com.ibm.fhir.model.resource.SubstanceProtein Maven / Gradle / Ivy
/*
* (C) Copyright IBM Corp. 2019, 2021
*
* SPDX-License-Identifier: Apache-2.0
*/
package com.ibm.fhir.model.resource;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.util.Objects;
import javax.annotation.Generated;
import com.ibm.fhir.model.annotation.Maturity;
import com.ibm.fhir.model.annotation.Summary;
import com.ibm.fhir.model.type.Attachment;
import com.ibm.fhir.model.type.BackboneElement;
import com.ibm.fhir.model.type.Code;
import com.ibm.fhir.model.type.CodeableConcept;
import com.ibm.fhir.model.type.Extension;
import com.ibm.fhir.model.type.Identifier;
import com.ibm.fhir.model.type.Integer;
import com.ibm.fhir.model.type.Meta;
import com.ibm.fhir.model.type.Narrative;
import com.ibm.fhir.model.type.String;
import com.ibm.fhir.model.type.Uri;
import com.ibm.fhir.model.type.code.StandardsStatus;
import com.ibm.fhir.model.util.ValidationSupport;
import com.ibm.fhir.model.visitor.Visitor;
/**
* A SubstanceProtein is defined as a single unit of a linear amino acid sequence, or a combination of subunits that are
* either covalently linked or have a defined invariant stoichiometric relationship. This includes all synthetic,
* recombinant and purified SubstanceProteins of defined sequence, whether the use is therapeutic or prophylactic. This
* set of elements will be used to describe albumins, coagulation factors, cytokines, growth factors,
* peptide/SubstanceProtein hormones, enzymes, toxins, toxoids, recombinant vaccines, and immunomodulators.
*
* Maturity level: FMM0 (Trial Use)
*/
@Maturity(
level = 0,
status = StandardsStatus.Value.TRIAL_USE
)
@Generated("com.ibm.fhir.tools.CodeGenerator")
public class SubstanceProtein extends DomainResource {
@Summary
private final CodeableConcept sequenceType;
@Summary
private final Integer numberOfSubunits;
@Summary
private final List disulfideLinkage;
@Summary
private final List subunit;
private SubstanceProtein(Builder builder) {
super(builder);
sequenceType = builder.sequenceType;
numberOfSubunits = builder.numberOfSubunits;
disulfideLinkage = Collections.unmodifiableList(builder.disulfideLinkage);
subunit = Collections.unmodifiableList(builder.subunit);
}
/**
* The SubstanceProtein descriptive elements will only be used when a complete or partial amino acid sequence is
* available or derivable from a nucleic acid sequence.
*
* @return
* An immutable object of type {@link CodeableConcept} that may be null.
*/
public CodeableConcept getSequenceType() {
return sequenceType;
}
/**
* Number of linear sequences of amino acids linked through peptide bonds. The number of subunits constituting the
* SubstanceProtein shall be described. It is possible that the number of subunits can be variable.
*
* @return
* An immutable object of type {@link Integer} that may be null.
*/
public Integer getNumberOfSubunits() {
return numberOfSubunits;
}
/**
* The disulphide bond between two cysteine residues either on the same subunit or on two different subunits shall be
* described. The position of the disulfide bonds in the SubstanceProtein shall be listed in increasing order of subunit
* number and position within subunit followed by the abbreviation of the amino acids involved. The disulfide linkage
* positions shall actually contain the amino acid Cysteine at the respective positions.
*
* @return
* An unmodifiable list containing immutable objects of type {@link String} that may be empty.
*/
public List getDisulfideLinkage() {
return disulfideLinkage;
}
/**
* This subclause refers to the description of each subunit constituting the SubstanceProtein. A subunit is a linear
* sequence of amino acids linked through peptide bonds. The Subunit information shall be provided when the finished
* SubstanceProtein is a complex of multiple sequences; subunits are not used to delineate domains within a single
* sequence. Subunits are listed in order of decreasing length; sequences of the same length will be ordered by
* decreasing molecular weight; subunits that have identical sequences will be repeated multiple times.
