p2s_mapper 1.0.0

package/esm/coordinates.js

@@ -0,0 +1,58 @@
+import { structurePositionToAlignmentMap, structureSeqVsTranscriptSeqMap, transcriptPositionToAlignmentMap, } from "./mappings.js";
+import { invertMap } from "./invertMap.js";
+export const structurePos = (n) => n;
+export const transcriptPos = (n) => n;
+export const alignmentCol = (n) => n;
+/**
+ * Builds every coordinate conversion once from a pairwise alignment, replacing
+ * the scatter of per-getter map builds + repeated invertMap calls. The branded
+ * methods are the preferred API; `maps` stays unbranded for whole-map consumers.
+ */
+export function makeCoordinateMapper(pairwiseAlignment) {
+    const { structureSeqToTranscriptSeqPosition, transcriptSeqToStructureSeqPosition, } = structureSeqVsTranscriptSeqMap(pairwiseAlignment);
+    const s2aln = structurePositionToAlignmentMap(pairwiseAlignment);
+    const t2aln = transcriptPositionToAlignmentMap(pairwiseAlignment);
+    const aln2s = invertMap(s2aln);
+    const aln2t = invertMap(t2aln);
+    // The `as` casts below are the single brand-crossing point: indexing a
+    // Record<number,number> yields a plain number that we re-brand to its output
+    // space. Isolated here so the rest of the codebase stays brand-clean.
+    return {
+        structureToTranscript: p => structureSeqToTranscriptSeqPosition[p],
+        transcriptToStructure: p => transcriptSeqToStructureSeqPosition[p],
+        structureToAlignment: p => s2aln[p],
+        alignmentToStructure: c => aln2s[c],
+        transcriptToAlignment: p => t2aln[p],
+        alignmentToTranscript: c => aln2t[c],
+        maps: {
+            structureSeqToTranscriptSeqPosition,
+            transcriptSeqToStructureSeqPosition,
+            structurePositionToAlignmentMap: s2aln,
+            transcriptPositionToAlignmentMap: t2aln,
+            alignmentToStructurePosition: aln2s,
+            alignmentToTranscriptPosition: aln2t,
+        },
+    };
+}
+/**
+ * The 0-based half-open structure-position range covering an inclusive range
+ * of 1-based transcript residues, the numbering a UniProt feature or a domain
+ * map uses. Residues the structure lacks are skipped, so a range that runs
+ * past a fragment's end clamps to the last modeled residue; undefined when none
+ * of the range aligns to the structure.
+ */
+export function transcriptRangeToStructureRange(mapper, range) {
+    let first;
+    let last;
+    for (let residue = range.start; residue <= range.end; residue++) {
+        const pos = mapper.transcriptToStructure(transcriptPos(residue - 1));
+        if (pos !== undefined) {
+            first = first === undefined ? pos : Math.min(first, pos);
+            last = last === undefined ? pos : Math.max(last, pos);
+        }
+    }
+    return first === undefined || last === undefined
+        ? undefined
+        : { start: first, end: last + 1 };
+}
+//# sourceMappingURL=coordinates.js.map

package/esm/coordinates.js.map

@@ -0,0 +1 @@
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package/esm/dbIds.d.ts

@@ -0,0 +1,16 @@
+type DbType = 'ensembl' | 'refseq' | 'ccds' | 'hgnc';
+export declare function matchDbIdPattern(id: string): {
+    db: DbType;
+    pattern: RegExp;
+    label: string;
+} | undefined;
+/** Whether an ID is a database identifier UniProt can map. */
+export declare function isRecognizedDatabaseId(id: string): boolean;
+/** Human-readable label for an ID, e.g. "ENST00000123 (Ensembl transcript)".
+ * Unrecognized IDs are returned unadorned. */
+export declare function getDbIdLabel(id: string): string;
+/** The UniProt xref query fragment for a recognized ID, e.g.
+ * "xref:ensembl-ENST00000123". HGNC strips its redundant "HGNC:" prefix. */
+export declare function buildUniProtXrefQuery(id: string): string | undefined;
+export declare function stripTrailingVersion(s?: string): string | undefined;
+export {};

