return null if bad scan * unit test for skipping scan with missing spectrum * updated unit test * test update and comments * remove unread scans Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu> Co-authored-by: Anthony <anthony.cesnik@gmail.com>
* correct Within calculation * update unit tests * this is the spot * Added Kullback Leibler to spectrum similarity * make sure numerator not zero in log * dont allow negative mz or intensity values * test for negative mz and intensity * code format Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu>
* correct Within calculation * update unit tests * this is the spot * searleMeasureOfSpectralSimilarity * Searle Similarity for identical spectra is double.maxvalue * eliminate unnecessary check * ternary * add comment Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu>
* First commit * Improved test for SpectralEntropy * Fixed what Shortreed broke * Deleted redundant check in SpectralEntropy method Co-authored-by: trishorts <mshort@chem.wisc.edu>
* correct Within calculation * update unit tests * this is the spot * use legacy uniprot to temporarily fullfill download requests Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu>
* fixed queries * Returned line to original
* Added hash for identifying matching targets and decoys * Added hash codes to pair target peptides to their decoys. * Cleaned up code * Added comments to better annotate pairing. Co-authored-by: zdanaceau <danaceau@wisc.edu>
* Added a function to generate decoys from scrambled targets. * Added function to generate decoys by scrambling targets * Fixed GetPercentIdentity to account for modifications and count cleavage motifs * Fixed comments and cleaned up code * Added more complex test cases * Added insulin protein as a more complex example to scramble. * Added target/decoy pairing to GetScrambledDecoyFromTarget * Added a test to ensure that peptides are mirrored once the maximum number of scramble attempts is reached. Co-authored-by: zdanaceau <danaceau@wisc.edu>
* correct Within calculation * update unit tests * this is the spot * unused namespaces * degree and star to ammonia and water * waterAndAmmoniaLossProductTypeMethods * ammonia and water loss fragment product ion unit tests Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu>
* correct Within calculation * update unit tests * this is the spot * unused namespaces * degree and star to ammonia and water * waterAndAmmoniaLossProductTypeMethods * ammonia and water loss fragment product ion unit tests * works bro * renamingBCproblemsInMM Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu>
* correct Within calculation * update unit tests * this is the spot * fds * final incremental changes Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu>
* correct Within calculation * update unit tests * this is the spot * add period tolerant get filename utility * now handles compressed files skipping the compressed file extension Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu>
* correct Within calculation * update unit tests * this is the spot * revert netSerializer and select AnyCPU * revert testadapter to nunit3testadapter * f Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu>
* Added correction to KullbackLeibler * Added using clause to LoadPsiMod to fix failing test * KullbackLeibler now returns null in situations where no peaks match * Added optional param to KullbackLeibler to fine tune correction values for 0 peaks * deleted unreachable code in KL * added missing return * Restructured for clarity * Reworked Kullback Leibler to prevent modification of YArrays * Commented out test lines * Removed duplicated code in SpectralSim, refactored IntensityPairs to take optional Array arguments
* Added Spectral averaging extensions to mzlib tested a few classes including Spectra Outputting * Tested Spectral Averaging Extensions * Fixed broken tests * Added additional Test Coverage * Adjusted code coverage to not look at the tests * Dealt with some possible null reference warnings and renamed tests to fit convention * One more potential null error * Changed Dynamic MzML test to wait for the writing to finish and not repeat a test case * Implemented Hash Code for MzSpectrum to resolve error and Alex's comment * Removed Json as it was not utilized and unnecessary, adjusted the exceptions being thrown to be MzLib Exceptions * Changed a few more exceptions to MzLib Exceptions * Adjusted configuration manager
* correct Within calculation * update unit tests * this is the spot * remove trailing tabs from quantified peaks peptides and proteins * flashlfq ToString unit tests Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu>
… negative values. (#659) * Fixed Obo parsing for mods.
