p2s_mapper 1.4.0 → 2.1.0

package/dist/structureSources.d.ts

@@ -1,6 +1,8 @@
 import type { FetchOptions } from './fetchUtils.ts';
+export declare const RCSB_SEQUENCE_COORDINATES_URL = "https://sequence-coordinates.rcsb.org/graphql";
 export interface ExperimentalStructure {
     pdbId: string;
+    /** RCSB's name for it: 'X-ray', 'EM', 'NMR', ... */
     method: string;
     /** Å; absent for NMR and some EM entries */
     resolution?: number;
@@ -9,20 +11,42 @@ export interface ExperimentalStructure {
     end: number;
     /** fraction of the UniProt sequence the entry covers, 0..1 */
     coverage: number;
+    /** author chain ids of the protein */
+    chains: string[];
 }
-export declare function beaconsSummaryUrl(uniprotId: string): string;
+/** One polymer entity aligned to the accession. */
+export interface EntityAlignment {
+    /** RCSB's id, "1TUP_3" */
+    entityId: string;
+    pdbId: string;
+    start: number;
+    end: number;
+    coverage: number;
+}
+export interface EntityDetails {
+    method: string;
+    resolution?: number;
+    chains: string[];
+}
+export declare function entityAlignmentsQuery(uniprotId: string): string;
+export declare const ENTITY_DETAILS_QUERY = "query($ids: [String!]!) { polymer_entities(entity_ids: $ids) {\n  rcsb_id\n  rcsb_polymer_entity_container_identifiers { auth_asym_ids }\n  entry { rcsb_entry_info { experimental_method resolution_combined } }\n} }";
+/**
+ * PDB entities only: the same list carries RCSB's computed models
+ * (`AF_AFP04637F1_1`), which a residue mapping does not exist for. The range
+ * spans every aligned region, as 3D-Beacons reported it.
+ */
+export declare function parseEntityAlignments(data: unknown): EntityAlignment[];
+export declare function parseEntityDetails(data: unknown): Map<string, EntityDetails>;
+/**
+ * One row per entry, best coverage first and sharpest within a tie. An entry
+ * with several entities of the protein (a construct crystallised beside a
+ * different fragment of itself) takes the best-covering entity's range and
+ * every entity's chains.
+ */
+export declare function experimentalStructures(alignments: EntityAlignment[], details: ReadonlyMap<string, EntityDetails>): ExperimentalStructure[];
 /**
- * PDBe entries only, best-covering first and sharpest within a tie.
- *
- * Predicted entries (AlphaFold, SWISS-MODEL, AlphaFill) are left out because a
- * prediction comes from AlphaFold's own API, which answers per model. And
- * 3D-Beacons files SASBDB's small-angle-scattering fits under "experimentally
- * determined" too, with numeric ids and near-full coverage — dystrophin's best
- * "structure" by coverage was SASBDB 436 — which are not entries a residue
- * mapping exists for. Hence the `provider === 'PDBe'` gate rather than the
- * category alone.
+ * Every PDB entry aligned to the accession. An accession with none, or one
+ * RCSB does not know, is `[]`; an isoform accession is asked as its entry,
+ * which is what the alignment is numbered on.
  */
-export declare function parseExperimentalStructures(json: unknown): ExperimentalStructure[];
-/** Best-effort: an unreachable API reads as "no entries", which costs a
- * structure suggestion and nothing else. */
 export declare function fetchExperimentalStructures(uniprotId: string, opts?: FetchOptions): Promise<ExperimentalStructure[]>;

package/dist/structureSources.js

@@ -1,87 +1,174 @@
 "use strict";
-// The experimental structures 3D-Beacons knows for a UniProt entry: every PDBe
-// entry mapped to the accession, with the UniProt range it covers and its
-// resolution, in one CORS-enabled call. That is what lets a page offer a
-// crystal structure beside a prediction without a PDB search of its own; take
-// the entry id from here and ask `fetchUniProtStructureMappings` for its
+// The experimental structures RCSB aligns to a UniProt entry: every PDB entity
+// carrying the accession, with the UniProt range it covers, then each entry's
+// method, resolution and chains. Two CORS-enabled calls, which is what lets a
+// page offer a crystal structure beside a prediction without a PDB search of
+// its own; take the entry id from here and ask `fetchPdbEntry` for its
 // residue mapping.
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.beaconsSummaryUrl = beaconsSummaryUrl;
-exports.parseExperimentalStructures = parseExperimentalStructures;
+exports.ENTITY_DETAILS_QUERY = exports.RCSB_SEQUENCE_COORDINATES_URL = void 0;
+exports.entityAlignmentsQuery = entityAlignmentsQuery;
+exports.parseEntityAlignments = parseEntityAlignments;
+exports.parseEntityDetails = parseEntityDetails;
+exports.experimentalStructures = experimentalStructures;
 exports.fetchExperimentalStructures = fetchExperimentalStructures;
-const fetchUtils_ts_1 = require("./fetchUtils.js");
-// Unfiltered: the `?provider=pdbe` form answered BRAF, HBB and BRCA2 with a 404
-// about one time in three (2026-10-09), and the parser keeps PDBe's entries
-// anyway.
-function beaconsSummaryUrl(uniprotId) {
-    return `https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/${encodeURIComponent(uniprotId)}.json`;
+const pdbEntry_ts_1 = require("./pdbEntry.js");
+const structureUrls_ts_1 = require("./structureUrls.js");
+exports.RCSB_SEQUENCE_COORDINATES_URL = 'https://sequence-coordinates.rcsb.org/graphql';
+function entityAlignmentsQuery(uniprotId) {
+    return `{ alignments(from: UNIPROT, to: PDB_ENTITY, queryId: "${uniprotId}") {
+  target_alignments {
+    target_id
+    coverage { query_coverage }
+    aligned_regions { query_begin query_end }
+  }
+} }`;
 }
+exports.ENTITY_DETAILS_QUERY = `query($ids: [String!]!) { polymer_entities(entity_ids: $ids) {
+  rcsb_id
+  rcsb_polymer_entity_container_identifiers { auth_asym_ids }
+  entry { rcsb_entry_info { experimental_method resolution_combined } }
+} }`;
+// RCSB's cap on ids per batch request
+const DETAILS_BATCH = 1000;
 function isRecord(value) {
     return typeof value === 'object' && value !== null && !Array.isArray(value);
 }
 function finiteNumber(value) {
     return typeof value === 'number' && Number.isFinite(value) ? value : undefined;
 }
+function strings(value) {
+    return Array.isArray(value)
+        ? value.filter((v) => typeof v === 'string')
+        : [];
+}
 /**
- * PDBe entries only, best-covering first and sharpest within a tie.
- *
- * Predicted entries (AlphaFold, SWISS-MODEL, AlphaFill) are left out because a
- * prediction comes from AlphaFold's own API, which answers per model. And
- * 3D-Beacons files SASBDB's small-angle-scattering fits under "experimentally
- * determined" too, with numeric ids and near-full coverage — dystrophin's best
- * "structure" by coverage was SASBDB 436 — which are not entries a residue
- * mapping exists for. Hence the `provider === 'PDBe'` gate rather than the
- * category alone.
+ * PDB entities only: the same list carries RCSB's computed models
+ * (`AF_AFP04637F1_1`), which a residue mapping does not exist for. The range
+ * spans every aligned region, as 3D-Beacons reported it.
  */
-function parseExperimentalStructures(json) {
-    const structures = isRecord(json) ? json.structures : undefined;
-    if (!Array.isArray(structures)) {
+function parseEntityAlignments(data) {
+    const alignments = isRecord(data) ? data.alignments : undefined;
+    const targets = isRecord(alignments)
+        ? alignments.target_alignments
+        : undefined;
+    if (!Array.isArray(targets)) {
         return [];
     }
-    return structures
-        .flatMap(entry => {
-        const s = isRecord(entry) ? entry.summary : undefined;
-        if (!isRecord(s)) {
+    return targets.flatMap(target => {
+        if (!isRecord(target) || typeof target.target_id !== 'string') {
             return [];
         }
-        const start = finiteNumber(s.uniprot_start);
-        const end = finiteNumber(s.uniprot_end);
-        const coverage = finiteNumber(s.coverage);
-        return typeof s.model_identifier === 'string' &&
-            s.provider === 'PDBe' &&
-            s.model_category === 'EXPERIMENTALLY DETERMINED' &&
-            start !== undefined &&
-            end !== undefined &&
-            coverage !== undefined
+        const [pdbId] = target.target_id.split('_');
+        const coverage = isRecord(target.coverage)
+            ? finiteNumber(target.coverage.query_coverage)
+            : undefined;
+        const regions = Array.isArray(target.aligned_regions)
+            ? target.aligned_regions.filter(isRecord)
+            : [];
+        const begins = regions.map(r => finiteNumber(r.query_begin));
+        const ends = regions.map(r => finiteNumber(r.query_end));
+        return pdbId !== undefined &&
+            (0, structureUrls_ts_1.isPdbId)(pdbId) &&
+            coverage !== undefined &&
+            begins.length > 0 &&
+            begins.every(b => b !== undefined) &&
+            ends.every(e => e !== undefined)
             ? [
                 {
-                    pdbId: s.model_identifier.toLowerCase(),
-                    method: typeof s.experimental_method === 'string'
-                        ? s.experimental_method
-                        : 'experimental',
-                    resolution: finiteNumber(s.resolution),
-                    start,
-                    end,
+                    entityId: target.target_id,
+                    pdbId: pdbId.toLowerCase(),
+                    start: Math.min(...begins),
+                    end: Math.max(...ends),
                     coverage,
                 },
             ]
             : [];
-    })
-        .sort((a, b) => b.coverage - a.coverage ||
+    });
+}
+function parseEntityDetails(data) {
+    const entities = isRecord(data) ? data.polymer_entities : undefined;
+    const details = new Map();
+    for (const entity of Array.isArray(entities) ? entities : []) {
+        if (!isRecord(entity) || typeof entity.rcsb_id !== 'string') {
+            continue;
+        }
+        const ids = entity.rcsb_polymer_entity_container_identifiers;
+        const info = isRecord(entity.entry)
+            ? entity.entry.rcsb_entry_info
+            : undefined;
+        const resolutions = isRecord(info) ? info.resolution_combined : undefined;
+        const resolution = Array.isArray(resolutions)
+            ? finiteNumber(resolutions[0])
+            : undefined;
+        details.set(entity.rcsb_id, {
+            method: isRecord(info) && typeof info.experimental_method === 'string'
+                ? info.experimental_method
+                : 'experimental',
+            ...(resolution === undefined ? {} : { resolution }),
+            chains: strings(isRecord(ids) ? ids.auth_asym_ids : undefined),
+        });
+    }
+    return details;
+}
+/**
+ * One row per entry, best coverage first and sharpest within a tie. An entry
+ * with several entities of the protein (a construct crystallised beside a
+ * different fragment of itself) takes the best-covering entity's range and
+ * every entity's chains.
+ */
+function experimentalStructures(alignments, details) {
+    const byEntry = new Map();
+    for (const a of alignments) {
+        const d = details.get(a.entityId);
+        if (!d) {
+            continue;
+        }
+        const existing = byEntry.get(a.pdbId);
+        if (!existing) {
+            byEntry.set(a.pdbId, {
+                pdbId: a.pdbId,
+                method: d.method,
+                ...(d.resolution === undefined ? {} : { resolution: d.resolution }),
+                start: a.start,
+                end: a.end,
+                coverage: a.coverage,
+                chains: [...d.chains],
+            });
+            continue;
+        }
+        for (const chain of d.chains) {
+            if (!existing.chains.includes(chain)) {
+                existing.chains.push(chain);
+            }
+        }
+        if (a.coverage > existing.coverage) {
+            Object.assign(existing, {
+                start: a.start,
+                end: a.end,
+                coverage: a.coverage,
+            });
+        }
+    }
+    return [...byEntry.values()].sort((a, b) => b.coverage - a.coverage ||
         (a.resolution ?? Infinity) - (b.resolution ?? Infinity));
 }
-/** Best-effort: an unreachable API reads as "no entries", which costs a
- * structure suggestion and nothing else. */
+const ISOFORM_SUFFIX = /-\d+$/;
+/**
+ * Every PDB entry aligned to the accession. An accession with none, or one
+ * RCSB does not know, is `[]`; an isoform accession is asked as its entry,
+ * which is what the alignment is numbered on.
+ */
 async function fetchExperimentalStructures(uniprotId, opts) {
-    for (let attempt = 0; attempt < 2; attempt++) {
-        const res = await (0, fetchUtils_ts_1.rawfetch)(beaconsSummaryUrl(uniprotId), opts).catch(() => undefined);
-        if (res?.ok) {
-            return parseExperimentalStructures(await res.json());
-        }
-        if (res?.status === 404 || opts?.signal?.aborted) {
-            return [];
+    const alignments = parseEntityAlignments(await (0, pdbEntry_ts_1.graphqlFetch)(exports.RCSB_SEQUENCE_COORDINATES_URL, entityAlignmentsQuery(uniprotId.replace(ISOFORM_SUFFIX, '')), undefined, opts));
+    const ids = alignments.map(a => a.entityId);
+    const details = new Map();
+    for (let i = 0; i < ids.length; i += DETAILS_BATCH) {
+        const batch = parseEntityDetails(await (0, pdbEntry_ts_1.graphqlFetch)(pdbEntry_ts_1.RCSB_DATA_GRAPHQL_URL, exports.ENTITY_DETAILS_QUERY, { ids: ids.slice(i, i + DETAILS_BATCH) }, opts));
+        for (const [id, d] of batch) {
+            details.set(id, d);
         }
     }
-    return [];
+    return experimentalStructures(alignments, details);
 }
 //# sourceMappingURL=structureSources.js.map

