A C D E G H I J M N O P R S T U V W X

A

addConstraintAndValidator(Class<A>, Class<V>, boolean) - Method in class de.isas.mztab2.validation.MzTabBeanValidator

Allows registration of custom constraint / validator pairs on the validation configuration.

addConstraintAndValidator(Class<T>, Class<A>, Class<V>, boolean) - Method in class de.isas.mztab2.validation.MzTabBeanValidator

Allows registration of custom constraint / validator pairs on the validation configuration for a specific (unannotated) type.

AndValidationHandler - Class in de.isas.mztab2.validation.handlers

AndValidationHandler() - Constructor for class de.isas.mztab2.validation.handlers.AndValidationHandler

asParameter(Term) - Static method in class de.isas.mztab2.cvmapping.CvMappingUtils

asParameter(CvTerm) - Static method in class de.isas.mztab2.cvmapping.CvMappingUtils

C

clearCaches() - Method in class de.isas.mztab2.cvmapping.CvParameterLookupService

complement(Set<T>, Set<T>) - Static method in class de.isas.mztab2.cvmapping.SetOperations

Returns the complement (a without elements also in b) of a and b.

CvDefinitionValidationHandler - Class in de.isas.mztab2.validation

Validates that controlled vocabularies used by parameters are defined in the metadata CV section.

CvDefinitionValidationHandler() - Constructor for class de.isas.mztab2.validation.CvDefinitionValidationHandler

CvMappingUtils - Class in de.isas.mztab2.cvmapping

Utility methods for conversion between the mapping file domain and the mzTab domain.

CvMappingUtils() - Constructor for class de.isas.mztab2.cvmapping.CvMappingUtils

CvMappingValidator - Class in de.isas.mztab2.validation

Validator implementation that uses a provided xml mapping file with rules for required, recommended and optional CV parameters to assert that an mzTab follows these rules.

CvMappingValidator() - Constructor for class de.isas.mztab2.validation.CvMappingValidator

CvParameterLookupService - Class in de.isas.mztab2.cvmapping

Abstraction over OLSClient to autoconvert Terms to Parameters and to allow easy matching of Parameters against parent terms and their children.

CvParameterLookupService() - Constructor for class de.isas.mztab2.cvmapping.CvParameterLookupService

CvParameterLookupService(OLSClient) - Constructor for class de.isas.mztab2.cvmapping.CvParameterLookupService

CvParameterLookupService(OLSWsConfig) - Constructor for class de.isas.mztab2.cvmapping.CvParameterLookupService

CvRuleHandler - Interface in de.isas.mztab2.validation

CvTermSelectionHandler - Interface in de.isas.mztab2.validation

CvTermValidationHandler - Interface in de.isas.mztab2.validation

D

de.isas.mztab2.cvmapping - package de.isas.mztab2.cvmapping

de.isas.mztab2.validation - package de.isas.mztab2.validation

de.isas.mztab2.validation.handlers - package de.isas.mztab2.validation.handlers

E

EmptyRuleHandler - Class in de.isas.mztab2.validation.handlers

EmptyRuleHandler() - Constructor for class de.isas.mztab2.validation.handlers.EmptyRuleHandler

equals(Object) - Method in class de.isas.mztab2.cvmapping.RuleEvaluationResult

ExtraParametersValidationHandler - Class in de.isas.mztab2.validation.handlers

ExtraParametersValidationHandler() - Constructor for class de.isas.mztab2.validation.handlers.ExtraParametersValidationHandler

G

getAllowedParameters() - Method in class de.isas.mztab2.cvmapping.RuleEvaluationResult

getFilteredSelection() - Method in class de.isas.mztab2.cvmapping.RuleEvaluationResult

getFoundParameters() - Method in class de.isas.mztab2.cvmapping.RuleEvaluationResult

getPathLocatorString(ConstraintViolation<?>) - Method in class de.isas.mztab2.validation.MzTabBeanValidator

getPathLocatorString.