* correct Within calculation * update unit tests * this is the spot * updatePsiModObo * eliminateUnusedUsings * deleteEmptyLine * copyAlways * unused lines * improved unit test coverage for file updates on existing file Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu>
…stitution mods (#964) * rename sequence variant description as variant call format * final unit test * undo accidental change of descripton to call format * more vcf tests * comprehensive vcf examples * test invalid variant * add line to proteindbloader * unit tests * chasing updates to variant call format * copilot suggestions * h * copilot
* did it * fixed some equality * Additional test coverage
Co-authored-by: Alexander-Sol <41119316+Alexander-Sol@users.noreply.github.com>
* rename sequence variant description as variant call format * final unit test * undo accidental change of descripton to call format * more vcf tests * comprehensive vcf examples * test invalid variant * add line to proteindbloader * unit tests * chasing updates to variant call format * copilot suggestions * h * added new paramater location to proteinxmlentry to reference specific isoform * primitive tweaks to SequenceVariation * lets see * copilot * g * space * test read protein xml with variant out of range gets filtered * some helpful comments * Update mzLib/UsefulProteomicsDatabases/ProteinXmlEntry.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update mzLib/Omics/BioPolymer/SequenceVariation.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update mzLib/UsefulProteomicsDatabases/ProteinXmlEntry.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update mzLib/UsefulProteomicsDatabases/ProteinXmlEntry.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update mzLib/Test/DatabaseTests/TestProteinReader.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update mzLib/UsefulProteomicsDatabases/ProteinXmlEntry.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * delete empty line * test variants for different isoforms * Update mzLib/UsefulProteomicsDatabases/ProteinXmlEntry.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update mzLib/UsefulProteomicsDatabases/ProteinXmlEntry.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
* Implemented and tested casanova mztab reader. * Updated from fasta maping * fix test by adding parameterless constructor
… value from .raw file trailer to Thermo Raw File Reader, and added appropriate test with data file containing CV values (#978) Co-authored-by: Nic Bollis <nbollis@comcast.net> Co-authored-by: trishorts <mshort@chem.wisc.edu>
… of expected changes to quantification (#986) * move flashlfq spectrafileinfo into massspectrometry * not there yet * er * we will see * fixed * responded to comments * micro changes
…o mzlib functions (#988) * minimal ISpectralMatch and ISpectralMatchHypothesis * some basic unit tests * response to copilot suggestions * remove empty comareto * eliminate ispectralmatchhypothesis * remove test infrastructure related to ispectralmatchhypothesis * updated CompareTo to use all fields of ISpectralMatch and favor high score * nitpics * yo * added scan number to ISpectralMatch * ScanNumber to OneBasedScanNumber * minus the compare to method
* Initial Project Creation * Moved ssrCalc * +- on n-terminal in full seq with mass shifts * Base Implmentation from Copilot * Implmented base in Proteomics * Removed chronologer estimator * Moved remaining RT code here * Incorporated CZE into the structure * Embedded chronologer weights * Restructured to remove redundant classes * Namespace formatting * Added class diagram * PR Cleanup * Basic enum testing * Use Canonical array for base sequence checks and added prediction error failure reason to base class * Made mod parsing of Type:IdwithMotiff allow the type component to be optional * Prediction specific unit testing * Updated project configuration and Nuget to ensure it works in MM * Ensured backwards compatibility * Removed extra constructors * small optimization per alex feedback * namespace adjustment * fix chronologer mod detection
… for both LFQ and IsoBaricQuant (#992) * g * sdg * tests * final changes * SpectraFileInfo and tests updated * isobaric quant tests * all revisions and test updates complete
* Enabling Support for Koina Models. WIP * Cleaned up and Tested. Still, reading a SpectralLibrary input for the model would be nice... * Fixed wrong input peptide validation logic (AND to OR) and added an intensity filter to not have fragment intensities less than the filter. * Made the inference calls batched, so now we can practically send any number of peptides for inference (previously capped at 1000). Cleaned up some methods. * Fixed indexing issues when parsing batches to create predicted library spectra. Fixed timing out issues in for the HttpClient and ensured disposal after use. Improved validation of input sequences and charge states when creating model object. * bunch of validation stuff + fixing filename typo * Bunch of updates and safety checks. * Restructured project. Reverted changes to CPU configuration in solution file. * adding to release build * adding predictions project to nuspec * Adding Nic and Alex smaller recommendations * implementing copilot suggestions * forgot copilot suggestion regarding always disposing client regardless of exceptions. * Added Shortreed tests and a summary for the model on implementation and use. * Added catch for try/finally.
