Class PhenopacketData
java.lang.Object
org.monarchinitiative.lirical.io.analysis.PhenopacketData
- All Implemented Interfaces:
SanitationInputs
Phenopacket attributes that are relevant for LIRICAL.
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Method Summary
Modifier and TypeMethodDescriptionage()
List<org.monarchinitiative.phenol.ontology.data.TermId>
boolean
Stream<org.monarchinitiative.phenol.ontology.data.TermId>
int
hashCode()
parseAge()
Try to parse the age and return an empty optional if the parsing fails.parseSex()
Try to parse the sex and return an empty optional if the parsing fails.Stream<org.monarchinitiative.phenol.ontology.data.TermId>
sampleId()
sex()
toString()
variants()
vcf()
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Method Details
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sampleId
- Specified by:
sampleId
in interfaceSanitationInputs
- Returns:
- a string with the sample ID or
null
if not available.
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presentHpoTerms
- Specified by:
presentHpoTerms
in interfaceSanitationInputs
- Returns:
- a list with CURIEs of HPO terms that represent the phenotypic features observed in the index patient.
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presentHpoTermIds
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excludedHpoTerms
- Specified by:
excludedHpoTerms
in interfaceSanitationInputs
- Returns:
- a list with CURIEs of HPO terms that represent the phenotypic features that were investigated and excluded in the index patient.
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excludedHpoTermIds
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age
- Specified by:
age
in interfaceSanitationInputs
- Returns:
- a string with the age or
null
if not available.
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parseAge
Try to parse the age and return an empty optional if the parsing fails. -
sex
- Specified by:
sex
in interfaceSanitationInputs
- Returns:
- a string with the sex or
null
if not available.
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parseSex
Try to parse the sex and return an empty optional if the parsing fails. -
vcf
- Specified by:
vcf
in interfaceSanitationInputs
- Returns:
- a string with the path of the VCF file with variants or
null
if not available.
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genomeAssembly
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variants
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diseaseIds
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equals
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hashCode
public int hashCode() -
toString
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