*
* @return
* An unmodifiable list containing immutable objects of type {@link Subunit} that may be empty.
*/
public List getSubunit() {
return subunit;
}
@Override
public boolean hasChildren() {
return super.hasChildren() ||
(sequenceType != null) ||
(numberOfSubunits != null) ||
!disulfideLinkage.isEmpty() ||
!subunit.isEmpty();
}
@Override
public void accept(java.lang.String elementName, int elementIndex, Visitor visitor) {
if (visitor.preVisit(this)) {
visitor.visitStart(elementName, elementIndex, this);
if (visitor.visit(elementName, elementIndex, this)) {
// visit children
accept(id, "id", visitor);
accept(meta, "meta", visitor);
accept(implicitRules, "implicitRules", visitor);
accept(language, "language", visitor);
accept(text, "text", visitor);
accept(contained, "contained", visitor, Resource.class);
accept(extension, "extension", visitor, Extension.class);
accept(modifierExtension, "modifierExtension", visitor, Extension.class);
accept(sequenceType, "sequenceType", visitor);
accept(numberOfSubunits, "numberOfSubunits", visitor);
accept(disulfideLinkage, "disulfideLinkage", visitor, String.class);
accept(subunit, "subunit", visitor, Subunit.class);
}
visitor.visitEnd(elementName, elementIndex, this);
visitor.postVisit(this);
}
}
@Override
public boolean equals(Object obj) {
if (this == obj) {
return true;
}
if (obj == null) {
return false;
}
if (getClass() != obj.getClass()) {
return false;
}
SubstanceProtein other = (SubstanceProtein) obj;
return Objects.equals(id, other.id) &&
Objects.equals(meta, other.meta) &&
Objects.equals(implicitRules, other.implicitRules) &&
Objects.equals(language, other.language) &&
Objects.equals(text, other.text) &&
Objects.equals(contained, other.contained) &&
Objects.equals(extension, other.extension) &&
Objects.equals(modifierExtension, other.modifierExtension) &&
Objects.equals(sequenceType, other.sequenceType) &&
Objects.equals(numberOfSubunits, other.numberOfSubunits) &&
Objects.equals(disulfideLinkage, other.disulfideLinkage) &&
Objects.equals(subunit, other.subunit);
}
@Override
public int hashCode() {
int result = hashCode;
if (result == 0) {
result = Objects.hash(id,
meta,
implicitRules,
language,
text,
contained,
extension,
modifierExtension,
sequenceType,
numberOfSubunits,
disulfideLinkage,
subunit);
hashCode = result;
}
return result;
}
@Override
public Builder toBuilder() {
return new Builder().from(this);
}
public static Builder builder() {
return new Builder();
}
public static class Builder extends DomainResource.Builder {
private CodeableConcept sequenceType;
private Integer numberOfSubunits;
private List disulfideLinkage = new ArrayList<>();
private List subunit = new ArrayList<>();
private Builder() {
super();
}
/**
* The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.
*
* @param id
* Logical id of this artifact
*
* @return
* A reference to this Builder instance
*/
@Override
public Builder id(java.lang.String id) {
return (Builder) super.id(id);
}
/**
* 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.
*
* @param meta
* Metadata about the resource
*
* @return
* A reference to this Builder instance
*/
@Override
public Builder meta(Meta meta) {
return (Builder) super.meta(meta);
}
/**
* 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.
*
* @param implicitRules
* A set of rules under which this content was created
*
* @return
* A reference to this Builder instance
*/
@Override
public Builder implicitRules(Uri implicitRules) {
return (Builder) super.implicitRules(implicitRules);
}
/**
* The base language in which the resource is written.
*
* @param language
* Language of the resource content
*
* @return
* A reference to this Builder instance
*/
@Override
public Builder language(Code language) {
return (Builder) super.language(language);
}
/**
* 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.
