phenopackets 0.2.2-post2

// This file is @generated by prost-build.

// The serde stuff has been added manually.
#[cfg(feature = "serde")]
use serde::{Deserialize, Serialize};

/// <https://vrsatile.readthedocs.io/en/latest/value_object_descriptor/vod_index.html#extension>
#[derive(Clone, PartialEq, ::prost::Message)]
#[cfg_attr(
    feature = "serde",
    derive(Serialize, Deserialize),
    serde(rename_all = "camelCase")
)]
pub struct Extension {
    #[prost(string, tag = "1")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "String::is_empty", default)
    )]
    pub name: ::prost::alloc::string::String,
    #[prost(string, tag = "2")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "String::is_empty", default)
    )]
    pub value: ::prost::alloc::string::String,
}
/// <https://vrsatile.readthedocs.io/en/latest/value_object_descriptor/vod_index.html#expression>
#[derive(Clone, PartialEq, ::prost::Message)]
#[cfg_attr(
    feature = "serde",
    derive(Serialize, Deserialize),
    serde(rename_all = "camelCase")
)]
pub struct Expression {
    #[prost(string, tag = "1")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "String::is_empty", default)
    )]
    pub syntax: ::prost::alloc::string::String,
    #[prost(string, tag = "2")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "String::is_empty", default)
    )]
    pub value: ::prost::alloc::string::String,
    #[prost(string, tag = "3")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "String::is_empty", default)
    )]
    pub version: ::prost::alloc::string::String,
}
#[derive(Clone, PartialEq, ::prost::Message)]
#[cfg_attr(
    feature = "serde",
    derive(Serialize, Deserialize),
    serde(rename_all = "camelCase")
)]
pub struct VcfRecord {
    #[prost(string, tag = "1")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "String::is_empty", default)
    )]
    pub genome_assembly: ::prost::alloc::string::String,
    #[prost(string, tag = "2")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "String::is_empty", default)
    )]
    pub chrom: ::prost::alloc::string::String,
    #[prost(uint64, tag = "3")]
    pub pos: u64,
    #[prost(string, tag = "4")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "String::is_empty", default)
    )]
    pub id: ::prost::alloc::string::String,
    #[prost(string, tag = "5")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "String::is_empty", default)
    )]
    pub r#ref: ::prost::alloc::string::String,
    #[prost(string, tag = "6")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "String::is_empty", default)
    )]
    pub alt: ::prost::alloc::string::String,
    #[prost(string, tag = "7")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "String::is_empty", default)
    )]
    pub qual: ::prost::alloc::string::String,
    #[prost(string, tag = "8")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "String::is_empty", default)
    )]
    pub filter: ::prost::alloc::string::String,
    #[prost(string, tag = "9")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "String::is_empty", default)
    )]
    pub info: ::prost::alloc::string::String,
}
#[derive(Clone, PartialEq, ::prost::Message)]
#[cfg_attr(
    feature = "serde",
    derive(Serialize, Deserialize),
    serde(rename_all = "camelCase")
)]
pub struct VariationDescriptor {
    #[prost(string, tag = "1")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "String::is_empty", default)
    )]
    pub id: ::prost::alloc::string::String,
    #[prost(message, optional, tag = "2")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Option::is_none", default)
    )]
    pub variation: ::core::option::Option<crate::ga4gh::vrs::v1::Variation>,
    #[prost(string, tag = "3")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "String::is_empty", default)
    )]
    pub label: ::prost::alloc::string::String,
    #[prost(string, tag = "4")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "String::is_empty", default)
    )]
    pub description: ::prost::alloc::string::String,
    /// A specific gene context that applies to this variant.
    #[prost(message, optional, tag = "5")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Option::is_none", default)
    )]
    pub gene_context: ::core::option::Option<GeneDescriptor>,
    /// HGVS, SPDI, and gnomAD-style strings should be represented as Expressions
    #[prost(message, repeated, tag = "6")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Vec::is_empty", default)
    )]
    pub expressions: ::prost::alloc::vec::Vec<Expression>,
    /// A VCF Record of the variant. This SHOULD be a single allele, the VCF genotype (GT) field should be represented in
    /// the allelic_state
    #[prost(message, optional, tag = "7")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Option::is_none", default)
    )]
    pub vcf_record: ::core::option::Option<VcfRecord>,
    /// Allele registry, ClinVar, or other related IDs should be included as xrefs
    #[prost(string, repeated, tag = "8")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Vec::is_empty", default)
    )]
    pub xrefs: ::prost::alloc::vec::Vec<::prost::alloc::string::String>,
    /// Common aliases for a variant, e.g. EGFR vIII, are alternate labels
