org.hl7.fhir.dstu2016may.model

Class Sequence.SequenceVariationComponent

java.lang.Object

org.hl7.fhir.dstu2016may.model.Base

org.hl7.fhir.dstu2016may.model.Element

org.hl7.fhir.dstu2016may.model.BackboneElement

org.hl7.fhir.dstu2016may.model.Sequence.SequenceVariationComponent

All Implemented Interfaces:

ca.uhn.fhir.model.api.IElement, Serializable, org.hl7.fhir.instance.model.api.IBase, org.hl7.fhir.instance.model.api.IBaseBackboneElement, org.hl7.fhir.instance.model.api.IBaseElement, org.hl7.fhir.instance.model.api.IBaseHasExtensions, org.hl7.fhir.instance.model.api.IBaseHasModifierExtensions

Enclosing class:

Sequence

public static class Sequence.SequenceVariationComponent
extends BackboneElement
implements org.hl7.fhir.instance.model.api.IBaseBackboneElement

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected StringType	cigar Extended CIGAR string for aligning the sequence with reference bases.
protected IntegerType	end 0-based end position (exclusive) of the variation on the reference sequence.
protected StringType	observedAllele Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence.
protected StringType	referenceAllele Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence.
protected IntegerType	start 0-based start position (inclusive) of the variation on the reference sequence.

Fields inherited from class org.hl7.fhir.dstu2016may.model.BackboneElement

modifierExtension

Fields inherited from class org.hl7.fhir.dstu2016may.model.Element

extension, id

Constructor Summary

Constructors

Constructor and Description
SequenceVariationComponent() Constructor

Method Summary

Modifier and Type	Method and Description
Base	addChild(String name)
Sequence.SequenceVariationComponent	copy()
boolean	equalsDeep(Base other)
boolean	equalsShallow(Base other)
String	fhirType()
String	getCigar()
StringType	getCigarElement()
int	getEnd()
IntegerType	getEndElement()
String	getObservedAllele()
StringType	getObservedAlleleElement()
Base[]	getProperty(int hash, String name, boolean checkValid)
String	getReferenceAllele()
StringType	getReferenceAlleleElement()
int	getStart()
IntegerType	getStartElement()
boolean	hasCigar()
boolean	hasCigarElement()
boolean	hasEnd()
boolean	hasEndElement()
boolean	hasObservedAllele()
boolean	hasObservedAlleleElement()
boolean	hasReferenceAllele()
boolean	hasReferenceAlleleElement()
boolean	hasStart()
boolean	hasStartElement()
boolean	isEmpty()
protected void	listChildren(List<Property> childrenList)
Base	makeProperty(int hash, String name)
Sequence.SequenceVariationComponent	setCigar(String value)
Sequence.SequenceVariationComponent	setCigarElement(StringType value)
Sequence.SequenceVariationComponent	setEnd(int value)
Sequence.SequenceVariationComponent	setEndElement(IntegerType value)
Sequence.SequenceVariationComponent	setObservedAllele(String value)
Sequence.SequenceVariationComponent	setObservedAlleleElement(StringType value)
void	setProperty(int hash, String name, Base value)
void	setProperty(String name, Base value)
Sequence.SequenceVariationComponent	setReferenceAllele(String value)
Sequence.SequenceVariationComponent	setReferenceAlleleElement(StringType value)
Sequence.SequenceVariationComponent	setStart(int value)
Sequence.SequenceVariationComponent	setStartElement(IntegerType value)

Methods inherited from class org.hl7.fhir.dstu2016may.model.BackboneElement

addModifierExtension, addModifierExtension, copyValues, getModifierExtension, hasModifierExtension

Methods inherited from class org.hl7.fhir.dstu2016may.model.Element

addExtension, addExtension, copyValues, getExtension, getExtensionsByUrl, getExtensionString, getId, getIdElement, hasExtension, hasExtension, hasId, hasIdElement, setId, setIdElement

