@cyanheads/interpro-mcp-server 0.0.0-stage → 0.1.1

package/dist/mcp-server/tools/definitions/interpro-get-protein-domains.tool.d.ts

@@ -0,0 +1,172 @@
+/**
+ * @fileoverview Protein annotation maps in budget-bounded segments of whole, discontinuous matches.
+ * @module mcp-server/tools/definitions/interpro-get-protein-domains.tool
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+/** Map signatures to sequence coordinates in budget-bounded segments with explicit coverage. */
+export declare const interproGetProteinDomains: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
+    accession: z.ZodString;
+    residuePosition: z.ZodOptional<z.ZodNumber>;
+    includeExtraFeatures: z.ZodDefault<z.ZodBoolean>;
+    cursor: z.ZodPreprocess<z.ZodOptional<z.ZodString>, unknown>;
+}, z.core.$strip>, z.ZodObject<{
+    accession: z.ZodString;
+    protein: z.ZodOptional<z.ZodObject<{
+        accession: z.ZodString;
+        length: z.ZodNumber;
+        source_database: z.ZodString;
+        name: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        gene: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        source_organism: z.ZodOptional<z.ZodObject<{
+            taxId: z.ZodUnion<readonly [z.ZodString, z.ZodNumber]>;
+            scientificName: z.ZodString;
+            fullName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        }, z.core.$catchall<z.ZodJSONSchema>>>;
+    }, z.core.$catchall<z.ZodJSONSchema>>>;
+    matches: z.ZodArray<z.ZodObject<{
+        metadata: z.ZodObject<{
+            accession: z.ZodString;
+            source_database: z.ZodString;
+            name: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+            type: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+            integrated: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+            member_databases: z.ZodOptional<z.ZodNullable<z.ZodRecord<z.ZodString, z.ZodRecord<z.ZodString, z.ZodString>>>>;
+            go_terms: z.ZodOptional<z.ZodNullable<z.ZodArray<z.ZodObject<{
+                identifier: z.ZodString;
+                name: z.ZodString;
+                category: z.ZodObject<{
+                    code: z.ZodString;
+                    name: z.ZodString;
+                }, z.core.$catchall<z.ZodJSONSchema>>;
+            }, z.core.$catchall<z.ZodJSONSchema>>>>>;
+        }, z.core.$catchall<z.ZodJSONSchema>>;
+        proteins: z.ZodArray<z.ZodObject<{
+            accession: z.ZodString;
+            entry_protein_locations: z.ZodArray<z.ZodObject<{
+                fragments: z.ZodArray<z.ZodObject<{
+                    start: z.ZodNumber;
+                    end: z.ZodNumber;
+                    'dc-status': z.ZodOptional<z.ZodString>;
+                }, z.core.$catchall<z.ZodJSONSchema>>>;
+                representative: z.ZodOptional<z.ZodNullable<z.ZodBoolean>>;
+                model: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+                score: z.ZodOptional<z.ZodNullable<z.ZodNumber>>;
+            }, z.core.$catchall<z.ZodJSONSchema>>>;
+        }, z.core.$catchall<z.ZodJSONSchema>>>;
+    }, z.core.$catchall<z.ZodJSONSchema>>>;
+    extraFeatures: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodObject<{
+        accession: z.ZodString;
+        source_database: z.ZodString;
+        locations: z.ZodArray<z.ZodObject<{
+            fragments: z.ZodArray<z.ZodObject<{
+                start: z.ZodNumber;
+                end: z.ZodNumber;
+                'dc-status': z.ZodOptional<z.ZodString>;
+            }, z.core.$catchall<z.ZodJSONSchema>>>;
+            representative: z.ZodOptional<z.ZodNullable<z.ZodBoolean>>;
+            model: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+            score: z.ZodOptional<z.ZodNullable<z.ZodNumber>>;
+        }, z.core.$catchall<z.ZodJSONSchema>>>;
+    }, z.core.$catchall<z.ZodJSONSchema>>>>;
+    selection: z.ZodObject<{
+        residuePosition: z.ZodOptional<z.ZodNumber>;
+        includeExtraFeatures: z.ZodBoolean;
+    }, z.core.$strip>;
+    coverage: z.ZodObject<{
+        totalMatches: z.ZodNumber;
+        scannedMatches: z.ZodNumber;
+        returnedMatches: z.ZodNumber;
+        totalFeatures: z.ZodOptional<z.ZodNumber>;
+        returnedFeatures: z.ZodOptional<z.ZodNumber>;
+        complete: z.ZodBoolean;
+        hasMore: z.ZodBoolean;
+        nextCursor: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>;
+    url: z.ZodString;
+    sourceUrl: z.ZodString;
+}, z.core.$strip>, readonly [{
+    readonly reason: "retry_deadline_exceeded";
+    readonly code: JsonRpcErrorCode.Timeout;
