Add multi-term ProForma parsing/writing (chimeric +, charge /z, multi-chain //)

[trishorts]

Summary

Adds first-class support for the ProForma 2.0 constructs that live above a single proteoform term, which ParseString (single-term) rejects today:

• Chimeric peptidoforms — + (section 7.2)
• Charge state and ion adducts — /z, /z[adducts] (section 7.1)
• Inter-chain crosslinks / branches — // (sections 4.2.3.2, 4.2.4)

The approach is intentionally thin and additive: the string is split on the top-level +, /, and // operators (respecting bracket nesting), and each chain is parsed and written by the existing single-term ProFormaParser / ProFormaWriter. Single-term behavior is untouched.

var parser = new ProFormaParser();
var writer = new ProFormaWriter();

var group = parser.ParseProteoformGroupString("EMEVEESPEK/2+ELVISLIVER/3");
group.Peptidoforms.Count;            // 2  (chimeric)
group.Peptidoforms[0].Charge;        // 2
writer.WriteString(group);           // "EMEVEESPEK/2+ELVISLIVER/3"

parser.ParseProteoformGroupString("EMEVEESPEK/2[+2Na+,+H+]");                 // charge + adducts
parser.ParseProteoformGroupString("SEK[XLMOD:02001#XL1]UENCE//EMEVTK[#XL1]SESPEK"); // inter-chain //
parser.ParseProteoformGroupString("EM[Oxidation]EVEES[Phospho]PEK");         // plain term -> 1 peptidoform, 1 chain

API added

• ProFormaPeptidoform — one peptidoform: IList<ProFormaTerm> Chains (joined by //), int? Charge, string? IonAdducts.
• ProFormaProteoformGroup — IList<ProFormaPeptidoform> Peptidoforms (chimeric, joined by +).
• ProFormaParser.ParseProteoformGroupString(string) and a ProFormaWriter.WriteString(ProFormaProteoformGroup) overload.

🟨 API shape is open to your preference

This is a feature proposal — the naming and placement are yours to shape. Reasonable alternatives include folding charge onto ProFormaTerm, or exposing these as a separate ProFormaMultiTermParser. Happy to adjust to whatever fits the SDK's direction; the parsing/writing logic is the same regardless.

Tests

• Charge / negative charge / adducts, chimeric, multi-chain, branch, and "plain term -> single peptidoform".
• RoundTripIsCanonicallyIdempotent over the section 4.2.3.2 / 4.2.4 / 7.1 / 7.2 specification examples.
• Full suite green: 249 passed, 7 skipped, 0 failed (net472 + net6.0).

🤖 Generated with Claude Code

https://claude.ai/code/session_01JNnpzBNwfnTbZxtZdtAzLG

[rfellers]

I like the approach of keeping things separate. One could argue that together is better, but it all comes down to what someone considers a ProForma 'term'. From a practical standpoint, we already have code using the existing API and a breaking change doesn't seem worth it.

[codecov]

Codecov Report

❌ Patch coverage is 94.01709% with 7 lines in your changes missing coverage. Please review.
✅ Project coverage is 89.37%. Comparing base (b4d1949) to head (91abd85).

Files with missing lines	Patch %	Lines
src/TopDownProteomics/ProForma/ProFormaParser.cs	92.13%	3 Missing and 4 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #118      +/-   ##
==========================================
+ Coverage   89.23%   89.37%   +0.14%     
==========================================
  Files         103      105       +2     
  Lines        5721     5838     +117     
  Branches      882      908      +26     
==========================================
+ Hits         5105     5218     +113     
- Misses        429      431       +2     
- Partials      187      189       +2     

Files with missing lines	Coverage Δ
.../TopDownProteomics/ProForma/ProFormaPeptidoform.cs	100.00% <100.00%> (ø)
...DownProteomics/ProForma/ProFormaProteoformGroup.cs	100.00% <100.00%> (ø)
src/TopDownProteomics/ProForma/ProFormaWriter.cs	91.39% <100.00%> (+2.33%)	⬆️
src/TopDownProteomics/ProForma/ProFormaParser.cs	92.80% <92.13%> (-0.20%)	⬇️

... and 1 file with indirect coverage changes

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