All Classes and Interfaces
Class
Description
Create a VRS Allele object such as
{'_id': 'ga4gh:VA.GuPzvZoansqNHPoXkQLXKo31VkTpDKsM',
'type': 'Allele',
'location': {'type': 'SequenceLocation',
'sequence_id': 'ga4gh:SQ.FOWokFmA__GgqWLtqFoWWDLuNEvvGwIJ',
'interval': {'type': 'SequenceInterval',
'start': {'type': 'Number', 'value': 48941647},
'end': {'type': 'Number', 'value': 48941648}}},
'state': {'type': 'LiteralSequenceExpression', 'sequence': 'T'}}
A
PhenopacketToolsException that is thrown by PhenopacketConverter
in case the provided data has incorrect format.Make an educated guess regarding which top-level element of Phenopacket schema is represented in the provided
byte[] or InputStream.Make an educated guess of the format of a top-level element of Phenopacket schema.
An exception thrown when sniffing of the top-level element of Phenopacket schema cannot be performed.
A class with constants that correspond to the upper-level HPO organ-system phenotypic abnormalities.
Static factory class for getting
PhenopacketValidators for top-level Phenopacket schema components.A static factory class for providing validators for pointing out violations of the annotation propagation rule.
A static factory class for providing validators for checking annotation of organ systems.
A static factory class for providing
PhenopacketValidators
that check if HPO terms of the Phenopacket schema elements are present in
a given Ontology and if the terms are non-obsolete.An Individual in the version 2 phenopacket can have these attributes.
JsonSchemaValidationWorkflowRunner<T extends com.google.protobuf.MessageOrBuilder>
Validates if given top-level element satisfies the following criteria:
data format requirements - for instance if the element is a valid JSON document if JSON input is provided
basic Phenopacket schema syntax requirements - the requirements described by the reference documentation.
JsonSchemaValidationWorkflowRunnerBuilder<T extends com.google.protobuf.MessageOrBuilder>
A builder for
JsonSchemaValidationWorkflowRunner.Static factory class for providing
PhenopacketValidators for performing metadata validation.The enum members represent the top-level elements of the Phenopacket schema.
The enum members represent the supported representations of the top-level elements of the Phenopacket schema.
PhenopacketFormatConverter<T extends com.google.protobuf.MessageOrBuilder>
The implementors allow to convert between formats of the top-level elements of Phenopacket schema.
Static class to get
PhenopacketFormatConverters for top-level elements of the Phenopacket schema.The implementors can serialize a top-level element of Phenopacket schema into provided
OutputStream.The implementors provide
PhenopacketPrinters for serializing top-level phenopacket elements
into PhenopacketFormat using PhenopacketSchemaVersion.A static utility class for obtaining JsonFormat.Parser and JsonFormat.Printer
configured for printing Phenopacket Schema elements.
An enum with currently supported Phenopacket schema versions.
Base checked exception thrown by phenopacket-tools.
Base unchecked exception thrown by phenopacket-tools.
PhenopacketValidator<T extends com.google.protobuf.MessageOrBuilder>
PhenopacketValidator represents a single step of the validation workflow.This has convenience methods for building PhenotypicFeature messages with some
commonly used options.
Simple wrapper for a ReferenceRange
unit:
id: "UO:0000316"
label: "cells per microliter"
low: 150000.0
high: 450000.0
A checked exception thrown in case of encountering some content sniffing issues.
Catch-all class for succinct provision of status codes.
A class to serve comprehensive but not necessarily medically correct top-level elements of
the Phenopacket schema, mainly usable for testing.
The TimeElement is used in many places in the Phenopacket.
Convert top-level elements of the phenopacket schema from v1 to v2 format.
ValidationLevel represents a severity level for ValidationResult.ValidationResult contains results of a single validation step performed by a PhenopacketValidator.ValidationResults contain validation results for one Phenopacket schema top-level element
(Phenopacket, Family,
or Cohort).A builder for creating
ValidationResults.A record to use for writing
ValidationResults by ValidationResultsWriter.Write out validation results obtained from validation of a top-level Phenopacket schema element.
ValidationWorkflowDispatcher exposes endpoints for validating top-level elements of Phenopacket Schema
and dispatches the data into the appropriate ValidationWorkflowRunner.ValidationWorkflowRunner<T extends com.google.protobuf.MessageOrBuilder>
ValidationWorkflowRunner validates selected top-level element of the Phenopacket Schema.ValidationWorkflowRunnerBuilder<T extends com.google.protobuf.MessageOrBuilder>
The base builder for constructing
ValidationWorkflowRunner.A description of a
PhenopacketValidator.