Ptm stoichiometry#2
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…culation in mzlibutils were copied from the previous branch onto this one. Need to add/remake the tests next.
…s. Need tests for the protein groups and the occupancy set up (currently called CalculateOccupancies).
…ts population) from SetUpQuantificationObjects method for now.
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…tide input for setting up the protein groups and the quantifications.
…bug when merging QuantifiedPeptides that caused the resulting mods to have greater intensity than total base peptide intensity.
…into PTMStoichiometry
Copilot suggestions for PFA class Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
copilot suggestions for creating deep copy on peptide mod stoich method as well as cleaner AND/OR conditional priority Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
comment fix Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
comment fix Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
…ote: the util occupancy code will be kept for now in the event it can be useful in the future due to its simpler code structure.
…for occupancy reporting. Updating quant to always have per group psm count, psm occupancy, and additionally intensity and intensity occupancy if lfq provided. NEEDS TESTS.
…roperties to ensure string and headers are always writeable.
…ould be call before writing quantification columns.
…into PTMStoichiometry
…PSM recounting the psm intensity for the unambiguous mods in that PSM.
code review revisions and additional unit tests
…oupType categories. Occupancy is now only reported from unamibiguous PSMs (will be enhanced later).
…s PSMs (FullSequence != null) are used for occupancy; 2) Generalized enum types of BioPolymerGroupType to Parent and DigestionProductTypes, which are general to proteomics and transcriptomics.
…into PTMStoichiometry
… fixes the integration issue.
* Changed ProteinXML writer to no longer produce empty position tags (e.g., <begin position="" />" in the .xml database * No longer write malformed entries * Small modificatoins to protein db writer of questionable quality * Updated .gitignore * Added UniprotEntry class, modified ProteinDbWriter for ProSight Compatibility * Added test for fasta -> xml writing * Updated proteinDbWriter, tests, add new protein constructor * Added new flag to WriteProteinDb * Fixed non variant protein assignment issue * Addressed Shortreed PR comments
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test PR on fork to track diffs prior to PR on upstream.