One page per schema, each with its properties, definitions, and the conformance fixtures every binding is tested against.
Schema | Description |
|---|---|
A multiple sequence alignment: a list of Sequence records. | |
A GFF3-derived sequence feature (gene model) node. | |
A full BLAST search result, matching blastserver’s parsed-XML shape: hit-level, with nested HSPs and taxonomy/cluster enrichment. | |
A pairwise distance matrix, shared by react-bio-viz and acacia (via @holmrenser/nj’s DistanceResult). | |
A single biological sequence record, shared by picea, react-bio-viz, and acacia (FASTA-derived). | |
A phylogenetic (or other hierarchical) tree node, shared by picea, react-bio-viz, acacia, and iqtreeserver. |
Core primitives¶
Reusable shapes the schemas above $ref.
Schema | Description |
|---|---|
IUPAC nucleotide codes for DNA: A/C/G/T plus the standard ambiguity codes (R,Y,S,W,K,M,B,D,H,V,N). | |
A short, stable identifier/label string: a sequence identifier, a GFF3 feature ID, a BLAST accession, etc. | |
A 1-based inclusive interval on a named reference sequence (GFF3 convention). | |
Free-form key/value metadata, GFF3-attribute-style: each value is a single string, or a list of strings for multi-valued tags. | |
IUPAC amino acid codes: the standard 20 (A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y) plus the ambiguity/special codes B (Asx), Z (Glx), X (any), J (Leu/Ile), U (selenocysteine), O (pyrrolysine) -- together these cover all 26 letters, so this pattern is effectively any letter. | |
IUPAC nucleotide codes for RNA: A/C/G/U plus the standard ambiguity codes (R,Y,S,W,K,M,B,D,H,V,N). | |
A pointer to a Sequence by identifier, without embedding the sequence itself. |