Biosample - Documentation

Biosample

new Biosample(opt_dataopt)

Description:

Generated by JsPbCodeGenerator.

Source:

phenopackets/schema/v1/base_pb.js, line 235

Parameters:

Name	Type	Attributes	Description
`opt_data`	Array	<optional>	Optional initial data array, typically from a server response, or constructed directly in Javascript. The array is used in place and becomes part of the constructed object. It is not cloned. If no data is provided, the constructed object will be empty, but still valid.

Extends

jspb.Message

Members

(static) IndividualAgeAtCollectionCase :number

Source:

phenopackets/schema/v1/base_pb.js, line 2991

Properties:

Name	Type	Description
`INDIVIDUAL_AGE_AT_COLLECTION_NOT_SET`	number
`AGE_OF_INDIVIDUAL_AT_COLLECTION`	number
`AGE_RANGE_OF_INDIVIDUAL_AT_COLLECTION`	number

Type:

number

(static) displayName

Source:

phenopackets/schema/v1/base_pb.js, line 244

(private, static, constant) oneofGroups_

Description:

Oneof group definitions for this message. Each group defines the field numbers belonging to that group. When of these fields' value is set, all other fields in the group are cleared. During deserialization, if multiple fields are encountered for a group, only the last value seen will be kept.

Source:

phenopackets/schema/v1/base_pb.js, line 2986

Oneof group definitions for this message. Each group defines the field numbers belonging to that group. When of these fields' value is set, all other fields in the group are cleared. During deserialization, if multiple fields are encountered for a group, only the last value seen will be kept.

(private, static, constant) repeatedFields_

Description:

List of repeated fields within this message type.

Source:

phenopackets/schema/v1/base_pb.js, line 2976

List of repeated fields within this message type.

Methods

addDiagnosticMarkers(opt_valueopt, non-null, opt_indexopt) → (non-null) {proto.org.phenopackets.schema.v1.core.OntologyClass}

Source:

phenopackets/schema/v1/base_pb.js, line 3698

Parameters:

Name	Type	Attributes	Description
`opt_value`	proto.org.phenopackets.schema.v1.core.OntologyClass	<optional>
`opt_index`	number	<optional>

Returns:

Type: proto.org.phenopackets.schema.v1.core.OntologyClass

addHtsFiles(opt_valueopt, non-null, opt_indexopt) → (non-null) {proto.org.phenopackets.schema.v1.core.HtsFile}

Source:

phenopackets/schema/v1/base_pb.js, line 3773

Parameters:

Name	Type	Attributes	Description
`opt_value`	proto.org.phenopackets.schema.v1.core.HtsFile	<optional>
`opt_index`	number	<optional>

Returns:

Type: proto.org.phenopackets.schema.v1.core.HtsFile

addPhenotypicFeatures(opt_valueopt, non-null, opt_indexopt) → (non-null) {proto.org.phenopackets.schema.v1.core.PhenotypicFeature}

Source:

phenopackets/schema/v1/base_pb.js, line 3438

Parameters:

Name	Type	Attributes	Description
`opt_value`	proto.org.phenopackets.schema.v1.core.PhenotypicFeature	<optional>
`opt_index`	number	<optional>

Returns:

Type: proto.org.phenopackets.schema.v1.core.PhenotypicFeature

addVariants(opt_valueopt, non-null, opt_indexopt) → (non-null) {proto.org.phenopackets.schema.v1.core.Variant}

Source:

phenopackets/schema/v1/base_pb.js, line 3811

Parameters:

Name	Type	Attributes	Description
`opt_value`	proto.org.phenopackets.schema.v1.core.Variant	<optional>
`opt_index`	number	<optional>

Returns:

Type: proto.org.phenopackets.schema.v1.core.Variant

clearAgeOfIndividualAtCollection() → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Description:

Clears the message field making it undefined.

Source:

phenopackets/schema/v1/base_pb.js, line 3512

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

clearAgeRangeOfIndividualAtCollection() → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Description:

Clears the message field making it undefined.

Source:

phenopackets/schema/v1/base_pb.js, line 3549

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

clearDiagnosticMarkersList() → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Description:

Clears the list making it empty but non-null.

Source:

phenopackets/schema/v1/base_pb.js, line 3707

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

clearHistologicalDiagnosis() → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Description:

Clears the message field making it undefined.

Source:

phenopackets/schema/v1/base_pb.js, line 3586

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

clearHtsFilesList() → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Description:

Clears the list making it empty but non-null.

Source:

phenopackets/schema/v1/base_pb.js, line 3782

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

clearPhenotypicFeaturesList() → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Description:

Clears the list making it empty but non-null.

