Package com.ibm.fhir.model.resource

Class MolecularSequence.Builder

    • Method Detail

      • id

        public MolecularSequence.Builder id​(java.lang.String id)
        The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.
        Overrides:
        id in class DomainResource.Builder
        Parameters:
        id - Logical id of this artifact
        Returns:
        A reference to this Builder instance

      • meta

        public MolecularSequence.Builder meta​(Meta meta)
        The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource.
        Overrides:
        meta in class DomainResource.Builder
        Parameters:
        meta - Metadata about the resource
        Returns:
        A reference to this Builder instance

      • implicitRules

        public MolecularSequence.Builder implicitRules​(Uri implicitRules)
        A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc.
        Overrides:
        implicitRules in class DomainResource.Builder
        Parameters:
        implicitRules - A set of rules under which this content was created
        Returns:
        A reference to this Builder instance

      • text

        public MolecularSequence.Builder text​(Narrative text)
        A human-readable narrative that contains a summary of the resource and can be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it "clinically safe" for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety.
        Overrides:
        text in class DomainResource.Builder
        Parameters:
        text - Text summary of the resource, for human interpretation
        Returns:
        A reference to this Builder instance

      • contained

        public MolecularSequence.Builder contained​(Resource... contained)
        These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope.

        Adds new element(s) to the existing list. If any of the elements are null, calling build() will fail.

        Overrides:
        contained in class DomainResource.Builder
        Parameters:
        contained - Contained, inline Resources
        Returns:
        A reference to this Builder instance

      • contained

        public MolecularSequence.Builder contained​(java.util.Collection<Resource> contained)
        These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope.

        Replaces the existing list with a new one containing elements from the Collection. If any of the elements are null, calling build() will fail.

        Overrides:
        contained in class DomainResource.Builder
        Parameters:
        contained - Contained, inline Resources
        Returns:
        A reference to this Builder instance
        Throws:
        java.lang.NullPointerException - If the passed collection is null

      • extension

        public MolecularSequence.Builder extension​(Extension... extension)
        May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

        Adds new element(s) to the existing list. If any of the elements are null, calling build() will fail.

        Overrides:
        extension in class DomainResource.Builder
        Parameters:
        extension - Additional content defined by implementations
        Returns:
        A reference to this Builder instance

      • extension

        public MolecularSequence.Builder extension​(java.util.Collection<Extension> extension)
        May be used to represent additional information that is not part of the basic definition of the resource. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer can define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension.

        Replaces the existing list with a new one containing elements from the Collection. If any of the elements are null, calling build() will fail.

        Overrides:
        extension in class DomainResource.Builder
        Parameters:
        extension - Additional content defined by implementations
        Returns:
        A reference to this Builder instance
        Throws:
        java.lang.NullPointerException - If the passed collection is null

      • modifierExtension

        public MolecularSequence.Builder modifierExtension​(Extension... modifierExtension)
        May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

        Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

        Adds new element(s) to the existing list. If any of the elements are null, calling build() will fail.

        Overrides:
        modifierExtension in class DomainResource.Builder
        Parameters:
        modifierExtension - Extensions that cannot be ignored
        Returns:
        A reference to this Builder instance

      • modifierExtension

        public MolecularSequence.Builder modifierExtension​(java.util.Collection<Extension> modifierExtension)
        May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. To make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions.

        Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself).

        Replaces the existing list with a new one containing elements from the Collection. If any of the elements are null, calling build() will fail.

        Overrides:
        modifierExtension in class DomainResource.Builder
        Parameters:
        modifierExtension - Extensions that cannot be ignored
        Returns:
        A reference to this Builder instance
        Throws:
        java.lang.NullPointerException - If the passed collection is null

      • identifier

        public MolecularSequence.Builder identifier​(Identifier... identifier)
        A unique identifier for this particular sequence instance. This is a FHIR-defined id.

        Adds new element(s) to the existing list. If any of the elements are null, calling build() will fail.

        Parameters:
        identifier - Unique ID for this particular sequence. This is a FHIR-defined id
        Returns:
        A reference to this Builder instance

      • identifier

        public MolecularSequence.Builder identifier​(java.util.Collection<Identifier> identifier)
        A unique identifier for this particular sequence instance. This is a FHIR-defined id.

        Replaces the existing list with a new one containing elements from the Collection. If any of the elements are null, calling build() will fail.

        Parameters:
        identifier - Unique ID for this particular sequence. This is a FHIR-defined id
        Returns:
        A reference to this Builder instance
        Throws:
        java.lang.NullPointerException - If the passed collection is null

      • type

        public MolecularSequence.Builder type​(SequenceType type)
        Amino Acid Sequence/ DNA Sequence / RNA Sequence.
        Parameters:
        type - aa | dna | rna
        Returns:
        A reference to this Builder instance

      • coordinateSystem

        public MolecularSequence.Builder coordinateSystem​(java.lang.Integer coordinateSystem)
        Convenience method for setting coordinateSystem.

        This element is required.

        Parameters:
        coordinateSystem - Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1- based numbering, inclusive start, inclusive end)
        Returns:
        A reference to this Builder instance
        See Also:
        coordinateSystem(com.ibm.fhir.model.type.Integer)

      • coordinateSystem

        public MolecularSequence.Builder coordinateSystem​(Integer 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).

        This element is required.

        Parameters:
        coordinateSystem - Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1- based numbering, inclusive start, inclusive end)
        Returns:
        A reference to this Builder instance

      • patient

        public MolecularSequence.Builder patient​(Reference patient)
        The patient whose sequencing results are described by this resource.

        Allowed resource types for this reference:

        Parameters:
        patient - Who and/or what this is about
        Returns:
        A reference to this Builder instance

      • specimen

        public MolecularSequence.Builder specimen​(Reference specimen)
        Specimen used for sequencing.