+    readonly when: "The shared fifty-second budget expires across protein metadata, match pages, and extra features.";
+    readonly retryable: true;
+    readonly recovery: "Retry interpro_get_protein_domains after waiting; omit extra features when they are not needed.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "invalid_cursor";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "Cursor decoding or scope fails, the records it resumes inside changed or disagree with it, or upstream rejects continuation.";
+    readonly retryable: false;
+    readonly recovery: "Repeat the same tool without cursor to restart pagination, keeping the intended filters.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "entry_withdrawn";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "InterPro reports a withdrawn record with HTTP 410.";
+    readonly retryable: false;
+    readonly recovery: "Call interpro_search_entries for a current replacement; consult interpro_list_reference with topic databases for source names.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "upstream_shape_invalid";
+    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: "Upstream JSON, structure, or continuation is incompatible.";
+    readonly retryable: false;
+    readonly recovery: "Retry the same tool later; call interpro_list_reference with topic release to check upstream availability.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: 'upstream_response_too_large';
+    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: 'An upstream response exceeds 4 MiB.';
+    readonly retryable: false;
+    readonly recovery: 'Retry list tools with a smaller limit, or retrieve individual members with interpro_get_entry instead of a large clan.';
+    readonly thrownBy: 'service';
+}, {
+    readonly reason: 'upstream_rejected';
+    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: 'InterPro returns an unhandled redirect or client rejection.';
+    readonly retryable: false;
+    readonly recovery: 'Retry the same tool later; call interpro_list_reference with topic release to check upstream availability.';
+    readonly thrownBy: 'service';
+}, {
+    readonly reason: 'upstream_unavailable';
+    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: 'InterPro has a network or server failure; HTTP 501 is not retryable.';
+    readonly retryable: true;
+    readonly recovery: 'Retry the same tool later; call interpro_list_reference with topic release to check upstream availability.';
+    readonly thrownBy: 'service';
+}, {
+    readonly reason: 'upstream_timeout';
+    readonly code: JsonRpcErrorCode.Timeout;
+    readonly when: 'InterPro returns HTTP 408/504 or an attempt exceeds its deadline.';
+    readonly retryable: true;
+    readonly recovery: 'Retry with a smaller limit where available, then repeat the same tool after waiting.';
+    readonly thrownBy: 'service';
+}, {
+    readonly reason: 'upstream_rate_limited';
+    readonly code: JsonRpcErrorCode.RateLimited;
+    readonly when: 'InterPro returns HTTP 429.';
+    readonly retryable: true;
+    readonly recovery: 'Wait for retryAfter when supplied, then repeat the same tool with fewer concurrent calls.';
+    readonly thrownBy: 'service';
+}, {
+    readonly reason: "protein_not_found";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "Canonical protein detail returns HTTP 204 or 404.";
+    readonly retryable: false;
+    readonly recovery: "Use a canonical UniProt accession returned by interpro_find_proteins_by_domain, then retry interpro_get_protein_domains.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "residue_out_of_range";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "Requested position exceeds the fetched protein length.";
+    readonly retryable: false;
+    readonly recovery: "Retry interpro_get_protein_domains with residuePosition between one and the returned protein length.";
+}], {
+    readonly notice: z.ZodOptional<z.ZodString>;
+    readonly totalCount: z.ZodOptional<z.ZodNumber>;
+    readonly truncated: z.ZodOptional<z.ZodBoolean>;
+    readonly shown: z.ZodOptional<z.ZodNumber>;
+    readonly cap: z.ZodOptional<z.ZodNumber>;
+    readonly effectiveQuery: z.ZodOptional<z.ZodString>;
+}>;
+//# sourceMappingURL=interpro-get-protein-domains.tool.d.ts.map

package/dist/mcp-server/tools/definitions/interpro-get-protein-domains.tool.d.ts.map

@@ -0,0 +1 @@
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package/dist/mcp-server/tools/definitions/interpro-get-protein-domains.tool.js

@@ -0,0 +1,374 @@
+/**
+ * @fileoverview Protein annotation maps in budget-bounded segments of whole, discontinuous matches.
