Package org.hl7.fhir.r4.model

Class MolecularSequence

java.lang.Object
org.hl7.fhir.r4.model.Base
org.hl7.fhir.r4.model.BaseResource
org.hl7.fhir.r4.model.Resource
org.hl7.fhir.r4.model.DomainResource
org.hl7.fhir.r4.model.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:

  • Field Details

    • identifier

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

    • type

      protected Enumeration<MolecularSequence.SequenceType> type
      Amino Acid Sequence/ DNA Sequence / RNA Sequence.

    • 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.)

    • specimen

      protected Reference specimen
      Specimen used for sequencing.

    • 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).

    • referenceSeq

      protected MolecularSequence.MolecularSequenceReferenceSeqComponent referenceSeq
      A sequence that is used as a reference to describe variants that are present in a sequence analyzed.

    • 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.

    • quality

      protected List<MolecularSequence.MolecularSequenceQualityComponent> quality
      An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686)).

    • readCoverage

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

    • repository

      protected List<MolecularSequence.MolecularSequenceRepositoryComponent> repository
      Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.

    • 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.)

    • structureVariant

      protected List<MolecularSequence.MolecularSequenceStructureVariantComponent> structureVariant
      Information about chromosome structure variation.

    • 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:

    • 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 invalid input: '<'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:

    • 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 invalid input: '<'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:

    • 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:

    • 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:

    • 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:

    • 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:

    • 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 invalid input: '<'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:

    • 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 invalid input: '<'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:

    • 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:

    • 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 invalid input: '<'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:

    • 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 invalid input: '<'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 invalid input: '<'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:

    • 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 invalid input: '<'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:

    • 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

  • Constructor Details

  • Method Details