*
* @param text
* Text summary of the resource, for human interpretation
*
* @return
* A reference to this Builder instance
*/
@Override
public Builder text(Narrative text) {
return (Builder) super.text(text);
}
/**
* 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
*
* @param contained
* Contained, inline Resources
*
* @return
* A reference to this Builder instance
*/
@Override
public Builder contained(Resource... contained) {
return (Builder) super.contained(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
*
* @param contained
* Contained, inline Resources
*
* @return
* A reference to this Builder instance
*/
@Override
public Builder contained(Collection contained) {
return (Builder) super.contained(contained);
}
/**
* 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
*
* @param extension
* Additional content defined by implementations
*
* @return
* A reference to this Builder instance
*/
@Override
public Builder extension(Extension... extension) {
return (Builder) super.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
*
* @param extension
* Additional content defined by implementations
*
* @return
* A reference to this Builder instance
*/
@Override
public Builder extension(Collection extension) {
return (Builder) super.extension(extension);
}
/**
* 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
*
* @param modifierExtension
* Extensions that cannot be ignored
*
* @return
* A reference to this Builder instance
*/
@Override
public Builder modifierExtension(Extension... modifierExtension) {
return (Builder) super.modifierExtension(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
*
* @param modifierExtension
* Extensions that cannot be ignored
*
* @return
* A reference to this Builder instance
*/
@Override
public Builder modifierExtension(Collection modifierExtension) {
return (Builder) super.modifierExtension(modifierExtension);
}
/**
* The SubstanceProtein descriptive elements will only be used when a complete or partial amino acid sequence is
* available or derivable from a nucleic acid sequence.
*
* @param sequenceType
* The SubstanceProtein descriptive elements will only be used when a complete or partial amino acid sequence is
* available or derivable from a nucleic acid sequence
*
* @return
* A reference to this Builder instance
*/
public Builder sequenceType(CodeableConcept sequenceType) {
this.sequenceType = sequenceType;
return this;
}
/**
* Number of linear sequences of amino acids linked through peptide bonds. The number of subunits constituting the
* SubstanceProtein shall be described. It is possible that the number of subunits can be variable.
*
* @param numberOfSubunits
* Number of linear sequences of amino acids linked through peptide bonds. The number of subunits constituting the
* SubstanceProtein shall be described. It is possible that the number of subunits can be variable
*
* @return
* A reference to this Builder instance
*/
public Builder numberOfSubunits(Integer numberOfSubunits) {
this.numberOfSubunits = numberOfSubunits;
return this;
}
/**
* The disulphide bond between two cysteine residues either on the same subunit or on two different subunits shall be
* described. The position of the disulfide bonds in the SubstanceProtein shall be listed in increasing order of subunit
* number and position within subunit followed by the abbreviation of the amino acids involved. The disulfide linkage
* positions shall actually contain the amino acid Cysteine at the respective positions.
*
* Adds new element(s) to the existing list
*
* @param disulfideLinkage
* The disulphide bond between two cysteine residues either on the same subunit or on two different subunits shall be
* described. The position of the disulfide bonds in the SubstanceProtein shall be listed in increasing order of subunit
* number and position within subunit followed by the abbreviation of the amino acids involved. The disulfide linkage
* positions shall actually contain the amino acid Cysteine at the respective positions
*
* @return
* A reference to this Builder instance
*/
public Builder disulfideLinkage(String... disulfideLinkage) {
for (String value : disulfideLinkage) {
this.disulfideLinkage.add(value);
}
return this;
}
/**
* The disulphide bond between two cysteine residues either on the same subunit or on two different subunits shall be
* described. The position of the disulfide bonds in the SubstanceProtein shall be listed in increasing order of subunit
* number and position within subunit followed by the abbreviation of the amino acids involved. The disulfide linkage
* positions shall actually contain the amino acid Cysteine at the respective positions.
