Class MolecularSequence.Quality
- java.lang.Object
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- org.linuxforhealth.fhir.model.visitor.AbstractVisitable
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- org.linuxforhealth.fhir.model.type.Element
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- org.linuxforhealth.fhir.model.type.BackboneElement
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- org.linuxforhealth.fhir.model.resource.MolecularSequence.Quality
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- All Implemented Interfaces:
Visitable
- Enclosing class:
- MolecularSequence
public static class MolecularSequence.Quality extends BackboneElement
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)).
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
MolecularSequence.Quality.Builder
static class
MolecularSequence.Quality.Roc
Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff.
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Field Summary
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Fields inherited from class org.linuxforhealth.fhir.model.type.BackboneElement
modifierExtension
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
accept(java.lang.String elementName, int elementIndex, Visitor visitor)
Accept a Visitor and invoke the appropriate visit methods.static MolecularSequence.Quality.Builder
builder()
boolean
equals(java.lang.Object obj)
Integer
getEnd()
End position of the sequence.Decimal
getFScore()
Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).Decimal
getGtFP()
The number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e.CodeableConcept
getMethod()
Which method is used to get sequence quality.Decimal
getPrecision()
QUERY.TP / (QUERY.TP + QUERY.FP).Decimal
getQueryFP()
False positives, i.e.Decimal
getQueryTP()
True positives, from the perspective of the query data, i.e.Decimal
getRecall()
TRUTH.TP / (TRUTH.TP + TRUTH.FN).MolecularSequence.Quality.Roc
getRoc()
Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff.Quantity
getScore()
The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.CodeableConcept
getStandardSequence()
Gold standard sequence used for comparing against.Integer
getStart()
Start position of the sequence.Decimal
getTruthFN()
False negatives, i.e.Decimal
getTruthTP()
True positives, from the perspective of the truth data, i.e.QualityType
getType()
INDEL / SNP / Undefined variant.boolean
hasChildren()
int
hashCode()
MolecularSequence.Quality.Builder
toBuilder()
Create a new Builder from the contents of this Element-
Methods inherited from class org.linuxforhealth.fhir.model.type.BackboneElement
getModifierExtension
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Methods inherited from class org.linuxforhealth.fhir.model.type.Element
as, getExtension, getId, hasValue, is
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Method Detail
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getType
public QualityType getType()
INDEL / SNP / Undefined variant.- Returns:
- An immutable object of type
QualityType
that is non-null.
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getStandardSequence
public CodeableConcept getStandardSequence()
Gold standard sequence used for comparing against.- Returns:
- An immutable object of type
CodeableConcept
that may be null.
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getStart
public Integer getStart()
Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.- Returns:
- An immutable object of type
Integer
that may be null.
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getEnd
public Integer getEnd()
End position of the 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.- Returns:
- An immutable object of type
Integer
that may be null.
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getScore
public Quantity getScore()
The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology. org/browser/current_svn/term/SO:0001685)).- Returns:
- An immutable object of type
Quantity
that may be null.
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getMethod
public CodeableConcept getMethod()
Which method is used to get sequence quality.- Returns:
- An immutable object of type
CodeableConcept
that may be null.
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getTruthTP
public Decimal getTruthTP()
True positives, from the perspective of the truth data, i.e. the number of sites in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.- Returns:
- An immutable object of type
Decimal
that may be null.
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getQueryTP
public Decimal getQueryTP()
True positives, from the perspective of the query data, i.e. the number of sites in the Query Call Set for which there are paths through the Truth Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.- Returns:
- An immutable object of type
Decimal
that may be null.
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getTruthFN
public Decimal getTruthFN()
False negatives, i.e. the number of sites in the Truth Call Set for which there is no path through the Query Call Set that is consistent with all of the alleles at this site, or sites for which there is an inaccurate genotype call for the event. Sites with correct variant but incorrect genotype are counted here.- Returns:
- An immutable object of type
Decimal
that may be null.
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getQueryFP
public Decimal getQueryFP()
False positives, i.e. the number of sites in the Query Call Set for which there is no path through the Truth Call Set that is consistent with this site. Sites with correct variant but incorrect genotype are counted here.- Returns:
- An immutable object of type
Decimal
that may be null.
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getGtFP
public Decimal getGtFP()
The number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e. cases where the truth is 1/1 and the query is 0/1 or similar).- Returns:
- An immutable object of type
Decimal
that may be null.
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getPrecision
public Decimal getPrecision()
QUERY.TP / (QUERY.TP + QUERY.FP).- Returns:
- An immutable object of type
Decimal
that may be null.
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getRecall
public Decimal getRecall()
TRUTH.TP / (TRUTH.TP + TRUTH.FN).- Returns:
- An immutable object of type
Decimal
that may be null.
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getFScore
public Decimal getFScore()
Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).- Returns:
- An immutable object of type
Decimal
that may be null.
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getRoc
public MolecularSequence.Quality.Roc getRoc()
Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff.- Returns:
- An immutable object of type
MolecularSequence.Quality.Roc
that may be null.
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hasChildren
public boolean hasChildren()
- Overrides:
hasChildren
in classBackboneElement
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accept
public void accept(java.lang.String elementName, int elementIndex, Visitor visitor)
Description copied from interface:Visitable
Accept a Visitor and invoke the appropriate visit methods. A typical implementation would look like this:if (visitor.preVisit(this)) { visitor.visitStart(elementName, elementIndex, this); if (visitor.visit(elementName, elementIndex, this)) { // visit children } visitor.visitEnd(elementName, elementIndex, this); visitor.postVisit(this); }
- Specified by:
accept
in interfaceVisitable
- Specified by:
accept
in classAbstractVisitable
- Parameters:
elementName
- the name of the element in the context of this visitelementIndex
- the index of the element in a list or -1 if it is not contained within a Listvisitor
- the visitor to use
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equals
public boolean equals(java.lang.Object obj)
- Overrides:
equals
in classjava.lang.Object
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hashCode
public int hashCode()
- Overrides:
hashCode
in classjava.lang.Object
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toBuilder
public MolecularSequence.Quality.Builder toBuilder()
Description copied from class:Element
Create a new Builder from the contents of this Element- Specified by:
toBuilder
in classBackboneElement
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builder
public static MolecularSequence.Quality.Builder builder()
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