    #[prost(string, repeated, tag = "9")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Vec::is_empty", default)
    )]
    pub alternate_labels: ::prost::alloc::vec::Vec<::prost::alloc::string::String>,
    #[prost(message, repeated, tag = "10")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Vec::is_empty", default)
    )]
    pub extensions: ::prost::alloc::vec::Vec<Extension>,
    /// The molecular context of the vrs variation. Must be one of “genomic”, “transcript”, or “protein”.
    /// Defaults to "unspecified_molecule_context"
    #[prost(enumeration = "MoleculeContext", tag = "11")]
    #[cfg_attr(
        feature = "serde",
        serde(
            serialize_with = "crate::serde::helpers::serialize_molecule_context",
            deserialize_with = "crate::serde::helpers::deserialize_molecule_context",
            default,
        )
    )]
    pub molecule_context: i32,
    /// The structural variant type associated with this variant, such as a substitution, deletion, or fusion.
    /// We RECOMMEND using a descendent term of SO:0001537.
    #[prost(message, optional, tag = "12")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Option::is_none", default)
    )]
    pub structural_type: ::core::option::Option<crate::schema::v2::core::OntologyClass>,
    /// A Sequence corresponding to a “ref allele”, describing the sequence expected at a SequenceLocation reference.
    #[prost(string, tag = "13")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "String::is_empty", default)
    )]
    pub vrs_ref_allele_seq: ::prost::alloc::string::String,
    /// We RECOMMEND that the allelic_state of variant be described by terms from the Genotype Ontology (GENO).
    /// These SHOULD descend from concept GENO:0000875.
    #[prost(message, optional, tag = "14")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Option::is_none", default)
    )]
    pub allelic_state: ::core::option::Option<crate::schema::v2::core::OntologyClass>,
}
/// <https://vrsatile.readthedocs.io/en/latest/value_object_descriptor/vod_index.html#gene-descriptor>
#[derive(Clone, PartialEq, ::prost::Message)]
#[cfg_attr(
    feature = "serde",
    derive(Serialize, Deserialize),
    serde(rename_all = "camelCase")
)]
pub struct GeneDescriptor {
    /// The official gene identifier as designated by the organism gene nomenclature committee e.g. HGNC:3477 or MGI:2385071
    /// This should be a CURIE linking the reference to a namespace where it can be retrieved.
    /// Mirrors the value_id field of a generic value object descriptor
    #[prost(string, tag = "1")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "String::is_empty", default)
    )]
    pub value_id: ::prost::alloc::string::String,
    /// The primary gene symbol. Takes the place of the label field in a generic descriptor
    #[prost(string, tag = "2")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "String::is_empty", default)
    )]
    pub symbol: ::prost::alloc::string::String,
    /// A free-text description of the value object
    #[prost(string, tag = "3")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "String::is_empty", default)
    )]
    pub description: ::prost::alloc::string::String,
    /// Alternate IDs (should be CURIE) for the same concept may be placed in alternate_ids
    #[prost(string, repeated, tag = "4")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Vec::is_empty", default)
    )]
    pub alternate_ids: ::prost::alloc::vec::Vec<::prost::alloc::string::String>,
    /// Takes the place of alternate_labels field in a generic descriptor
    #[prost(string, repeated, tag = "5")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Vec::is_empty", default)
    )]
    pub alternate_symbols: ::prost::alloc::vec::Vec<::prost::alloc::string::String>,
    /// Related concept IDs (e.g. gene ortholog IDs) may be placed in xrefs
    #[prost(string, repeated, tag = "6")]
    #[cfg_attr(
        feature = "serde",
        serde(skip_serializing_if = "Vec::is_empty", default)
    )]
    pub xrefs: ::prost::alloc::vec::Vec<::prost::alloc::string::String>,
}
#[derive(Clone, Copy, Debug, PartialEq, Eq, Hash, PartialOrd, Ord, ::prost::Enumeration)]
#[repr(i32)]
pub enum MoleculeContext {
    UnspecifiedMoleculeContext = 0,
    Genomic = 1,
    Transcript = 2,
    Protein = 3,
}
impl MoleculeContext {
    /// String value of the enum field names used in the ProtoBuf definition.
    ///
    /// The values are not transformed in any way and thus are considered stable
    /// (if the ProtoBuf definition does not change) and safe for programmatic use.
    pub fn as_str_name(&self) -> &'static str {
        match self {
            Self::UnspecifiedMoleculeContext => "unspecified_molecule_context",
            Self::Genomic => "genomic",
            Self::Transcript => "transcript",
            Self::Protein => "protein",
        }
    }
    /// Creates an enum from field names used in the ProtoBuf definition.
    pub fn from_str_name(value: &str) -> ::core::option::Option<Self> {
        match value {
            "unspecified_molecule_context" => Some(Self::UnspecifiedMoleculeContext),
            "genomic" => Some(Self::Genomic),
            "transcript" => Some(Self::Transcript),
            "protein" => Some(Self::Protein),
            _ => None,
        }
    }
}