getRule() - Method in class de.isas.mztab2.cvmapping.RuleEvaluationResult

H

handleParameters(RuleEvaluationResult, boolean) - Method in interface de.isas.mztab2.validation.CvTermValidationHandler

handleParameters(RuleEvaluationResult, boolean) - Method in class de.isas.mztab2.validation.handlers.AndValidationHandler

handleParameters(RuleEvaluationResult, boolean) - Method in class de.isas.mztab2.validation.handlers.ExtraParametersValidationHandler

handleParameters(RuleEvaluationResult, boolean) - Method in class de.isas.mztab2.validation.handlers.OrValidationHandler

handleParameters(RuleEvaluationResult, boolean) - Method in class de.isas.mztab2.validation.handlers.SharedParametersValidationHandler

handleParameters(RuleEvaluationResult, boolean) - Method in class de.isas.mztab2.validation.handlers.XorValidationHandler

handleRule(CvMappingRule, List<Pair<Pointer, Parameter>>) - Method in interface de.isas.mztab2.validation.CvRuleHandler

handleRule(CvMappingRule, List<Pair<Pointer, Parameter>>) - Method in class de.isas.mztab2.validation.handlers.EmptyRuleHandler

handleRule(CvMappingRule, List<Pair<Pointer, Parameter>>) - Method in class de.isas.mztab2.validation.handlers.ResolvingCvRuleHandler

handleSelection(List<Pair<Pointer, Parameter>>) - Method in class de.isas.mztab2.cvmapping.RemoveUserParams

handleSelection(List<Pair<Pointer, Parameter>>) - Method in interface de.isas.mztab2.validation.CvTermSelectionHandler

hashCode() - Method in class de.isas.mztab2.cvmapping.RuleEvaluationResult

I

intersection(Set<T>, Set<T>) - Static method in class de.isas.mztab2.cvmapping.SetOperations

Returns the intersection (a \cap b, all common elements) of a and b.

isChildOfOrSame(Parameter, Parameter) - Method in class de.isas.mztab2.cvmapping.CvParameterLookupService

isEqualTo(Term, Parameter) - Static method in class de.isas.mztab2.cvmapping.CvMappingUtils

isEqualTo(Parameter, Parameter) - Static method in class de.isas.mztab2.cvmapping.CvMappingUtils

J

JxPathElement - Class in de.isas.mztab2.cvmapping

Utility methods for simpler Java 8 compatible handling of JXPath selections and pointers.

JxPathElement() - Constructor for class de.isas.mztab2.cvmapping.JxPathElement

M

MzTabBeanValidator - Class in de.isas.mztab2.validation

This validator used the HibernateValidator bean validation reference implementation.

MzTabBeanValidator() - Constructor for class de.isas.mztab2.validation.MzTabBeanValidator

Default constructor.

MzTabBeanValidator(boolean) - Constructor for class de.isas.mztab2.validation.MzTabBeanValidator

Constructor setting up the validator configuration and default constraint mapping.

N

newSet(Collection<? extends T>) - Static method in class de.isas.mztab2.cvmapping.SetOperations

Creates a new typed LinkedHashSet (preserving order of insertion) from the given collection.

niceToString(CvMappingRule) - Static method in class de.isas.mztab2.cvmapping.CvMappingUtils

O

of(File, boolean) - Static method in class de.isas.mztab2.validation.CvMappingValidator

of(File, CvParameterLookupService, boolean) - Static method in class de.isas.mztab2.validation.CvMappingValidator

of(URL, boolean) - Static method in class de.isas.mztab2.validation.CvMappingValidator

of(URL, CvParameterLookupService, boolean) - Static method in class de.isas.mztab2.validation.CvMappingValidator

of(CvMapping, CvParameterLookupService, boolean) - Static method in class de.isas.mztab2.validation.CvMappingValidator

OrValidationHandler - Class in de.isas.mztab2.validation.handlers

OrValidationHandler() - Constructor for class de.isas.mztab2.validation.handlers.OrValidationHandler

P

ParameterComparisonResult - Enum in de.isas.mztab2.cvmapping

Result of a comparison of a CvTerm T defined in a CvRule against the parameter P found via JXPath.

R

RemoveUserParams - Class in de.isas.mztab2.cvmapping

Removes user parameters from the provided selection.