package/dist/structureSources.js.map

@@ -1 +1 @@
-{"version":3,"file":"structureSources.js","sourceRoot":"","sources":["../src/structureSources.ts"],"names":[],"mappings":";AAAA,+EAA+E;AAC/E,0EAA0E;AAC1E,yEAAyE;AACzE,8EAA8E;AAC9E,yEAAyE;AACzE,mBAAmB;;AAqBnB,8CAEC;AAqBD,kEA0CC;AAID,kEAgBC;AAxGD,mDAA0C;AAgB1C,gFAAgF;AAChF,4EAA4E;AAC5E,UAAU;AACV,SAAgB,iBAAiB,CAAC,SAAiB;IACjD,OAAO,oEAAoE,kBAAkB,CAAC,SAAS,CAAC,OAAO,CAAA;AACjH,CAAC;AAED,SAAS,QAAQ,CAAC,KAAc;IAC9B,OAAO,OAAO,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;AAC7E,CAAC;AAED,SAAS,YAAY,CAAC,KAAc;IAClC,OAAO,OAAO,KAAK,KAAK,QAAQ,IAAI,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,SAAS,CAAA;AAChF,CAAC;AAED;;;;;;;;;;GAUG;AACH,SAAgB,2BAA2B,CACzC,IAAa;IAEb,MAAM,UAAU,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,SAAS,CAAA;IAC/D,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,EAAE,CAAC;QAC/B,OAAO,EAAE,CAAA;IACX,CAAC;IACD,OAAO,UAAU;SACd,OAAO,CAAC,KAAK,CAAC,EAAE;QACf,MAAM,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,SAAS,CAAA;QACrD,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC;YACjB,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,KAAK,GAAG,YAAY,CAAC,CAAC,CAAC,aAAa,CAAC,CAAA;QAC3C,MAAM,GAAG,GAAG,YAAY,CAAC,CAAC,CAAC,WAAW,CAAC,CAAA;QACvC,MAAM,QAAQ,GAAG,YAAY,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAA;QACzC,OAAO,OAAO,CAAC,CAAC,gBAAgB,KAAK,QAAQ;YAC3C,CAAC,CAAC,QAAQ,KAAK,MAAM;YACrB,CAAC,CAAC,cAAc,KAAK,2BAA2B;YAChD,KAAK,KAAK,SAAS;YACnB,GAAG,KAAK,SAAS;YACjB,QAAQ,KAAK,SAAS;YACtB,CAAC,CAAC;gBACE;oBACE,KAAK,EAAE,CAAC,CAAC,gBAAgB,CAAC,WAAW,EAAE;oBACvC,MAAM,EACJ,OAAO,CAAC,CAAC,mBAAmB,KAAK,QAAQ;wBACvC,CAAC,CAAC,CAAC,CAAC,mBAAmB;wBACvB,CAAC,CAAC,cAAc;oBACpB,UAAU,EAAE,YAAY,CAAC,CAAC,CAAC,UAAU,CAAC;oBACtC,KAAK;oBACL,GAAG;oBACH,QAAQ;iBACT;aACF;YACH,CAAC,CAAC,EAAE,CAAA;IACR,CAAC,CAAC;SACD,IAAI,CACH,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CACP,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,QAAQ;QACvB,CAAC,CAAC,CAAC,UAAU,IAAI,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,UAAU,IAAI,QAAQ,CAAC,CAC1D,CAAA;AACL,CAAC;AAED;4CAC4C;AACrC,KAAK,UAAU,2BAA2B,CAC/C,SAAiB,EACjB,IAAmB;IAEnB,KAAK,IAAI,OAAO,GAAG,CAAC,EAAE,OAAO,GAAG,CAAC,EAAE,OAAO,EAAE,EAAE,CAAC;QAC7C,MAAM,GAAG,GAAG,MAAM,IAAA,wBAAQ,EAAC,iBAAiB,CAAC,SAAS,CAAC,EAAE,IAAI,CAAC,CAAC,KAAK,CAClE,GAAG,EAAE,CAAC,SAAS,CAChB,CAAA;QACD,IAAI,GAAG,EAAE,EAAE,EAAE,CAAC;YACZ,OAAO,2BAA2B,CAAC,MAAM,GAAG,CAAC,IAAI,EAAE,CAAC,CAAA;QACtD,CAAC;QACD,IAAI,GAAG,EAAE,MAAM,KAAK,GAAG,IAAI,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE,CAAC;YACjD,OAAO,EAAE,CAAA;QACX,CAAC;IACH,CAAC;IACD,OAAO,EAAE,CAAA;AACX,CAAC"}
+{"version":3,"file":"structureSources.js","sourceRoot":"","sources":["../src/structureSources.ts"],"names":[],"mappings":";AAAA,+EAA+E;AAC/E,8EAA8E;AAC9E,8EAA8E;AAC9E,6EAA6E;AAC7E,uEAAuE;AACvE,mBAAmB;;;AAyCnB,sDAQC;AA8BD,sDAsCC;AAED,gDAyBC;AAQD,wDAyCC;AASD,kEA4BC;AApOD,+CAAmE;AACnE,yDAA4C;AAI/B,QAAA,6BAA6B,GACxC,+CAA+C,CAAA;AAiCjD,SAAgB,qBAAqB,CAAC,SAAiB;IACrD,OAAO,yDAAyD,SAAS;;;;;;IAMvE,CAAA;AACJ,CAAC;AAEY,QAAA,oBAAoB,GAAG;;;;IAIhC,CAAA;AAEJ,sCAAsC;AACtC,MAAM,aAAa,GAAG,IAAI,CAAA;AAE1B,SAAS,QAAQ,CAAC,KAAc;IAC9B,OAAO,OAAO,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;AAC7E,CAAC;AAED,SAAS,YAAY,CAAC,KAAc;IAClC,OAAO,OAAO,KAAK,KAAK,QAAQ,IAAI,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,SAAS,CAAA;AAChF,CAAC;AAED,SAAS,OAAO,CAAC,KAAc;IAC7B,OAAO,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC;QACzB,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAe,EAAE,CAAC,OAAO,CAAC,KAAK,QAAQ,CAAC;QACzD,CAAC,CAAC,EAAE,CAAA;AACR,CAAC;AAED;;;;GAIG;AACH,SAAgB,qBAAqB,CAAC,IAAa;IACjD,MAAM,UAAU,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,SAAS,CAAA;IAC/D,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,CAAC;QAClC,CAAC,CAAC,UAAU,CAAC,iBAAiB;QAC9B,CAAC,CAAC,SAAS,CAAA;IACb,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE,CAAC;QAC5B,OAAO,EAAE,CAAA;IACX,CAAC;IACD,OAAO,OAAO,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE;QAC9B,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,IAAI,OAAO,MAAM,CAAC,SAAS,KAAK,QAAQ,EAAE,CAAC;YAC9D,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,CAAC,KAAK,CAAC,GAAG,MAAM,CAAC,SAAS,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QAC3C,MAAM,QAAQ,GAAG,QAAQ,CAAC,MAAM,CAAC,QAAQ,CAAC;YACxC,CAAC,CAAC,YAAY,CAAC,MAAM,CAAC,QAAQ,CAAC,cAAc,CAAC;YAC9C,CAAC,CAAC,SAAS,CAAA;QACb,MAAM,OAAO,GAAG,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,eAAe,CAAC;YACnD,CAAC,CAAC,MAAM,CAAC,eAAe,CAAC,MAAM,CAAC,QAAQ,CAAC;YACzC,CAAC,CAAC,EAAE,CAAA;QACN,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,YAAY,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAA;QAC5D,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,YAAY,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAA;QACxD,OAAO,KAAK,KAAK,SAAS;YACxB,IAAA,0BAAO,EAAC,KAAK,CAAC;YACd,QAAQ,KAAK,SAAS;YACtB,MAAM,CAAC,MAAM,GAAG,CAAC;YACjB,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,SAAS,CAAC;YAClC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,SAAS,CAAC;YAChC,CAAC,CAAC;gBACE;oBACE,QAAQ,EAAE,MAAM,CAAC,SAAS;oBAC1B,KAAK,EAAE,KAAK,CAAC,WAAW,EAAE;oBAC1B,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC;oBAC1B,GAAG,EAAE,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC;oBACtB,QAAQ;iBACT;aACF;YACH,CAAC,CAAC,EAAE,CAAA;IACR,CAAC,CAAC,CAAA;AACJ,CAAC;AAED,SAAgB,kBAAkB,CAAC,IAAa;IAC9C,MAAM,QAAQ,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC,CAAC,SAAS,CAAA;IACnE,MAAM,OAAO,GAAG,IAAI,GAAG,EAAyB,CAAA;IAChD,KAAK,MAAM,MAAM,IAAI,KAAK,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC;QAC7D,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,IAAI,OAAO,MAAM,CAAC,OAAO,KAAK,QAAQ,EAAE,CAAC;YAC5D,SAAQ;QACV,CAAC;QACD,MAAM,GAAG,GAAG,MAAM,CAAC,yCAAyC,CAAA;QAC5D,MAAM,IAAI,GAAG,QAAQ,CAAC,MAAM,CAAC,KAAK,CAAC;YACjC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,eAAe;YAC9B,CAAC,CAAC,SAAS,CAAA;QACb,MAAM,WAAW,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,mBAAmB,CAAC,CAAC,CAAC,SAAS,CAAA;QACzE,MAAM,UAAU,GAAG,KAAK,CAAC,OAAO,CAAC,WAAW,CAAC;YAC3C,CAAC,CAAC,YAAY,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC;YAC9B,CAAC,CAAC,SAAS,CAAA;QACb,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,OAAO,EAAE;YAC1B,MAAM,EACJ,QAAQ,CAAC,IAAI,CAAC,IAAI,OAAO,IAAI,CAAC,mBAAmB,KAAK,QAAQ;gBAC5D,CAAC,CAAC,IAAI,CAAC,mBAAmB;gBAC1B,CAAC,CAAC,cAAc;YACpB,GAAG,CAAC,UAAU,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,UAAU,EAAE,CAAC;YACnD,MAAM,EAAE,OAAO,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,aAAa,CAAC,CAAC,CAAC,SAAS,CAAC;SAC/D,CAAC,CAAA;IACJ,CAAC;IACD,OAAO,OAAO,CAAA;AAChB,CAAC;AAED;;;;;GAKG;AACH,SAAgB,sBAAsB,CACpC,UAA6B,EAC7B,OAA2C;IAE3C,MAAM,OAAO,GAAG,IAAI,GAAG,EAAiC,CAAA;IACxD,KAAK,MAAM,CAAC,IAAI,UAAU,EAAE,CAAC;QAC3B,MAAM,CAAC,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAA;QACjC,IAAI,CAAC,CAAC,EAAE,CAAC;YACP,SAAQ;QACV,CAAC;QACD,MAAM,QAAQ,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;QACrC,IAAI,CAAC,QAAQ,EAAE,CAAC;YACd,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE;gBACnB,KAAK,EAAE,CAAC,CAAC,KAAK;gBACd,MAAM,EAAE,CAAC,CAAC,MAAM;gBAChB,GAAG,CAAC,CAAC,CAAC,UAAU,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,UAAU,EAAE,CAAC,CAAC,UAAU,EAAE,CAAC;gBACnE,KAAK,EAAE,CAAC,CAAC,KAAK;gBACd,GAAG,EAAE,CAAC,CAAC,GAAG;gBACV,QAAQ,EAAE,CAAC,CAAC,QAAQ;gBACpB,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC;aACtB,CAAC,CAAA;YACF,SAAQ;QACV,CAAC;QACD,KAAK,MAAM,KAAK,IAAI,CAAC,CAAC,MAAM,EAAE,CAAC;YAC7B,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAE,CAAC;gBACrC,QAAQ,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YAC7B,CAAC;QACH,CAAC;QACD,IAAI,CAAC,CAAC,QAAQ,GAAG,QAAQ,CAAC,QAAQ,EAAE,CAAC;YACnC,MAAM,CAAC,MAAM,CAAC,QAAQ,EAAE;gBACtB,KAAK,EAAE,CAAC,CAAC,KAAK;gBACd,GAAG,EAAE,CAAC,CAAC,GAAG;gBACV,QAAQ,EAAE,CAAC,CAAC,QAAQ;aACrB,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;IACD,OAAO,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,CAAC,IAAI,CAC/B,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CACP,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,QAAQ;QACvB,CAAC,CAAC,CAAC,UAAU,IAAI,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,UAAU,IAAI,QAAQ,CAAC,CAC1D,CAAA;AACH,CAAC;AAED,MAAM,cAAc,GAAG,OAAO,CAAA;AAE9B;;;;GAIG;AACI,KAAK,UAAU,2BAA2B,CAC/C,SAAiB,EACjB,IAAmB;IAEnB,MAAM,UAAU,GAAG,qBAAqB,CACtC,MAAM,IAAA,0BAAY,EAChB,qCAA6B,EAC7B,qBAAqB,CAAC,SAAS,CAAC,OAAO,CAAC,cAAc,EAAE,EAAE,CAAC,CAAC,EAC5D,SAAS,EACT,IAAI,CACL,CACF,CAAA;IACD,MAAM,GAAG,GAAG,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAA;IAC3C,MAAM,OAAO,GAAG,IAAI,GAAG,EAAyB,CAAA;IAChD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,IAAI,aAAa,EAAE,CAAC;QACnD,MAAM,KAAK,GAAG,kBAAkB,CAC9B,MAAM,IAAA,0BAAY,EAChB,mCAAqB,EACrB,4BAAoB,EACpB,EAAE,GAAG,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,aAAa,CAAC,EAAE,EACxC,IAAI,CACL,CACF,CAAA;QACD,KAAK,MAAM,CAAC,EAAE,EAAE,CAAC,CAAC,IAAI,KAAK,EAAE,CAAC;YAC5B,OAAO,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAA;QACpB,CAAC;IACH,CAAC;IACD,OAAO,sBAAsB,CAAC,UAAU,EAAE,OAAO,CAAC,CAAA;AACpD,CAAC"}

