Package org.hl7.fhir.r4.model

Class MolecularSequence

  • All Implemented Interfaces:
    ca.uhn.fhir.model.api.IElement, Serializable, org.hl7.fhir.instance.model.api.IAnyResource, org.hl7.fhir.instance.model.api.IBase, org.hl7.fhir.instance.model.api.IBaseHasExtensions, org.hl7.fhir.instance.model.api.IBaseHasModifierExtensions, org.hl7.fhir.instance.model.api.IBaseResource, org.hl7.fhir.instance.model.api.IDomainResource
    public class MolecularSequence
extends DomainResource
    Raw data describing a biological sequence.
    See Also:
    Serialized Form

    • Field Detail

      • identifier

        protected List<Identifier> identifier
        A unique identifier for this particular sequence instance. This is a FHIR-defined id.

      • coordinateSystem

        protected IntegerType coordinateSystem
        Whether the sequence is numbered starting at 0 (0-based numbering or coordinates, inclusive start, exclusive end) or starting at 1 (1-based numbering, inclusive start and inclusive end).

      • patient

        protected Reference patient
        The patient whose sequencing results are described by this resource.

      • patientTarget

        protected Patient patientTarget
        The actual object that is the target of the reference (The patient whose sequencing results are described by this resource.)

      • specimenTarget

        protected Specimen specimenTarget
        The actual object that is the target of the reference (Specimen used for sequencing.)

      • device

        protected Reference device
        The method for sequencing, for example, chip information.

      • deviceTarget

        protected Device deviceTarget
        The actual object that is the target of the reference (The method for sequencing, for example, chip information.)

      • performer

        protected Reference performer
        The organization or lab that should be responsible for this result.

      • performerTarget

        protected Organization performerTarget
        The actual object that is the target of the reference (The organization or lab that should be responsible for this result.)

      • quantity

        protected Quantity quantity
        The number of copies of the sequence of interest. (RNASeq).

      • variant

        protected List<MolecularSequence.MolecularSequenceVariantComponent> variant
        The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.) It can represent some complex mutation or segment variation with the assist of CIGAR string.

      • observedSeq

        protected StringType observedSeq
        Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall start from referenceSeq.windowStart and end by referenceSeq.windowEnd.

      • readCoverage

        protected IntegerType readCoverage
        Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.

      • pointer

        protected List<Reference> pointer
        Pointer to next atomic sequence which at most contains one variant.

      • pointerTarget

        protected List<MolecularSequence> pointerTarget
        The actual objects that are the target of the reference (Pointer to next atomic sequence which at most contains one variant.)

      • SP_IDENTIFIER

        public static final String SP_IDENTIFIER
        Search parameter: identifier

        Description: The unique identity for a particular sequence
        Type: token
        Path: MolecularSequence.identifier

        See Also:
        Constant Field Values

      • IDENTIFIER

        public static final ca.uhn.fhir.rest.gclient.TokenClientParam IDENTIFIER
        Fluent Client search parameter constant for identifier

        Description: The unique identity for a particular sequence
        Type: token
        Path: MolecularSequence.identifier

      • SP_REFERENCESEQID_VARIANT_COORDINATE

        public static final String SP_REFERENCESEQID_VARIANT_COORDINATE
        Search parameter: referenceseqid-variant-coordinate

        Description: Search parameter by reference sequence and variant coordinate. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `referenceSeqId-variant-coordinate=NC_000001.11$lt345$gt123`, this means it will search for the MolecularSequence resource with variants on NC_000001.11 and with position >123 and <345, where in 1-based system resource, all strings within region NC_000001.11:124-344 will be revealed, while in 0-based system resource, all strings within region NC_000001.11:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.
        Type: composite
        Path:

        See Also:
        Constant Field Values

      • REFERENCESEQID_VARIANT_COORDINATE

        public static final ca.uhn.fhir.rest.gclient.CompositeClientParam<ca.uhn.fhir.rest.gclient.TokenClientParam,​ca.uhn.fhir.rest.gclient.NumberClientParam> REFERENCESEQID_VARIANT_COORDINATE
        Fluent Client search parameter constant for referenceseqid-variant-coordinate

        Description: Search parameter by reference sequence and variant coordinate. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `referenceSeqId-variant-coordinate=NC_000001.11$lt345$gt123`, this means it will search for the MolecularSequence resource with variants on NC_000001.11 and with position >123 and <345, where in 1-based system resource, all strings within region NC_000001.11:124-344 will be revealed, while in 0-based system resource, all strings within region NC_000001.11:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.
        Type: composite
        Path:

      • SP_CHROMOSOME

        public static final String SP_CHROMOSOME
        Search parameter: chromosome

        Description: Chromosome number of the reference sequence
        Type: token
        Path: MolecularSequence.referenceSeq.chromosome

