| /** |
| */ |
| package org.hl7.fhir; |
| |
| import org.eclipse.emf.common.util.EList; |
| |
| /** |
| * <!-- begin-user-doc --> |
| * A representation of the model object '<em><b>Molecular Sequence</b></em>'. |
| * <!-- end-user-doc --> |
| * |
| * <!-- begin-model-doc --> |
| * Raw data describing a biological sequence. |
| * If the element is present, it must have either a @value, an @id, or extensions |
| * <!-- end-model-doc --> |
| * |
| * <p> |
| * The following features are supported: |
| * </p> |
| * <ul> |
| * <li>{@link org.hl7.fhir.MolecularSequence#getIdentifier <em>Identifier</em>}</li> |
| * <li>{@link org.hl7.fhir.MolecularSequence#getType <em>Type</em>}</li> |
| * <li>{@link org.hl7.fhir.MolecularSequence#getCoordinateSystem <em>Coordinate System</em>}</li> |
| * <li>{@link org.hl7.fhir.MolecularSequence#getPatient <em>Patient</em>}</li> |
| * <li>{@link org.hl7.fhir.MolecularSequence#getSpecimen <em>Specimen</em>}</li> |
| * <li>{@link org.hl7.fhir.MolecularSequence#getDevice <em>Device</em>}</li> |
| * <li>{@link org.hl7.fhir.MolecularSequence#getPerformer <em>Performer</em>}</li> |
| * <li>{@link org.hl7.fhir.MolecularSequence#getQuantity <em>Quantity</em>}</li> |
| * <li>{@link org.hl7.fhir.MolecularSequence#getReferenceSeq <em>Reference Seq</em>}</li> |
| * <li>{@link org.hl7.fhir.MolecularSequence#getVariant <em>Variant</em>}</li> |
| * <li>{@link org.hl7.fhir.MolecularSequence#getObservedSeq <em>Observed Seq</em>}</li> |
| * <li>{@link org.hl7.fhir.MolecularSequence#getQuality <em>Quality</em>}</li> |
| * <li>{@link org.hl7.fhir.MolecularSequence#getReadCoverage <em>Read Coverage</em>}</li> |
| * <li>{@link org.hl7.fhir.MolecularSequence#getRepository <em>Repository</em>}</li> |
| * <li>{@link org.hl7.fhir.MolecularSequence#getPointer <em>Pointer</em>}</li> |
| * <li>{@link org.hl7.fhir.MolecularSequence#getStructureVariant <em>Structure Variant</em>}</li> |
| * </ul> |
| * |
| * @see org.hl7.fhir.FhirPackage#getMolecularSequence() |
| * @model extendedMetaData="name='MolecularSequence' kind='elementOnly'" |
| * @generated |
| */ |
| public interface MolecularSequence extends DomainResource { |
| /** |
| * Returns the value of the '<em><b>Identifier</b></em>' containment reference list. |
| * The list contents are of type {@link org.hl7.fhir.Identifier}. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * <!-- begin-model-doc --> |
| * A unique identifier for this particular sequence instance. This is a FHIR-defined id. |
| * <!-- end-model-doc --> |
| * @return the value of the '<em>Identifier</em>' containment reference list. |
| * @see org.hl7.fhir.FhirPackage#getMolecularSequence_Identifier() |
| * @model containment="true" |
| * extendedMetaData="kind='element' name='identifier' namespace='##targetNamespace'" |
| * @generated |
| */ |
| EList<Identifier> getIdentifier(); |
| |
| /** |
| * Returns the value of the '<em><b>Type</b></em>' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * <!-- begin-model-doc --> |
| * Amino Acid Sequence/ DNA Sequence / RNA Sequence. |
| * <!-- end-model-doc --> |
| * @return the value of the '<em>Type</em>' containment reference. |
| * @see #setType(SequenceType) |
| * @see org.hl7.fhir.FhirPackage#getMolecularSequence_Type() |
| * @model containment="true" |
| * extendedMetaData="kind='element' name='type' namespace='##targetNamespace'" |
| * @generated |
| */ |
| SequenceType getType(); |
| |
| /** |
| * Sets the value of the '{@link org.hl7.fhir.MolecularSequence#getType <em>Type</em>}' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @param value the new value of the '<em>Type</em>' containment reference. |
| * @see #getType() |
| * @generated |
| */ |
| void setType(SequenceType value); |
| |
| /** |
| * Returns the value of the '<em><b>Coordinate System</b></em>' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * <!-- begin-model-doc --> |
| * 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). |
| * <!-- end-model-doc --> |