RemoveUserParams() - Constructor for class de.isas.mztab2.cvmapping.RemoveUserParams

resolveChildren(Parameter, int) - Method in class de.isas.mztab2.cvmapping.CvParameterLookupService

resolveChildren(Parameter) - Method in class de.isas.mztab2.cvmapping.CvParameterLookupService

resolveParents(Parameter) - Method in class de.isas.mztab2.cvmapping.CvParameterLookupService

resolveParents(Parameter, int) - Method in class de.isas.mztab2.cvmapping.CvParameterLookupService

ResolvingCvRuleHandler - Class in de.isas.mztab2.validation.handlers

ResolvingCvRuleHandler(CvParameterLookupService) - Constructor for class de.isas.mztab2.validation.handlers.ResolvingCvRuleHandler

RuleEvaluationResult - Class in de.isas.mztab2.cvmapping

Captures results of applying a rule to a parameter selection.

RuleEvaluationResult(CvMappingRule, List<Pair<Pointer, Parameter>>, Map<String, Parameter>, Map<String, Pair<Pointer, Parameter>>) - Constructor for class de.isas.mztab2.cvmapping.RuleEvaluationResult

S

SetOperations - Class in de.isas.mztab2.cvmapping

Utility methods for sets with common names.

SetOperations() - Constructor for class de.isas.mztab2.cvmapping.SetOperations

SharedParametersValidationHandler - Class in de.isas.mztab2.validation.handlers

SharedParametersValidationHandler() - Constructor for class de.isas.mztab2.validation.handlers.SharedParametersValidationHandler

symmetricDifference(Set<T>, Set<T>) - Static method in class de.isas.mztab2.cvmapping.SetOperations

Returns the symmetric set difference (union(complement(a,b),complement(b,a))) on a and b.

T

toErrorLevel(CvMappingRule.RequirementLevel) - Static method in class de.isas.mztab2.cvmapping.CvMappingUtils

toList(Pointer, Class<? extends T>) - Static method in class de.isas.mztab2.cvmapping.JxPathElement

toList(JXPathContext, String, Class<? extends T>) - Static method in class de.isas.mztab2.cvmapping.JxPathElement

toStream(Pointer, Class<? extends T>) - Static method in class de.isas.mztab2.cvmapping.JxPathElement

toStream(Iterator, Class<? extends T>) - Static method in class de.isas.mztab2.cvmapping.JxPathElement

toStream(Iterator<? extends T>) - Static method in class de.isas.mztab2.cvmapping.JxPathElement

toString(CvMappingRule) - Static method in class de.isas.mztab2.cvmapping.CvMappingUtils

toString(List<CvTerm>) - Static method in class de.isas.mztab2.cvmapping.CvMappingUtils

toString() - Method in class de.isas.mztab2.cvmapping.RuleEvaluationResult

typedIter(Iterator, Class<? extends T>) - Static method in class de.isas.mztab2.cvmapping.JxPathElement

U

union(Set<T>, Set<T>) - Static method in class de.isas.mztab2.cvmapping.SetOperations

Returns the union (a+b) of a and b.

V

validate(MzTab) - Method in class de.isas.mztab2.validation.CvDefinitionValidationHandler

validate(MzTab) - Method in class de.isas.mztab2.validation.CvMappingValidator

validate(MzTab) - Method in class de.isas.mztab2.validation.MzTabBeanValidator

valueOf(String) - Static method in enum de.isas.mztab2.cvmapping.ParameterComparisonResult

Returns the enum constant of this type with the specified name.

values() - Static method in enum de.isas.mztab2.cvmapping.ParameterComparisonResult

Returns an array containing the constants of this enum type, in the order they are declared.

W

withPostValidator(Validator<MzTab>) - Method in class de.isas.mztab2.validation.CvMappingValidator

withPreValidator(Validator<MzTab>) - Method in class de.isas.mztab2.validation.CvMappingValidator

X

XorValidationHandler - Class in de.isas.mztab2.validation.handlers

XorValidationHandler() - Constructor for class de.isas.mztab2.validation.handlers.XorValidationHandler

A C D E G H I J M N O P R S T U V W X