package/dist/structureUrls.d.ts

@@ -9,21 +9,18 @@ export declare function uniprotEntryUrl(uniprotId: string): string;
  */
 export declare function getAlphaFoldStructureUrl(uniprotId: string, version?: string): string;
 export declare function getPdbStructureUrl(pdbId: string): string;
+export declare function isPdbId(value: string): boolean;
+export declare function rcsbEntryUrl(pdbId: string): string;
 /**
- * Resolve the `{ pdbId }` shorthand to a concrete structure URL, so a
- * hand-authored snapshot or a short launch URL doesn't have to know RCSB's
- * filename format. An explicit `url` (or inline `data`) always wins.
- * Idempotent: re-resolving an already-resolved spec returns the same url.
+ * Resolve the `{ pdbId }` shorthand to a structure URL, so a hand-written config
+ * or a short launch URL needs no RCSB filename. An explicit `url` (or inline
+ * `data`) always wins, and resolving an already-resolved spec returns the same
+ * url.
  *
- * `uniprotId` deliberately resolves to no url here, and still outranks a
- * `pdbId`. An accession's files are whatever AlphaFold DB currently holds — an
- * isoform model, several fragments, a new model version — so the structure
- * keeps the accession and the structure loader asks the prediction API which
- * file to open.
- *
- * Shared by the Structure model's snapshot preprocessor and the
- * LaunchView-ProteinView extension point, which would otherwise each carry
- * their own copy of the same precedence rule.
+ * `uniprotId` resolves to no url and still outranks a `pdbId`. AlphaFold DB's
+ * files for an accession change (an isoform model, several fragments, a new
+ * model version), so the caller keeps the accession and asks
+ * `fetchAlphaFoldModels` which file to open.
  */
 export declare function resolveStructureUrl({ url, data, uniprotId, pdbId, }: {
     url?: string;
@@ -43,9 +40,9 @@ export declare function getUniprotIdFromAlphaFoldTarget(target: string): string
 export declare function getStructureUrlFromTarget(target: string, db: string): string | undefined;
 export declare function getConfidenceUrlFromTarget(target: string): string | undefined;
 /**
- * What a structure is called in the UI: its PDB id, its AlphaFold accession,
- * else the file's name. Shared by the view title, the alignment panel heading
- * and the hover readout, so one structure reads the same everywhere.
+ * The name to show for a structure: its PDB id, its AlphaFold accession, else
+ * the file's name. Use it wherever a structure is named, so each place shows
+ * the same name.
  */
 export declare function structureDisplayLabel({ url, data, uniprotId, }: {
     url?: string;

package/dist/structureUrls.js

@@ -1,13 +1,13 @@
 "use strict";
-// Pure structure-URL builders and target parsers. Kept dependency-free so both
-// the launch flow and the ProteinView model (e.g. resolving a `uniprotId`/`pdbId`
-// shorthand at hydration) can import them without pulling in heavy launch code.
+// Structure URL builders and target parsers, with no dependencies.
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.uniprotGffUrl = uniprotGffUrl;
 exports.uniprotFastaUrl = uniprotFastaUrl;
 exports.uniprotEntryUrl = uniprotEntryUrl;
 exports.getAlphaFoldStructureUrl = getAlphaFoldStructureUrl;
 exports.getPdbStructureUrl = getPdbStructureUrl;
+exports.isPdbId = isPdbId;
+exports.rcsbEntryUrl = rcsbEntryUrl;
 exports.resolveStructureUrl = resolveStructureUrl;
 exports.getPdbIdFromUrl = getPdbIdFromUrl;
 exports.getUniprotIdFromAlphaFoldTarget = getUniprotIdFromAlphaFoldTarget;
@@ -15,10 +15,8 @@ exports.getStructureUrlFromTarget = getStructureUrlFromTarget;
 exports.getConfidenceUrlFromTarget = getConfidenceUrlFromTarget;
 exports.structureDisplayLabel = structureDisplayLabel;
 const ALPHAFOLD_VERSION = 'v6';
-// UniProt endpoints. rest.* is the machine API (the GFF the feature tracks and
-// the alignment's annotation rows both read, the FASTA the temporary protein
-// assembly is built from); www.*/entry is the human-facing entry page the UI
-// links to. Centralized so a path change is one edit rather than a grep.
+// UniProt endpoints. rest.* is the machine API, serving the features as GFF
+// and the sequence as FASTA; www.*/entry is the entry page for people.
 function uniprotGffUrl(uniprotId) {
     return `https://rest.uniprot.org/uniprotkb/${uniprotId}.gff`;
 }
@@ -40,21 +38,25 @@ function getAlphaFoldStructureUrl(uniprotId, version = ALPHAFOLD_VERSION) {
 function getPdbStructureUrl(pdbId) {
     return `https://files.rcsb.org/download/${pdbId}.cif`;
 }
+// A PDB id is four characters, the first a digit: 1TUP, 6ZIO. Checked before
+// a typed one reaches a fetch, so three characters on the way to four are not
+// a 404 apiece.
+function isPdbId(value) {
+    return /^[1-9][A-Za-z0-9]{3}$/.test(value);
+}
+function rcsbEntryUrl(pdbId) {
+    return `https://www.rcsb.org/structure/${pdbId.toUpperCase()}`;
+}
 /**
- * Resolve the `{ pdbId }` shorthand to a concrete structure URL, so a
- * hand-authored snapshot or a short launch URL doesn't have to know RCSB's
- * filename format. An explicit `url` (or inline `data`) always wins.
- * Idempotent: re-resolving an already-resolved spec returns the same url.
- *
- * `uniprotId` deliberately resolves to no url here, and still outranks a
- * `pdbId`. An accession's files are whatever AlphaFold DB currently holds — an
- * isoform model, several fragments, a new model version — so the structure
- * keeps the accession and the structure loader asks the prediction API which
- * file to open.
+ * Resolve the `{ pdbId }` shorthand to a structure URL, so a hand-written config
+ * or a short launch URL needs no RCSB filename. An explicit `url` (or inline
+ * `data`) always wins, and resolving an already-resolved spec returns the same
+ * url.
  *
- * Shared by the Structure model's snapshot preprocessor and the
- * LaunchView-ProteinView extension point, which would otherwise each carry
- * their own copy of the same precedence rule.
+ * `uniprotId` resolves to no url and still outranks a `pdbId`. AlphaFold DB's
+ * files for an accession change (an isoform model, several fragments, a new
+ * model version), so the caller keeps the accession and asks
+ * `fetchAlphaFoldModels` which file to open.
  */
 function resolveStructureUrl({ url, data, uniprotId, pdbId, }) {
     if (url !== undefined || data !== undefined) {
@@ -121,9 +123,9 @@ function getConfidenceUrlFromTarget(target) {
     return undefined;
 }
 /**
- * What a structure is called in the UI: its PDB id, its AlphaFold accession,
- * else the file's name. Shared by the view title, the alignment panel heading
- * and the hover readout, so one structure reads the same everywhere.
+ * The name to show for a structure: its PDB id, its AlphaFold accession, else
+ * the file's name. Use it wherever a structure is named, so each place shows
+ * the same name.
  */
 function structureDisplayLabel({ url, data, uniprotId, }) {
     if (url === undefined) {