| * @return the value of the '<em>Coordinate System</em>' containment reference. |
| * @see #setCoordinateSystem(org.hl7.fhir.Integer) |
| * @see org.hl7.fhir.FhirPackage#getMolecularSequence_CoordinateSystem() |
| * @model containment="true" required="true" |
| * extendedMetaData="kind='element' name='coordinateSystem' namespace='##targetNamespace'" |
| * @generated |
| */ |
| org.hl7.fhir.Integer getCoordinateSystem(); |
| |
| /** |
| * Sets the value of the '{@link org.hl7.fhir.MolecularSequence#getCoordinateSystem <em>Coordinate System</em>}' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @param value the new value of the '<em>Coordinate System</em>' containment reference. |
| * @see #getCoordinateSystem() |
| * @generated |
| */ |
| void setCoordinateSystem(org.hl7.fhir.Integer value); |
| |
| /** |
| * Returns the value of the '<em><b>Patient</b></em>' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * <!-- begin-model-doc --> |
| * The patient whose sequencing results are described by this resource. |
| * <!-- end-model-doc --> |
| * @return the value of the '<em>Patient</em>' containment reference. |
| * @see #setPatient(Reference) |
| * @see org.hl7.fhir.FhirPackage#getMolecularSequence_Patient() |
| * @model containment="true" |
| * extendedMetaData="kind='element' name='patient' namespace='##targetNamespace'" |
| * @generated |
| */ |
| Reference getPatient(); |
| |
| /** |
| * Sets the value of the '{@link org.hl7.fhir.MolecularSequence#getPatient <em>Patient</em>}' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @param value the new value of the '<em>Patient</em>' containment reference. |
| * @see #getPatient() |
| * @generated |
| */ |
| void setPatient(Reference value); |
| |
| /** |
| * Returns the value of the '<em><b>Specimen</b></em>' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * <!-- begin-model-doc --> |
| * Specimen used for sequencing. |
| * <!-- end-model-doc --> |
| * @return the value of the '<em>Specimen</em>' containment reference. |
| * @see #setSpecimen(Reference) |
| * @see org.hl7.fhir.FhirPackage#getMolecularSequence_Specimen() |
| * @model containment="true" |
| * extendedMetaData="kind='element' name='specimen' namespace='##targetNamespace'" |
| * @generated |
| */ |
| Reference getSpecimen(); |
| |
| /** |
| * Sets the value of the '{@link org.hl7.fhir.MolecularSequence#getSpecimen <em>Specimen</em>}' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @param value the new value of the '<em>Specimen</em>' containment reference. |
| * @see #getSpecimen() |
| * @generated |
| */ |
| void setSpecimen(Reference value); |
| |
| /** |
| * Returns the value of the '<em><b>Device</b></em>' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * <!-- begin-model-doc --> |
| * The method for sequencing, for example, chip information. |
| * <!-- end-model-doc --> |
| * @return the value of the '<em>Device</em>' containment reference. |
| * @see #setDevice(Reference) |
| * @see org.hl7.fhir.FhirPackage#getMolecularSequence_Device() |
| * @model containment="true" |
| * extendedMetaData="kind='element' name='device' namespace='##targetNamespace'" |
| * @generated |
| */ |
| Reference getDevice(); |
| |
| /** |
| * Sets the value of the '{@link org.hl7.fhir.MolecularSequence#getDevice <em>Device</em>}' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @param value the new value of the '<em>Device</em>' containment reference. |
| * @see #getDevice() |
| * @generated |
| */ |
| void setDevice(Reference value); |
| |
| /** |
| * Returns the value of the '<em><b>Performer</b></em>' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * <!-- begin-model-doc --> |
| * The organization or lab that should be responsible for this result. |
| * <!-- end-model-doc --> |
| * @return the value of the '<em>Performer</em>' containment reference. |
| * @see #setPerformer(Reference) |
| * @see org.hl7.fhir.FhirPackage#getMolecularSequence_Performer() |
| * @model containment="true" |