+ * @module mcp-server/tools/definitions/interpro-get-protein-domains.tool
+ */
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+import { BUDGET_LABEL, fitWithinBudget, jsonByteLength, RESPONSE_BYTE_BUDGET, } from '../../../services/interpro/budget.js';
+import { compareText, continuation, cursorScope, decodePositionCursor, encodePositionCursor, } from '../../../services/interpro/cursors.js';
+import { formatInterpro, normalizeImages } from '../../../services/interpro/format.js';
+import { getInterproService } from '../../../services/interpro/interpro-service.js';
+import { detailSchema, ExtraFeaturesSchema, isAccession, listSchema, MatchSchema, optionalString, ProteinAccessionSchema, ProteinMetadataSchema, } from '../../../services/interpro/schemas.js';
+import { UPSTREAM_ERRORS } from '../../../services/interpro/upstream-errors.js';
+const OPERATION = 'interpro_get_protein_domains';
+const PAGE_SIZE = 200;
+const MAX_PAGES = 3;
+const SelectionSchema = z.object({
+    residuePosition: z
+        .number()
+        .int()
+        .positive()
+        .optional()
+        .describe('Selected 1-based inclusive residue position.'),
+    includeExtraFeatures: z.boolean().describe('Whether extra predicted features were requested.'),
+});
+const CoverageSchema = z.object({
+    totalMatches: z
+        .number()
+        .int()
+        .nonnegative()
+        .describe('Upstream unfiltered total match count; a segment holding only extra features repeats the count the match list reported.'),
+    scannedMatches: z
+        .number()
+        .int()
+        .nonnegative()
+        .describe('Match records this segment covered, before residue filtering; across a complete walk the segments sum to totalMatches.'),
+    returnedMatches: z
+        .number()
+        .int()
+        .nonnegative()
+        .describe('Selected match records in this segment.'),
+    totalFeatures: z
+        .number()
+        .int()
+        .nonnegative()
+        .optional()
+        .describe('Selected extra features for this protein and residue; present with extraFeatures.'),
+    returnedFeatures: z
+        .number()
+        .int()
+        .nonnegative()
+        .optional()
+        .describe('Extra features in this segment; present with extraFeatures.'),
+    complete: z
+        .boolean()
+        .describe('True only when this call starts without a cursor and returns the whole map: every match and every requested extra feature.'),
+    hasMore: z
+        .boolean()
+        .describe('Whether another segment remains, holding more matches or requested extra features.'),
+    nextCursor: z
+        .string()
+        .optional()
+        .describe('Opaque cursor resuming at the next whole match or extra feature, for the same protein and selection.'),
+});
+/**
+ * Where a continuation resumes: `skip` records into an upstream match page (`page` is that
+ * page's upstream cursor, absent for the first page), or `features` selected extra features into
+ * the feature list that follows the last match. `after` names the last record an earlier segment
+ * covered, so a page or feature list that changed since the cursor was minted is rejected.
+ */
+const PositionSchema = z.union([
+    z
+        .object({
+        page: z.string().min(1).optional(),
+        skip: z.number().int().nonnegative(),
+        after: z.string().min(1).optional(),
+    })
+        .strict()
+        .refine((point) => point.skip > 0 === (point.after !== undefined) &&
+        (point.page !== undefined || point.skip > 0)),
+    z
+        .object({
+        features: z.number().int().nonnegative(),
+        after: z.string().min(1).optional(),
+        totalMatches: z.number().int().nonnegative(),
+    })
+        .strict()
+        .refine((point) => point.features > 0 === (point.after !== undefined)),
+]);
+function contains(locations, position) {
+    return locations.some((location) => location.fragments.some((fragment) => fragment.start <= position && position <= fragment.end));
+}
+function earliest(match) {
+    return Math.min(...match.proteins.flatMap((protein) => protein.entry_protein_locations.flatMap((location) => location.fragments.map((fragment) => fragment.start))));
+}
+/** Earliest fragment start, then accession, then canonical JSON: one total order for any page. */
+function byCoordinate(left, right) {
+    return (earliest(left) - earliest(right) ||
+        compareText(left.metadata.accession, right.metadata.accession) ||
+        compareText(cursorScope(left), cursorScope(right)));
+}
+/** Map signatures to sequence coordinates in budget-bounded segments with explicit coverage. */
+export const interproGetProteinDomains = tool('interpro_get_protein_domains', {
+    title: 'Map protein domains',
+    description: 'Retrieve InterPro and member-signature matches on a canonical UniProt protein, preserving every location and discontinuous fragment. Optionally retain matches covering a residue and include extra predicted features. Large maps arrive in segments of whole matches that fit the response budget: the first segment carries the protein metadata, requested extra features follow the last match, and coverage.nextCursor continues until hasMore is false.',
+    annotations: { readOnlyHint: true, idempotentHint: true, openWorldHint: true },
+    auth: ['tool:interpro_get_protein_domains:read'],