package/dist/structureUrls.js.map

@@ -1 +1 @@
-{"version":3,"file":"structureUrls.js","sourceRoot":"","sources":["../src/structureUrls.ts"],"names":[],"mappings":";AAAA,+EAA+E;AAC/E,kFAAkF;AAClF,gFAAgF;;AAQhF,sCAEC;AAED,0CAEC;AAED,0CAEC;AAQD,4DAKC;AAED,gDAEC;AAkBD,kDAiBC;AAYD,0CAiBC;AAUD,0EAGC;AAID,8DAUC;AAED,gEAOC;AAOD,sDA0BC;AAtKD,MAAM,iBAAiB,GAAG,IAAI,CAAA;AAE9B,+EAA+E;AAC/E,6EAA6E;AAC7E,6EAA6E;AAC7E,yEAAyE;AACzE,SAAgB,aAAa,CAAC,SAAiB;IAC7C,OAAO,sCAAsC,SAAS,MAAM,CAAA;AAC9D,CAAC;AAED,SAAgB,eAAe,CAAC,SAAiB;IAC/C,OAAO,sCAAsC,SAAS,QAAQ,CAAA;AAChE,CAAC;AAED,SAAgB,eAAe,CAAC,SAAiB;IAC/C,OAAO,qCAAqC,SAAS,QAAQ,CAAA;AAC/D,CAAC;AAED;;;;;GAKG;AACH,SAAgB,wBAAwB,CACtC,SAAiB,EACjB,OAAO,GAAG,iBAAiB;IAE3B,OAAO,wCAAwC,SAAS,aAAa,OAAO,MAAM,CAAA;AACpF,CAAC;AAED,SAAgB,kBAAkB,CAAC,KAAa;IAC9C,OAAO,mCAAmC,KAAK,MAAM,CAAA;AACvD,CAAC;AAED;;;;;;;;;;;;;;;GAeG;AACH,SAAgB,mBAAmB,CAAC,EAClC,GAAG,EACH,IAAI,EACJ,SAAS,EACT,KAAK,GAMN;IACC,IAAI,GAAG,KAAK,SAAS,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;QAC5C,OAAO,GAAG,CAAA;IACZ,CAAC;IACD,OAAO,SAAS,KAAK,SAAS,IAAI,KAAK,KAAK,SAAS;QACnD,CAAC,CAAC,SAAS;QACX,CAAC,CAAC,kBAAkB,CAAC,KAAK,CAAC,CAAA;AAC/B,CAAC;AAED,8EAA8E;AAC9E,iFAAiF;AACjF,8DAA8D;AAC9D,MAAM,iBAAiB,GAAG,CAAC,gBAAgB,EAAE,eAAe,EAAE,eAAe,CAAC,CAAA;AAE9E;;;;GAIG;AACH,SAAgB,eAAe,CAAC,GAAW;IACzC,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,CAAC,GAAG,EAAE;QAC3B,IAAI,CAAC;YACH,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,GAAG,CAAC,CAAA;YAC3B,OAAO,EAAE,IAAI,EAAE,MAAM,CAAC,QAAQ,EAAE,IAAI,EAAE,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE,CAAA;QAC1E,CAAC;QAAC,MAAM,CAAC;YACP,OAAO,EAAE,IAAI,EAAE,SAAS,EAAE,IAAI,EAAE,SAAS,EAAE,CAAA;QAC7C,CAAC;IACH,CAAC,CAAC,EAAE,CAAA;IACJ,IAAI,IAAI,KAAK,SAAS,IAAI,CAAC,iBAAiB,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC;QAC5D,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,KAAK,GACT,2EAA2E,CAAC,IAAI,CAC9E,IAAI,IAAI,EAAE,CACX,CAAA;IACH,OAAO,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,CAAA;AAClC,CAAC;AAED,yEAAyE;AACzE,yEAAyE;AACzE,SAAS,eAAe,CAAC,MAAc;IACrC,OAAO,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAE,CAAA;AAC9B,CAAC;AAED;+EAC+E;AAC/E,SAAgB,+BAA+B,CAAC,MAAc;IAC5D,MAAM,KAAK,GAAG,8BAA8B,CAAC,IAAI,CAAC,eAAe,CAAC,MAAM,CAAC,CAAC,CAAA;IAC1E,OAAO,KAAK,EAAE,CAAC,CAAC,CAAC,CAAA;AACnB,CAAC;AAED,0EAA0E;AAC1E,wEAAwE;AACxE,SAAgB,yBAAyB,CAAC,MAAc,EAAE,EAAU;IAClE,MAAM,QAAQ,GAAG,eAAe,CAAC,MAAM,CAAC,CAAA;IACxC,IAAI,QAAQ,CAAC,UAAU,CAAC,KAAK,CAAC,EAAE,CAAC;QAC/B,OAAO,qCAAqC,QAAQ,MAAM,CAAA;IAC5D,CAAC;IACD,MAAM,KAAK,GACT,EAAE,KAAK,QAAQ;QACb,CAAC,CAAC,iCAAiC,CAAC,IAAI,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAC;QACvD,CAAC,CAAC,SAAS,CAAA;IACf,OAAO,KAAK,CAAC,CAAC,CAAC,kBAAkB,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;AACtD,CAAC;AAED,SAAgB,0BAA0B,CAAC,MAAc;IACvD,MAAM,QAAQ,GAAG,eAAe,CAAC,MAAM,CAAC,CAAA;IACxC,IAAI,QAAQ,CAAC,UAAU,CAAC,KAAK,CAAC,EAAE,CAAC;QAC/B,MAAM,YAAY,GAAG,QAAQ,CAAC,OAAO,CAAC,SAAS,EAAE,cAAc,CAAC,CAAA;QAChE,OAAO,qCAAqC,YAAY,OAAO,CAAA;IACjE,CAAC;IACD,OAAO,SAAS,CAAA;AAClB,CAAC;AAED;;;;GAIG;AACH,SAAgB,qBAAqB,CAAC,EACpC,GAAG,EACH,IAAI,EACJ,SAAS,GAKV;IACC,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;QACtB,OAAO,IAAI,KAAK,SAAS;YACvB,CAAC,CAAC,oBAAoB;YACtB,CAAC,CAAC,SAAS;gBACT,CAAC,CAAC,aAAa,SAAS,EAAE;gBAC1B,CAAC,CAAC,EAAE,CAAA;IACV,CAAC;IACD,MAAM,KAAK,GAAG,eAAe,CAAC,GAAG,CAAC,CAAA;IAClC,IAAI,KAAK,EAAE,CAAC;QACV,OAAO,KAAK,CAAC,WAAW,EAAE,CAAA;IAC5B,CAAC;IACD,MAAM,YAAY,GAAG,+BAA+B,CAAC,GAAG,CAAC,CAAA;IACzD,IAAI,YAAY,EAAE,CAAC;QACjB,OAAO,aAAa,YAAY,EAAE,CAAA;IACpC,CAAC;IACD,MAAM,IAAI,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;IAChD,OAAO,IAAI,KAAK,SAAS,IAAI,IAAI,KAAK,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAA;AACvD,CAAC"}
+{"version":3,"file":"structureUrls.js","sourceRoot":"","sources":["../src/structureUrls.ts"],"names":[],"mappings":";AAAA,mEAAmE;;AAMnE,sCAEC;AAED,0CAEC;AAED,0CAEC;AAQD,4DAKC;AAED,gDAEC;AAKD,0BAEC;AAED,oCAEC;AAaD,kDAiBC;AAYD,0CAiBC;AAUD,0EAGC;AAID,8DAUC;AAED,gEAOC;AAOD,sDA0BC;AA1KD,MAAM,iBAAiB,GAAG,IAAI,CAAA;AAE9B,4EAA4E;AAC5E,uEAAuE;AACvE,SAAgB,aAAa,CAAC,SAAiB;IAC7C,OAAO,sCAAsC,SAAS,MAAM,CAAA;AAC9D,CAAC;AAED,SAAgB,eAAe,CAAC,SAAiB;IAC/C,OAAO,sCAAsC,SAAS,QAAQ,CAAA;AAChE,CAAC;AAED,SAAgB,eAAe,CAAC,SAAiB;IAC/C,OAAO,qCAAqC,SAAS,QAAQ,CAAA;AAC/D,CAAC;AAED;;;;;GAKG;AACH,SAAgB,wBAAwB,CACtC,SAAiB,EACjB,OAAO,GAAG,iBAAiB;IAE3B,OAAO,wCAAwC,SAAS,aAAa,OAAO,MAAM,CAAA;AACpF,CAAC;AAED,SAAgB,kBAAkB,CAAC,KAAa;IAC9C,OAAO,mCAAmC,KAAK,MAAM,CAAA;AACvD,CAAC;AAED,6EAA6E;AAC7E,8EAA8E;AAC9E,gBAAgB;AAChB,SAAgB,OAAO,CAAC,KAAa;IACnC,OAAO,uBAAuB,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;AAC5C,CAAC;AAED,SAAgB,YAAY,CAAC,KAAa;IACxC,OAAO,kCAAkC,KAAK,CAAC,WAAW,EAAE,EAAE,CAAA;AAChE,CAAC;AAED;;;;;;;;;;GAUG;AACH,SAAgB,mBAAmB,CAAC,EAClC,GAAG,EACH,IAAI,EACJ,SAAS,EACT,KAAK,GAMN;IACC,IAAI,GAAG,KAAK,SAAS,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;QAC5C,OAAO,GAAG,CAAA;IACZ,CAAC;IACD,OAAO,SAAS,KAAK,SAAS,IAAI,KAAK,KAAK,SAAS;QACnD,CAAC,CAAC,SAAS;QACX,CAAC,CAAC,kBAAkB,CAAC,KAAK,CAAC,CAAA;AAC/B,CAAC;AAED,8EAA8E;AAC9E,iFAAiF;AACjF,8DAA8D;AAC9D,MAAM,iBAAiB,GAAG,CAAC,gBAAgB,EAAE,eAAe,EAAE,eAAe,CAAC,CAAA;AAE9E;;;;GAIG;AACH,SAAgB,eAAe,CAAC,GAAW;IACzC,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,CAAC,GAAG,EAAE;QAC3B,IAAI,CAAC;YACH,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,GAAG,CAAC,CAAA;YAC3B,OAAO,EAAE,IAAI,EAAE,MAAM,CAAC,QAAQ,EAAE,IAAI,EAAE,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE,CAAA;QAC1E,CAAC;QAAC,MAAM,CAAC;YACP,OAAO,EAAE,IAAI,EAAE,SAAS,EAAE,IAAI,EAAE,SAAS,EAAE,CAAA;QAC7C,CAAC;IACH,CAAC,CAAC,EAAE,CAAA;IACJ,IAAI,IAAI,KAAK,SAAS,IAAI,CAAC,iBAAiB,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC;QAC5D,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,KAAK,GACT,2EAA2E,CAAC,IAAI,CAC9E,IAAI,IAAI,EAAE,CACX,CAAA;IACH,OAAO,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,CAAA;AAClC,CAAC;AAED,yEAAyE;AACzE,yEAAyE;AACzE,SAAS,eAAe,CAAC,MAAc;IACrC,OAAO,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAE,CAAA;AAC9B,CAAC;AAED;+EAC+E;AAC/E,SAAgB,+BAA+B,CAAC,MAAc;IAC5D,MAAM,KAAK,GAAG,8BAA8B,CAAC,IAAI,CAAC,eAAe,CAAC,MAAM,CAAC,CAAC,CAAA;IAC1E,OAAO,KAAK,EAAE,CAAC,CAAC,CAAC,CAAA;AACnB,CAAC;AAED,0EAA0E;AAC1E,wEAAwE;AACxE,SAAgB,yBAAyB,CAAC,MAAc,EAAE,EAAU;IAClE,MAAM,QAAQ,GAAG,eAAe,CAAC,MAAM,CAAC,CAAA;IACxC,IAAI,QAAQ,CAAC,UAAU,CAAC,KAAK,CAAC,EAAE,CAAC;QAC/B,OAAO,qCAAqC,QAAQ,MAAM,CAAA;IAC5D,CAAC;IACD,MAAM,KAAK,GACT,EAAE,KAAK,QAAQ;QACb,CAAC,CAAC,iCAAiC,CAAC,IAAI,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAC;QACvD,CAAC,CAAC,SAAS,CAAA;IACf,OAAO,KAAK,CAAC,CAAC,CAAC,kBAAkB,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;AACtD,CAAC;AAED,SAAgB,0BAA0B,CAAC,MAAc;IACvD,MAAM,QAAQ,GAAG,eAAe,CAAC,MAAM,CAAC,CAAA;IACxC,IAAI,QAAQ,CAAC,UAAU,CAAC,KAAK,CAAC,EAAE,CAAC;QAC/B,MAAM,YAAY,GAAG,QAAQ,CAAC,OAAO,CAAC,SAAS,EAAE,cAAc,CAAC,CAAA;QAChE,OAAO,qCAAqC,YAAY,OAAO,CAAA;IACjE,CAAC;IACD,OAAO,SAAS,CAAA;AAClB,CAAC;AAED;;;;GAIG;AACH,SAAgB,qBAAqB,CAAC,EACpC,GAAG,EACH,IAAI,EACJ,SAAS,GAKV;IACC,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;QACtB,OAAO,IAAI,KAAK,SAAS;YACvB,CAAC,CAAC,oBAAoB;YACtB,CAAC,CAAC,SAAS;gBACT,CAAC,CAAC,aAAa,SAAS,EAAE;gBAC1B,CAAC,CAAC,EAAE,CAAA;IACV,CAAC;IACD,MAAM,KAAK,GAAG,eAAe,CAAC,GAAG,CAAC,CAAA;IAClC,IAAI,KAAK,EAAE,CAAC;QACV,OAAO,KAAK,CAAC,WAAW,EAAE,CAAA;IAC5B,CAAC;IACD,MAAM,YAAY,GAAG,+BAA+B,CAAC,GAAG,CAAC,CAAA;IACzD,IAAI,YAAY,EAAE,CAAC;QACjB,OAAO,aAAa,YAAY,EAAE,CAAA;IACpC,CAAC;IACD,MAAM,IAAI,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;IAChD,OAAO,IAAI,KAAK,SAAS,IAAI,IAAI,KAAK,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAA;AACvD,CAAC"}