| * extendedMetaData="kind='element' name='performer' namespace='##targetNamespace'" |
| * @generated |
| */ |
| Reference getPerformer(); |
| |
| /** |
| * Sets the value of the '{@link org.hl7.fhir.MolecularSequence#getPerformer <em>Performer</em>}' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @param value the new value of the '<em>Performer</em>' containment reference. |
| * @see #getPerformer() |
| * @generated |
| */ |
| void setPerformer(Reference value); |
| |
| /** |
| * Returns the value of the '<em><b>Quantity</b></em>' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * <!-- begin-model-doc --> |
| * The number of copies of the sequence of interest. (RNASeq). |
| * <!-- end-model-doc --> |
| * @return the value of the '<em>Quantity</em>' containment reference. |
| * @see #setQuantity(Quantity) |
| * @see org.hl7.fhir.FhirPackage#getMolecularSequence_Quantity() |
| * @model containment="true" |
| * extendedMetaData="kind='element' name='quantity' namespace='##targetNamespace'" |
| * @generated |
| */ |
| Quantity getQuantity(); |
| |
| /** |
| * Sets the value of the '{@link org.hl7.fhir.MolecularSequence#getQuantity <em>Quantity</em>}' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @param value the new value of the '<em>Quantity</em>' containment reference. |
| * @see #getQuantity() |
| * @generated |
| */ |
| void setQuantity(Quantity value); |
| |
| /** |
| * Returns the value of the '<em><b>Reference Seq</b></em>' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * <!-- begin-model-doc --> |
| * A sequence that is used as a reference to describe variants that are present in a sequence analyzed. |
| * <!-- end-model-doc --> |
| * @return the value of the '<em>Reference Seq</em>' containment reference. |
| * @see #setReferenceSeq(MolecularSequenceReferenceSeq) |
| * @see org.hl7.fhir.FhirPackage#getMolecularSequence_ReferenceSeq() |
| * @model containment="true" |
| * extendedMetaData="kind='element' name='referenceSeq' namespace='##targetNamespace'" |
| * @generated |
| */ |
| MolecularSequenceReferenceSeq getReferenceSeq(); |
| |
| /** |
| * Sets the value of the '{@link org.hl7.fhir.MolecularSequence#getReferenceSeq <em>Reference Seq</em>}' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @param value the new value of the '<em>Reference Seq</em>' containment reference. |
| * @see #getReferenceSeq() |
| * @generated |
| */ |
| void setReferenceSeq(MolecularSequenceReferenceSeq value); |
| |
| /** |
| * Returns the value of the '<em><b>Variant</b></em>' containment reference list. |
| * The list contents are of type {@link org.hl7.fhir.MolecularSequenceVariant}. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * <!-- begin-model-doc --> |
| * 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. |
| * <!-- end-model-doc --> |
| * @return the value of the '<em>Variant</em>' containment reference list. |
| * @see org.hl7.fhir.FhirPackage#getMolecularSequence_Variant() |
| * @model containment="true" |
| * extendedMetaData="kind='element' name='variant' namespace='##targetNamespace'" |
| * @generated |
| */ |
| EList<MolecularSequenceVariant> getVariant(); |
| |
| /** |
| * Returns the value of the '<em><b>Observed Seq</b></em>' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * <!-- begin-model-doc --> |
| * 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. |
| * <!-- end-model-doc --> |
| * @return the value of the '<em>Observed Seq</em>' containment reference. |
| * @see #setObservedSeq(org.hl7.fhir.String) |
| * @see org.hl7.fhir.FhirPackage#getMolecularSequence_ObservedSeq() |
| * @model containment="true" |
| * extendedMetaData="kind='element' name='observedSeq' namespace='##targetNamespace'" |
| * @generated |
| */ |
| org.hl7.fhir.String getObservedSeq(); |
| |
| /** |
| * Sets the value of the '{@link org.hl7.fhir.MolecularSequence#getObservedSeq <em>Observed Seq</em>}' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @param value the new value of the '<em>Observed Seq</em>' containment reference. |
