> ## Documentation Index
> Fetch the complete documentation index at: https://docs.rafflesia.ai/llms.txt
> Use this file to discover all available pages before exploring further.

# List immutable homology results

> Pages the stable ranked results of a completed homology search. Each result carries typed measurements and provenance.



## OpenAPI

````yaml /api-reference/openapi.json get /v1/homology/{homology_search_id}/results
openapi: 3.1.0
info:
  description: >-
    Deterministic biological evidence primitives. Every response is the same
    envelope: ok, data, warnings, provenance.
  title: Rafflesia API
  version: 0.1.0
servers:
  - description: Production
    url: https://api.rafflesia.ai
security:
  - bearerAuth: []
paths:
  /v1/homology/{homology_search_id}/results:
    get:
      tags:
        - Homology
      summary: List immutable homology results
      description: >-
        Pages the stable ranked results of a completed homology search. Each
        result carries typed measurements and provenance.
      operationId: homology_results
      parameters:
        - in: path
          name: homology_search_id
          required: true
          schema:
            type: string
        - explode: false
          in: query
          name: limit
          schema:
            default: 100
            format: int64
            maximum: 100
            minimum: 1
            type: integer
        - explode: false
          in: query
          name: starting_after
          schema:
            type: string
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/EnvelopeHomologySearchResultList'
          description: OK
          headers:
            Rafflesia-Contract-Digest:
              schema:
                type: string
            Rafflesia-Version:
              schema:
                type: string
            X-Request-ID:
              schema:
                type: string
        default:
          content:
            application/problem+json:
              schema:
                $ref: '#/components/schemas/ErrorModel'
          description: Error
components:
  schemas:
    EnvelopeHomologySearchResultList:
      additionalProperties: false
      properties:
        $schema:
          description: A URL to the JSON Schema for this object.
          examples:
            - https://example.com/schemas/EnvelopeHomologySearchResultList.json
          format: uri
          readOnly: true
          type: string
        data:
          $ref: '#/components/schemas/HomologySearchResultList'
          description: Operation result data.
        error:
          $ref: '#/components/schemas/APIError'
          description: Structured error information.
        evidence:
          $ref: '#/components/schemas/EvidenceSummary'
          description: Mechanical evidence summary for agent inspection and chaining.
        ok:
          description: Whether the operation succeeded.
          type: boolean
        provenance:
          $ref: '#/components/schemas/Provenance'
          description: Execution provenance.
        warnings:
          description: Non-fatal warnings.
          items:
            $ref: '#/components/schemas/Warning'
          type:
            - array
            - 'null'
      required:
        - ok
        - warnings
        - provenance
      type: object
    ErrorModel:
      additionalProperties: false
      properties:
        $schema:
          description: A URL to the JSON Schema for this object.
          examples:
            - https://example.com/schemas/ErrorModel.json
          format: uri
          readOnly: true
          type: string
        detail:
          description: >-
            A human-readable explanation specific to this occurrence of the
            problem.
          examples:
            - Property foo is required but is missing.
          type: string
        errors:
          description: Optional list of individual error details
          items:
            $ref: '#/components/schemas/ErrorDetail'
          type:
            - array
            - 'null'
        instance:
          description: >-
            A URI reference that identifies the specific occurrence of the
            problem.
          examples:
            - https://example.com/error-log/abc123
          format: uri
          type: string
        status:
          description: HTTP status code
          examples:
            - 400
          format: int64
          type: integer
        title:
          description: >-
            A short, human-readable summary of the problem type. This value
            should not change between occurrences of the error.
          examples:
            - Bad Request
          type: string
        type:
          default: about:blank
          description: A URI reference to human-readable documentation for the error.
          examples:
            - https://example.com/errors/example
          format: uri
          type: string
      type: object
    HomologySearchResultList:
      additionalProperties: false
      properties:
        data:
          items:
            $ref: '#/components/schemas/HomologySearchResult'
          type:
            - array
            - 'null'
        has_more:
          type: boolean
        next_cursor:
          type: string
        object:
          type: string
        url:
          type: string
      required:
        - object
        - url
        - data
        - has_more
      type: object
    APIError:
      additionalProperties: false
      properties:
        code:
          description: Stable specific error code.
          type: string
        details:
          additionalProperties: {}
          description: Additional structured error details.
          type: object
        doc_url:
          description: Stable documentation URL for this error code.
          type: string
        message:
          description: Human-readable error message.
          type: string
        param:
          description: Request field responsible for the error when known.
          type: string
        type:
          description: Stable coarse error category.
          enum:
            - invalid_request_error
            - resource_missing
            - conflict_error
            - rate_limit_error
            - authentication_error
            - permission_error
            - billing_error
            - api_error
          type: string
      required:
        - type
        - code
        - message
        - doc_url
      type: object
    EvidenceSummary:
      additionalProperties: false
      properties:
        duration_ms:
          description: >-
            Primary elapsed duration in milliseconds when the response exposes
            one.
          format: int64
          type: integer
        input_refs:
          description: >-
            Input references detected from request fields such as object_id,
            structure_id, target_id, and sequence_id.
          items:
            type: string
          type:
            - array
            - 'null'
        object_refs:
          description: Object ids or object refs visible in the response/provenance.
          items:
            type: string
          type:
            - array
            - 'null'
        output_refs:
          description: Output references detected from response data and generated objects.
          items:
            type: string
          type:
            - array
            - 'null'
        row_count:
          description: >-
            Primary row count or returned row count when the response exposes
            one.
          format: int64
          type: integer
        warnings_count:
          description: Number of non-fatal warnings in the envelope.
          format: int64
          type: integer