package/dist/types.d.ts

@@ -5,10 +5,7 @@ export declare const ALIGNMENT_ALGORITHMS: {
 };
 export declare const DEFAULT_ALIGNMENT_ALGORITHM: AlignmentAlgorithm;
 export declare const ALIGNMENT_ALGORITHM_VALUES: AlignmentAlgorithm[];
-/**
- * Parses an untrusted algorithm name (a URL session-spec param) into the union.
- * The only place a coercion is needed: the model property is an enumeration, so
- * everything downstream of hydration is already typed.
- */
+/** Parses an untrusted algorithm name, such as a URL parameter, falling back
+ * to Smith-Waterman. */
 export declare function coerceAlignmentAlgorithm(value: string): AlignmentAlgorithm;
 export declare const ALIGNMENT_ALGORITHM_LABELS: Record<AlignmentAlgorithm, string>;

package/dist/types.js

@@ -11,11 +11,8 @@ exports.ALIGNMENT_ALGORITHM_VALUES = [
     'needleman_wunsch',
     'smith_waterman',
 ];
-/**
- * Parses an untrusted algorithm name (a URL session-spec param) into the union.
- * The only place a coercion is needed: the model property is an enumeration, so
- * everything downstream of hydration is already typed.
- */
+/** Parses an untrusted algorithm name, such as a URL parameter, falling back
+ * to Smith-Waterman. */
 function coerceAlignmentAlgorithm(value) {
     return (exports.ALIGNMENT_ALGORITHM_VALUES.find(v => v === value) ??
         exports.DEFAULT_ALIGNMENT_ALGORITHM);

package/dist/types.js.map

@@ -1 +1 @@
-{"version":3,"file":"types.js","sourceRoot":"","sources":["../src/types.ts"],"names":[],"mappings":";;;AAmBA,4DAKC;AAtBY,QAAA,oBAAoB,GAAG;IAClC,gBAAgB,EAAE,kBAAkB;IACpC,cAAc,EAAE,gBAAgB;CACxB,CAAA;AAEG,QAAA,2BAA2B,GAAuB,gBAAgB,CAAA;AAElE,QAAA,0BAA0B,GAAyB;IAC9D,kBAAkB;IAClB,gBAAgB;CACjB,CAAA;AAED;;;;GAIG;AACH,SAAgB,wBAAwB,CAAC,KAAa;IACpD,OAAO,CACL,kCAA0B,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,KAAK,CAAC;QACjD,mCAA2B,CAC5B,CAAA;AACH,CAAC;AAEY,QAAA,0BAA0B,GAAuC;IAC5E,gBAAgB,EAAE,kBAAkB;IACpC,cAAc,EAAE,gBAAgB;CACjC,CAAA"}
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../src/types.ts"],"names":[],"mappings":";;;AAgBA,4DAKC;AAnBY,QAAA,oBAAoB,GAAG;IAClC,gBAAgB,EAAE,kBAAkB;IACpC,cAAc,EAAE,gBAAgB;CACxB,CAAA;AAEG,QAAA,2BAA2B,GAAuB,gBAAgB,CAAA;AAElE,QAAA,0BAA0B,GAAyB;IAC9D,kBAAkB;IAClB,gBAAgB;CACjB,CAAA;AAED;wBACwB;AACxB,SAAgB,wBAAwB,CAAC,KAAa;IACpD,OAAO,CACL,kCAA0B,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,KAAK,CAAC;QACjD,mCAA2B,CAC5B,CAAA;AACH,CAAC;AAEY,QAAA,0BAA0B,GAAuC;IAC5E,gBAAgB,EAAE,kBAAkB;IACpC,cAAc,EAAE,gBAAgB;CACjC,CAAA"}

package/dist/uniProtSearch.js

@@ -51,7 +51,6 @@ async function searchByXref(id, opts) {
         return { entries: await searchUniProt(query, 10, opts), error: undefined };
     }
     catch (e) {
-        console.error(`xref search failed for ${id}:`, e);
         return { entries: [], error: e };
     }
 }
@@ -63,18 +62,14 @@ async function searchByGeneName(geneName, organismId, opts) {
         // are 284812. The descendants are asked only on a miss, because for a
         // species with reviewed subspecies entries (human and Neanderthal) they
         // turn one answer into two.
-        // The taxon itself has answered, so the wider question failing leaves
-        // that answer standing rather than turning an empty result into an error.
+        // When the descendant search fails, the taxon's own empty result stands
+        // rather than becoming an error.
         const entries = exact.length === 0 && organismId
-            ? await searchUniProt(buildGeneNameQuery(geneName, organismId, 'taxonomy_id'), 5, opts).catch((e) => {
-                console.error(`descendant-taxon search failed for ${geneName}:`, e);
-                return exact;
-            })
+            ? await searchUniProt(buildGeneNameQuery(geneName, organismId, 'taxonomy_id'), 5, opts).catch(() => exact)
             : exact;
         return { entries, error: undefined };
     }
     catch (e) {
-        console.error(`gene name search failed for ${geneName}:`, e);
         return { entries: [], error: e };
     }
 }