package/esm/dbIds.js

@@ -0,0 +1,35 @@
+const DB_ID_PATTERNS = [
+    { db: 'ensembl', pattern: /^ENS[A-Z]*G\d+/i, label: 'Ensembl gene' },
+    { db: 'ensembl', pattern: /^ENS[A-Z]*T\d+/i, label: 'Ensembl transcript' },
+    { db: 'ensembl', pattern: /^ENS[A-Z]*P\d+/i, label: 'Ensembl protein' },
+    { db: 'refseq', pattern: /^[NX]M_\d+/i, label: 'RefSeq mRNA' },
+    { db: 'refseq', pattern: /^[NX]R_\d+/i, label: 'RefSeq ncRNA' },
+    { db: 'refseq', pattern: /^[NX]P_\d+/i, label: 'RefSeq protein' },
+    { db: 'ccds', pattern: /^CCDS\d+/i, label: 'CCDS' },
+    { db: 'hgnc', pattern: /^HGNC:\d+/i, label: 'HGNC' },
+];
+export function matchDbIdPattern(id) {
+    return DB_ID_PATTERNS.find(p => p.pattern.test(id));
+}
+/** Whether an ID is a database identifier UniProt can map. */
+export function isRecognizedDatabaseId(id) {
+    return matchDbIdPattern(id) !== undefined;
+}
+/** Human-readable label for an ID, e.g. "ENST00000123 (Ensembl transcript)".
+ * Unrecognized IDs are returned unadorned. */
+export function getDbIdLabel(id) {
+    const match = matchDbIdPattern(id);
+    return match ? `${id} (${match.label})` : id;
+}
+/** The UniProt xref query fragment for a recognized ID, e.g.
+ * "xref:ensembl-ENST00000123". HGNC strips its redundant "HGNC:" prefix. */
+export function buildUniProtXrefQuery(id) {
+    const match = matchDbIdPattern(id);
+    return match
+        ? `xref:${match.db}-${match.db === 'hgnc' ? id.replace('HGNC:', '') : id}`
+        : undefined;
+}
+export function stripTrailingVersion(s) {
+    return s?.replace(/\.[^./]+$/, '');
+}
+//# sourceMappingURL=dbIds.js.map

package/esm/dbIds.js.map

@@ -0,0 +1 @@
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package/esm/extractPerResidueConfidence.d.ts

@@ -0,0 +1,49 @@
+interface ConfidenceModel {
+    obj?: {
+        data: {
+            atomicConformation: {
+                B_iso_or_equiv: {
+                    value: (row: number) => number;
+                };
+            };
+            atomicHierarchy: {
+                residueAtomSegments: {
+                    offsets: ArrayLike<number>;
+                    count: number;
+                };
+                chainAtomSegments: {
+                    index: ArrayLike<number>;
+                };
+                chains: {
+                    label_entity_id: {
+                        value: (row: number) => string;
+                    };
+                };
+                residues: {
+                    label_seq_id: {
+                        value: (row: number) => number;
+                    };
+                };
+            };
+        };
+    };
+}
+/**
+ * Per-residue B-factor / pLDDT of one polymer entity, keyed by molstar's
+ * `label_seq_id`. Keyed by id rather than by residue order because the atomic
+ * hierarchy only holds *observed* residues: a chain with an unmodeled loop, or
+ * a chain that is not the first in the file, would otherwise plot every value
+ * against the wrong SEQRES position. Convert through `Entity.seqIds`.
+ */
+export interface EntityConfidence {
+    entityId: string;
+    byLabelSeqId: Map<number, number>;
+}
+export declare function extractPerResidueConfidence(model: ConfidenceModel): EntityConfidence[] | undefined;
+/**
+ * AlphaFold-style pLDDT lives in [0, 100] and varies across residues. A
+ * constant column (common when a PDB has no B-factors) or out-of-range values
+ * indicate the track wouldn't be meaningful as confidence.
+ */
+export declare function looksLikePlddt(values: number[] | undefined): values is number[];
+export {};