Methods inherited from class org.hl7.fhir.dstu2016may.model.Base

castToActionDefinition, castToAddress, castToAnnotation, castToAttachment, castToBase64Binary, castToBoolean, castToCode, castToCodeableConcept, castToCoding, castToContactPoint, castToDataRequirement, castToDate, castToDateTime, castToDecimal, castToDuration, castToElementDefinition, castToExtension, castToHumanName, castToId, castToIdentifier, castToInstant, castToInteger, castToMarkdown, castToMeta, castToModuleMetadata, castToMoney, castToNarrative, castToOid, castToParameterDefinition, castToPeriod, castToPositiveInt, castToQuantity, castToRange, castToRatio, castToReference, castToResource, castToSampledData, castToSignature, castToSimpleQuantity, castToString, castToTime, castToTiming, castToTriggerDefinition, castToUnsignedInt, castToUri, children, compareDeep, compareDeep, compareDeep, compareValues, compareValues, equals, getChildByName, getFormatCommentsPost, getFormatCommentsPre, getUserData, getUserInt, getUserString, hasFormatComment, hasPrimitiveValue, hasType, hasUserData, isMetadataBased, isPrimitive, listChildrenByName, listChildrenByName, primitiveValue, setUserData, setUserDataINN

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.hl7.fhir.instance.model.api.IBase

getFormatCommentsPost, getFormatCommentsPre, hasFormatComment

Methods inherited from interface org.hl7.fhir.instance.model.api.IBaseHasExtensions

addExtension, getExtension, hasExtension

Methods inherited from interface org.hl7.fhir.instance.model.api.IBaseHasModifierExtensions

addModifierExtension, getModifierExtension, hasModifierExtension

Field Detail

start

protected IntegerType start

0-based start position (inclusive) of the variation on the reference sequence.

end

protected IntegerType end

0-based end position (exclusive) of the variation on the reference sequence.

observedAllele

protected StringType observedAllele

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.

referenceAllele

protected StringType referenceAllele

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.

cigar

protected StringType cigar

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).

Constructor Detail

SequenceVariationComponent

public SequenceVariationComponent()

Constructor

Method Detail

getStartElement

public IntegerType getStartElement()

Returns:

start (0-based start position (inclusive) of the variation on the reference sequence.). This is the underlying object with id, value and extensions. The accessor "getStart" gives direct access to the value

hasStartElement

public boolean hasStartElement()

hasStart

public boolean hasStart()

setStartElement

public Sequence.SequenceVariationComponent setStartElement(IntegerType value)

Parameters:

value - start (0-based start position (inclusive) of the variation on the reference sequence.). This is the underlying object with id, value and extensions. The accessor "getStart" gives direct access to the value

getStart

public int getStart()

Returns:

0-based start position (inclusive) of the variation on the reference sequence.

setStart

public Sequence.SequenceVariationComponent setStart(int value)

Parameters:

value - 0-based start position (inclusive) of the variation on the reference sequence.

getEndElement

public IntegerType getEndElement()

Returns:

end (0-based end position (exclusive) of the variation on the reference sequence.). This is the underlying object with id, value and extensions. The accessor "getEnd" gives direct access to the value

hasEndElement

public boolean hasEndElement()

hasEnd

public boolean hasEnd()

setEndElement

public Sequence.SequenceVariationComponent setEndElement(IntegerType value)

Parameters:

value - end (0-based end position (exclusive) of the variation on the reference sequence.). This is the underlying object with id, value and extensions. The accessor "getEnd" gives direct access to the value

getEnd

public int getEnd()

Returns:

0-based end position (exclusive) of the variation on the reference sequence.

setEnd

public Sequence.SequenceVariationComponent setEnd(int value)

Parameters:

value - 0-based end position (exclusive) of the variation on the reference sequence.

getObservedAlleleElement

public StringType getObservedAlleleElement()