… Omics (#993) * g * sdg * tests * final changes * add IBioPolymerGroup * protein group * draft 1 complete * g * ProteinGroupTests * improved coverage * merge upstream and resolve conflicts * remove score from IBioPolymerGroup interface * add Omics Dot BioPolymerGroup concrete class * biopolymergrouptests * biopolymergroup tests * update CompareTo order in SpectraFileInfo and unit test * remove ProteinGroup class and associated tests * add sequence coverage method to BioPolymerGroup * add class SpectralMatch as concrete instantiation of ISpectralMatch * sequence coverage added to BioPolymerGroup * GetSequenceCoverage added to BioPolymerGroup * change GetAminoAcidCoverage to GetSequenceCoverage and adapt for BioPolymer * spectral match tests * unit tests for SpectralMatch and GetSequenceCoverage * add interface IHasSequenceCoverageFromFragments * testing fixed using new SequenceCoverage interface * finish migration to ihassequencefragments * rename SpectralMatch as SpectralMatchWithSequenceCoverage * streamline get coverage * fresh comments on interface * final comments * rename spectral match class for specificity * Update mzLib/Omics/BioPolymerGroup/BioPolymerGroup.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update mzLib/Omics/BioPolymerGroup/BioPolymerGroup.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * update score handling by adding a new class and changing IBioPolymerGroup and BioPolymerGroup accordingly * slimfast BioPolymerGroup * make the tests adapt * biopolymer group sequence coverage tests * slimmer spectral match class * Update mzLib/Test/Omics/SpectraFileInfoTests.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * copilot review tweaks. * tests stolen from metamorpheus * keep essential BioPolymerGroupSequenceCoverage tests * essential BioPolymerGroup tests * essential cross class tests * lean and mean * summary comments * recover lost sequence coverage * Did a bunch of tweaks * Reconciled after shortreed changes * added accession and decoy information * PR Cleanup * critical unit tests to improve coverage of BioPolymerGroup * none * revert spectrafile info changes * remove unneccesary ibiopolymergroup extension methods * remove protected from IHasSequenceCoverage * summary statement update * provide default values for Accession and IsDecoy in BaseSpectralMatch constructor --------- Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: nbollis <nbollis@comcast.net>
* added trimMsN in filteringParams * . * . * comment * Update mzLib/MassSpectrometry/FilteringParams.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * comment --------- Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> Co-authored-by: trishorts <mshort@chem.wisc.edu>
* lets make the proteases dot tsv be the one used by metamorpheus in the same was as the digestion agent for rna * woops * eliminate cleave before proline * eliminate unused columns from proteases dot tsv and add comments clearly explaining all the rules * rename trypsin to follow naming conventin * test missing embedded resource * test embedded resource exists and loads * copilot suggestions * more suggestions * test coverage * removed hard coded column index ofr proteases tsv and ensured backward compatibility * enable custom proteases * test custom protease dictionary * explainer for embedded resource * remove parentheses from protease tsv * simpler naming * resolve namine conflicts * update toml * set default trypsin * revert changes caused by using wrong protease * revert flashlfq test toml * eliminate unneccessary changes to test proteases * let's see if this works * add embedded rnase dictionary and enabled backward compatibility for dont cleave before proline * no change * remove references to proteases and rrnas tsv in dot nuspec * no change * update nuspec * copilot review comments * fix nuspec * eliminate semi trypsin and semi elastase * that was dumb * eliminate test for protease that no longer exists
…to SequenceVariation (#967) * rename sequence variant description as variant call format * final unit test * undo accidental change of descripton to call format * more vcf tests * comprehensive vcf examples * test invalid variant * add line to proteindbloader * unit tests * chasing updates to variant call format * copilot suggestions * h * added new paramater location to proteinxmlentry to reference specific isoform * primitive tweaks to SequenceVariation * lets see * expand test AppliedVariants * expand test AppliedVariants_AsIBioPolymer * expand test stop gained * three new tests * expand test stop gained decoys and digestion * expand test SequenceVariationIsValid * expand TestThatProteinVariantsAreGeneratedDuringRead * two new tests * one more * this fucking test * name changeroo * two new vcf constructors in SequenceVariation * close * h * u * l * it fucking works * copilot * copilot * comments * unwoops * g * space * test read protein xml with variant out of range gets filtered * some helpful comments * Update mzLib/UsefulProteomicsDatabases/ProteinXmlEntry.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update mzLib/Omics/BioPolymer/SequenceVariation.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update mzLib/UsefulProteomicsDatabases/ProteinXmlEntry.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update mzLib/UsefulProteomicsDatabases/ProteinXmlEntry.