+    input: z.object({
+        accession: ProteinAccessionSchema,
+        residuePosition: z
+            .number()
+            .int()
+            .positive()
+            .optional()
+            .describe('Residue position, 1-based and inclusive; must not exceed protein length.'),
+        includeExtraFeatures: z
+            .boolean()
+            .default(false)
+            .describe('Include complete extra predicted features, returned after the last match; defaults to false.'),
+        cursor: optionalString(z.string().trim().max(4096)).describe('Opaque coverage.nextCursor with unchanged accession, residuePosition, and includeExtraFeatures.'),
+    }),
+    output: z.object({
+        accession: z.string().describe('Canonical UniProt accession.'),
+        protein: ProteinMetadataSchema.optional().describe('Complete upstream protein metadata on the first segment, the call without cursor; continuation segments omit it.'),
+        matches: z
+            .array(MatchSchema.describe('Complete entry match record.'))
+            .describe('Whole selected match records in this segment, sorted by earliest coordinate then accession; a match is never split across segments.'),
+        extraFeatures: ExtraFeaturesSchema.optional().describe('Whole selected extra features in this segment, in feature-key order; {} when none are selected. Omitted when not requested or when this segment ends before the features that follow the last match.'),
+        selection: SelectionSchema.describe('Applied residue and extra-feature selection.'),
+        coverage: CoverageSchema.describe('Where this segment sits in the protein map: every match, then requested extra features.'),
+        url: z.string().describe('Canonical protein website URL.'),
+        sourceUrl: z.string().describe('Official protein API source URL.'),
+    }),
+    enrichment: {
+        notice: z.string().optional().describe('Interpretation, continuation, or recovery guidance.'),
+        totalCount: z.number().optional().describe('Upstream total matching records.'),
+        truncated: z.boolean().optional().describe('More segments remain.'),
+        shown: z.number().int().optional().describe('Selected match records in this segment.'),
+        cap: z
+            .number()
+            .int()
+            .optional()
+            .describe('Most match records one call reads; a segment can stop sooner at the response byte budget.'),
+        effectiveQuery: z.string().optional().describe('Applied selection as JSON.'),
+    },
+    errors: [
+        {
+            reason: 'retry_deadline_exceeded',
+            code: JsonRpcErrorCode.Timeout,
+            when: 'The shared fifty-second budget expires across protein metadata, match pages, and extra features.',
+            retryable: true,
+            recovery: 'Retry interpro_get_protein_domains after waiting; omit extra features when they are not needed.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'invalid_cursor',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'Cursor decoding or scope fails, the records it resumes inside changed or disagree with it, or upstream rejects continuation.',
+            retryable: false,
+            recovery: 'Repeat the same tool without cursor to restart pagination, keeping the intended filters.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'entry_withdrawn',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'InterPro reports a withdrawn record with HTTP 410.',
+            retryable: false,
+            recovery: 'Call interpro_search_entries for a current replacement; consult interpro_list_reference with topic databases for source names.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'upstream_shape_invalid',
+            code: JsonRpcErrorCode.ServiceUnavailable,
+            when: 'Upstream JSON, structure, or continuation is incompatible.',
+            retryable: false,
+            recovery: 'Retry the same tool later; call interpro_list_reference with topic release to check upstream availability.',
+            thrownBy: 'service',
+        },
+        ...UPSTREAM_ERRORS,
+        {
+            reason: 'protein_not_found',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'Canonical protein detail returns HTTP 204 or 404.',
+            retryable: false,
+            recovery: 'Use a canonical UniProt accession returned by interpro_find_proteins_by_domain, then retry interpro_get_protein_domains.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'residue_out_of_range',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'Requested position exceeds the fetched protein length.',
+            retryable: false,
+            recovery: 'Retry interpro_get_protein_domains with residuePosition between one and the returned protein length.',
+        },
+    ],
+    async handler(input, ctx) {
+        const accession = input.accession.toUpperCase();
+        const residue = input.residuePosition;
+        const selection = {
+            ...(residue !== undefined ? { residuePosition: residue } : {}),
+            includeExtraFeatures: input.includeExtraFeatures,
+        };
+        const scope = { accession, ...selection };
+        const start = decodePositionCursor(input.cursor, OPERATION, scope, PositionSchema);