package/esm/extractPerResidueConfidence.js

@@ -0,0 +1,38 @@
+export function extractPerResidueConfidence(model) {
+    const data = model.obj?.data;
+    if (!data) {
+        return undefined;
+    }
+    const { B_iso_or_equiv } = data.atomicConformation;
+    const { residueAtomSegments, chainAtomSegments, chains, residues } = data.atomicHierarchy;
+    const byEntity = new Map();
+    for (let residue = 0; residue < residueAtomSegments.count; residue++) {
+        const atom = residueAtomSegments.offsets[residue];
+        const entityId = chains.label_entity_id.value(chainAtomSegments.index[atom]);
+        let values = byEntity.get(entityId);
+        if (!values) {
+            values = new Map();
+            byEntity.set(entityId, values);
+        }
+        const seqId = residues.label_seq_id.value(residue);
+        if (!values.has(seqId)) {
+            values.set(seqId, B_iso_or_equiv.value(atom));
+        }
+    }
+    return [...byEntity].map(([entityId, byLabelSeqId]) => ({
+        entityId,
+        byLabelSeqId,
+    }));
+}
+/**
+ * AlphaFold-style pLDDT lives in [0, 100] and varies across residues. A
+ * constant column (common when a PDB has no B-factors) or out-of-range values
+ * indicate the track wouldn't be meaningful as confidence.
+ */
+export function looksLikePlddt(values) {
+    return (!!values &&
+        values.length > 1 &&
+        values.every(v => v >= 0 && v <= 100) &&
+        new Set(values).size > 1);
+}
+//# sourceMappingURL=extractPerResidueConfidence.js.map

package/esm/extractPerResidueConfidence.js.map

@@ -0,0 +1 @@
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package/esm/extractStructureSequences.d.ts

@@ -0,0 +1,142 @@
+/** A polymer entity of a loaded structure: its mmCIF entity id, its one-letter
+ * sequence, and the molstar `label_seq_id` of each of those residues.
+ *
+ * The entity id is what lets every downstream step talk about "the gene's
+ * protein" by identity instead of by the fragile entity-[0] position.
+ *
+ * `seqIds` is what lets it talk about a *residue* by identity. Structure
+ * positions in this plugin are 0-based indices into `seq`; molstar addresses
+ * residues by `label_seq_id`. Those are related by `+1` only when the entity's
+ * sequence covers every residue from 1 — true for any mmCIF with an
+ * `entity_poly_seq` category (all of RCSB and AlphaFold) and for PDB files
+ * carrying SEQRES records, because molstar synthesizes the category from them.
+ *
+ * A PDB-format file with no SEQRES has no such category, so molstar falls back
+ * to `StructureSequence.fromHierarchy` and takes `label_seq_id` straight from
+ * the observed residues' author numbering: a chain whose coordinates start at
+ * residue 94 yields seqIds 94.., and an unobserved loop leaves a hole. Deriving
+ * the id arithmetically there is off by the whole offset, in both directions —
+ * every hover reads the wrong residue and every highlight paints the wrong one.
+ * So carry the real ids and convert through them.
+ */
+export interface Entity {
+    entityId: string;
+    seq: string;
+    seqIds: number[];
+    /** author chain ids carrying this entity, e.g. ['A', 'B'] for a homodimer;
+     * what a user recognises from the PDB entry page, where the entity id is
+     * molstar's own bookkeeping */
+    chains: string[];
+    /** DNA, RNA or a hybrid, by molstar's entity subtype. Its one-letter
+     * sequence spells amino acids too (A, C, G, T, U), so it has to be kept
+     * out of the transcript alignment rather than merely scoring low. */
+    nucleicAcid?: boolean;
+    /** `auth_seq_id` per position: the numbering the depositors chose, which
+     * for an RCSB entry is the one papers and UniProt cite (1TUP's position 154
+     * is R248) and what Mol*'s own hover label shows. Display only; every
+     * coordinate the plugin computes with stays a 0-based position, and molstar
+     * is addressed through `seqIds`. Absent when the model has no atomic
+     * hierarchy to read it from. See `residueNumber`. */
+    authSeqIds?: number[];
+}
+interface Column<T> {
+    rowCount: number;
+    value(row: number): T;
+}
+interface StructureModel {
+    obj?: {
+        data: {
+            entities?: {
+                subtype: Column<string>;
+                getEntityIndex(id: string): number;
+            };
+            sourceData?: {
+                data: unknown;
+            };
+            sequence: {
+                sequences: readonly {
+                    entityId: string;
+                    sequence: {
+                        code: {
+                            toArray(): ArrayLike<string>;
+                        };
+                        seqId: {
+                            toArray(): ArrayLike<number>;
+                        };
+                    };
+                }[];
+            };
+            atomicHierarchy?: {
+                chains: {
+                    label_entity_id: Column<string>;
+                    auth_asym_id: Column<string>;
+                };
+                residues?: {
+                    label_seq_id: Column<number>;
+                    auth_seq_id: Column<number>;
+                };
+                residueAtomSegments?: {
+                    offsets: ArrayLike<number>;
+                    count: number;
+                };
+                chainAtomSegments?: {
+                    index: ArrayLike<number>;
+                };
+            };
+        };
+    };
+}
+/**
+ * Author numbering for every SEQRES position, observed or not. A residue with
+ * no atoms has no auth_seq_id of its own, so it takes the offset of the nearest
+ * observed residue before it (after it, at an unobserved N-terminus): a
+ * disordered loop keeps counting the way the paper does. With nothing observed
+ * the label numbering stands.
+ */
+export declare function fillAuthSeqIds(seqIds: number[], observed: Map<number, number> | undefined): number[];
+/** The number a residue is called by: author numbering when the file carries
+ * it, else molstar's label_seq_id, which is the author numbering already for a
+ * SEQRES-less PDB and 1..N for everything else. */
+export declare function residueNumber(entity: Entity | undefined, pos: number): number;
+/**
+ * The 0-based half-open position range covering an inclusive range of author
+ * residue numbers, the form a paper or a spec names a site by ("R248",
+ * "residues 102-292"). Undefined when no residue of the entity carries a number
+ * in the range, so a typo selects nothing rather than something else.
+ */
+export declare function residueRangeToPositions(entity: Entity | undefined, range: {
+    start: number;
+    end: number;
+}): {
+    start: number;
+    end: number;
+} | undefined;
+/**
+ * One letter per position, so `seq[pos]` and `seqIds[pos]` name the same
+ * residue. Molstar's `label` column is not that: it spells a residue with no
+ * one-letter code by its component id (MSE, TPO, ACE) and an alternate site as
+ * "(S|P)", which shifted every later position. `code` writes X for those; the
+ * mmCIF canonical sequence then supplies the parent residue (MSE is M) when it
+ * has one letter per position, which a chromophore spelled "TYG" does not.
+ */
+export declare function oneLetterSequence(codes: ArrayLike<string>, canonical: string | undefined): string;
+export declare function extractEntities(model: StructureModel): Entity[] | undefined;
+/** A user-facing name for an entity: its chains when known, else its id. */
+export declare function entityLabel(entity: Entity): string;
+/** The protein chains' sequences, for the launch dialog's isoform matching,
+ * which has no use for a DNA strand that happens to align. */
+export declare function extractStructureSequences(model: StructureModel): string[] | undefined;
+/**
+ * The molstar `label_seq_id`s for a set of 0-based structure positions. Unknown
+ * positions are dropped rather than guessed, so an out-of-range position paints
+ * nothing instead of painting something wrong.
+ */
+export declare function toLabelSeqIds(entity: Entity | undefined, positions: Iterable<number>): number[];
+/** As toLabelSeqIds, for a half-open [start, end) structure-position range. */
+export declare function rangeToLabelSeqIds(entity: Entity | undefined, range: {
+    start: number;
+    end: number;
+} | undefined): number[];
+/** Reverse of `seqIds`: molstar's label_seq_id -> 0-based structure position. */
+export declare function makeLabelSeqIdIndex(entity: Entity | undefined): Map<number, number>;
+export {};

