feat(fragindex): phase 1 — data structures + codecs#21
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feat(fragindex): phase 1 — data structures + codecs#21
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Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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✨ Finishing Touches🧪 Generate unit tests (beta)
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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
540f194EliasFanostub + empty-list codece4b01d6EliasFanonaive int[] encoding4c7e68fEliasFano.Cursorzero-copy iteratorf129d55Fingerprint128128-bit b/y bit-set + popcounte450891Slab(immutable view) +SlabBuilder(writable, single-use)276fe08FragmentIndexStoreinterface +DirectStorein-memory implAll six commits are individually revertible.
Files
New package
edu.ucsd.msjava.fragindex:EliasFano.java— sorted-int[] codec with zero-copyCursoriteration. 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/HiBitsfor zero-allocation reads;bucketCursor(int)returnsEliasFano.Cursor.SlabBuilder.java— writable construction buffer. Single-use (IllegalStateExceptionafterfinish()).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)DBScanner/MSGFPlus/ scoring code pathsdevCompactSuffixArrayor other external stateReviews
Each task went through spec compliance review + code quality review:
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.mdfor the 7-phase plan; Phase 1 is gated on this PR merging.🤖 Generated with Claude Code