feat(fragindex): phase 1 — data structures + codecs

[ypriverol]

Summary

Phase 1 of the fragment-indexed two-tier search design (spec at /Users/yperez/.claude/plans/msgfplus-fragment-index/design.md). Internal-only — adds the data-structure foundation with full unit-test coverage. No CLI surface, no runtime behaviour change.

Safe to merge as a no-op addition; Phases 2-7 build on top.

What landed

Commit	Component
540f194	EliasFano stub + empty-list codec
e4b01d6	EliasFano naive int[] encoding
4c7e68f	EliasFano.Cursor zero-copy iterator
f129d55	Fingerprint128 128-bit b/y bit-set + popcount
e450891	Slab (immutable view) + SlabBuilder (writable, single-use)
276fe08	FragmentIndexStore interface + DirectStore in-memory impl

All six commits are individually revertible.

Files

New package edu.ucsd.msjava.fragindex:

• EliasFano.java — sorted-int[] codec with zero-copy Cursor iteration. Naive layout; compact Elias-Fano bit-packing lands in Phase 4.
• Fingerprint128.java — 128-bit fragment fingerprint, low-64 = b-ion bits, high-64 = y-ion bits. setBIonBucket / setYIonBucket / popcountAnd.
• Slab.java — immutable read-only per-slab view. fingerprint(int) returns a fresh snapshot (no internal-state leak); fingerprintLoBits/HiBits for zero-allocation reads; bucketCursor(int) returns EliasFano.Cursor.
• SlabBuilder.java — writable construction buffer. Single-use (IllegalStateException after finish()).
• FragmentIndexStore.java — storage backend interface.
• DirectStore.java — in-memory impl of the store.

Test plan

• mvn -B verify — 184 tests pass (166 baseline + 18 new Phase 1 tests)
• No change to existing DBScanner / MSGFPlus / scoring code paths
• No new CLI flags; no behaviour change on dev
• All Phase 1 test files are self-contained; no dependency on CompactSuffixArray or other external state

Reviews

Each task went through spec compliance review + code quality review:

• Task 6 (Slab + SlabBuilder) initially flagged two Must-fix issues by reviewer (mutable Fingerprint128 return leaked internal state; SlabBuilder not idempotent). Both addressed in the same commit.
• Task 7 reviewer flagged a Javadoc clarification on concurrent-build thread-safety (deferred to Phase 2 when the build pipeline is added).

Not in this PR

Phase 2 (build pipeline via extended BuildSA -buildFragIndex 1) will be its own PR on top. See /Users/yperez/.claude/plans/msgfplus-fragment-index/plan.md for the 7-phase plan; Phase 1 is gated on this PR merging.

🤖 Generated with Claude Code

[coderabbitai]

Important

Review skipped

Draft detected.

Please check the settings in the CodeRabbit UI or the .coderabbit.yaml file in this repository. To trigger a single review, invoke the @coderabbitai review command.

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 26e397f6-64eb-4583-affe-520675fe0140

You can disable this status message by setting the reviews.review_status to false in the CodeRabbit configuration file.

Use the checkbox below for a quick retry:

• 🔍 Trigger review

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch feat/frag-index-phase1

---

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

_{Comment @coderabbitai help to get the list of available commands and usage tips.}