| * @see #getObservedSeq() |
| * @generated |
| */ |
| void setObservedSeq(org.hl7.fhir.String value); |
| |
| /** |
| * Returns the value of the '<em><b>Quality</b></em>' containment reference list. |
| * The list contents are of type {@link org.hl7.fhir.MolecularSequenceQuality}. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * <!-- begin-model-doc --> |
| * 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)). |
| * <!-- end-model-doc --> |
| * @return the value of the '<em>Quality</em>' containment reference list. |
| * @see org.hl7.fhir.FhirPackage#getMolecularSequence_Quality() |
| * @model containment="true" |
| * extendedMetaData="kind='element' name='quality' namespace='##targetNamespace'" |
| * @generated |
| */ |
| EList<MolecularSequenceQuality> getQuality(); |
| |
| /** |
| * Returns the value of the '<em><b>Read Coverage</b></em>' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * <!-- begin-model-doc --> |
| * Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence. |
| * <!-- end-model-doc --> |
| * @return the value of the '<em>Read Coverage</em>' containment reference. |
| * @see #setReadCoverage(org.hl7.fhir.Integer) |
| * @see org.hl7.fhir.FhirPackage#getMolecularSequence_ReadCoverage() |
| * @model containment="true" |
| * extendedMetaData="kind='element' name='readCoverage' namespace='##targetNamespace'" |
| * @generated |
| */ |
| org.hl7.fhir.Integer getReadCoverage(); |
| |
| /** |
| * Sets the value of the '{@link org.hl7.fhir.MolecularSequence#getReadCoverage <em>Read Coverage</em>}' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @param value the new value of the '<em>Read Coverage</em>' containment reference. |
| * @see #getReadCoverage() |
| * @generated |
| */ |
| void setReadCoverage(org.hl7.fhir.Integer value); |
| |
| /** |
| * Returns the value of the '<em><b>Repository</b></em>' containment reference list. |
| * The list contents are of type {@link org.hl7.fhir.MolecularSequenceRepository}. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * <!-- begin-model-doc --> |
| * Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq. |
| * <!-- end-model-doc --> |
| * @return the value of the '<em>Repository</em>' containment reference list. |
| * @see org.hl7.fhir.FhirPackage#getMolecularSequence_Repository() |
| * @model containment="true" |
| * extendedMetaData="kind='element' name='repository' namespace='##targetNamespace'" |
| * @generated |
| */ |
| EList<MolecularSequenceRepository> getRepository(); |
| |
| /** |
| * Returns the value of the '<em><b>Pointer</b></em>' containment reference list. |
| * The list contents are of type {@link org.hl7.fhir.Reference}. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * <!-- begin-model-doc --> |
| * Pointer to next atomic sequence which at most contains one variant. |
| * <!-- end-model-doc --> |
| * @return the value of the '<em>Pointer</em>' containment reference list. |
| * @see org.hl7.fhir.FhirPackage#getMolecularSequence_Pointer() |
| * @model containment="true" |
| * extendedMetaData="kind='element' name='pointer' namespace='##targetNamespace'" |
| * @generated |
| */ |
| EList<Reference> getPointer(); |
| |
| /** |
| * Returns the value of the '<em><b>Structure Variant</b></em>' containment reference list. |
| * The list contents are of type {@link org.hl7.fhir.MolecularSequenceStructureVariant}. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * <!-- begin-model-doc --> |
| * Information about chromosome structure variation. |
| * <!-- end-model-doc --> |
| * @return the value of the '<em>Structure Variant</em>' containment reference list. |
| * @see org.hl7.fhir.FhirPackage#getMolecularSequence_StructureVariant() |
| * @model containment="true" |
| * extendedMetaData="kind='element' name='structureVariant' namespace='##targetNamespace'" |
| * @generated |
| */ |
| EList<MolecularSequenceStructureVariant> getStructureVariant(); |
| |
| } // MolecularSequence |