      required:
        - warnings_count
      type: object
    Provenance:
      additionalProperties: false
      properties:
        cache_hit:
          description: Whether cached output was reused.
          type: boolean
        created_at:
          description: UTC timestamp.
          type: string
        database_snapshots:
          description: Database snapshots used.
          items:
            $ref: '#/components/schemas/DatabaseSnapshot'
          type:
            - array
            - 'null'
        generated_object_ids:
          description: Object ids created by the operation.
          items:
            type: string
          type:
            - array
            - 'null'
        input_hash:
          description: SHA-256 hash of canonical request input.
          type: string
        operation:
          description: Primitive operation id.
          type: string
        parameters_hash:
          description: SHA-256 hash of parameters.
          type: string
        request_id:
          description: Unique request identifier.
          type: string
        server_version:
          description: Server version.
          type: string
        tool_versions:
          description: Tool versions used.
          items:
            $ref: '#/components/schemas/ToolVersion'
          type:
            - array
            - 'null'
      required:
        - request_id
        - operation
        - created_at
        - server_version
      type: object
    Warning:
      additionalProperties: false
      properties:
        code:
          description: Stable warning code.
          type: string
        details:
          additionalProperties: {}
          description: Additional structured warning details.
          type: object
        message:
          description: Human-readable warning message.
          type: string
      required:
        - code
        - message
      type: object
    ErrorDetail:
      additionalProperties: false
      properties:
        location:
          description: >-
            Where the error occurred, e.g. 'body.items[3].tags' or
            'path.thing-id'
          type: string
        message:
          description: Error message text
          type: string
        value:
          description: The value at the given location
      type: object
    HomologySearchResult:
      additionalProperties: false
      properties:
        evidence:
          $ref: '#/components/schemas/HomologySearchResultEvidence'
        id:
          type: string
        object:
          type: string
        rank:
          format: int64
          type: integer
        target:
          $ref: '#/components/schemas/HomologySearchResultTarget'
      required:
        - id
        - object
        - rank
        - target
        - evidence
      type: object
    DatabaseSnapshot:
      additionalProperties: false
      properties:
        digest:
          type: string
        kind:
          type: string
        name:
          type: string
        version:
          type: string
      required:
        - name
        - version
      type: object
    ToolVersion:
      additionalProperties: false
      properties:
        name:
          type: string
        path:
          type: string
        version:
          type: string
      required:
        - name
        - version
      type: object
    HomologySearchResultEvidence:
      additionalProperties: false
      properties:
        affine:
          $ref: '#/components/schemas/HomologyAffineMeasurements'
        alignment:
          $ref: '#/components/schemas/HomologyPairwiseAlignment'
        kind:
          type: string
        maxsim:
          $ref: '#/components/schemas/HomologyMaxSimMeasurements'
        object:
          type: string
        significance:
          $ref: '#/components/schemas/HomologySignificanceMeasurements'
      required:
        - object
        - kind
        - maxsim
      type: object
    HomologySearchResultTarget:
      additionalProperties: false
      properties:
        database_release_id:
          type: string
        kind:
          type: string
        record_id:
          type: string
        target_ordinal:
          format: int64
          type: integer
      required:
        - kind
        - record_id
        - database_release_id
        - target_ordinal
      type: object
    HomologyAffineMeasurements:
      additionalProperties: false
      properties:
        normalized_score:
          format: double
          type: number
        raw_score:
          format: double
          type: number
      required:
        - raw_score
        - normalized_score
      type: object
    HomologyPairwiseAlignment:
      additionalProperties: false
      properties:
        aligned_residue_count:
          format: int64
          type: integer
        cigar:
          type: string
        cigar_dialect:
          type: string
        coordinate_system:
          type: string
        gap_opening_count:
          format: int64
          type: integer
        gap_residue_count:
          format: int64
          type: integer
        identical_residue_count:
          format: int64
          type: integer
        query_coverage_ratio:
          format: double
          type: number
        query_end:
          format: int64
          type: integer
        query_length:
          format: int64
          type: integer
        query_start:
          format: int64
          type: integer
        target_coverage_ratio:
          format: double
          type: number
        target_end:
          format: int64
          type: integer
        target_length:
          format: int64
          type: integer
        target_start:
          format: int64
          type: integer
      required:
        - coordinate_system
        - cigar_dialect
        - query_length
        - target_length
        - query_start
        - query_end
        - target_start
        - target_end
        - query_coverage_ratio
        - target_coverage_ratio
        - aligned_residue_count
        - identical_residue_count
        - gap_residue_count
        - gap_opening_count
        - cigar
      type: object
    HomologyMaxSimMeasurements:
      additionalProperties: false
      properties:
        bidirectional:
          format: double
          type: number
        query_to_target:
          format: double
          type: number
        target_to_query:
          format: double
          type: number
      required:
        - query_to_target
        - target_to_query
        - bidirectional
      type: object
    HomologySignificanceMeasurements:
      additionalProperties: false
      properties:
        calibration_bin:
          type: string
        calibration_id:
          type: string
        calibration_sample_count:
          format: int64
          type: integer
        expected_false_hits:
          format: double
          type: number
        family_wise_exceedance_probability:
          format: double
          type: number
        minimum_resolvable_probability:
          format: double
          type: number
        pair_tail_probability:
          format: double
          type: number
        q_value:
          format: double
          type: number
        support_status:
          enum:
            - supported_empirical
            - supported_tail_model
            - insufficient_tail_resolution
            - out_of_support
            - missing_calibration
          type: string
      required:
        - calibration_sample_count
        - support_status
        - calibration_id
      type: object
  securitySchemes:
    bearerAuth:
      description: 'A Rafflesia API key, sent as `Authorization: Bearer <key>`.'
      scheme: bearer
      type: http

````