*
*
Replaces the existing list with a new one containing elements from the Collection
*
* @param disulfideLinkage
* The disulphide bond between two cysteine residues either on the same subunit or on two different subunits shall be
* described. The position of the disulfide bonds in the SubstanceProtein shall be listed in increasing order of subunit
* number and position within subunit followed by the abbreviation of the amino acids involved. The disulfide linkage
* positions shall actually contain the amino acid Cysteine at the respective positions
*
* @return
* A reference to this Builder instance
*/
public Builder disulfideLinkage(Collection disulfideLinkage) {
this.disulfideLinkage = new ArrayList<>(disulfideLinkage);
return this;
}
/**
* This subclause refers to the description of each subunit constituting the SubstanceProtein. A subunit is a linear
* sequence of amino acids linked through peptide bonds. The Subunit information shall be provided when the finished
* SubstanceProtein is a complex of multiple sequences; subunits are not used to delineate domains within a single
* sequence. Subunits are listed in order of decreasing length; sequences of the same length will be ordered by
* decreasing molecular weight; subunits that have identical sequences will be repeated multiple times.
*
* Adds new element(s) to the existing list
*
* @param subunit
* This subclause refers to the description of each subunit constituting the SubstanceProtein. A subunit is a linear
* sequence of amino acids linked through peptide bonds. The Subunit information shall be provided when the finished
* SubstanceProtein is a complex of multiple sequences; subunits are not used to delineate domains within a single
* sequence. Subunits are listed in order of decreasing length; sequences of the same length will be ordered by
* decreasing molecular weight; subunits that have identical sequences will be repeated multiple times
*
* @return
* A reference to this Builder instance
*/
public Builder subunit(Subunit... subunit) {
for (Subunit value : subunit) {
this.subunit.add(value);
}
return this;
}
/**
* This subclause refers to the description of each subunit constituting the SubstanceProtein. A subunit is a linear
* sequence of amino acids linked through peptide bonds. The Subunit information shall be provided when the finished
* SubstanceProtein is a complex of multiple sequences; subunits are not used to delineate domains within a single
* sequence. Subunits are listed in order of decreasing length; sequences of the same length will be ordered by
* decreasing molecular weight; subunits that have identical sequences will be repeated multiple times.
*
*
Replaces the existing list with a new one containing elements from the Collection
*
* @param subunit
* This subclause refers to the description of each subunit constituting the SubstanceProtein. A subunit is a linear
* sequence of amino acids linked through peptide bonds. The Subunit information shall be provided when the finished
* SubstanceProtein is a complex of multiple sequences; subunits are not used to delineate domains within a single
* sequence. Subunits are listed in order of decreasing length; sequences of the same length will be ordered by
* decreasing molecular weight; subunits that have identical sequences will be repeated multiple times
*
* @return
* A reference to this Builder instance
*/
public Builder subunit(Collection subunit) {
this.subunit = new ArrayList<>(subunit);
return this;
}
/**
* Build the {@link SubstanceProtein}
*
* @return
* An immutable object of type {@link SubstanceProtein}
* @throws IllegalStateException
* if the current state cannot be built into a valid SubstanceProtein per the base specification
*/
@Override
public SubstanceProtein build() {
SubstanceProtein substanceProtein = new SubstanceProtein(this);
if (validating) {
validate(substanceProtein);
}
return substanceProtein;
}
protected void validate(SubstanceProtein substanceProtein) {
super.validate(substanceProtein);
ValidationSupport.checkList(substanceProtein.disulfideLinkage, "disulfideLinkage", String.class);
ValidationSupport.checkList(substanceProtein.subunit, "subunit", Subunit.class);
}
protected Builder from(SubstanceProtein substanceProtein) {
super.from(substanceProtein);
sequenceType = substanceProtein.sequenceType;
numberOfSubunits = substanceProtein.numberOfSubunits;
disulfideLinkage.addAll(substanceProtein.disulfideLinkage);
subunit.addAll(substanceProtein.subunit);
return this;
}
}
/**
* This subclause refers to the description of each subunit constituting the SubstanceProtein. A subunit is a linear
* sequence of amino acids linked through peptide bonds. The Subunit information shall be provided when the finished
* SubstanceProtein is a complex of multiple sequences; subunits are not used to delineate domains within a single
* sequence. Subunits are listed in order of decreasing length; sequences of the same length will be ordered by
* decreasing molecular weight; subunits that have identical sequences will be repeated multiple times.