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update mzLib/Test/DatabaseTests/TestProteinReader.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update mzLib/UsefulProteomicsDatabases/ProteinXmlEntry.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * delete empty line * test variants for different isoforms * Update mzLib/UsefulProteomicsDatabases/ProteinXmlEntry.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update mzLib/UsefulProteomicsDatabases/ProteinXmlEntry.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update mzLib/Omics/BioPolymer/VariantApplication.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update mzLib/Test/DatabaseTests/TestVariantProtein.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update mzLib/Test/DatabaseTests/TestVariantProtein.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update mzLib/Test/DatabaseTests/TestVariantProtein.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update mzLib/Test/DatabaseTests/TestVariantProtein.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update mzLib/Test/DatabaseTests/TestVariantProtein.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * test sequence variant constructor * check intersects * apply variants with null vcf * more variant application tests * test variants in decoy protein generator * test variants in decoy proteins * Update mzLib/Test/DatabaseTests/TestVariantProtein.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update mzLib/Test/DatabaseTests/TestVariantProtein.cs Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * Update mzLib/mzLib.nuspec Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> * make sure test decoy protein has only critical tests * remove unneccessary tests * evaluate TestPeptideWithSetMods for criticality to function --------- Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
* Restructuring Predictions project. Adding Prosit2020iRTTMT, PFly2024FineTuned, and Prosit2019iRT model drafts. Need to add tests. Need to also revisit modification rules from how the python api handles them. * temp * Implemeted Abstract classes for Fragment Intensity and Retention Time prediction models. The Flyability model does not need an abstract class, yet, since 1) there is only one Koina model and 2) these models will likely vary more in terms of outputs. Also, restructure the Koina project to organize the code a bit more logically. Lastly, renamed the project to PredictionClients. We have prediction tools that make sense to live in other parts of MzLib, so it seems better to focus this project to handle any query-based model usage. * rename prosit2020intensityhcd test file * fragment ion and retention time prediction tests done for now. * Flyability model tests added. Now just need to document everything well. * Added comments to Fragment intensity abstract and derived classes * Added commenting for retention time and flyability models. * Removed some irrelevant tests as mod code was changed. * copilot suggestions * check if nuspec is the issue * Shortreed suggestions minus additional layer of abstraction. * temp * refactor for additional model abstraction layer * fixed warning and duplicates handling when generating spectral library * Models are now IDisposable. Makes it obvious more obvious that model will only infer properties of constructor validated peptides. Then, no more inference calls are valid (disposed) though results prevail. * small copilot suggestions. * api consistency * oops. --------- Co-authored-by: trishorts <mshort@chem.wisc.edu>
* added locking * Copilot Suggestions --------- Co-authored-by: trishorts <mshort@chem.wisc.edu>
* firstUpdate * tested * made null the default --------- Co-authored-by: trishorts <mshort@chem.wisc.edu>
* Averaging supports different CV voltages. * Faims Snipping * Tested averaging with faims * Responded to copilot and shortreed suggestions * dummy commit --------- Co-authored-by: trishorts <mshort@chem.wisc.edu>
* ssrcalc changes * ssrcal speed up memory reduction unit test update * some fixes * d * final changes question mark * negligible * comments
* add protease_mods as an embedded resource * fully tested * Update version number in mzLib.nuspec
* Mod Reading moved to Omics * cleanup * tested public facing methods * renamed dictioanries * fix bug * PR Cleanup * PWSM and OWSM implementaiton * PR Cleanup and Code Coverage * scrub scrub
* Added new extensions * Added backbone modifications * PR Cleanup * Expanded test coverage * More comments * MRS change request * AS comments. * made indexing more clear * Account for terminal mods
* Added new extensions * Added backbone modifications * PR Cleanup * Expanded test coverage * Base implementation * Tested base mod * PrCleanup * Swalled the Roach * additional comments * More comments * MRS change request * AS comments. * made indexing more clear * Account for terminal mods * Converted fragmentation parameters to an interface for better toml handling * MOre test * Fix M-Ion issues * Fully Removed PtmListLoader * Fully Removed PtmListLoader * added ammonia loss
* fix bug that occurs when applying variant combinations that shift the coordinates with unit tests * that was difficult * fix summary statement * revert unintended changes * undo more unneeded changes * unit test with variant overlap in combo and bug fix --------- Co-authored-by: Nic Bollis <nbollis@comcast.net>
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