package/esm/extractStructureSequences.js

@@ -0,0 +1,205 @@
+/** Observed residues' label_seq_id -> auth_seq_id, per entity. The first chain
+ * carrying an entity wins, so a homodimer's copies agree. */
+function authSeqIdsByEntity(model) {
+    const hierarchy = model.obj?.data.atomicHierarchy;
+    const byEntity = new Map();
+    const { residues, residueAtomSegments, chainAtomSegments, chains } = hierarchy ?? {};
+    if (!residues || !residueAtomSegments || !chainAtomSegments || !chains) {
+        return undefined;
+    }
+    for (let residue = 0; residue < residueAtomSegments.count; residue++) {
+        const atom = residueAtomSegments.offsets[residue];
+        const entityId = chains.label_entity_id.value(chainAtomSegments.index[atom]);
+        let ids = byEntity.get(entityId);
+        if (!ids) {
+            ids = new Map();
+            byEntity.set(entityId, ids);
+        }
+        const labelSeqId = residues.label_seq_id.value(residue);
+        if (!ids.has(labelSeqId)) {
+            ids.set(labelSeqId, residues.auth_seq_id.value(residue));
+        }
+    }
+    return byEntity;
+}
+/**
+ * Author numbering for every SEQRES position, observed or not. A residue with
+ * no atoms has no auth_seq_id of its own, so it takes the offset of the nearest
+ * observed residue before it (after it, at an unobserved N-terminus): a
+ * disordered loop keeps counting the way the paper does. With nothing observed
+ * the label numbering stands.
+ */
+export function fillAuthSeqIds(seqIds, observed) {
+    const out = [];
+    let offset;
+    const firstObserved = seqIds.find(id => observed?.has(id));
+    if (firstObserved !== undefined) {
+        offset = observed.get(firstObserved) - firstObserved;
+    }
+    for (const id of seqIds) {
+        const auth = observed?.get(id);
+        if (auth !== undefined) {
+            offset = auth - id;
+        }
+        out.push(id + (offset ?? 0));
+    }
+    return out;
+}
+/** The number a residue is called by: author numbering when the file carries
+ * it, else molstar's label_seq_id, which is the author numbering already for a
+ * SEQRES-less PDB and 1..N for everything else. */
+export function residueNumber(entity, pos) {
+    return entity?.authSeqIds?.[pos] ?? entity?.seqIds[pos] ?? pos + 1;
+}
+/**
+ * The 0-based half-open position range covering an inclusive range of author
+ * residue numbers, the form a paper or a spec names a site by ("R248",
+ * "residues 102-292"). Undefined when no residue of the entity carries a number
+ * in the range, so a typo selects nothing rather than something else.
+ */
+export function residueRangeToPositions(entity, range) {
+    if (!entity) {
+        return undefined;
+    }
+    let first;
+    let last;
+    for (let pos = 0; pos < entity.seq.length; pos++) {
+        const n = residueNumber(entity, pos);
+        if (n >= range.start && n <= range.end) {
+            first ??= pos;
+            last = pos;
+        }
+    }
+    return first === undefined || last === undefined
+        ? undefined
+        : { start: first, end: last + 1 };
+}
+function chainsByEntity(model) {
+    const chains = model.obj?.data.atomicHierarchy?.chains;
+    const byEntity = new Map();
+    if (chains) {
+        for (let i = 0; i < chains.label_entity_id.rowCount; i++) {
+            const entityId = chains.label_entity_id.value(i);
+            const chain = chains.auth_asym_id.value(i);
+            const list = byEntity.get(entityId) ?? [];
+            if (!list.includes(chain)) {
+                list.push(chain);
+            }
+            byEntity.set(entityId, list);
+        }
+    }
+    return byEntity;
+}
+// mmCIF entity_poly.type values for nucleic-acid polymers. Molstar derives the
+// subtype from residue components when a file (PDB format) carries no
+// entity_poly, so the flag is available for either format.
+const NUCLEIC_ACID_SUBTYPES = new Set([
+    'polydeoxyribonucleotide',
+    'polyribonucleotide',
+    'polydeoxyribonucleotide/polyribonucleotide hybrid',
+    'peptide nucleic acid',
+]);
+function isNucleicAcid(model, entityId) {
