feat: ProForma 2.0 reader/writer and Layer-2 modification converter#1072
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feat: ProForma 2.0 reader/writer and Layer-2 modification converter#1072trishorts wants to merge 20 commits into
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Adds the authoritative ProForma test set (123 strings: 26 from the v1.0 paper, 89 valid + 8 counter-examples from the v2.0 spec) as a TSV plus a CorpusLoaderTests fixture that guards its completeness and integrity. This is the foundation the reader/writer will be developed against, test-first. Test data loads via TestContext.CurrentContext.TestDirectory, matching the existing FileReadingTests convention. Phase 0: setup + corpus. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Adds ProFormaReader.Read and ProFormaWriter.Write — thin mzLib entry points that delegate Layer-1 parse/write to the TopDownProteomics reference parser, so callers depend on mzLib types rather than the SDK directly. Includes a shared ProFormaTestCorpus loader and base-level round-trip tests asserting canonical idempotence of write(parse(s)). Surfaces the first SDK coverage gap: ProFormaWriter throws on a range bearing multiple modifications (spec 4.5); parsing succeeds, only writing fails. The case is pinned by KnownGap_MultiModRange_ParsesButSdkWriterThrows so a future SDK fix is detected. Phase 1: Readers/ProForma facade. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Widens the round-trip sweep to every valid corpus example. The wrapped SDK round-trips all single-proteoform-term forms (99/110): single-chain crosslinks, disulfides, glycans, formulas/isotopes, ranges, localization groups, scored sites, unknown position, global mods, termini, and the common v1.0 syntaxes. Three gaps are pinned with dedicated tests so each is tracked: - v1.0 default-source prefix [SOURCE]+SEQ — intentionally unsupported (v2.0 removed it). - charge /z, chimeric +, multi-chain // (13 rows) — valid v2.0 features that live above a single term; planned facade work. - writer throws on a multi-mod range (gap #1, pinned earlier). 106 ProForma tests green. Phase 2-3: Layer-1 coverage map. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Adds ProFormaConverter mapping between a ProFormaTerm and mzLib's
(base sequence + AllModsOneIsNterminus) representation that
IBioPolymerWithSetMods consumes, mirroring the index convention and lookup
idiom of GetModificationDictionaryFromFullSequence/DetermineFullSequence
(N-terminus = 1, residue r = r + 2, C-terminus = length + 2).
This first slice resolves per-residue Name descriptors via the
"{name} on {residue}" IdWithMotif key and round-trips them back through the
writer. A guard throws MzLibException on features outside the Layer-2 subset
(tag groups/crosslinks, labile, unlocalized, global mods, ranges, sequence
ambiguity) and on modifications absent from the supplied database, so callers
never silently drop data.
Phase 10: Layer-2 converter (slice 1).
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Extends ProFormaConverter to map Identifier descriptors (e.g. [UNIMOD:35], [MOD:00719]) to mzLib Modifications via a DatabaseReference accession index, and to emit accession descriptors on the inverse path when a modification carries a recognized ontology reference (else a Name). Resolution is motif-aware: a single accession such as UNIMOD:21 maps to several modifications differing only by target residue, so the residue at the tagged position disambiguates. Alias maps bridge mzLib's DatabaseReference keys and ProForma prefixes (Unimod<->UNIMOD, PSI-MOD<->MOD, RESID<->RESID). Phase 10: Layer-2 converter (slice 2, accessions). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Makes ProFormaConverter resolution terminus-aware: interior residues match on
target motif, while N-/C-terminal descriptors match on LocationRestriction
(N-terminal./Peptide N-terminal. and the C-terminal equivalents). The Name
path tries the usual "{name} on X" terminal id first, then any same-named
terminus-compatible modification.
Round-trips terminal mods by both name ([Acetyl]-...-[Amidation]) and
accession ([UNIMOD:214]-...), placing them at the AllModsOneIsNterminus
terminal keys (1 and length + 2).
Phase 10: Layer-2 converter (slice 3, terminal mods).