*/
public static class Subunit extends BackboneElement {
@Summary
private final Integer subunit;
@Summary
private final String sequence;
@Summary
private final Integer length;
@Summary
private final Attachment sequenceAttachment;
@Summary
private final Identifier nTerminalModificationId;
@Summary
private final String nTerminalModification;
@Summary
private final Identifier cTerminalModificationId;
@Summary
private final String cTerminalModification;
private Subunit(Builder builder) {
super(builder);
subunit = builder.subunit;
sequence = builder.sequence;
length = builder.length;
sequenceAttachment = builder.sequenceAttachment;
nTerminalModificationId = builder.nTerminalModificationId;
nTerminalModification = builder.nTerminalModification;
cTerminalModificationId = builder.cTerminalModificationId;
cTerminalModification = builder.cTerminalModification;
}
/**
* Index of primary sequences of amino acids linked through peptide bonds in order of decreasing length. Sequences of the
* same length will be ordered by molecular weight. Subunits that have identical sequences will be repeated and have
* sequential subscripts.
*
* @return
* An immutable object of type {@link Integer} that may be null.
*/
public Integer getSubunit() {
return subunit;
}
/**
* The sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-
* letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed
* SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids
* that are not represented with a single letter code an X should be used within the sequence. The modified amino acids
* will be distinguished by their position in the sequence.
*
* @return
* An immutable object of type {@link String} that may be null.
*/
public String getSequence() {
return sequence;
}
/**
* Length of linear sequences of amino acids contained in the subunit.
*
* @return
* An immutable object of type {@link Integer} that may be null.
*/
public Integer getLength() {
return length;
}
/**
* The sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-
* letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed
* SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids
* that are not represented with a single letter code an X should be used within the sequence. The modified amino acids
* will be distinguished by their position in the sequence.
*
* @return
* An immutable object of type {@link Attachment} that may be null.
*/
public Attachment getSequenceAttachment() {
return sequenceAttachment;
}
/**
* Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID.
*
* @return
* An immutable object of type {@link Identifier} that may be null.
*/
public Identifier getNTerminalModificationId() {
return nTerminalModificationId;
}
/**
* The name of the fragment modified at the N-terminal of the SubstanceProtein shall be specified.
*
* @return
* An immutable object of type {@link String} that may be null.
*/
public String getNTerminalModification() {
return nTerminalModification;
}
/**
* Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID.
*
* @return
* An immutable object of type {@link Identifier} that may be null.
*/
public Identifier getCTerminalModificationId() {
return cTerminalModificationId;
}
/**
* The modification at the C-terminal shall be specified.
*
* @return
* An immutable object of type {@link String} that may be null.
