Fix ProForma writer for ranges bearing multiple modifications (§4.5)

[trishorts]

Problem

ProFormaWriter.WriteString throws ProFormaParseException: "Can't nest ranges within each other." whenever a term contains a sequence range that carries more than one modification — the ProForma 2.0 §4.5 construct (SEQ)[mod1][mod2]…. The parser accepts these strings, so they cannot currently be round-tripped: parsing succeeds but writing the resulting term fails.

Reproduce

var parser = new ProFormaParser();
var writer = new ProFormaWriter();
var term = parser.ParseString("PRT(ESFRMS)[Oxidation][Oxidation][half cystine][half cystine]ISK");
writer.WriteString(term);   // throws: Can't nest ranges within each other.

This also blocks real specification examples (e.g. the §4.5 insulin-style range bearing multiple oxidations and half-cystines).

Root cause

Each modification on a range is parsed as a separate ProFormaTag spanning the same (ZeroBasedStartIndex, ZeroBasedEndIndex) — the parser keeps the range open across consecutive )[mod][mod] until the next residue resets it. When the writer reaches the range, its inner loop scans the tags that fall within the range and unconditionally throws for any whose start != end. But a co-located range modification legitimately has start != end (it spans the whole range), so these were mistaken for nested ranges.

Fix

In the range branch of WriteString, a tag whose start and end equal the current range's start and end is treated as another modification on that same range and emitted as a consecutive [descriptor] after the range closes. Genuinely nested ranges (a different start != end inside the range) still throw as before.

After

PRT(ESFRMS)[Oxidation][Oxidation][half cystine][half cystine]ISK   // round-trips unchanged
SE(QUEN)[+14.05][Oxidation]CE                                       // two modifications on one range

Tests

• WriteMultipleModificationsOnSameRange — constructs a range carrying two modifications and asserts SE(QUEN)[+14.05][Oxidation]CE.
• RoundTripMultipleModificationsOnRange — parse→write round-trip of a four-modification range.
• Full suite green: 235 passed, 7 skipped, 0 failed (net472 + net6.0).

🤖 Generated with Claude Code

https://claude.ai/code/session_01JNnpzBNwfnTbZxtZdtAzLG