package/dist/uniProtSearch.js.map

@@ -1 +1 @@
-{"version":3,"file":"uniProtSearch.js","sourceRoot":"","sources":["../src/uniProtSearch.ts"],"names":[],"mappings":";;AAmFA,gDAYC;AA6ED,oDAgEC;AA5OD,mDAA2C;AAC3C,yCAImB;AAsCnB,MAAM,cAAc,GAClB,6DAA6D,CAAA;AAE/D,SAAS,mBAAmB,CAC1B,MAAsC;IAEtC,OAAO;QACL,SAAS,EAAE,MAAM,CAAC,gBAAgB;QAClC,EAAE,EAAE,MAAM,CAAC,WAAW;QACtB,QAAQ,EAAE,MAAM,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,QAAQ,EAAE,KAAK;QAC5C,YAAY,EACV,MAAM,CAAC,QAAQ,EAAE,UAAU,IAAI,MAAM,CAAC,QAAQ,EAAE,cAAc;QAChE,WAAW,EAAE,MAAM,CAAC,kBAAkB,EAAE,eAAe,EAAE,QAAQ,EAAE,KAAK;QACxE,UAAU,EAAE,MAAM,CAAC,SAAS,KAAK,iCAAiC;KACnE,CAAA;AACH,CAAC;AAED,KAAK,UAAU,aAAa,CAC1B,KAAa,EACb,IAAY,EACZ,IAAmB;IAEnB,MAAM,GAAG,GAAG,mDAAmD,kBAAkB,CAAC,KAAK,CAAC,WAAW,cAAc,SAAS,IAAI,EAAE,CAAA;IAChI,MAAM,IAAI,GAAG,MAAM,IAAA,yBAAS,EAAmB,GAAG,EAAE,IAAI,CAAC,CAAA;IACzD,OAAO,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,mBAAmB,CAAC,CAAA;AAC9C,CAAC;AAED;;;;;;;;;;;;GAYG;AACH,SAAgB,kBAAkB,CAChC,QAAgB,EAChB,UAAmB,EACnB,QAAuC,aAAa;IAEpD,OAAO;QACL,eAAe,QAAQ,CAAC,UAAU,CAAC,GAAG,EAAE,KAAK,CAAC,GAAG;QACjD,UAAU,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,UAAU,EAAE,CAAC,CAAC,CAAC,SAAS;QACjD,eAAe;KAChB;SACE,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,SAAS,CAAC;SAC5B,IAAI,CAAC,OAAO,CAAC,CAAA;AAClB,CAAC;AAOD,KAAK,UAAU,YAAY,CACzB,EAAU,EACV,IAAmB;IAEnB,MAAM,KAAK,GAAG,IAAA,gCAAqB,EAAC,EAAE,CAAC,CAAA;IACvC,IAAI,CAAC,KAAK,EAAE,CAAC;QACX,OAAO,EAAE,OAAO,EAAE,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,CAAA;IAC1C,CAAC;IACD,IAAI,CAAC;QACH,OAAO,EAAE,OAAO,EAAE,MAAM,aAAa,CAAC,KAAK,EAAE,EAAE,EAAE,IAAI,CAAC,EAAE,KAAK,EAAE,SAAS,EAAE,CAAA;IAC5E,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,OAAO,CAAC,KAAK,CAAC,0BAA0B,EAAE,GAAG,EAAE,CAAC,CAAC,CAAA;QACjD,OAAO,EAAE,OAAO,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,CAAA;IAClC,CAAC;AACH,CAAC;AAED,KAAK,UAAU,gBAAgB,CAC7B,QAAgB,EAChB,UAA8B,EAC9B,IAAmB;IAEnB,IAAI,CAAC;QACH,MAAM,KAAK,GAAG,MAAM,aAAa,CAC/B,kBAAkB,CAAC,QAAQ,EAAE,UAAU,CAAC,EACxC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,EACnB,IAAI,CACL,CAAA;QACD,0EAA0E;QAC1E,0EAA0E;QAC1E,sEAAsE;QACtE,wEAAwE;QACxE,4BAA4B;QAC5B,sEAAsE;QACtE,0EAA0E;QAC1E,MAAM,OAAO,GACX,KAAK,CAAC,MAAM,KAAK,CAAC,IAAI,UAAU;YAC9B,CAAC,CAAC,MAAM,aAAa,CACjB,kBAAkB,CAAC,QAAQ,EAAE,UAAU,EAAE,aAAa,CAAC,EACvD,CAAC,EACD,IAAI,CACL,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBACrB,OAAO,CAAC,KAAK,CAAC,sCAAsC,QAAQ,GAAG,EAAE,CAAC,CAAC,CAAA;gBACnE,OAAO,KAAK,CAAA;YACd,CAAC,CAAC;YACJ,CAAC,CAAC,KAAK,CAAA;QACX,OAAO,EAAE,OAAO,EAAE,KAAK,EAAE,SAAS,EAAE,CAAA;IACtC,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,OAAO,CAAC,KAAK,CAAC,+BAA+B,QAAQ,GAAG,EAAE,CAAC,CAAC,CAAA;QAC5D,OAAO,EAAE,OAAO,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,CAAA;IAClC,CAAC;AACH,CAAC;AAED,SAAS,kBAAkB,CAAC,OAAuB;IACjD,MAAM,IAAI,GAAG,IAAI,GAAG,EAAU,CAAA;IAC9B,MAAM,MAAM,GAAmB,EAAE,CAAA;IACjC,KAAK,MAAM,KAAK,IAAI,OAAO,EAAE,CAAC;QAC5B,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE,CAAC;YAC/B,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,SAAS,CAAC,CAAA;YACzB,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QACpB,CAAC;IACH,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAQM,KAAK,UAAU,oBAAoB,CACxC,EACE,aAAa,GAAG,EAAE,EAClB,MAAM,EACN,QAAQ,EACR,UAAU,GAOX,EACD,IAAmB;IAEnB,MAAM,WAAW,GAAG,IAAI,GAAG,CAAC,aAAa,CAAC,CAAA;IAC1C,MAAM,cAAc,GAAG,MAAM,CAAC,CAAC,CAAC,IAAA,+BAAoB,EAAC,MAAM,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACxE,IAAI,cAAc,IAAI,IAAA,iCAAsB,EAAC,cAAc,CAAC,EAAE,CAAC;QAC7D,WAAW,CAAC,GAAG,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;IAED,6EAA6E;IAC7E,2EAA2E;IAC3E,uEAAuE;IACvE,MAAM,CAAC,WAAW,EAAE,UAAU,CAAC,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC;QAClD,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,WAAW,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC,YAAY,CAAC,EAAE,EAAE,IAAI,CAAC,CAAC,CAAC;QAC/D,QAAQ,CAAC,CAAC,CAAC,gBAAgB,CAAC,QAAQ,EAAE,UAAU,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC,SAAS;KACpE,CAAC,CAAA;IAEF,IAAI,OAAO,GAAG,kBAAkB,CAAC,WAAW,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAA;IACrE,wEAAwE;IACxE,6EAA6E;IAC7E,yEAAyE;IACzE,MAAM,mBAAmB,GACvB,UAAU,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,SAAS,CAAA;IACzE,IAAI,mBAAmB,EAAE,CAAC;QACxB,OAAO,GAAG,kBAAkB,CAAC,CAAC,GAAG,OAAO,EAAE,GAAG,mBAAmB,CAAC,OAAO,CAAC,CAAC,CAAA;IAC5E,CAAC;IAED,MAAM,cAAc,GAAG,WAAW,CAAC,IAAI,GAAG,CAAC,mBAAmB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACvE,MAAM,WAAW,GACf,WAAW,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,KAAK,SAAS,CAAC,CAAC,MAAM;QACrD,CAAC,mBAAmB,EAAE,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAEpD,4EAA4E;IAC5E,6EAA6E;IAC7E,IACE,OAAO,CAAC,MAAM,KAAK,CAAC;QACpB,cAAc,GAAG,CAAC;QAClB,cAAc,KAAK,WAAW,EAC9B,CAAC;QACD,MAAM,CACJ,mBAAmB,EAAE,KAAK;YAC1B,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,KAAK,SAAS,CAAC,EAAE,KAAK,CACpD,CAAA;IACH,CAAC;IAED,OAAO;QACL,OAAO,EAAE,OAAO,CAAC,QAAQ,CACvB,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,MAAM,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,MAAM,CAAC,CAAC,CAAC,UAAU,CAAC,CACtD;QACD,cAAc;QACd,WAAW;KACZ,CAAA;AACH,CAAC"}