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Adds a fixture that loads the bundled Unimod database (~2700 modifications) via Loaders.LoadUnimod and exercises ProFormaConverter on real data rather than hand-built mods: resolves names (Oxidation, Phospho) and accessions (UNIMOD:35, UNIMOD:21), selects the correct motif amid real accession ambiguity (UNIMOD:21 maps to Phospho on S/T/Y), and round-trips. Confirms the per-residue/terminal, name/accession converter behaves on the actual modification dictionary MetaMorpheus loads, de-risking integration. Phase 10: Layer-2 converter (slice 4, real-Unimod validation). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Adds ToProFormaString/ToProFormaTerm extension methods on IBioPolymerWithSetMods so a scored peptide or proteoform converts to its ProForma 2.0 string in one call. This is the surface MetaMorpheus top-down output will consume; it composes the existing converter and writer. End-to-end tests build a PeptideWithSetModifications from its native mzLib FullSequence and assert the ProForma output for both a name modification ([Oxidation]) and an accession-bearing one ([UNIMOD:35]). Phase 10: Layer-2 converter (slice 5, peptide bridge). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Adds the "ProForma" column constant to SpectrumMatchFromTsvHeader so search output can carry the ProForma 2.0 string alongside Full Sequence. The value is populated by MetaMorpheus's PsmTsvWriter via IBioPolymerWithSetMods .ToProFormaString(); the column appears on the standard PSM/proteoform path (crosslink/glyco use their own headers). Phase 10: ProForma output column. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Adds SpectrumMatchFromTsv.ProForma, registers the column in ParseHeader, and reads it via GetOptionalValue so it round-trips with the writer. The column is optional (IndexOf returns -1 for pre-ProForma files, treated as absent), so older result files still read unchanged. In the ambiguity-disambiguation constructor the parent value is carried as-is rather than split on '|', because ProForma uses '|' as an internal descriptor separator and cannot be split per candidate. Phase 10: ProForma reader round-trip. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Companion PR (consumes this): smith-chem-wisc/MetaMorpheus#2663 |
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## master #1072 +/- ##
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+ Coverage 82.33% 86.77% +4.44%
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Files 382 396 +14
Lines 50509 51137 +628
Branches 6102 6236 +134
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+ Hits 41585 44373 +2788
+ Misses 7734 5547 -2187
- Partials 1190 1217 +27
🚀 New features to boost your workflow:
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Add 7 NUnit tests for the fail-loud paths in ProFormaConverter that had no patch coverage: - the five EnsureLayer2Supported guards (labile, unlocalized, global, position-range, sequence-ambiguity modifications) - the unresolved-terminal-mod throw (N- and C-terminus) - the terminal name-resolution fallback (mod stored with a residue motif rather than the wildcard X) Lifts ProFormaConverter.cs patch coverage from ~80% well above 90%. The two lines left uncovered (SelectCandidate count==1 fallback, IsTerminusCompatible default arm) are provably unreachable from the public API. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
…der-writer # Conflicts: # mzLib/Readers/Readers.csproj
Fixes from the PR smith-chem-wisc#1072 review of the ProForma Layer-2 converter: - Match the motif's modified residue instead of the whole motif string, so context-bearing motifs (e.g. the N-glyc sequon Nxs) resolve instead of throwing MzLibException for an otherwise-known modification. - Cache the accession index per allModsKnown instance (ConditionalWeakTable) rather than rebuilding it over the full mod database on every term, removing O(mods x references) work per converted PSM in batch consumption. - Fail loud (MzLibException) when two tags target the same residue index instead of silently overwriting one, per the converter's stated contract. - Throw a descriptive MzLibException, not a raw IndexOutOfRangeException, for an out-of-range tag index. - Emit ontology accessions in a fixed UNIMOD > MOD > RESID order so ToProFormaString output is deterministic when a mod has multiple references. - Guard null arguments in ToModificationDictionary/ToProFormaTerm. Addresses 6 findings (2 Major, 4 Minor) from the PR smith-chem-wisc#1072 review. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Fixes from the PR smith-chem-wisc#1072 review of the ProForma test suite: - Assert the exact v2-spec valid corpus count (EqualTo(89)) instead of a weak GreaterThan(70), matching the precise-count sibling tests so a deleted or mistyped row is caught. - Assert the crosslink guard's message ("tag group") so the test confirms the tag-group path fired rather than passing on an incidental missing-mod throw against the empty dictionary. - Use a unique per-test temp filename (Test.ID) instead of a fixed name in the shared test directory, removing a parallelization/leftover hazard. Addresses 3 Minor findings from the PR smith-chem-wisc#1072 review. