Module org.phenopackets.phenopackettools.builder
Package org.phenopackets.phenopackettools.builder.builders

Class BiosampleBuilder

java.lang.Object
org.phenopackets.phenopackettools.builder.builders.BiosampleBuilder
public class BiosampleBuilder extends Object

  • Method Details

    • builder

      public static BiosampleBuilder builder(String id)

    • individualId

      public BiosampleBuilder individualId(String id)

    • derivedFromId

      public BiosampleBuilder derivedFromId(String id)

    • description

      public BiosampleBuilder description(String desc)

    • sampledTissue

      public BiosampleBuilder sampledTissue(org.phenopackets.schema.v2.core.OntologyClass tissue)

    • sampledType

      public BiosampleBuilder sampledType(org.phenopackets.schema.v2.core.OntologyClass tissue)

    • addPhenotypicFeature

      public BiosampleBuilder addPhenotypicFeature(String id, String label)

    • addPhenotypicFeature

      public BiosampleBuilder addPhenotypicFeature(org.phenopackets.schema.v2.core.PhenotypicFeature feature)

    • addAllPhenotypicFeatures

      public BiosampleBuilder addAllPhenotypicFeatures(List<org.phenopackets.schema.v2.core.PhenotypicFeature> features)

    • addMeasurement

      public BiosampleBuilder addMeasurement(org.phenopackets.schema.v2.core.Measurement measurement)

    • addAllMeasurements

      public BiosampleBuilder addAllMeasurements(List<org.phenopackets.schema.v2.core.Measurement> measurements)

    • taxonomy

      public BiosampleBuilder taxonomy(org.phenopackets.schema.v2.core.OntologyClass taxon)

    • timeOfCollection

      public BiosampleBuilder timeOfCollection(org.phenopackets.schema.v2.core.TimeElement time)

    • histologicalDiagnosis

      public BiosampleBuilder histologicalDiagnosis(org.phenopackets.schema.v2.core.OntologyClass histologicalDiagnosis)

    • tumorProgression

      public BiosampleBuilder tumorProgression(org.phenopackets.schema.v2.core.OntologyClass progression)

    • tumorGrade

      public BiosampleBuilder tumorGrade(org.phenopackets.schema.v2.core.OntologyClass grade)

    • pathologicalStage

      public BiosampleBuilder pathologicalStage(org.phenopackets.schema.v2.core.OntologyClass stage)

    • addPathologicalTnmFinding

      public BiosampleBuilder addPathologicalTnmFinding(org.phenopackets.schema.v2.core.OntologyClass tnmFinding)

    • addAllPathologicalTnmFindings

      public BiosampleBuilder addAllPathologicalTnmFindings(List<org.phenopackets.schema.v2.core.OntologyClass> tnmFindings)

    • addDiagnosticMarker

      public BiosampleBuilder addDiagnosticMarker(org.phenopackets.schema.v2.core.OntologyClass marker)

    • addAllDiagnosticMarkers

      public BiosampleBuilder addAllDiagnosticMarkers(List<org.phenopackets.schema.v2.core.OntologyClass> markers)

    • procedure

      public BiosampleBuilder procedure(org.phenopackets.schema.v2.core.Procedure procedure)

    • addFile

      public BiosampleBuilder addFile(org.phenopackets.schema.v2.core.File file)

    • addAllFiles

      public BiosampleBuilder addAllFiles(List<org.phenopackets.schema.v2.core.File> files)

    • materialSample

      public BiosampleBuilder materialSample(org.phenopackets.schema.v2.core.OntologyClass material)

    • sampleProcessing

      public BiosampleBuilder sampleProcessing(org.phenopackets.schema.v2.core.OntologyClass processing)

    • sampleStorage

      public BiosampleBuilder sampleStorage(org.phenopackets.schema.v2.core.OntologyClass storage)

    • build

      public org.phenopackets.schema.v2.core.Biosample build()