A C D E G H I J M N O P R S T U V W X
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All Classes All Packages
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A
- addConstraintAndValidator(Class<A>, Class<V>, boolean) - Method in class de.isas.mztab2.validation.MzTabBeanValidator
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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
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Allows registration of custom constraint / validator pairs on the validation configuration for a specific (unannotated) type.
- AndValidationHandler - Class in de.isas.mztab2.validation.handlers
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Implements 'AND' logic, meaning all alternative possible terms or term roots for an object must occur.
- AndValidationHandler() - Constructor for class de.isas.mztab2.validation.handlers.AndValidationHandler
- asParameter(CvTerm) - Static method in class de.isas.mztab2.cvmapping.CvMappingUtils
- asParameter(Term) - Static method in class de.isas.mztab2.cvmapping.CvMappingUtils
C
- CHILD_OF - de.isas.mztab2.cvmapping.ParameterComparisonResult
- clearCaches() - Method in class de.isas.mztab2.cvmapping.CvParameterLookupService
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Clears all query result caches (parent and child).
- complement(Set<T>, Set<T>) - Static method in class de.isas.mztab2.cvmapping.SetOperations
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Returns the complement (a without elements also in b) of
aandb. - CvDefinitionValidationHandler - Class in de.isas.mztab2.validation
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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
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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
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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
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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
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Create a new instance of the lookup service with default OLS configuration.
- CvParameterLookupService(OLSClient) - Constructor for class de.isas.mztab2.cvmapping.CvParameterLookupService
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Create a new instance of the lookup service with a custom OLSClient.
- CvParameterLookupService(OLSWsConfig) - Constructor for class de.isas.mztab2.cvmapping.CvParameterLookupService
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Create a new instance of the lookup service with a custom OLSWsConfig configuration.
- CvRuleHandler - Interface in de.isas.mztab2.validation
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Interface for rule logic handling implementations.
- CvTermSelectionHandler - Interface in de.isas.mztab2.validation
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Interface for JxPath subtree selection handling.
- CvTermValidationHandler - Interface in de.isas.mztab2.validation
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Interface for handling of rule evaluation results.
D
- de.isas.mztab2.cvmapping - package de.isas.mztab2.cvmapping
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This package contains classes for controlled vocabulary term access, comparison, results and external cv parameter resolution.
- de.isas.mztab2.validation - package de.isas.mztab2.validation
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This package contains interfaces and implementations for the semantic validation via CvTerms.
- de.isas.mztab2.validation.handlers - package de.isas.mztab2.validation.handlers
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This package contains implementations for the semantic validation controlled vocabulary term rules.
E
- EmptyRuleHandler - Class in de.isas.mztab2.validation.handlers
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Implements handling of rules that have no cv parameter match.
- EmptyRuleHandler() - Constructor for class de.isas.mztab2.validation.handlers.EmptyRuleHandler
- ExtraParametersValidationHandler - Class in de.isas.mztab2.validation.handlers
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Implements handling of cv parameters (not user params) that are found at the object.
- ExtraParametersValidationHandler() - Constructor for class de.isas.mztab2.validation.handlers.ExtraParametersValidationHandler
G
- getPathLocatorString(ConstraintViolation<?>) - Method in class de.isas.mztab2.validation.MzTabBeanValidator
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getPathLocatorString.
H
- handleParameters(RuleEvaluationResult, boolean) - Method in interface de.isas.mztab2.validation.CvTermValidationHandler
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Implementations of this method should take care that they always return a list, even if it is empty.
- 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
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Handle the provided rule according to the implementor's logic.
- 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
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Handle the provided selection, e.g. by filtering it or by modifying elements therein.
I
- IDENTICAL - de.isas.mztab2.cvmapping.ParameterComparisonResult
- intersection(Set<T>, Set<T>) - Static method in class de.isas.mztab2.cvmapping.SetOperations
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Returns the intersection (a \cap b, all common elements) of
aandb. - isChildOfOrSame(Parameter, Parameter) - Method in class de.isas.mztab2.cvmapping.CvParameterLookupService
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Compares two parameters for their parent to child relationship.
- isEqualTo(Parameter, Parameter) - Static method in class de.isas.mztab2.cvmapping.CvMappingUtils
- isEqualTo(Term, Parameter) - Static method in class de.isas.mztab2.cvmapping.CvMappingUtils
J
- JxPathElement - Class in de.isas.mztab2.cvmapping
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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
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This validator used the HibernateValidator bean validation reference implementation.
- MzTabBeanValidator() - Constructor for class de.isas.mztab2.validation.MzTabBeanValidator
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Default constructor.
- MzTabBeanValidator(boolean) - Constructor for class de.isas.mztab2.validation.MzTabBeanValidator
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Constructor setting up the validator configuration and default constraint mapping.
N
- newSet(Collection<? extends T>) - Static method in class de.isas.mztab2.cvmapping.SetOperations
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Creates a new typed
LinkedHashSet(preserving order of insertion) from the given collection. - niceToString(CvMappingRule) - Static method in class de.isas.mztab2.cvmapping.CvMappingUtils
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Creates a user-friendly string of a mapping rule.
- NOT_RELATED - de.isas.mztab2.cvmapping.ParameterComparisonResult
O
- of(CvMapping, CvParameterLookupService, boolean) - Static method in class de.isas.mztab2.validation.CvMappingValidator
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Create a new instance of CvMappingValidator.
- of(File, boolean) - Static method in class de.isas.mztab2.validation.CvMappingValidator
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Create a new instance of CvMappingValidator.