+        const stale = () => ctx.fail('invalid_cursor', 'Cursor no longer matches the InterPro records it resumes inside.');
+        if (start && 'features' in start && !input.includeExtraFeatures)
+            throw stale();
+        const resumed = start !== undefined;
+        const covers = (locations) => residue === undefined || contains(locations, residue);
+        const service = getInterproService();
+        const call = service.begin(ctx);
+        const detail = await service.request(call, ['protein', 'uniprot', accession], {}, detailSchema(ProteinMetadataSchema), { missing: { reason: 'protein_not_found', accession, sourceDatabase: 'uniprot' } });
+        if (!detail.data)
+            throw ctx.fail('upstream_shape_invalid', 'Protein metadata response is missing.');
+        const protein = normalizeImages(detail.data.metadata);
+        if (residue !== undefined && residue > protein.length)
+            throw ctx.fail('residue_out_of_range', `Residue ${residue} exceeds the ${protein.length}-residue length of ${accession}.`, { accession, proteinLength: protein.length, residuePosition: residue });
+        /** Whole candidate items in walk order: every match, then every selected extra feature. */
+        const items = [];
+        let scanned = 0;
+        let totalMatches = start && 'features' in start ? start.totalMatches : 0;
+        let totalFeatures;
+        /** Where the walk resumes after the last gathered item; undefined once the walk ends. */
+        let end;
+        const segment = (count) => {
+            const stop = items[count];
+            const resume = stop ? stop.at : end;
+            const matches = [];
+            const features = [];
+            for (const item of items.slice(0, count))
+                if (item.kind === 'match')
+                    matches.push(item.match);
+                else
+                    features.push([item.key, item.feature]);
+            const featureTotal = totalFeatures;
+            const reachedFeatures = featureTotal !== undefined && (features.length > 0 || resume === undefined);
+            return {
+                accession,
+                ...(resumed ? {} : { protein }),
+                matches: matches.toSorted(byCoordinate),
+                ...(reachedFeatures ? { extraFeatures: Object.fromEntries(features) } : {}),
+                selection,
+                coverage: {
+                    totalMatches,
+                    scannedMatches: stop ? stop.scannedBefore : scanned,
+                    returnedMatches: matches.length,
+                    ...(reachedFeatures
+                        ? { totalFeatures: featureTotal, returnedFeatures: features.length }
+                        : {}),
+                    complete: !resumed && resume === undefined,
+                    hasMore: resume !== undefined,
+                    ...(resume ? { nextCursor: encodePositionCursor(OPERATION, scope, resume) } : {}),
+                },
+                url: `https://www.ebi.ac.uk/interpro/protein/UniProt/${accession}/`,
+                sourceUrl: detail.sourceUrl,
+            };
+        };
+        const overflows = () => items.length > 0 && jsonByteLength(segment(items.length)) > RESPONSE_BYTE_BUDGET;
+        if (!start || 'skip' in start) {
+            let page = start?.page;
+            let skip = start?.skip ?? 0;
+            const seen = new Set(page ? [page] : []);
+            for (let read = 1;; read++) {
+                const response = await service.request(call, ['entry', 'all', 'protein', 'uniprot', accession], { page_size: PAGE_SIZE, cursor: page }, listSchema(MatchSchema), { continuation: page !== undefined });
+                if (read === 1)
+                    totalMatches = response.data?.count ?? 0;
+                const records = normalizeImages(response.data?.results ?? []).toSorted(byCoordinate);
+                if (skip > 0 &&
+                    (skip >= records.length || records[skip - 1]?.metadata.accession !== start?.after))
+                    throw stale();
+                for (let index = skip; index < records.length; index++) {
+                    const match = records[index];
+                    if (match.proteins.some((record) => covers(record.entry_protein_locations)))
+                        items.push({
+                            kind: 'match',
+                            match,
+                            scannedBefore: scanned,
+                            at: {
+                                ...(page ? { page } : {}),
+                                skip: index,
+                                ...(index ? { after: records[index - 1].metadata.accession } : {}),
+                            },
+                        });
+                    scanned += 1;
+                }
+                const next = continuation(response.data?.next ?? null, seen);
+                end = next ? { page: next, skip: 0 } : undefined;
+                if (!next)
+                    break;
+                seen.add(next);
+                page = next;
+                skip = 0;
+                if (read === MAX_PAGES || overflows())
+                    break;
+            }
+        }
+        if (input.includeExtraFeatures && end === undefined) {
+            // Read extras only when the matches fit beside the cursor that would resume at them.
