Package com.babylonhealth.lit.hl7_java.builders

Class MolecularSequenceBuilder.Impl

    • Constructor Detail

      • Impl

        public Impl​(java.lang.Integer coordinateSystem)
        Required fields for MolecularSequence
        Parameters:
        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).

    • Method Detail

      • withId

        public MolecularSequenceBuilder.Impl withId​(@NonNull
                                            @NonNull java.lang.String id)
        Parameters:
        id - - The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.

      • withMeta

        public MolecularSequenceBuilder.Impl withMeta​(@NonNull
                                              @NonNull com.babylonhealth.lit.core.model.Meta meta)
        Parameters:
        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.

      • withText

        public MolecularSequenceBuilder.Impl withText​(@NonNull
                                              @NonNull com.babylonhealth.lit.hl7.model.Narrative text)
        Parameters:
        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.

      • withType

        public MolecularSequenceBuilder.Impl withType​(@NonNull
                                              @NonNull com.babylonhealth.lit.hl7.SEQUENCE_TYPE _type)
        Parameters:
        _type - - Amino Acid Sequence/ DNA Sequence / RNA Sequence.

      • withDevice

        public MolecularSequenceBuilder.Impl withDevice​(@NonNull
                                                @NonNull com.babylonhealth.lit.core.model.Reference device)
        Parameters:
        device - - The method for sequencing, for example, chip information.

      • withDevice

        public MolecularSequenceBuilder.Impl withDevice​(@NonNull
                                                @NonNull com.babylonhealth.lit.core_java.builders.ReferenceBuilder device)

      • withPatient

        public MolecularSequenceBuilder.Impl withPatient​(@NonNull
                                                 @NonNull com.babylonhealth.lit.core.model.Reference patient)
        Parameters:
        patient - - The patient whose sequencing results are described by this resource.

      • withPatient

        public MolecularSequenceBuilder.Impl withPatient​(@NonNull
                                                 @NonNull com.babylonhealth.lit.core_java.builders.ReferenceBuilder patient)

      • withPointer

        public MolecularSequenceBuilder.Impl withPointer​(@NonNull
                                                 @NonNull com.babylonhealth.lit.core.model.Reference... pointer)
        Parameters:
        pointer - - Pointer to next atomic sequence which at most contains one variant.

      • withPointer

        public MolecularSequenceBuilder.Impl withPointer​(@NonNull
                                                 @NonNull java.util.Collection<com.babylonhealth.lit.core.model.Reference> pointer)
        Parameters:
        pointer - - Pointer to next atomic sequence which at most contains one variant.

      • withPointer

        public MolecularSequenceBuilder.Impl withPointer​(@NonNull
                                                 @NonNull com.babylonhealth.lit.core_java.builders.ReferenceBuilder... pointer)

      • withLanguage

        public MolecularSequenceBuilder.Impl withLanguage​(@NonNull
                                                  @NonNull com.babylonhealth.lit.core.LANGUAGES language)
        Parameters:
        language - - The base language in which the resource is written.

      • withSpecimen

        public MolecularSequenceBuilder.Impl withSpecimen​(@NonNull
                                                  @NonNull com.babylonhealth.lit.core.model.Reference specimen)
        Parameters:
        specimen - - Specimen used for sequencing.

      • withSpecimen

        public MolecularSequenceBuilder.Impl withSpecimen​(@NonNull
                                                  @NonNull com.babylonhealth.lit.core_java.builders.ReferenceBuilder specimen)

      • withQuantity

        public MolecularSequenceBuilder.Impl withQuantity​(@NonNull
                                                  @NonNull com.babylonhealth.lit.core.model.Quantity quantity)
        Parameters:
        quantity - - The number of copies of the sequence of interest. (RNASeq).

      • withQuantity

        public MolecularSequenceBuilder.Impl withQuantity​(@NonNull
                                                  @NonNull com.babylonhealth.lit.core_java.builders.QuantityBuilder quantity)

      • withContained

        public MolecularSequenceBuilder.Impl withContained​(@NonNull
                                                   @NonNull com.babylonhealth.lit.core.model.Resource... contained)
        Parameters:
        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.

      • withContained

        public MolecularSequenceBuilder.Impl withContained​(@NonNull
                                                   @NonNull java.util.Collection<com.babylonhealth.lit.core.model.Resource> contained)
        Parameters:
        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.

      • withContained

        public MolecularSequenceBuilder.Impl withContained​(@NonNull
                                                   @NonNull com.babylonhealth.lit.core_java.builders.ResourceBuilder... contained)

      • withExtension

        public MolecularSequenceBuilder.Impl withExtension​(@NonNull
                                                   @NonNull com.babylonhealth.lit.core.model.Extension... extension)
        Parameters:
        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.

      • withExtension

        public MolecularSequenceBuilder.Impl withExtension​(@NonNull
                                                   @NonNull java.util.Collection<com.babylonhealth.lit.core.model.Extension> extension)
        Parameters:
        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.

      • withExtension

        public MolecularSequenceBuilder.Impl withExtension​(@NonNull
                                                   @NonNull com.babylonhealth.lit.core_java.builders.ExtensionBuilder... extension)

      • withPerformer

        public MolecularSequenceBuilder.Impl withPerformer​(@NonNull
                                                   @NonNull com.babylonhealth.lit.core.model.Reference performer)
        Parameters:
        performer - - The organization or lab that should be responsible for this result.