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…-chain forms Add a layer above the single-term TopDownProteomics parser so ProForma 2.0 constructs that live above one proteoform term round-trip losslessly: chimeric peptidoforms (+), charge states (/z[adducts]), and inter-chain crosslink / branch chains (//). - ProFormaMultiTerm / ProFormaPeptidoform: model a chimeric set of peptidoforms, each one or more // chains plus an optional /charge[adducts]. - ProFormaMultiTermReader / ProFormaMultiTermWriter: split on the top-level +, /, and // operators (bracket-depth-aware), delegating each chain to the wrapped single-term ProFormaReader/ProFormaWriter and reassembling on write. Covers the 13 corpus forms previously pinned as "above a single term" (charge x7, chimeric x1, inter-chain crosslink x3, branch x2). 17 new multi-term round-trip tests pass; the single-term parser is unchanged. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JNnpzBNwfnTbZxtZdtAzLG
The 0.0.299 ProFormaWriter now serializes a range bearing multiple modifications (spec 4.5), closing the only known SDK writer gap. The KnownGap_MultiModRange guard test fired as designed: drop it, remove v2-4.5-01 from the writer-gap exclusion set, and let that example flow through the standard round-trip suite. 144 ProForma tests green. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
- Treat the wildcard "X" motif as matching any residue, so an interior mod stored against an X-motif Modification resolves on read instead of throwing (previously broke the round-trip for that whole class of mods). - Accept "Anywhere." LocationRestriction at a terminus so a terminal- position mod that ToProFormaTerm writes is also resolvable on read. - Reject IonAdducts without a Charge in the ProFormaPeptidoform ctor, since the writer can only emit adducts inside /z[...] and would otherwise drop them silently. Addresses 3 findings (1 Major, 2 Minor) from the PR smith-chem-wisc#1072 review. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
- Assert exact input preservation for an inter-chain crosslink form and a branch // form, plus chain-sequence content for the chimeric and multi-chain splits; idempotence alone would miss a consistent drop/reorder of chains or crosslink labels. - ProFormaTestCorpus.Load() throws InvalidDataException on a malformed row instead of calling NUnit Assert, so a bad corpus fails cleanly at execution rather than as a TestCaseSource discovery error. Addresses 3 findings from the PR smith-chem-wisc#1072 review (fix_007/008/009 were already fixed in-branch; fix_010 informational, skipped). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Author
Manual unit-test reviewAll 36 unit test(s) added by this PR were reviewed individually by the author (not only by automated/AI-generated checks): 33 approved as written, 3 edited, 0 flagged. This satisfies the author's standing AI-use policy that AI-assisted tests receive human review before relying on them. Recorded 2026-06-30 15:14. |
Pins the fix that lets IsTerminusCompatible accept an "Anywhere." LocationRestriction at a terminus: ToProFormaTerm writes any position-1 mod as an N-terminal descriptor regardless of restriction, so the read path must resolve it. Fails before that change. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Overview
This PR adds HUPO-PSI ProForma 2.0 reading and writing to mzLib. Layer 1 (string ↔
ProFormaTerm) is delegated to the TopDownProteomics SDK — already a production dependency of mzLib — through a thinReaders/ProFormafacade (ProFormaReader,ProFormaWriter), so callers depend on stable mzLib entry points rather than the SDK directly. Layer 2 (ProFormaTerm↔IBioPolymerWithSetMods) is new work:ProFormaConvertermaps per-residue and N-/C-terminal modifications to and from mzLibModificationobjects, mirroring the existingGetModificationDictionaryFromFullSequence/DetermineFullSequenceidiom (N-term = 1, residue = index + 2, C-term = length + 2). Resolution is motif-aware for interior residues andLocationRestriction-aware at termini, handling both names ([Oxidation]) and ontology accessions ([UNIMOD:35]). A one-callIBioPolymerWithSetMods.ToProFormaString()bridge plus aProFormapsmtsv column (written and re-read) complete the round-trip. Unsupported constructs fail loud.What's included
Readers/ProForma/—ProFormaReader.Read,ProFormaWriter.Write(wrap the SDK parser/writer);ProFormaConverter(Layer-2, both directions);ProFormaExtensions.ToProFormaString()/ToProFormaTerm().SpectrumMatchFromTsvHeader.ProForma;SpectrumMatchFromTsv.ProFormaparsed viaParseHeader+GetOptionalValue(optional — pre-ProForma files still read).TopDownProteomicsPackageReference added toReaders.csproj(already transitive viaUsefulProteomicsDatabases).Design notes for reviewers
IResultFile: ProForma is an in-memory string codec, not a file-on-disk with an extension. Documented, not an oversight.MzLibException): crosslinks/tag groups, branches, labile mods, ambiguity groups, ranges, sequence ambiguity, global isotope mods.[SOURCE]+default-source prefix not parsed (removed in v2.0; intentionally unsupported); (3) charge/z, chimeric+, multi-chain//need a multi-term facade (planned).Testing
120 ProForma tests (corpus of 123 manuscript examples; Layer-1 round-trip idempotence; Layer-2 round-trips incl. real bundled Unimod validation). Full
FileReadingTestssuite green (716). Baseline unchanged.🤖 Generated with Claude Code