+{"version":3,"file":"uniProtSearch.js","sourceRoot":"","sources":["../src/uniProtSearch.ts"],"names":[],"mappings":";;AAmFA,gDAYC;AAwED,oDAgEC;AAvOD,mDAA2C;AAC3C,yCAImB;AAsCnB,MAAM,cAAc,GAClB,6DAA6D,CAAA;AAE/D,SAAS,mBAAmB,CAC1B,MAAsC;IAEtC,OAAO;QACL,SAAS,EAAE,MAAM,CAAC,gBAAgB;QAClC,EAAE,EAAE,MAAM,CAAC,WAAW;QACtB,QAAQ,EAAE,MAAM,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,QAAQ,EAAE,KAAK;QAC5C,YAAY,EACV,MAAM,CAAC,QAAQ,EAAE,UAAU,IAAI,MAAM,CAAC,QAAQ,EAAE,cAAc;QAChE,WAAW,EAAE,MAAM,CAAC,kBAAkB,EAAE,eAAe,EAAE,QAAQ,EAAE,KAAK;QACxE,UAAU,EAAE,MAAM,CAAC,SAAS,KAAK,iCAAiC;KACnE,CAAA;AACH,CAAC;AAED,KAAK,UAAU,aAAa,CAC1B,KAAa,EACb,IAAY,EACZ,IAAmB;IAEnB,MAAM,GAAG,GAAG,mDAAmD,kBAAkB,CAAC,KAAK,CAAC,WAAW,cAAc,SAAS,IAAI,EAAE,CAAA;IAChI,MAAM,IAAI,GAAG,MAAM,IAAA,yBAAS,EAAmB,GAAG,EAAE,IAAI,CAAC,CAAA;IACzD,OAAO,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,mBAAmB,CAAC,CAAA;AAC9C,CAAC;AAED;;;;;;;;;;;;GAYG;AACH,SAAgB,kBAAkB,CAChC,QAAgB,EAChB,UAAmB,EACnB,QAAuC,aAAa;IAEpD,OAAO;QACL,eAAe,QAAQ,CAAC,UAAU,CAAC,GAAG,EAAE,KAAK,CAAC,GAAG;QACjD,UAAU,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,UAAU,EAAE,CAAC,CAAC,CAAC,SAAS;QACjD,eAAe;KAChB;SACE,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,SAAS,CAAC;SAC5B,IAAI,CAAC,OAAO,CAAC,CAAA;AAClB,CAAC;AAOD,KAAK,UAAU,YAAY,CACzB,EAAU,EACV,IAAmB;IAEnB,MAAM,KAAK,GAAG,IAAA,gCAAqB,EAAC,EAAE,CAAC,CAAA;IACvC,IAAI,CAAC,KAAK,EAAE,CAAC;QACX,OAAO,EAAE,OAAO,EAAE,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,CAAA;IAC1C,CAAC;IACD,IAAI,CAAC;QACH,OAAO,EAAE,OAAO,EAAE,MAAM,aAAa,CAAC,KAAK,EAAE,EAAE,EAAE,IAAI,CAAC,EAAE,KAAK,EAAE,SAAS,EAAE,CAAA;IAC5E,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,OAAO,EAAE,OAAO,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,CAAA;IAClC,CAAC;AACH,CAAC;AAED,KAAK,UAAU,gBAAgB,CAC7B,QAAgB,EAChB,UAA8B,EAC9B,IAAmB;IAEnB,IAAI,CAAC;QACH,MAAM,KAAK,GAAG,MAAM,aAAa,CAC/B,kBAAkB,CAAC,QAAQ,EAAE,UAAU,CAAC,EACxC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,EACnB,IAAI,CACL,CAAA;QACD,0EAA0E;QAC1E,0EAA0E;QAC1E,sEAAsE;QACtE,wEAAwE;QACxE,4BAA4B;QAC5B,wEAAwE;QACxE,iCAAiC;QACjC,MAAM,OAAO,GACX,KAAK,CAAC,MAAM,KAAK,CAAC,IAAI,UAAU;YAC9B,CAAC,CAAC,MAAM,aAAa,CACjB,kBAAkB,CAAC,QAAQ,EAAE,UAAU,EAAE,aAAa,CAAC,EACvD,CAAC,EACD,IAAI,CACL,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC;YACtB,CAAC,CAAC,KAAK,CAAA;QACX,OAAO,EAAE,OAAO,EAAE,KAAK,EAAE,SAAS,EAAE,CAAA;IACtC,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,OAAO,EAAE,OAAO,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,CAAA;IAClC,CAAC;AACH,CAAC;AAED,SAAS,kBAAkB,CAAC,OAAuB;IACjD,MAAM,IAAI,GAAG,IAAI,GAAG,EAAU,CAAA;IAC9B,MAAM,MAAM,GAAmB,EAAE,CAAA;IACjC,KAAK,MAAM,KAAK,IAAI,OAAO,EAAE,CAAC;QAC5B,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE,CAAC;YAC/B,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,SAAS,CAAC,CAAA;YACzB,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QACpB,CAAC;IACH,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAQM,KAAK,UAAU,oBAAoB,CACxC,EACE,aAAa,GAAG,EAAE,EAClB,MAAM,EACN,QAAQ,EACR,UAAU,GAOX,EACD,IAAmB;IAEnB,MAAM,WAAW,GAAG,IAAI,GAAG,CAAC,aAAa,CAAC,CAAA;IAC1C,MAAM,cAAc,GAAG,MAAM,CAAC,CAAC,CAAC,IAAA,+BAAoB,EAAC,MAAM,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACxE,IAAI,cAAc,IAAI,IAAA,iCAAsB,EAAC,cAAc,CAAC,EAAE,CAAC;QAC7D,WAAW,CAAC,GAAG,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;IAED,6EAA6E;IAC7E,2EAA2E;IAC3E,uEAAuE;IACvE,MAAM,CAAC,WAAW,EAAE,UAAU,CAAC,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC;QAClD,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,WAAW,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC,YAAY,CAAC,EAAE,EAAE,IAAI,CAAC,CAAC,CAAC;QAC/D,QAAQ,CAAC,CAAC,CAAC,gBAAgB,CAAC,QAAQ,EAAE,UAAU,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC,SAAS;KACpE,CAAC,CAAA;IAEF,IAAI,OAAO,GAAG,kBAAkB,CAAC,WAAW,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAA;IACrE,wEAAwE;IACxE,6EAA6E;IAC7E,yEAAyE;IACzE,MAAM,mBAAmB,GACvB,UAAU,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,SAAS,CAAA;IACzE,IAAI,mBAAmB,EAAE,CAAC;QACxB,OAAO,GAAG,kBAAkB,CAAC,CAAC,GAAG,OAAO,EAAE,GAAG,mBAAmB,CAAC,OAAO,CAAC,CAAC,CAAA;IAC5E,CAAC;IAED,MAAM,cAAc,GAAG,WAAW,CAAC,IAAI,GAAG,CAAC,mBAAmB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACvE,MAAM,WAAW,GACf,WAAW,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,KAAK,SAAS,CAAC,CAAC,MAAM;QACrD,CAAC,mBAAmB,EAAE,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAEpD,4EAA4E;IAC5E,6EAA6E;IAC7E,IACE,OAAO,CAAC,MAAM,KAAK,CAAC;QACpB,cAAc,GAAG,CAAC;QAClB,cAAc,KAAK,WAAW,EAC9B,CAAC;QACD,MAAM,CACJ,mBAAmB,EAAE,KAAK;YAC1B,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,KAAK,SAAS,CAAC,EAAE,KAAK,CACpD,CAAA;IACH,CAAC;IAED,OAAO;QACL,OAAO,EAAE,OAAO,CAAC,QAAQ,CACvB,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,MAAM,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,MAAM,CAAC,CAAC,CAAC,UAAU,CAAC,CACtD;QACD,cAAc;QACd,WAAW;KACZ,CAAA;AACH,CAAC"}