Source:

phenopackets/schema/v1/base_pb.js, line 3447

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

clearProcedure() → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Description:

Clears the message field making it undefined.

Source:

phenopackets/schema/v1/base_pb.js, line 3735

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

clearSampledTissue() → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Description:

Clears the message field making it undefined.

Source:

phenopackets/schema/v1/base_pb.js, line 3400

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

clearTaxonomy() → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Description:

Clears the message field making it undefined.

Source:

phenopackets/schema/v1/base_pb.js, line 3475

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

clearTumorGrade() → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Description:

Clears the message field making it undefined.

Source:

phenopackets/schema/v1/base_pb.js, line 3660

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

clearTumorProgression() → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Description:

Clears the message field making it undefined.

Source:

phenopackets/schema/v1/base_pb.js, line 3623

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

clearVariantsList() → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Description:

Clears the list making it empty but non-null.

Source:

phenopackets/schema/v1/base_pb.js, line 3820

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

getAgeOfIndividualAtCollection() → (nullable) {proto.org.phenopackets.schema.v1.core.Age}

Description:

optional Age age_of_individual_at_collection = 7;

Source:

phenopackets/schema/v1/base_pb.js, line 3493

Returns:

Type: proto.org.phenopackets.schema.v1.core.Age

getAgeRangeOfIndividualAtCollection() → (nullable) {proto.org.phenopackets.schema.v1.core.AgeRange}

Description:

optional AgeRange age_range_of_individual_at_collection = 8;

Source:

phenopackets/schema/v1/base_pb.js, line 3530

Returns:

Type: proto.org.phenopackets.schema.v1.core.AgeRange

getDescription() → {string}

Description:

optional string description = 3;

Source:

phenopackets/schema/v1/base_pb.js, line 3363

Returns:

Type: string

getDiagnosticMarkersList() → (non-null) {Array.<!proto.org.phenopackets.schema.v1.core.OntologyClass>}

Description:

repeated OntologyClass diagnostic_markers = 12;

Source:

phenopackets/schema/v1/base_pb.js, line 3678

Returns:

Type: Array.<!proto.org.phenopackets.schema.v1.core.OntologyClass>

getHistologicalDiagnosis() → (nullable) {proto.org.phenopackets.schema.v1.core.OntologyClass}

Description:

optional OntologyClass histological_diagnosis = 9;

Source:

phenopackets/schema/v1/base_pb.js, line 3567

Returns:

Type: proto.org.phenopackets.schema.v1.core.OntologyClass

getHtsFilesList() → (non-null) {Array.<!proto.org.phenopackets.schema.v1.core.HtsFile>}

Description:

repeated HtsFile hts_files = 14;

Source:

phenopackets/schema/v1/base_pb.js, line 3753

Returns:

Type: Array.<!proto.org.phenopackets.schema.v1.core.HtsFile>

getId() → {string}

Description:

optional string id = 1;

Source:

phenopackets/schema/v1/base_pb.js, line 3327

Returns:

Type: string

getIndividualAgeAtCollectionCase() → {proto.org.phenopackets.schema.v1.core.Biosample.IndividualAgeAtCollectionCase}

Source:

phenopackets/schema/v1/base_pb.js, line 3000

Returns:

Type: proto.org.phenopackets.schema.v1.core.Biosample.IndividualAgeAtCollectionCase

getIndividualId() → {string}

Description:

optional string individual_id = 2;

Source:

phenopackets/schema/v1/base_pb.js, line 3345

Returns:

Type: string

getIsControlSample() → {boolean}

Description:

optional bool is_control_sample = 16;

Source:

phenopackets/schema/v1/base_pb.js, line 3829

Returns:

Type: boolean

getPhenotypicFeaturesList() → (non-null) {Array.<!proto.org.phenopackets.schema.v1.core.PhenotypicFeature>}

Description:

repeated PhenotypicFeature phenotypic_features = 5;

Source:

phenopackets/schema/v1/base_pb.js, line 3418

Returns:

Type: Array.<!proto.org.phenopackets.schema.v1.core.PhenotypicFeature>

getProcedure() → (nullable) {proto.org.phenopackets.schema.v1.core.Procedure}

Description:

optional Procedure procedure = 13;

Source:

phenopackets/schema/v1/base_pb.js, line 3716

Returns:

Type: proto.org.phenopackets.schema.v1.core.Procedure

getSampledTissue() → (nullable) {proto.org.phenopackets.schema.v1.core.OntologyClass}

Description:

optional OntologyClass sampled_tissue = 4;

Source:

phenopackets/schema/v1/base_pb.js, line 3381

Returns:

Type: proto.org.phenopackets.schema.v1.core.OntologyClass

getTaxonomy() → (nullable) {proto.org.phenopackets.schema.v1.core.OntologyClass}

Description:

optional OntologyClass taxonomy = 6;

Source:

phenopackets/schema/v1/base_pb.js, line 3456

Returns:

Type: proto.org.phenopackets.schema.v1.core.OntologyClass

getTumorGrade() → (nullable) {proto.org.phenopackets.schema.v1.core.OntologyClass}

Description:

optional OntologyClass tumor_grade = 11;

Source:

phenopackets/schema/v1/base_pb.js, line 3641

Returns:

Type: proto.org.phenopackets.schema.v1.core.OntologyClass

getTumorProgression() → (nullable) {proto.org.phenopackets.schema.v1.core.OntologyClass}

Description:

optional OntologyClass tumor_progression = 10;

Source:

phenopackets/schema/v1/base_pb.js, line 3604

Returns:

Type: proto.org.phenopackets.schema.v1.core.OntologyClass

getVariantsList() → (non-null) {Array.<!proto.org.phenopackets.schema.v1.core.Variant>}

Description:

repeated Variant variants = 15;

Source:

phenopackets/schema/v1/base_pb.js, line 3791

Returns:

Type: Array.<!proto.org.phenopackets.schema.v1.core.Variant>

hasAgeOfIndividualAtCollection() → {boolean}

Description:

Returns whether this field is set.

Source:

phenopackets/schema/v1/base_pb.js, line 3521

Returns:

Type: boolean

hasAgeRangeOfIndividualAtCollection() → {boolean}

Description:

Returns whether this field is set.

Source:

phenopackets/schema/v1/base_pb.js, line 3558

Returns:

Type: boolean

hasHistologicalDiagnosis() → {boolean}

Description:

Returns whether this field is set.

Source:

phenopackets/schema/v1/base_pb.js, line 3595

Returns:

Type: boolean

hasProcedure() → {boolean}

Description:

Returns whether this field is set.

Source:

phenopackets/schema/v1/base_pb.js, line 3744

Returns:

Type: boolean

hasSampledTissue() → {boolean}

Description:

Returns whether this field is set.

Source:

phenopackets/schema/v1/base_pb.js, line 3409

Returns:

Type: boolean

hasTaxonomy() → {boolean}

Description:

Returns whether this field is set.

Source:

phenopackets/schema/v1/base_pb.js, line 3484

Returns:

Type: boolean

hasTumorGrade() → {boolean}

Description:

Returns whether this field is set.

Source:

phenopackets/schema/v1/base_pb.js, line 3669

Returns:

Type: boolean

hasTumorProgression() → {boolean}

Description:

Returns whether this field is set.

Source:

phenopackets/schema/v1/base_pb.js, line 3632

Returns:

Type: boolean

serializeBinary() → (non-null) {Uint8Array}

Description:

Serializes the message to binary data (in protobuf wire format).

Source:

phenopackets/schema/v1/base_pb.js, line 3180

Returns:

Type: Uint8Array

setAgeOfIndividualAtCollection(value) → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Source:

phenopackets/schema/v1/base_pb.js, line 3503

Parameters:

Name	Type	Description
`value`	proto.org.phenopackets.schema.v1.core.Age \| undefined

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

setAgeRangeOfIndividualAtCollection(value) → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Source:

phenopackets/schema/v1/base_pb.js, line 3540

Parameters:

Name	Type	Description
`value`	proto.org.phenopackets.schema.v1.core.AgeRange \| undefined

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

setDescription(value) → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Source:

phenopackets/schema/v1/base_pb.js, line 3372

Parameters:

Name	Type	Description
`value`	string

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

setDiagnosticMarkersList(valuenon-null) → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Source:

phenopackets/schema/v1/base_pb.js, line 3688

Parameters:

Name	Type	Description
`value`	Array.<!proto.org.phenopackets.schema.v1.core.OntologyClass>

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

setHistologicalDiagnosis(value) → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Source:

phenopackets/schema/v1/base_pb.js, line 3577

Parameters:

Name	Type	Description
`value`	proto.org.phenopackets.schema.v1.core.OntologyClass \| undefined

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

setHtsFilesList(valuenon-null) → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Source:

phenopackets/schema/v1/base_pb.js, line 3763

Parameters:

Name	Type	Description
`value`	Array.<!proto.org.phenopackets.schema.v1.core.HtsFile>

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

setId(value) → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Source:

phenopackets/schema/v1/base_pb.js, line 3336

Parameters:

Name	Type	Description
`value`	string

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

setIndividualId(value) → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Source:

phenopackets/schema/v1/base_pb.js, line 3354

Parameters:

Name	Type	Description
`value`	string

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

setIsControlSample(value) → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Source:

phenopackets/schema/v1/base_pb.js, line 3838

Parameters:

Name	Type	Description
`value`	boolean

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

setPhenotypicFeaturesList(valuenon-null) → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Source:

phenopackets/schema/v1/base_pb.js, line 3428

Parameters:

Name	Type	Description
`value`	Array.<!proto.org.phenopackets.schema.v1.core.PhenotypicFeature>

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

setProcedure(value) → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Source:

phenopackets/schema/v1/base_pb.js, line 3726

Parameters:

Name	Type	Description
`value`	proto.org.phenopackets.schema.v1.core.Procedure \| undefined

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

setSampledTissue(value) → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Source:

phenopackets/schema/v1/base_pb.js, line 3391

Parameters:

Name	Type	Description
`value`	proto.org.phenopackets.schema.v1.core.OntologyClass \| undefined

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

setTaxonomy(value) → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Source:

phenopackets/schema/v1/base_pb.js, line 3466

Parameters:

Name	Type	Description
`value`	proto.org.phenopackets.schema.v1.core.OntologyClass \| undefined

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

setTumorGrade(value) → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Source:

phenopackets/schema/v1/base_pb.js, line 3651

Parameters:

Name	Type	Description
`value`	proto.org.phenopackets.schema.v1.core.OntologyClass \| undefined

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

setTumorProgression(value) → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Source:

phenopackets/schema/v1/base_pb.js, line 3614

Parameters:

Name	Type	Description
`value`	proto.org.phenopackets.schema.v1.core.OntologyClass \| undefined

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

setVariantsList(valuenon-null) → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Source:

phenopackets/schema/v1/base_pb.js, line 3801

Parameters:

Name	Type	Description
`value`	Array.<!proto.org.phenopackets.schema.v1.core.Variant>

Returns:

returns this

Type: proto.org.phenopackets.schema.v1.core.Biosample

toObject(opt_includeInstanceopt) → (non-null) {Object}

Description:

Creates an object representation of this proto. Field names that are reserved in JavaScript and will be renamed to pb_name. Optional fields that are not set will be set to undefined. To access a reserved field use, foo.pb_, eg, foo.pb_default. For the list of reserved names please see: net/proto2/compiler/js/internal/generator.cc#kKeyword.

Source:

phenopackets/schema/v1/base_pb.js, line 3019

Parameters:

Name	Type	Attributes	Description
`opt_includeInstance`	boolean	<optional>	Deprecated. whether to include the JSPB instance for transitional soy proto support: http://goto/soy-param-migration

Returns:

Type: Object

(static) deserializeBinary(bytes) → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Description:

Deserializes binary data (in protobuf wire format).

Source:

phenopackets/schema/v1/base_pb.js, line 3070

Parameters:

Name	Type	Description
`bytes`	jspb.ByteSource	The bytes to deserialize.

Returns:

Type: proto.org.phenopackets.schema.v1.core.Biosample

(static) deserializeBinaryFromReader(msgnon-null, readernon-null) → (non-null) {proto.org.phenopackets.schema.v1.core.Biosample}

Description:

Deserializes binary data (in protobuf wire format) from the given reader into the given message object.

Source:

phenopackets/schema/v1/base_pb.js, line 3084

Parameters:

Name	Type	Description
`msg`	proto.org.phenopackets.schema.v1.core.Biosample	The message object to deserialize into.
`reader`	jspb.BinaryReader	The BinaryReader to use.

Returns:

Type: proto.org.phenopackets.schema.v1.core.Biosample

(static) serializeBinaryToWriter(messagenon-null, writernon-null)

Description:

Serializes the given message to binary data (in protobuf wire format), writing to the given BinaryWriter.

Source:

phenopackets/schema/v1/base_pb.js, line 3194

Parameters:

Name	Type	Description
`message`	proto.org.phenopackets.schema.v1.core.Biosample
`writer`	jspb.BinaryWriter

(static) toObject(includeInstance, msgnon-null) → (non-null) {Object}

Description:

Static version of the {@see toObject} method.

Source:

phenopackets/schema/v1/base_pb.js, line 3033

Parameters:

Name	Type	Description
`includeInstance`	boolean \| undefined	Deprecated. Whether to include the JSPB instance for transitional soy proto support: http://goto/soy-param-migration
`msg`	proto.org.phenopackets.schema.v1.core.Biosample	The msg instance to transform.

Returns:

Type: Object