Class MolecularSequence.Builder
- java.lang.Object
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- org.linuxforhealth.fhir.model.builder.AbstractBuilder<Resource>
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- org.linuxforhealth.fhir.model.resource.Resource.Builder
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- org.linuxforhealth.fhir.model.resource.DomainResource.Builder
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- org.linuxforhealth.fhir.model.resource.MolecularSequence.Builder
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- Enclosing class:
- MolecularSequence
public static class MolecularSequence.Builder extends DomainResource.Builder
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Field Summary
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Fields inherited from class org.linuxforhealth.fhir.model.resource.DomainResource.Builder
contained, extension, modifierExtension, text
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Fields inherited from class org.linuxforhealth.fhir.model.resource.Resource.Builder
id, implicitRules, language, meta
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Fields inherited from class org.linuxforhealth.fhir.model.builder.AbstractBuilder
validating
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description MolecularSequence
build()
Build theMolecularSequence
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.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.MolecularSequence.Builder
coordinateSystem(java.lang.Integer coordinateSystem)
Convenience method for settingcoordinateSystem
.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).MolecularSequence.Builder
device(Reference device)
The method for sequencing, for example, chip information.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.MolecularSequence.Builder
extension(Extension... extension)
May be used to represent additional information that is not part of the basic definition of the resource.protected MolecularSequence.Builder
from(MolecularSequence molecularSequence)
MolecularSequence.Builder
id(java.lang.String id)
The logical id of the resource, as used in the URL for the resource.MolecularSequence.Builder
identifier(java.util.Collection<Identifier> identifier)
A unique identifier for this particular sequence instance.MolecularSequence.Builder
identifier(Identifier... identifier)
A unique identifier for this particular sequence instance.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.MolecularSequence.Builder
language(Code language)
The base language in which the resource is written.MolecularSequence.Builder
meta(Meta meta)
The metadata about the resource.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.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.MolecularSequence.Builder
observedSeq(java.lang.String observedSeq)
Convenience method for settingobservedSeq
.MolecularSequence.Builder
observedSeq(String observedSeq)
Sequence that was observed.MolecularSequence.Builder
patient(Reference patient)
The patient whose sequencing results are described by this resource.MolecularSequence.Builder
performer(Reference performer)
The organization or lab that should be responsible for this result.MolecularSequence.Builder
pointer(java.util.Collection<Reference> pointer)
Pointer to next atomic sequence which at most contains one variant.MolecularSequence.Builder
pointer(Reference... pointer)
Pointer to next atomic sequence which at most contains one variant.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)).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)).MolecularSequence.Builder
quantity(Quantity quantity)
The number of copies of the sequence of interest.MolecularSequence.Builder
readCoverage(java.lang.Integer readCoverage)
Convenience method for settingreadCoverage
.MolecularSequence.Builder
readCoverage(Integer readCoverage)
Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence.MolecularSequence.Builder
referenceSeq(MolecularSequence.ReferenceSeq referenceSeq)
A sequence that is used as a reference to describe variants that are present in a sequence analyzed.MolecularSequence.Builder
repository(java.util.Collection<MolecularSequence.Repository> repository)
Configurations of the external repository.MolecularSequence.Builder
repository(MolecularSequence.Repository... repository)
Configurations of the external repository.MolecularSequence.Builder
specimen(Reference specimen)
Specimen used for sequencing.MolecularSequence.Builder
structureVariant(java.util.Collection<MolecularSequence.StructureVariant> structureVariant)
Information about chromosome structure variation.MolecularSequence.Builder
structureVariant(MolecularSequence.StructureVariant... structureVariant)
Information about chromosome structure variation.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.MolecularSequence.Builder
type(SequenceType type)
Amino Acid Sequence/ DNA Sequence / RNA Sequence.protected void
validate(MolecularSequence molecularSequence)
MolecularSequence.Builder
variant(java.util.Collection<MolecularSequence.Variant> variant)
The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.MolecularSequence.Builder
variant(MolecularSequence.Variant... variant)
The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.-
Methods inherited from class org.linuxforhealth.fhir.model.resource.DomainResource.Builder
from, validate
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Methods inherited from class org.linuxforhealth.fhir.model.resource.Resource.Builder
from, validate
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Methods inherited from class org.linuxforhealth.fhir.model.builder.AbstractBuilder
isValidating, setValidating
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Method Detail
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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 classDomainResource.Builder
- Parameters:
id
- Logical id of this artifact- Returns:
- A reference to this Builder instance
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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 classDomainResource.Builder
- Parameters:
meta
- Metadata about the resource- Returns:
- A reference to this Builder instance
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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 classDomainResource.Builder
- Parameters:
implicitRules
- A set of rules under which this content was created- Returns:
- A reference to this Builder instance
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language
public MolecularSequence.Builder language(Code language)
The base language in which the resource is written.- Overrides:
language
in classDomainResource.Builder
- Parameters:
language
- Language of the resource content- Returns:
- A reference to this Builder instance
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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 classDomainResource.Builder
- Parameters:
text
- Text summary of the resource, for human interpretation- Returns:
- A reference to this Builder instance
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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 classDomainResource.Builder
- Parameters:
contained
- Contained, inline Resources- Returns:
- A reference to this Builder instance
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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 classDomainResource.Builder
- Parameters:
contained
- Contained, inline Resources- Returns:
- A reference to this Builder instance
- Throws:
java.lang.NullPointerException
- If the passed collection is null
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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 classDomainResource.Builder
- Parameters:
extension
- Additional content defined by implementations- Returns:
- A reference to this Builder instance
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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 classDomainResource.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
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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 classDomainResource.Builder
- Parameters:
modifierExtension
- Extensions that cannot be ignored- Returns:
- A reference to this Builder instance
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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 classDomainResource.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
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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
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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
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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
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coordinateSystem
public MolecularSequence.Builder coordinateSystem(java.lang.Integer coordinateSystem)
Convenience method for settingcoordinateSystem
.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(org.linuxforhealth.fhir.model.type.Integer)
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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
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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
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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
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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
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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
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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
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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
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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
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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
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observedSeq
public MolecularSequence.Builder observedSeq(java.lang.String observedSeq)
Convenience method for settingobservedSeq
.- Parameters:
observedSeq
- Sequence that was observed- Returns:
- A reference to this Builder instance
- See Also:
observedSeq(org.linuxforhealth.fhir.model.type.String)
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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
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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
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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
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readCoverage
public MolecularSequence.Builder readCoverage(java.lang.Integer readCoverage)
Convenience method for settingreadCoverage
.- Parameters:
readCoverage
- Average number of reads representing a given nucleotide in the reconstructed sequence- Returns:
- A reference to this Builder instance
- See Also:
readCoverage(org.linuxforhealth.fhir.model.type.Integer)
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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
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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
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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
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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
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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
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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
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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
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build
public MolecularSequence build()
- Specified by:
build
in interfaceBuilder<Resource>
- Specified by:
build
in classDomainResource.Builder
- Returns:
- An immutable object of type
MolecularSequence
- Throws:
java.lang.IllegalStateException
- if the current state cannot be built into a valid MolecularSequence per the base specification
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validate
protected void validate(MolecularSequence molecularSequence)
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from
protected MolecularSequence.Builder from(MolecularSequence molecularSequence)
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