Deprecated API

Contents

• Terminally Deprecated
• Fields
• Methods

Terminally Deprecated Elements

Element	Description
org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder.builder()	use VariationDescriptorBuilder.builder(String) instead. The id is a required field and it should not be possible to create a builder without an id.
org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators.cohortHpoPhenotypeValidator(MinimalOntology)	use HpoPhenotypeValidators.Primary.cohortHpoPhenotypeValidator(MinimalOntology) instead
org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators.familyHpoPhenotypeValidator(MinimalOntology)	use HpoPhenotypeValidators.Primary.familyHpoPhenotypeValidator(MinimalOntology) instead
org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators.phenopacketHpoPhenotypeValidator(MinimalOntology)	use HpoPhenotypeValidators.Primary.phenopacketHpoPhenotypeValidator(MinimalOntology) instead
org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunnerBuilder.addAllSemanticValidators(List<PhenopacketValidator<T>>)	use ValidationWorkflowRunnerBuilder.addValidators(Collection) instead
org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunnerBuilder.addAllSyntaxValidators(List<PhenopacketValidator<T>>)	use ValidationWorkflowRunnerBuilder.addValidators(Collection) instead
org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunnerBuilder.addSemanticValidator(PhenopacketValidator<T>)	use ValidationWorkflowRunnerBuilder.addValidator(PhenopacketValidator) instead
org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunnerBuilder.addSyntaxValidator(PhenopacketValidator<T>)	use ValidationWorkflowRunnerBuilder.addValidator(PhenopacketValidator) instead
org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunnerBuilder.semanticValidators	use ValidationWorkflowRunnerBuilder.validators instead
org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunnerBuilder.syntaxValidators	use ValidationWorkflowRunnerBuilder.validators instead

Deprecated Fields

Field	Description
org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunnerBuilder.semanticValidators	use ValidationWorkflowRunnerBuilder.validators instead
org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunnerBuilder.syntaxValidators	use ValidationWorkflowRunnerBuilder.validators instead

Deprecated Methods

Method	Description
org.phenopackets.phenopackettools.builder.builders.VariationDescriptorBuilder.builder()	use VariationDescriptorBuilder.builder(String) instead. The id is a required field and it should not be possible to create a builder without an id.
org.phenopackets.phenopackettools.util.format.ElementSniffer.sniff(byte[], PhenopacketSchemaVersion, PhenopacketFormat)	in favor of ElementSniffer.sniff(byte[], PhenopacketFormat)
org.phenopackets.phenopackettools.util.format.ElementSniffer.sniff(InputStream, PhenopacketSchemaVersion, PhenopacketFormat)	in favor of ElementSniffer.sniff(InputStream, PhenopacketFormat).
org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators.cohortHpoPhenotypeValidator(MinimalOntology)	use HpoPhenotypeValidators.Primary.cohortHpoPhenotypeValidator(MinimalOntology) instead
org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators.familyHpoPhenotypeValidator(MinimalOntology)	use HpoPhenotypeValidators.Primary.familyHpoPhenotypeValidator(MinimalOntology) instead
org.phenopackets.phenopackettools.validator.core.phenotype.HpoPhenotypeValidators.phenopacketHpoPhenotypeValidator(MinimalOntology)	use HpoPhenotypeValidators.Primary.phenopacketHpoPhenotypeValidator(MinimalOntology) instead
org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunnerBuilder.addAllSemanticValidators(List<PhenopacketValidator<T>>)	use ValidationWorkflowRunnerBuilder.addValidators(Collection) instead
org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunnerBuilder.addAllSyntaxValidators(List<PhenopacketValidator<T>>)	use ValidationWorkflowRunnerBuilder.addValidators(Collection) instead
org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunnerBuilder.addSemanticValidator(PhenopacketValidator<T>)	use ValidationWorkflowRunnerBuilder.addValidator(PhenopacketValidator) instead
org.phenopackets.phenopackettools.validator.core.ValidationWorkflowRunnerBuilder.addSyntaxValidator(PhenopacketValidator<T>)	use ValidationWorkflowRunnerBuilder.addValidator(PhenopacketValidator) instead