Crate gapsmith_find 

Pathway / reaction finder.

Mirrors the R reference implementation spread across src/prepare_batch_alignments.R, src/analyse_alignments.R, and src/gapseq_find.sh. The pipeline:

1. pathways::select picks a subset of gapsmith_db::PathwayRow to evaluate, based on a user keyword or pattern.
2. seqfile::resolve_for_reaction walks the dat/seq/ tree to find the reference FASTA(s) for each reaction.
3. runner::run_find builds one concatenated query.faa, runs the alignment (via gapsmith_align::Aligner) against the input genome, classifies every hit, and aggregates per-pathway completeness.
4. output emits *-Reactions.tbl and *-Pathways.tbl in gapseq’s column order.

Complex / subunit detection (src/complex_detection.R) lives in complex; it has point-by-point R-parity on 9 handcrafted cases (greek / latin numerals, size-dict synonyms, coverage edges). See crates/gapsmith-find/tests/complex_parity.rs.

End-to-end parity

runner::run_find produces byte-identical *-Pathways.tbl output against real gapseq on two test cases (-p PWY-6587 and -p amino on toy/ecore.faa). See crates/gapsmith-find/tests/pipeline_parity.rs.

Re-exports

pub use classify::classify_hits;

pub use classify::ClassifyOptions;

pub use output::write_pathways_tbl;

pub use output::write_reactions_tbl;

pub use pathways::select;

pub use pathways::ExpandedReaction;

pub use pathways::PathwaySelectOptions;

pub use runner::run_find;

pub use runner::FindError;

pub use runner::FindOptions;

pub use runner::FindReport;

pub use seqfile::resolve_for_reaction;

pub use seqfile::ResolvedSeq;

pub use seqfile::SeqfileOptions;

pub use types::HitStatus;

pub use types::PathwayResult;

pub use types::PwyStatus;

pub use types::ReactionHit;

Modules

classify

Hit classification — port of src/analyse_alignments.R:108–143.

complex

Port of src/complex_detection.R.

dbhit

Reaction → SEED reaction ID lookup (“dbhit”).

output

Emit *-Reactions.tbl and *-Pathways.tbl in gapseq’s column order.

pathways

Pathway selection and per-reaction expansion.

runner

End-to-end driver for gapsmith find.

seqfile

Reference-FASTA resolver.

taxonomy

Minimal loader for dat/taxonomy.tbl — used to filter pathways by their taxrange column.

types

Result types produced by the find pipeline.