+    const entities = model.obj?.data.entities;
+    if (!entities) {
+        return false;
+    }
+    const index = entities.getEntityIndex(entityId);
+    return index >= 0 && NUCLEIC_ACID_SUBTYPES.has(entities.subtype.value(index));
+}
+function canonicalSequencesByEntity(model) {
+    const source = model.obj?.data.sourceData?.data;
+    const entityPoly = source?.db?.entity_poly;
+    const byEntity = new Map();
+    if (entityPoly) {
+        for (let i = 0; i < entityPoly.entity_id.rowCount; i++) {
+            byEntity.set(entityPoly.entity_id.value(i), entityPoly.pdbx_seq_one_letter_code_can.value(i).replaceAll(/\s/g, ''));
+        }
+    }
+    return byEntity;
+}
+/**
+ * One letter per position, so `seq[pos]` and `seqIds[pos]` name the same
+ * residue. Molstar's `label` column is not that: it spells a residue with no
+ * one-letter code by its component id (MSE, TPO, ACE) and an alternate site as
+ * "(S|P)", which shifted every later position. `code` writes X for those; the
+ * mmCIF canonical sequence then supplies the parent residue (MSE is M) when it
+ * has one letter per position, which a chromophore spelled "TYG" does not.
+ */
+export function oneLetterSequence(codes, canonical) {
+    const letters = Array.from(codes);
+    return letters
+        .map((c, i) => c === 'X' && canonical?.length === letters.length ? canonical[i] : c)
+        .join('');
+}
+export function extractEntities(model) {
+    const chains = chainsByEntity(model);
+    const authIds = authSeqIdsByEntity(model);
+    const canonical = canonicalSequencesByEntity(model);
+    return model.obj?.data.sequence.sequences.map(s => {
+        const seqIds = Array.from(s.sequence.seqId.toArray());
+        return {
+            entityId: s.entityId,
+            seq: oneLetterSequence(s.sequence.code.toArray(), canonical.get(s.entityId)),
+            seqIds,
+            chains: chains.get(s.entityId) ?? [],
+            ...(isNucleicAcid(model, s.entityId) ? { nucleicAcid: true } : {}),
+            ...(authIds
+                ? { authSeqIds: fillAuthSeqIds(seqIds, authIds.get(s.entityId)) }
+                : {}),
+        };
+    });
+}
+/** A user-facing name for an entity: its chains when known, else its id. */
+export function entityLabel(entity) {
+    const chains = entity.chains.length > 0
+        ? `Chain ${entity.chains.join('/')}`
+        : `Entity ${entity.entityId}`;
+    return `${chains} (${entity.seq.length} ${entity.nucleicAcid ? 'nt' : 'aa'})`;
+}
+/** The protein chains' sequences, for the launch dialog's isoform matching,
+ * which has no use for a DNA strand that happens to align. */
+export function extractStructureSequences(model) {
+    return extractEntities(model)
+        ?.filter(e => !e.nucleicAcid)
+        .map(e => e.seq);
+}
+/**
+ * The molstar `label_seq_id`s for a set of 0-based structure positions. Unknown
+ * positions are dropped rather than guessed, so an out-of-range position paints
+ * nothing instead of painting something wrong.
+ */
+export function toLabelSeqIds(entity, positions) {
+    if (!entity) {
+        return [];
+    }
+    const out = [];
+    for (const pos of positions) {
+        const id = entity.seqIds[pos];
+        if (id !== undefined) {
+            out.push(id);
+        }
+    }
+    return out;
+}
+/** As toLabelSeqIds, for a half-open [start, end) structure-position range. */
+export function rangeToLabelSeqIds(entity, range) {
+    if (!entity || !range) {
+        return [];
+    }
+    const start = Math.max(0, range.start);
+    const end = Math.min(entity.seqIds.length, range.end);
+    return end > start ? entity.seqIds.slice(start, end) : [];
+}
+/** Reverse of `seqIds`: molstar's label_seq_id -> 0-based structure position. */
+export function makeLabelSeqIdIndex(entity) {
+    const index = new Map();
+    entity?.seqIds.forEach((id, pos) => {
+        // first wins: duplicate ids (micro-heterogeneity) collapse to one residue
+        if (!index.has(id)) {
+            index.set(id, pos);
+        }
+    });
+    return index;
+}
+//# sourceMappingURL=extractStructureSequences.js.map