        See Also:
        Constant Field Values

      • CHROMOSOME

        public static final ca.uhn.fhir.rest.gclient.TokenClientParam CHROMOSOME
        Fluent Client search parameter constant for chromosome

        Description: Chromosome number of the reference sequence
        Type: token
        Path: MolecularSequence.referenceSeq.chromosome

      • SP_WINDOW_END

        public static final String SP_WINDOW_END
        Search parameter: window-end

        Description: End position (0-based exclusive, which menas the acid at this position will not be included, 1-based inclusive, which means the acid at this position will be included) of the reference sequence.
        Type: number
        Path: MolecularSequence.referenceSeq.windowEnd

        See Also:
        Constant Field Values

      • WINDOW_END

        public static final ca.uhn.fhir.rest.gclient.NumberClientParam WINDOW_END
        Fluent Client search parameter constant for window-end

        Description: End position (0-based exclusive, which menas the acid at this position will not be included, 1-based inclusive, which means the acid at this position will be included) of the reference sequence.
        Type: number
        Path: MolecularSequence.referenceSeq.windowEnd

      • SP_TYPE

        public static final String SP_TYPE
        Search parameter: type

        Description: Amino Acid Sequence/ DNA Sequence / RNA Sequence
        Type: token
        Path: MolecularSequence.type

        See Also:
        Constant Field Values

      • TYPE

        public static final ca.uhn.fhir.rest.gclient.TokenClientParam TYPE
        Fluent Client search parameter constant for type

        Description: Amino Acid Sequence/ DNA Sequence / RNA Sequence
        Type: token
        Path: MolecularSequence.type

      • SP_WINDOW_START

        public static final String SP_WINDOW_START
        Search parameter: window-start

        Description: Start position (0-based inclusive, 1-based inclusive, that means the nucleic acid or amino acid at this position will be included) of the reference sequence.
        Type: number
        Path: MolecularSequence.referenceSeq.windowStart

        See Also:
        Constant Field Values

      • WINDOW_START

        public static final ca.uhn.fhir.rest.gclient.NumberClientParam WINDOW_START
        Fluent Client search parameter constant for window-start

        Description: Start position (0-based inclusive, 1-based inclusive, that means the nucleic acid or amino acid at this position will be included) of the reference sequence.
        Type: number
        Path: MolecularSequence.referenceSeq.windowStart

      • SP_VARIANT_END

        public static final String SP_VARIANT_END
        Search parameter: variant-end

        Description: End position (0-based exclusive, which menas the acid at this position will not be included, 1-based inclusive, which means the acid at this position will be included) of the variant.
        Type: number
        Path: MolecularSequence.variant.end

        See Also:
        Constant Field Values

      • VARIANT_END

        public static final ca.uhn.fhir.rest.gclient.NumberClientParam VARIANT_END
        Fluent Client search parameter constant for variant-end

        Description: End position (0-based exclusive, which menas the acid at this position will not be included, 1-based inclusive, which means the acid at this position will be included) of the variant.
        Type: number
        Path: MolecularSequence.variant.end

      • SP_CHROMOSOME_VARIANT_COORDINATE

        public static final String SP_CHROMOSOME_VARIANT_COORDINATE
        Search parameter: chromosome-variant-coordinate

        Description: Search parameter by chromosome and variant coordinate. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `chromosome-variant-coordinate=1$lt345$gt123`, this means it will search for the MolecularSequence resource with variants on chromosome 1 and with position >123 and <345, where in 1-based system resource, all strings within region 1:124-344 will be revealed, while in 0-based system resource, all strings within region 1:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.
        Type: composite
        Path:

        See Also:
        Constant Field Values

      • CHROMOSOME_VARIANT_COORDINATE

        public static final ca.uhn.fhir.rest.gclient.CompositeClientParam<ca.uhn.fhir.rest.gclient.TokenClientParam,​ca.uhn.fhir.rest.gclient.NumberClientParam> CHROMOSOME_VARIANT_COORDINATE
        Fluent Client search parameter constant for chromosome-variant-coordinate

        Description: Search parameter by chromosome and variant coordinate. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `chromosome-variant-coordinate=1$lt345$gt123`, this means it will search for the MolecularSequence resource with variants on chromosome 1 and with position >123 and <345, where in 1-based system resource, all strings within region 1:124-344 will be revealed, while in 0-based system resource, all strings within region 1:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.
        Type: composite
        Path:

      • SP_PATIENT

        public static final String SP_PATIENT
        Search parameter: patient

        Description: The subject that the observation is about
        Type: reference
        Path: MolecularSequence.patient

        See Also:
        Constant Field Values

      • PATIENT

        public static final ca.uhn.fhir.rest.gclient.ReferenceClientParam PATIENT
        Fluent Client search parameter constant for patient

        Description: The subject that the observation is about
        Type: reference
        Path: MolecularSequence.patient

      • INCLUDE_PATIENT

        public static final ca.uhn.fhir.model.api.Include INCLUDE_PATIENT
        Constant for fluent queries to be used to add include statements. Specifies the path value of "MolecularSequence:patient".