+            end = { features: 0, totalMatches };
+            if (!overflows()) {
+                end = undefined;
+                const extras = await service.request(call, ['protein', 'uniprot', accession], { extra_features: '' }, ExtraFeaturesSchema);
+                if (!extras.data)
+                    throw ctx.fail('upstream_shape_invalid', 'Extra feature response is missing.');
+                const selected = Object.entries(normalizeImages(extras.data))
+                    .filter(([, feature]) => covers(feature.locations))
+                    .toSorted(([a], [b]) => compareText(a, b));
+                const resumeAt = start && 'features' in start ? start : undefined;
+                const skip = resumeAt?.features ?? 0;
+                if (skip > 0 && (skip >= selected.length || selected[skip - 1]?.[0] !== resumeAt?.after))
+                    throw stale();
+                totalFeatures = selected.length;
+                for (let index = skip; index < selected.length; index++) {
+                    const [key, feature] = selected[index];
+                    items.push({
+                        kind: 'feature',
+                        key,
+                        feature,
+                        scannedBefore: scanned,
+                        at: {
+                            features: index,
+                            ...(index ? { after: selected[index - 1][0] } : {}),
+                            totalMatches,
+                        },
+                    });
+                }
+            }
+        }
+        const { count, output, oversized } = fitWithinBudget(items.length, segment);
+        const { coverage } = output;
+        const stop = items[count];
+        const notices = [];
+        if (oversized) {
+            const only = items[0];
+            const [named, unnamed, id] = only.kind === 'feature'
+                ? ['Extra feature', 'This extra feature', only.key]
+                : ['Match', 'This match', only.match.metadata.accession];
+            notices.push(`${isAccession(id) ? `${named} ${id}` : unnamed} cannot be split, so this segment holds it alone and exceeds the ${BUDGET_LABEL}.`);
+        }
+        if (coverage.nextCursor) {
+            const reason = stop
+                ? ` and stopped at the ${BUDGET_LABEL} before the next whole ${stop.kind === 'match' ? 'match' : 'extra feature'}`
+                : oversized
+                    ? ''
+                    : ` and reached the ${MAX_PAGES}-page read limit after ${coverage.scannedMatches} match records`;
+            const nextCall = {
+                accession,
+                ...(residue !== undefined ? { residuePosition: residue } : {}),
+                ...(input.includeExtraFeatures ? { includeExtraFeatures: true } : {}),
+                cursor: coverage.nextCursor,
+            };
+            notices.push(`This segment covers part of the protein map${reason}. Continue with interpro_get_protein_domains ${JSON.stringify(nextCall)} before concluding that a residue has no annotation.`);
+        }
+        else if (resumed)
+            notices.push('This is the final resumed segment. Only the combined segments cover the traversal; upstream pagination is not a snapshot.' +
+                (coverage.returnedMatches || 'features' in start
+                    ? ''
+                    : ' No match was selected in this segment.'));
+        else if (!coverage.returnedMatches)
+            notices.push(residue === undefined
+                ? 'The protein has no returned signature matches. Annotation is not a clinical interpretation.'
+                : 'No match contains this position. Annotation is not a clinical interpretation.');
+        if (resumed)
+            notices.push('Continuation segments omit the protein metadata the first segment returned.');
+        ctx.enrich.total(totalMatches);
+        ctx.enrich.echo(JSON.stringify(scope));
+        if (coverage.nextCursor)
+            ctx.enrich.truncated({ shown: coverage.returnedMatches, cap: MAX_PAGES * PAGE_SIZE });
+        if (notices.length)
+            ctx.enrich.notice(notices.join(' '));
+        return output;
+    },
+    format: formatInterpro,
+});
+//# sourceMappingURL=interpro-get-protein-domains.tool.js.map

package/dist/mcp-server/tools/definitions/interpro-get-protein-domains.tool.js.map

@@ -0,0 +1 @@
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