package/esm/alignmentQuality.d.ts

@@ -1,20 +1,20 @@
 import type { PairwiseAlignment } from './mappings.ts';
 export interface AlignmentQuality {
-    /** columns carrying a residue on both rows, i.e. mapped positions */
+    /** columns with a residue in both rows, i.e. mapped positions */
     aligned: number;
     identical: number;
     transcriptLength: number;
     structureLength: number;
     /** identical over aligned; 0 when nothing aligned */
     identity: number;
-    /** identical over the shorter of the two sequences: the statistic that
-     * separates a real match from a chance local alignment, see below */
+    /** identical over the shorter of the two sequences, which separates a
+     * real match from a chance local alignment (see LOW_IDENTITY_OVER_SHORTER) */
     identityOverShorter: number;
     /** aligned over the structure's length */
     structureCoverage: number;
     /** first and last transcript residue the alignment covers, 1-based
-     * inclusive; 0 when nothing aligned. A structure is usually a fragment, and
-     * which part of the protein it holds is the reader's first question. */
+     * inclusive; 0 when nothing aligned. A structure is usually a fragment, so
+     * these show which part of the protein it contains. */
     transcriptStart: number;
     transcriptEnd: number;
 }

package/esm/alphaFoldModels.d.ts

@@ -22,11 +22,11 @@ export declare function parseAlphaFoldModels(json: unknown): AlphaFoldModel[];
 export declare function fetchAlphaFoldModels(uniprotId: string, opts?: FetchOptions): Promise<AlphaFoldModel[]>;
 /**
  * The model to open for a gene's transcripts: one folded from exactly a
- * transcript's translation, canonical first, so the view maps it as an
- * identity; else the canonical model; else the longest isoform model.
+ * transcript's translation, canonical first, so every residue maps to itself;
+ * else the canonical model; else the longest isoform model.
  *
- * Takes any record of sequences, since the structure loader knows one
- * translation rather than a gene's isoforms.
+ * Takes any record of sequences, since a caller may know one translation rather
+ * than a gene's isoforms.
  */
 export declare function pickAlphaFoldModel(models: AlphaFoldModel[], isoformSequences: Record<string, {
     seq: string;