- of(File, CvParameterLookupService, boolean) - Static method in class de.isas.mztab2.validation.CvMappingValidator
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Create a new instance of CvMappingValidator.
- of(URL, boolean) - Static method in class de.isas.mztab2.validation.CvMappingValidator
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Create a new instance of CvMappingValidator.
- of(URL, CvParameterLookupService, boolean) - Static method in class de.isas.mztab2.validation.CvMappingValidator
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Create a new instance of CvMappingValidator.
- OrValidationHandler - Class in de.isas.mztab2.validation.handlers
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Implements 'OR' logic, meaning alternative possible terms or term roots for an object may be present.
- OrValidationHandler() - Constructor for class de.isas.mztab2.validation.handlers.OrValidationHandler
P
- ParameterComparisonResult - Enum in de.isas.mztab2.cvmapping
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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
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Removes user parameters from the provided selection.
- RemoveUserParams() - Constructor for class de.isas.mztab2.cvmapping.RemoveUserParams
- resolveChildren(Parameter) - Method in class de.isas.mztab2.cvmapping.CvParameterLookupService
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Resolve all children of a parameter up to an arbitrary depth.
- resolveChildren(Parameter, int) - Method in class de.isas.mztab2.cvmapping.CvParameterLookupService
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Resolve all children of a parameter up to a given maximum depth (1 meaning immediate children, -1 meaning all).
- resolveParents(Parameter) - Method in class de.isas.mztab2.cvmapping.CvParameterLookupService
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Resolve all parents of parameter up to an arbitrary depth (actually height, since we go from bottom to top).
- resolveParents(Parameter, int) - Method in class de.isas.mztab2.cvmapping.CvParameterLookupService
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Resolve all parents of a parameter up to a given maximum depth (1 meaning the immediate parents, -1 meaning all).
- ResolvingCvRuleHandler - Class in de.isas.mztab2.validation.handlers
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Implements resolution of cv parameters using the provided lookup service.
- ResolvingCvRuleHandler(CvParameterLookupService) - Constructor for class de.isas.mztab2.validation.handlers.ResolvingCvRuleHandler
- RuleEvaluationResult - Class in de.isas.mztab2.cvmapping
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Captures results of applying a rule to a parameter selection.
- RuleEvaluationResult() - Constructor for class de.isas.mztab2.cvmapping.RuleEvaluationResult
S
- SetOperations - Class in de.isas.mztab2.cvmapping
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Utility methods for sets with common names.
- SetOperations() - Constructor for class de.isas.mztab2.cvmapping.SetOperations
- SharedParametersValidationHandler - Class in de.isas.mztab2.validation.handlers
-
Implements support for validating multiple parameters and the intersection between terms as described by the rule and the actually found ones.
- SharedParametersValidationHandler() - Constructor for class de.isas.mztab2.validation.handlers.SharedParametersValidationHandler
- symmetricDifference(Set<T>, Set<T>) - Static method in class de.isas.mztab2.cvmapping.SetOperations
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Returns the symmetric set difference (
union(complement(a,b),complement(b,a))) onaandb.
T
- toErrorLevel(CvMappingRule.RequirementLevel) - Static method in class de.isas.mztab2.cvmapping.CvMappingUtils
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Maps the provided requirement level to the corresponding MZTabErrorType.Level.
- toList(JXPathContext, String, Class<? extends T>) - Static method in class de.isas.mztab2.cvmapping.JxPathElement
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Returns the elements selected by the xpath expression from the provided JXPathContext as a list of the given object type.
- toList(Pointer, Class<? extends T>) - Static method in class de.isas.mztab2.cvmapping.JxPathElement
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Wrap the provided pointer as a list of the given object type.
- toStream(Iterator<? extends T>) - Static method in class de.isas.mztab2.cvmapping.JxPathElement
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Wraps the provided typed iterator into a stream, based on Spliterators.
- toStream(Iterator, Class<? extends T>) - Static method in class de.isas.mztab2.cvmapping.JxPathElement
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Creates a typed stream from an untyped (pre Java 6) iterator.
- toStream(Pointer, Class<? extends T>) - Static method in class de.isas.mztab2.cvmapping.JxPathElement
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Wrap the provided pointer as a stream of the given object type.
- toString(CvMappingRule) - Static method in class de.isas.mztab2.cvmapping.CvMappingUtils
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Creates a string representation of a mapping rule.
- toString(List<CvTerm>) - Static method in class de.isas.mztab2.cvmapping.CvMappingUtils
- typedIter(Iterator, Class<? extends T>) - Static method in class de.isas.mztab2.cvmapping.JxPathElement
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Creates a typed iterator from an untyped (pre Java 6) iterator.
U
- union(Set<T>, Set<T>) - Static method in class de.isas.mztab2.cvmapping.SetOperations
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Returns the union (a+b) of
aandb.
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
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Returns the enum constant of this type with the specified name.
- values() - Static method in enum de.isas.mztab2.cvmapping.ParameterComparisonResult
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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
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Add the provided validator implementation to the list of validators that run last.
- withPreValidator(Validator<MzTab>) - Method in class de.isas.mztab2.validation.CvMappingValidator
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Add the provided validator implementation to the list of validators that run first.
X
- XorValidationHandler - Class in de.isas.mztab2.validation.handlers
-
Implements 'XOR' logic, meaning mutually exclusive alternative possible terms or term roots for an object are allowed.
- XorValidationHandler() - Constructor for class de.isas.mztab2.validation.handlers.XorValidationHandler
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