| /** |
| */ |
| package org.hl7.fhir; |
| |
| |
| /** |
| * <!-- begin-user-doc --> |
| * A representation of the model object '<em><b>Molecular Sequence Variant</b></em>'. |
| * <!-- end-user-doc --> |
| * |
| * <!-- begin-model-doc --> |
| * Raw data describing a biological sequence. |
| * <!-- end-model-doc --> |
| * |
| * <p> |
| * The following features are supported: |
| * </p> |
| * <ul> |
| * <li>{@link org.hl7.fhir.MolecularSequenceVariant#getStart <em>Start</em>}</li> |
| * <li>{@link org.hl7.fhir.MolecularSequenceVariant#getEnd <em>End</em>}</li> |
| * <li>{@link org.hl7.fhir.MolecularSequenceVariant#getObservedAllele <em>Observed Allele</em>}</li> |
| * <li>{@link org.hl7.fhir.MolecularSequenceVariant#getReferenceAllele <em>Reference Allele</em>}</li> |
| * <li>{@link org.hl7.fhir.MolecularSequenceVariant#getCigar <em>Cigar</em>}</li> |
| * <li>{@link org.hl7.fhir.MolecularSequenceVariant#getVariantPointer <em>Variant Pointer</em>}</li> |
| * </ul> |
| * |
| * @see org.hl7.fhir.FhirPackage#getMolecularSequenceVariant() |
| * @model extendedMetaData="name='MolecularSequence.Variant' kind='elementOnly'" |
| * @generated |
| */ |
| public interface MolecularSequenceVariant extends BackboneElement { |
| /** |
| * Returns the value of the '<em><b>Start</b></em>' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * <!-- begin-model-doc --> |
| * Start position of the variant on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive. |
| * <!-- end-model-doc --> |
| * @return the value of the '<em>Start</em>' containment reference. |
| * @see #setStart(org.hl7.fhir.Integer) |
| * @see org.hl7.fhir.FhirPackage#getMolecularSequenceVariant_Start() |
| * @model containment="true" |
| * extendedMetaData="kind='element' name='start' namespace='##targetNamespace'" |
| * @generated |
| */ |
| org.hl7.fhir.Integer getStart(); |
| |
| /** |
| * Sets the value of the '{@link org.hl7.fhir.MolecularSequenceVariant#getStart <em>Start</em>}' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @param value the new value of the '<em>Start</em>' containment reference. |
| * @see #getStart() |
| * @generated |
| */ |
| void setStart(org.hl7.fhir.Integer value); |
| |
| /** |
| * Returns the value of the '<em><b>End</b></em>' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * <!-- begin-model-doc --> |
| * End position of the variant on the reference sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position. |
| * <!-- end-model-doc --> |
| * @return the value of the '<em>End</em>' containment reference. |
| * @see #setEnd(org.hl7.fhir.Integer) |
| * @see org.hl7.fhir.FhirPackage#getMolecularSequenceVariant_End() |
| * @model containment="true" |
| * extendedMetaData="kind='element' name='end' namespace='##targetNamespace'" |
| * @generated |
| */ |
| org.hl7.fhir.Integer getEnd(); |
| |
| /** |
| * Sets the value of the '{@link org.hl7.fhir.MolecularSequenceVariant#getEnd <em>End</em>}' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @param value the new value of the '<em>End</em>' containment reference. |
| * @see #getEnd() |
| * @generated |
| */ |
| void setEnd(org.hl7.fhir.Integer value); |
| |
| /** |
| * Returns the value of the '<em><b>Observed Allele</b></em>' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * <!-- begin-model-doc --> |
| * An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end. |
| * <!-- end-model-doc --> |
| * @return the value of the '<em>Observed Allele</em>' containment reference. |
| * @see #setObservedAllele(org.hl7.fhir.String) |
| * @see org.hl7.fhir.FhirPackage#getMolecularSequenceVariant_ObservedAllele() |
| * @model containment="true" |
| * extendedMetaData="kind='element' name='observedAllele' namespace='##targetNamespace'" |
| * @generated |
| */ |
| org.hl7.fhir.String getObservedAllele(); |
| |
| /** |
| * Sets the value of the '{@link org.hl7.fhir.MolecularSequenceVariant#getObservedAllele <em>Observed Allele</em>}' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @param value the new value of the '<em>Observed Allele</em>' containment reference. |
| * @see #getObservedAllele() |
| * @generated |
| */ |
| void setObservedAllele(org.hl7.fhir.String value); |
| |
| /** |
| * Returns the value of the '<em><b>Reference Allele</b></em>' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * <!-- begin-model-doc --> |
| * An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end. |
| * <!-- end-model-doc --> |
| * @return the value of the '<em>Reference Allele</em>' containment reference. |
| * @see #setReferenceAllele(org.hl7.fhir.String) |
| * @see org.hl7.fhir.FhirPackage#getMolecularSequenceVariant_ReferenceAllele() |
| * @model containment="true" |
| * extendedMetaData="kind='element' name='referenceAllele' namespace='##targetNamespace'" |
| * @generated |
| */ |
| org.hl7.fhir.String getReferenceAllele(); |
| |
| /** |
| * Sets the value of the '{@link org.hl7.fhir.MolecularSequenceVariant#getReferenceAllele <em>Reference Allele</em>}' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @param value the new value of the '<em>Reference Allele</em>' containment reference. |
| * @see #getReferenceAllele() |
| * @generated |
| */ |
| void setReferenceAllele(org.hl7.fhir.String value); |
| |
| /** |
| * Returns the value of the '<em><b>Cigar</b></em>' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * <!-- begin-model-doc --> |
| * Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm). |
| * <!-- end-model-doc --> |
| * @return the value of the '<em>Cigar</em>' containment reference. |
| * @see #setCigar(org.hl7.fhir.String) |
| * @see org.hl7.fhir.FhirPackage#getMolecularSequenceVariant_Cigar() |
| * @model containment="true" |
| * extendedMetaData="kind='element' name='cigar' namespace='##targetNamespace'" |
| * @generated |
| */ |
| org.hl7.fhir.String getCigar(); |
| |
| /** |
| * Sets the value of the '{@link org.hl7.fhir.MolecularSequenceVariant#getCigar <em>Cigar</em>}' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @param value the new value of the '<em>Cigar</em>' containment reference. |
| * @see #getCigar() |
| * @generated |
| */ |
| void setCigar(org.hl7.fhir.String value); |
| |
| /** |
| * Returns the value of the '<em><b>Variant Pointer</b></em>' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * <!-- begin-model-doc --> |
| * A pointer to an Observation containing variant information. |
| * <!-- end-model-doc --> |
| * @return the value of the '<em>Variant Pointer</em>' containment reference. |
| * @see #setVariantPointer(Reference) |
| * @see org.hl7.fhir.FhirPackage#getMolecularSequenceVariant_VariantPointer() |
| * @model containment="true" |
| * extendedMetaData="kind='element' name='variantPointer' namespace='##targetNamespace'" |
| * @generated |
| */ |
| Reference getVariantPointer(); |
| |
| /** |
| * Sets the value of the '{@link org.hl7.fhir.MolecularSequenceVariant#getVariantPointer <em>Variant Pointer</em>}' containment reference. |
| * <!-- begin-user-doc --> |
| * <!-- end-user-doc --> |
| * @param value the new value of the '<em>Variant Pointer</em>' containment reference. |
| * @see #getVariantPointer() |
| * @generated |
| */ |
| void setVariantPointer(Reference value); |
| |
| } // MolecularSequenceVariant |