      • SP_VARIANT_START

        public static final String SP_VARIANT_START
        Search parameter: variant-start

        Description: Start position (0-based inclusive, 1-based inclusive, that means the nucleic acid or amino acid at this position will be included) of the variant.
        Type: number
        Path: MolecularSequence.variant.start

        See Also:
        Constant Field Values

      • VARIANT_START

        public static final ca.uhn.fhir.rest.gclient.NumberClientParam VARIANT_START
        Fluent Client search parameter constant for variant-start

        Description: Start position (0-based inclusive, 1-based inclusive, that means the nucleic acid or amino acid at this position will be included) of the variant.
        Type: number
        Path: MolecularSequence.variant.start

      • SP_CHROMOSOME_WINDOW_COORDINATE

        public static final String SP_CHROMOSOME_WINDOW_COORDINATE
        Search parameter: chromosome-window-coordinate

        Description: Search parameter by chromosome and window. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `chromosome-window-coordinate=1$lt345$gt123`, this means it will search for the MolecularSequence resource with a window on chromosome 1 and with position >123 and <345, where in 1-based system resource, all strings within region 1:124-344 will be revealed, while in 0-based system resource, all strings within region 1:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.
        Type: composite
        Path:

        See Also:
        Constant Field Values

      • CHROMOSOME_WINDOW_COORDINATE

        public static final ca.uhn.fhir.rest.gclient.CompositeClientParam<ca.uhn.fhir.rest.gclient.TokenClientParam,​ca.uhn.fhir.rest.gclient.NumberClientParam> CHROMOSOME_WINDOW_COORDINATE
        Fluent Client search parameter constant for chromosome-window-coordinate

        Description: Search parameter by chromosome and window. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `chromosome-window-coordinate=1$lt345$gt123`, this means it will search for the MolecularSequence resource with a window on chromosome 1 and with position >123 and <345, where in 1-based system resource, all strings within region 1:124-344 will be revealed, while in 0-based system resource, all strings within region 1:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.
        Type: composite
        Path:

      • SP_REFERENCESEQID_WINDOW_COORDINATE

        public static final String SP_REFERENCESEQID_WINDOW_COORDINATE
        Search parameter: referenceseqid-window-coordinate

        Description: Search parameter by reference sequence and window. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `referenceSeqId-window-coordinate=NC_000001.11$lt345$gt123`, this means it will search for the MolecularSequence resource with a window on NC_000001.11 and with position >123 and <345, where in 1-based system resource, all strings within region NC_000001.11:124-344 will be revealed, while in 0-based system resource, all strings within region NC_000001.11:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.
        Type: composite
        Path:

        See Also:
        Constant Field Values

      • REFERENCESEQID_WINDOW_COORDINATE

        public static final ca.uhn.fhir.rest.gclient.CompositeClientParam<ca.uhn.fhir.rest.gclient.TokenClientParam,​ca.uhn.fhir.rest.gclient.NumberClientParam> REFERENCESEQID_WINDOW_COORDINATE
        Fluent Client search parameter constant for referenceseqid-window-coordinate

        Description: Search parameter by reference sequence and window. This will refer to part of a locus or part of a gene where search region will be represented in 1-based system. Since the coordinateSystem can either be 0-based or 1-based, this search query will include the result of both coordinateSystem that contains the equivalent segment of the gene or whole genome sequence. For example, a search for sequence can be represented as `referenceSeqId-window-coordinate=NC_000001.11$lt345$gt123`, this means it will search for the MolecularSequence resource with a window on NC_000001.11 and with position >123 and <345, where in 1-based system resource, all strings within region NC_000001.11:124-344 will be revealed, while in 0-based system resource, all strings within region NC_000001.11:123-344 will be revealed. You may want to check detail about 0-based v.s. 1-based above.
        Type: composite
        Path:

      • SP_REFERENCESEQID

        public static final String SP_REFERENCESEQID
        Search parameter: referenceseqid

        Description: Reference Sequence of the sequence
        Type: token
        Path: MolecularSequence.referenceSeq.referenceSeqId

        See Also:
        Constant Field Values

      • REFERENCESEQID

        public static final ca.uhn.fhir.rest.gclient.TokenClientParam REFERENCESEQID
        Fluent Client search parameter constant for referenceseqid

        Description: Reference Sequence of the sequence
        Type: token
        Path: MolecularSequence.referenceSeq.referenceSeqId