        Allowed resource types for this reference:

        Parameters:
        specimen - Specimen used for sequencing
        Returns:
        A reference to this Builder instance

      • device

        public MolecularSequence.Builder device​(Reference device)
        The method for sequencing, for example, chip information.

        Allowed resource types for this reference:

        Parameters:
        device - The method for sequencing
        Returns:
        A reference to this Builder instance

      • performer

        public MolecularSequence.Builder performer​(Reference performer)
        The organization or lab that should be responsible for this result.

        Allowed resource types for this reference:

        Parameters:
        performer - Who should be responsible for test result
        Returns:
        A reference to this Builder instance

      • quantity

        public MolecularSequence.Builder quantity​(Quantity quantity)
        The number of copies of the sequence of interest. (RNASeq).
        Parameters:
        quantity - The number of copies of the sequence of interest. (RNASeq)
        Returns:
        A reference to this Builder instance

      • referenceSeq

        public MolecularSequence.Builder referenceSeq​(MolecularSequence.ReferenceSeq referenceSeq)
        A sequence that is used as a reference to describe variants that are present in a sequence analyzed.
        Parameters:
        referenceSeq - A sequence used as reference
        Returns:
        A reference to this Builder instance

      • variant

        public MolecularSequence.Builder variant​(MolecularSequence.Variant... 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.

        Adds new element(s) to the existing list. If any of the elements are null, calling build() will fail.

        Parameters:
        variant - Variant in sequence
        Returns:
        A reference to this Builder instance

      • variant

        public MolecularSequence.Builder variant​(java.util.Collection<MolecularSequence.Variant> 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.

        Replaces the existing list with a new one containing elements from the Collection. If any of the elements are null, calling build() will fail.

        Parameters:
        variant - Variant in sequence
        Returns:
        A reference to this Builder instance
        Throws:
        java.lang.NullPointerException - If the passed collection is null

      • observedSeq

        public MolecularSequence.Builder observedSeq​(String 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.
        Parameters:
        observedSeq - Sequence that was observed
        Returns:
        A reference to this Builder instance

      • quality

        public MolecularSequence.Builder quality​(MolecularSequence.Quality... 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)).

        Adds new element(s) to the existing list. If any of the elements are null, calling build() will fail.

        Parameters:
        quality - An set of value as quality of sequence
        Returns:
        A reference to this Builder instance

      • quality

        public MolecularSequence.Builder quality​(java.util.Collection<MolecularSequence.Quality> 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)).

        Replaces the existing list with a new one containing elements from the Collection. If any of the elements are null, calling build() will fail.

        Parameters:
        quality - An set of value as quality of sequence
        Returns:
        A reference to this Builder instance
        Throws:
        java.lang.NullPointerException - If the passed collection is null

      • readCoverage

        public MolecularSequence.Builder readCoverage​(java.lang.Integer readCoverage)
        Convenience method for setting readCoverage.
        Parameters:
        readCoverage - Average number of reads representing a given nucleotide in the reconstructed sequence
        Returns:
        A reference to this Builder instance
        See Also:
        readCoverage(com.ibm.fhir.model.type.Integer)

      • readCoverage

        public MolecularSequence.Builder readCoverage​(Integer readCoverage)
        Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.
        Parameters:
        readCoverage - Average number of reads representing a given nucleotide in the reconstructed sequence
        Returns:
        A reference to this Builder instance

      • repository

        public MolecularSequence.Builder repository​(MolecularSequence.Repository... repository)
        Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.

        Adds new element(s) to the existing list. If any of the elements are null, calling build() will fail.

        Parameters:
        repository - External repository which contains detailed report related with observedSeq in this resource
        Returns:
        A reference to this Builder instance

      • repository

        public MolecularSequence.Builder repository​(java.util.Collection<MolecularSequence.Repository> repository)
        Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.

        Replaces the existing list with a new one containing elements from the Collection. If any of the elements are null, calling build() will fail.

        Parameters:
        repository - External repository which contains detailed report related with observedSeq in this resource
        Returns:
        A reference to this Builder instance
        Throws:
        java.lang.NullPointerException - If the passed collection is null

      • pointer

        public MolecularSequence.Builder pointer​(Reference... pointer)
        Pointer to next atomic sequence which at most contains one variant.

        Adds new element(s) to the existing list. If any of the elements are null, calling build() will fail.

        Allowed resource types for the references:

        Parameters:
        pointer - Pointer to next atomic sequence
        Returns:
        A reference to this Builder instance

      • pointer

        public MolecularSequence.Builder pointer​(java.util.Collection<Reference> pointer)
        Pointer to next atomic sequence which at most contains one variant.

        Replaces the existing list with a new one containing elements from the Collection. If any of the elements are null, calling build() will fail.

        Allowed resource types for the references:

        Parameters:
        pointer - Pointer to next atomic sequence
        Returns:
        A reference to this Builder instance
        Throws:
        java.lang.NullPointerException - If the passed collection is null

      • structureVariant

        public MolecularSequence.Builder structureVariant​(MolecularSequence.StructureVariant... structureVariant)
        Information about chromosome structure variation.

        Adds new element(s) to the existing list. If any of the elements are null, calling build() will fail.

        Parameters:
        structureVariant - Structural variant
        Returns:
        A reference to this Builder instance

      • structureVariant

        public MolecularSequence.Builder structureVariant​(java.util.Collection<MolecularSequence.StructureVariant> structureVariant)
        Information about chromosome structure variation.

        Replaces the existing list with a new one containing elements from the Collection. If any of the elements are null, calling build() will fail.

        Parameters:
        structureVariant - Structural variant
        Returns:
        A reference to this Builder instance
        Throws:
        java.lang.NullPointerException - If the passed collection is null