Struct BatchClusterAligner 

pub struct BatchClusterAligner {
    pub inner: Box<dyn Aligner>,
    pub cluster_identity: f32,
    pub cluster_coverage: f32,
}

Driver for the batch-cluster mode.

inner is any per-pair Aligner — typically crate::DiamondAligner or crate::Mmseqs2Aligner. It aligns query-vs-representative exactly once; the expansion layer then rebuilds per-genome hit sets.

Fields

inner: Box<dyn Aligner>

cluster_identity: f32

cluster_coverage: f32

Implementations

impl BatchClusterAligner

pub fn new(inner: Box<dyn Aligner>) -> Self

Sensible defaults: 0.5 identity / 0.8 coverage mirror mmseqs2’s own default easy-cluster parameters.

pub fn align_genomes( &self, query_fasta: &Path, genomes: &[GenomeInput], workdir: &Path, opts: &AlignOpts, ) -> Result<Vec<GenomeHitSet>, AlignError>

Run the full batch-cluster pipeline. workdir is where intermediate files live (concatenated FASTA, cluster outputs, alignment TSV); pass a tempfile::TempDir::path() if you don’t need to persist them.