Returns:

observedAllele (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 is the underlying object with id, value and extensions. The accessor "getObservedAllele" gives direct access to the value

hasObservedAlleleElement

public boolean hasObservedAlleleElement()

hasObservedAllele

public boolean hasObservedAllele()

setObservedAlleleElement

public Sequence.SequenceVariationComponent setObservedAlleleElement(StringType value)

Parameters:

value - observedAllele (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 is the underlying object with id, value and extensions. The accessor "getObservedAllele" gives direct access to the value

getObservedAllele

public String getObservedAllele()

Returns:

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.

setObservedAllele

public Sequence.SequenceVariationComponent setObservedAllele(String value)

Parameters:

value - 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.

getReferenceAlleleElement

public StringType getReferenceAlleleElement()

Returns:

referenceAllele (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 is the underlying object with id, value and extensions. The accessor "getReferenceAllele" gives direct access to the value

hasReferenceAlleleElement

public boolean hasReferenceAlleleElement()

hasReferenceAllele

public boolean hasReferenceAllele()

setReferenceAlleleElement

public Sequence.SequenceVariationComponent setReferenceAlleleElement(StringType value)

Parameters:

value - referenceAllele (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 is the underlying object with id, value and extensions. The accessor "getReferenceAllele" gives direct access to the value

getReferenceAllele

public String getReferenceAllele()

Returns:

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.

setReferenceAllele

public Sequence.SequenceVariationComponent setReferenceAllele(String value)

Parameters:

value - 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.

getCigarElement

public StringType getCigarElement()

Returns:

cigar (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).). This is the underlying object with id, value and extensions. The accessor "getCigar" gives direct access to the value

hasCigarElement

public boolean hasCigarElement()

hasCigar

public boolean hasCigar()

setCigarElement

public Sequence.SequenceVariationComponent setCigarElement(StringType value)

Parameters:

value - cigar (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).). This is the underlying object with id, value and extensions. The accessor "getCigar" gives direct access to the value

getCigar

public String getCigar()

Returns:

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).

setCigar

public Sequence.SequenceVariationComponent setCigar(String value)

Parameters:

value - 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).

listChildren

protected void listChildren(List<Property> childrenList)

Overrides:

listChildren in class BackboneElement

getProperty

public Base[] getProperty(int hash,
                          String name,
                          boolean checkValid)
                   throws org.hl7.fhir.exceptions.FHIRException

Overrides:

getProperty in class BackboneElement

Throws:

org.hl7.fhir.exceptions.FHIRException

setProperty

public void setProperty(int hash,
                        String name,
                        Base value)
                 throws org.hl7.fhir.exceptions.FHIRException

Overrides:

setProperty in class BackboneElement

Throws:

org.hl7.fhir.exceptions.FHIRException

setProperty

public void setProperty(String name,
                        Base value)
                 throws org.hl7.fhir.exceptions.FHIRException

Overrides:

setProperty in class BackboneElement

Throws:

org.hl7.fhir.exceptions.FHIRException

makeProperty

public Base makeProperty(int hash,
                         String name)
                  throws org.hl7.fhir.exceptions.FHIRException

Overrides:

makeProperty in class BackboneElement

Throws:

org.hl7.fhir.exceptions.FHIRException

addChild

public Base addChild(String name)
              throws org.hl7.fhir.exceptions.FHIRException

Overrides:

addChild in class BackboneElement

Throws:

org.hl7.fhir.exceptions.FHIRException

copy

public Sequence.SequenceVariationComponent copy()

Specified by:

copy in class BackboneElement

equalsDeep

public boolean equalsDeep(Base other)

Overrides:

equalsDeep in class BackboneElement

equalsShallow

public boolean equalsShallow(Base other)

Overrides:

equalsShallow in class BackboneElement

isEmpty

public boolean isEmpty()

Specified by:

isEmpty in interface org.hl7.fhir.instance.model.api.IBase

Overrides:

isEmpty in class BackboneElement

fhirType

public String fhirType()

Overrides:

fhirType in class BackboneElement