*/
public String getCTerminalModification() {
return cTerminalModification;
}
@Override
public boolean hasChildren() {
return super.hasChildren() ||
(subunit != null) ||
(sequence != null) ||
(length != null) ||
(sequenceAttachment != null) ||
(nTerminalModificationId != null) ||
(nTerminalModification != null) ||
(cTerminalModificationId != null) ||
(cTerminalModification != null);
}
@Override
public void accept(java.lang.String elementName, int elementIndex, Visitor visitor) {
if (visitor.preVisit(this)) {
visitor.visitStart(elementName, elementIndex, this);
if (visitor.visit(elementName, elementIndex, this)) {
// visit children
accept(id, "id", visitor);
accept(extension, "extension", visitor, Extension.class);
accept(modifierExtension, "modifierExtension", visitor, Extension.class);
accept(subunit, "subunit", visitor);
accept(sequence, "sequence", visitor);
accept(length, "length", visitor);
accept(sequenceAttachment, "sequenceAttachment", visitor);
accept(nTerminalModificationId, "nTerminalModificationId", visitor);
accept(nTerminalModification, "nTerminalModification", visitor);
accept(cTerminalModificationId, "cTerminalModificationId", visitor);
accept(cTerminalModification, "cTerminalModification", visitor);
}
visitor.visitEnd(elementName, elementIndex, this);
visitor.postVisit(this);
}
}
@Override
public boolean equals(Object obj) {
if (this == obj) {
return true;
}
if (obj == null) {
return false;
}
if (getClass() != obj.getClass()) {
return false;
}
Subunit other = (Subunit) obj;
return Objects.equals(id, other.id) &&
Objects.equals(extension, other.extension) &&
Objects.equals(modifierExtension, other.modifierExtension) &&
Objects.equals(subunit, other.subunit) &&
Objects.equals(sequence, other.sequence) &&
Objects.equals(length, other.length) &&
Objects.equals(sequenceAttachment, other.sequenceAttachment) &&
Objects.equals(nTerminalModificationId, other.nTerminalModificationId) &&
Objects.equals(nTerminalModification, other.nTerminalModification) &&
Objects.equals(cTerminalModificationId, other.cTerminalModificationId) &&
Objects.equals(cTerminalModification, other.cTerminalModification);
}
@Override
public int hashCode() {
int result = hashCode;
if (result == 0) {
result = Objects.hash(id,
extension,
modifierExtension,
subunit,
sequence,
length,
sequenceAttachment,
nTerminalModificationId,
nTerminalModification,
cTerminalModificationId,
cTerminalModification);
hashCode = result;
}
return result;
}
@Override
public Builder toBuilder() {
return new Builder().from(this);
}
public static Builder builder() {
return new Builder();
}
public static class Builder extends BackboneElement.Builder {
private Integer subunit;
private String sequence;
private Integer length;
private Attachment sequenceAttachment;
private Identifier nTerminalModificationId;
private String nTerminalModification;
private Identifier cTerminalModificationId;
private String cTerminalModification;
private Builder() {
super();
}
/**
* Unique id for the element within a resource (for internal references). This may be any string value that does not
* contain spaces.
*
* @param id
* Unique id for inter-element referencing
*
* @return
* A reference to this Builder instance
*/
@Override
public Builder id(java.lang.String id) {
return (Builder) super.id(id);
}
/**
* May be used to represent additional information that is not part of the basic definition of the element. 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
*
* @param extension
* Additional content defined by implementations
*
* @return
* A reference to this Builder instance
*/
@Override
public Builder extension(Extension... extension) {
return (Builder) super.extension(extension);
}
/**
* May be used to represent additional information that is not part of the basic definition of the element. 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
*
* @param extension
* Additional content defined by implementations
*
* @return
* A reference to this Builder instance
*/
@Override
public Builder extension(Collection extension) {
return (Builder) super.extension(extension);
}
/**
* May be used to represent additional information that is not part of the basic definition of the element and that
* modifies the understanding of the element in which it is contained 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 can 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
*
* @param modifierExtension
* Extensions that cannot be ignored even if unrecognized
*
* @return
* A reference to this Builder instance
*/
@Override
public Builder modifierExtension(Extension... modifierExtension) {
return (Builder) super.modifierExtension(modifierExtension);
}
/**
* May be used to represent additional information that is not part of the basic definition of the element and that
* modifies the understanding of the element in which it is contained 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 can 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
*
* @param modifierExtension
* Extensions that cannot be ignored even if unrecognized
*
* @return
* A reference to this Builder instance
*/
@Override
public Builder modifierExtension(Collection modifierExtension) {
return (Builder) super.modifierExtension(modifierExtension);
}
/**
* Index of primary sequences of amino acids linked through peptide bonds in order of decreasing length. Sequences of the
* same length will be ordered by molecular weight. Subunits that have identical sequences will be repeated and have
* sequential subscripts.