      • withPerformer

        public MolecularSequenceBuilder.Impl withPerformer​(@NonNull
                                                   @NonNull com.babylonhealth.lit.core_java.builders.ReferenceBuilder performer)

      • withIdentifier

        public MolecularSequenceBuilder.Impl withIdentifier​(@NonNull
                                                    @NonNull com.babylonhealth.lit.core.model.Identifier... identifier)
        Parameters:
        identifier - - A unique identifier for this particular sequence instance. This is a FHIR-defined id.

      • withIdentifier

        public MolecularSequenceBuilder.Impl withIdentifier​(@NonNull
                                                    @NonNull java.util.Collection<com.babylonhealth.lit.core.model.Identifier> identifier)
        Parameters:
        identifier - - A unique identifier for this particular sequence instance. This is a FHIR-defined id.

      • withIdentifier

        public MolecularSequenceBuilder.Impl withIdentifier​(@NonNull
                                                    @NonNull com.babylonhealth.lit.core_java.builders.IdentifierBuilder... identifier)

      • withObservedSeq

        public MolecularSequenceBuilder.Impl withObservedSeq​(@NonNull
                                                     @NonNull java.lang.String observedSeq)
        Parameters:
        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.

      • withReadCoverage

        public MolecularSequenceBuilder.Impl withReadCoverage​(@NonNull
                                                      @NonNull java.lang.Integer readCoverage)
        Parameters:
        readCoverage - - Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.

      • withImplicitRules

        public MolecularSequenceBuilder.Impl withImplicitRules​(@NonNull
                                                       @NonNull java.lang.String implicitRules)
        Parameters:
        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.

      • withModifierExtension

        public MolecularSequenceBuilder.Impl withModifierExtension​(@NonNull
                                                           @NonNull com.babylonhealth.lit.core.model.Extension... modifierExtension)
        Parameters:
        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).

      • withModifierExtension

        public MolecularSequenceBuilder.Impl withModifierExtension​(@NonNull
                                                           @NonNull java.util.Collection<com.babylonhealth.lit.core.model.Extension> modifierExtension)
        Parameters:
        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).

      • withModifierExtension

        public MolecularSequenceBuilder.Impl withModifierExtension​(@NonNull
                                                           @NonNull com.babylonhealth.lit.core_java.builders.ExtensionBuilder... modifierExtension)

      • withVariant

        public MolecularSequenceBuilder.Impl withVariant​(@NonNull
                                                 @NonNull com.babylonhealth.lit.hl7.model.MolecularSequence.Variant... variant)
        Parameters:
        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.

      • withVariant

        public MolecularSequenceBuilder.Impl withVariant​(@NonNull
                                                 @NonNull java.util.Collection<com.babylonhealth.lit.hl7.model.MolecularSequence.Variant> variant)
        Parameters:
        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.

      • withRepository

        public MolecularSequenceBuilder.Impl withRepository​(@NonNull
                                                    @NonNull com.babylonhealth.lit.hl7.model.MolecularSequence.Repository... repository)
        Parameters:
        repository - - Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.

      • withRepository

        public MolecularSequenceBuilder.Impl withRepository​(@NonNull
                                                    @NonNull java.util.Collection<com.babylonhealth.lit.hl7.model.MolecularSequence.Repository> repository)
        Parameters:
        repository - - Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq.

      • withQuality

        public MolecularSequenceBuilder.Impl withQuality​(@NonNull
                                                 @NonNull com.babylonhealth.lit.hl7.model.MolecularSequence.Quality... quality)
        Parameters:
        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)).

      • withQuality

        public MolecularSequenceBuilder.Impl withQuality​(@NonNull
                                                 @NonNull java.util.Collection<com.babylonhealth.lit.hl7.model.MolecularSequence.Quality> quality)
        Parameters:
        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)).

      • withReferenceSeq

        public MolecularSequenceBuilder.Impl withReferenceSeq​(@NonNull
                                                      com.babylonhealth.lit.hl7.model.MolecularSequence.ReferenceSeq referenceSeq)
        Parameters:
        referenceSeq - - A sequence that is used as a reference to describe variants that are present in a sequence analyzed.

      • withStructureVariant

        public MolecularSequenceBuilder.Impl withStructureVariant​(@NonNull
                                                          @NonNull com.babylonhealth.lit.hl7.model.MolecularSequence.StructureVariant... structureVariant)
        Parameters:
        structureVariant - - Information about chromosome structure variation.

      • withStructureVariant

        public MolecularSequenceBuilder.Impl withStructureVariant​(@NonNull
                                                          @NonNull java.util.Collection<com.babylonhealth.lit.hl7.model.MolecularSequence.StructureVariant> structureVariant)
        Parameters:
        structureVariant - - Information about chromosome structure variation.

      • build

        public com.babylonhealth.lit.hl7.model.MolecularSequence build()
        Specified by:
        build in interface DomainResourceBuilder
        Specified by:
        build in interface MolecularSequenceBuilder
        Specified by:
        build in interface com.babylonhealth.lit.core_java.builders.ResourceBuilder