package/esm/extractStructureSequences.js.map

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package/esm/fetchUtils.d.ts

@@ -0,0 +1,34 @@
+/**
+ * The error a failed response deserves: status and host, plus at most the first
+ * line of the body. A whole body is an HTML error page or a megabyte of JSON,
+ * and pasting it into the dialog buries the one line that says what went wrong.
+ */
+export declare function httpError(response: Response, url: string): Promise<Error>;
+/**
+ * `fetch` rejects with a bare `TypeError: Failed to fetch` for a DNS failure,
+ * an offline browser and a refused cross-origin request alike, naming neither
+ * the host nor the cause. Anything else — an abort, most notably — passes
+ * through untouched.
+ */
+export declare function networkError(url: string, cause: unknown): unknown;
+/**
+ * Request options plus the `fetch` to make the request with. Every network
+ * function here takes them, so a caller can hand in a host's instrumented
+ * fetch, a test double, or nothing at all and get `globalThis.fetch`. Resolved
+ * per call rather than captured at import, so a page that installs its fetch
+ * late is still honored.
+ */
+export interface FetchOptions extends RequestInit {
+    fetch?: typeof globalThis.fetch;
+}
+export declare function rawfetch(url: string, args?: FetchOptions): Promise<Response>;
+export declare function myfetch(url: string, args?: FetchOptions): Promise<Response>;
+export declare function jsonfetch<T = unknown>(url: string, args?: FetchOptions): Promise<T>;
+/**
+ * An AbortSignal's reason as a real Error. `signal.reason` is `any` — usually a
+ * DOMException, but a caller can abort with anything at all — and throwing a
+ * non-Error loses the stack and breaks `instanceof Error` checks in the UI's
+ * error rendering. Normalize at every throw site.
+ */
+export declare function abortError(signal: AbortSignal): Error;
+export declare function timeout(time: number, signal?: AbortSignal): Promise<void>;