*
* @param subunit
* Index of primary sequences of amino acids linked through peptide bonds in order of decreasing length. Sequences of the
* same length will be ordered by molecular weight. Subunits that have identical sequences will be repeated and have
* sequential subscripts
*
* @return
* A reference to this Builder instance
*/
public Builder subunit(Integer subunit) {
this.subunit = subunit;
return this;
}
/**
* The sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-
* letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed
* SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids
* that are not represented with a single letter code an X should be used within the sequence. The modified amino acids
* will be distinguished by their position in the sequence.
*
* @param sequence
* The sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-
* letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed
* SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids
* that are not represented with a single letter code an X should be used within the sequence. The modified amino acids
* will be distinguished by their position in the sequence
*
* @return
* A reference to this Builder instance
*/
public Builder sequence(String sequence) {
this.sequence = sequence;
return this;
}
/**
* Length of linear sequences of amino acids contained in the subunit.
*
* @param length
* Length of linear sequences of amino acids contained in the subunit
*
* @return
* A reference to this Builder instance
*/
public Builder length(Integer length) {
this.length = length;
return this;
}
/**
* The sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-
* letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed
* SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids
* that are not represented with a single letter code an X should be used within the sequence. The modified amino acids
* will be distinguished by their position in the sequence.
*
* @param sequenceAttachment
* The sequence information shall be provided enumerating the amino acids from N- to C-terminal end using standard single-
* letter amino acid codes. Uppercase shall be used for L-amino acids and lowercase for D-amino acids. Transcribed
* SubstanceProteins will always be described using the translated sequence; for synthetic peptide containing amino acids
* that are not represented with a single letter code an X should be used within the sequence. The modified amino acids
* will be distinguished by their position in the sequence
*
* @return
* A reference to this Builder instance
*/
public Builder sequenceAttachment(Attachment sequenceAttachment) {
this.sequenceAttachment = sequenceAttachment;
return this;
}
/**
* Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID.
*
* @param nTerminalModificationId
* Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID
*
* @return
* A reference to this Builder instance
*/
public Builder nTerminalModificationId(Identifier nTerminalModificationId) {
this.nTerminalModificationId = nTerminalModificationId;
return this;
}
/**
* The name of the fragment modified at the N-terminal of the SubstanceProtein shall be specified.
*
* @param nTerminalModification
* The name of the fragment modified at the N-terminal of the SubstanceProtein shall be specified
*
* @return
* A reference to this Builder instance
*/
public Builder nTerminalModification(String nTerminalModification) {
this.nTerminalModification = nTerminalModification;
return this;
}
/**
* Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID.
*
* @param cTerminalModificationId
* Unique identifier for molecular fragment modification based on the ISO 11238 Substance ID
*
* @return
* A reference to this Builder instance
*/
public Builder cTerminalModificationId(Identifier cTerminalModificationId) {
this.cTerminalModificationId = cTerminalModificationId;
return this;
}
/**
* The modification at the C-terminal shall be specified.
*
* @param cTerminalModification
* The modification at the C-terminal shall be specified
*
* @return
* A reference to this Builder instance
*/
public Builder cTerminalModification(String cTerminalModification) {
this.cTerminalModification = cTerminalModification;
return this;
}
/**
* Build the {@link Subunit}
*
* @return
* An immutable object of type {@link Subunit}
* @throws IllegalStateException
* if the current state cannot be built into a valid Subunit per the base specification
*/
@Override
public Subunit build() {
Subunit subunit = new Subunit(this);
if (validating) {
validate(subunit);
}
return subunit;
}
protected void validate(Subunit subunit) {
super.validate(subunit);
ValidationSupport.requireValueOrChildren(subunit);
}
protected Builder from(Subunit subunit) {
super.from(subunit);
this.subunit = subunit.subunit;
sequence = subunit.sequence;
length = subunit.length;
sequenceAttachment = subunit.sequenceAttachment;
nTerminalModificationId = subunit.nTerminalModificationId;
nTerminalModification = subunit.nTerminalModification;
cTerminalModificationId = subunit.cTerminalModificationId;
cTerminalModification = subunit.cTerminalModification;
return this;
}
}
}
}