B C D E F G I M N O R S T U V

B

Behavior - Enum in org.biopax.validator.jaxb

Java class for Behavior.

BiopaxValidatorClient - Class in org.biopax.validator

Simple (example) BioPAX Validator client to upload and check BioPAX OWL files.

BiopaxValidatorClient(String) - Constructor for class org.biopax.validator.BiopaxValidatorClient

Main Constructor It configures for the validator's URL (defined by DEFAULT_VALIDATOR_URL constant) and result format ().

BiopaxValidatorClient() - Constructor for class org.biopax.validator.BiopaxValidatorClient

Default Constructor It configures for the default validator (defined by DEFAULT_VALIDATOR_URL constant) to return XML result.

BiopaxValidatorClient.RetFormat - Enum in org.biopax.validator

C

Category - Enum in org.biopax.validator.jaxb

Java class for Category.

category - Variable in class org.biopax.validator.jaxb.ErrorType

code - Variable in class org.biopax.validator.jaxb.ErrorType

comment - Variable in class org.biopax.validator.jaxb.Validation

createErrorCaseType() - Method in class org.biopax.validator.jaxb.ObjectFactory

Create an instance of ErrorCaseType

createErrorType() - Method in class org.biopax.validator.jaxb.ObjectFactory

Create an instance of ErrorType

createValidation() - Method in class org.biopax.validator.jaxb.ObjectFactory

Create an instance of Validation

createValidatorResponse() - Method in class org.biopax.validator.jaxb.ObjectFactory

Create an instance of ValidatorResponse

createValidatorResponse(ValidatorResponse) - Method in class org.biopax.validator.jaxb.ObjectFactory

Create an instance of JAXBElement<ValidatorResponse>}

D

DEFAULT_VALIDATOR_URL - Static variable in class org.biopax.validator.BiopaxValidatorClient

Default BioPAX Validator's URL

description - Variable in class org.biopax.validator.jaxb.Validation

E

error - Variable in class org.biopax.validator.jaxb.Validation

errorCase - Variable in class org.biopax.validator.jaxb.ErrorType

ErrorCaseType - Class in org.biopax.validator.jaxb

Java class for ErrorCaseType complex type.

ErrorCaseType() - Constructor for class org.biopax.validator.jaxb.ErrorCaseType

ErrorType - Class in org.biopax.validator.jaxb

Java class for ErrorType complex type.

ErrorType() - Constructor for class org.biopax.validator.jaxb.ErrorType

F

fix - Variable in class org.biopax.validator.jaxb.Validation

fixed - Variable in class org.biopax.validator.jaxb.ErrorCaseType

fromValue(String) - Static method in enum org.biopax.validator.jaxb.Behavior

fromValue(String) - Static method in enum org.biopax.validator.jaxb.Category

G

getCategory() - Method in class org.biopax.validator.jaxb.ErrorType

Gets the value of the category property.

getCode() - Method in class org.biopax.validator.jaxb.ErrorType

Gets the value of the code property.

getComment() - Method in class org.biopax.validator.jaxb.Validation

Gets the value of the comment property.

getDescription() - Method in class org.biopax.validator.jaxb.Validation

Gets the value of the description property.

getError() - Method in class org.biopax.validator.jaxb.Validation

Gets the value of the error property.

getErrorCase() - Method in class org.biopax.validator.jaxb.ErrorType

Gets the value of the errorCase property.

getMaxErrors() - Method in class org.biopax.validator.jaxb.Validation

Gets the value of the maxErrors property.

getMessage() - Method in class org.biopax.validator.jaxb.ErrorCaseType

Gets the value of the message property.

getMessage() - Method in class org.biopax.validator.jaxb.ErrorType

Gets the value of the message property.

getModelSerialized() - Method in class org.biopax.validator.jaxb.Validation

Gets the value of the modelSerialized property.

getNotFixedCases() - Method in class org.biopax.validator.jaxb.ErrorType

Gets the value of the notFixedCases property.

getNotFixedErrors() - Method in class org.biopax.validator.jaxb.Validation

Gets the value of the notFixedErrors property.

getNotFixedProblems() - Method in class org.biopax.validator.jaxb.Validation

Gets the value of the notFixedProblems property.

getObject() - Method in class org.biopax.validator.jaxb.ErrorCaseType

Gets the value of the object property.

getReportedBy() - Method in class org.biopax.validator.jaxb.ErrorCaseType

Gets the value of the reportedBy property.

getSummary() - Method in class org.biopax.validator.jaxb.Validation

Gets the value of the summary property.

getThreshold() - Method in class org.biopax.validator.jaxb.Validation

Gets the value of the threshold property.

getTotalCases() - Method in class org.biopax.validator.jaxb.ErrorType

Gets the value of the totalCases property.

getTotalProblemsFound() - Method in class org.biopax.validator.jaxb.Validation

Gets the value of the totalProblemsFound property.

getType() - Method in class org.biopax.validator.jaxb.ErrorType

Gets the value of the type property.

getUrl() - Method in class org.biopax.validator.BiopaxValidatorClient

getValidationResult() - Method in class org.biopax.validator.jaxb.ValidatorResponse

Gets the value of the validationResult property.

I

isFix() - Method in class org.biopax.validator.jaxb.Validation

Gets the value of the fix property.

isFixed() - Method in class org.biopax.validator.jaxb.ErrorCaseType

Gets the value of the fixed property.

isNormalize() - Method in class org.biopax.validator.jaxb.Validation

Gets the value of the normalize property.

M

maxErrors - Variable in class org.biopax.validator.jaxb.Validation

message - Variable in class org.biopax.validator.jaxb.ErrorCaseType

message - Variable in class org.biopax.validator.jaxb.ErrorType

modelSerialized - Variable in class org.biopax.validator.jaxb.Validation

N

normalize - Variable in class org.biopax.validator.jaxb.Validation

notFixedCases - Variable in class org.biopax.validator.jaxb.ErrorType

notFixedErrors - Variable in class org.biopax.validator.jaxb.Validation

notFixedProblems - Variable in class org.biopax.validator.jaxb.Validation

O

object - Variable in class org.biopax.validator.jaxb.ErrorCaseType

ObjectFactory - Class in org.biopax.validator.jaxb

This object contains factory methods for each Java content interface and Java element interface generated in the org.biopax.validator.jaxb package.

ObjectFactory() - Constructor for class org.biopax.validator.jaxb.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: org.biopax.validator.jaxb

org.biopax.validator - package org.biopax.validator

org.biopax.validator.jaxb - package org.biopax.validator.jaxb

R

reportedBy - Variable in class org.biopax.validator.jaxb.ErrorCaseType

S

setCategory(Category) - Method in class org.biopax.validator.jaxb.ErrorType

Sets the value of the category property.

setCode(String) - Method in class org.biopax.validator.jaxb.ErrorType

Sets the value of the code property.

setDescription(String) - Method in class org.biopax.validator.jaxb.Validation

Sets the value of the description property.

setFix(boolean) - Method in class org.biopax.validator.jaxb.Validation

Sets the value of the fix property.

setFixed(boolean) - Method in class org.biopax.validator.jaxb.ErrorCaseType

Sets the value of the fixed property.

setMaxErrors(int) - Method in class org.biopax.validator.jaxb.Validation

Sets the value of the maxErrors property.

setMessage(String) - Method in class org.biopax.validator.jaxb.ErrorCaseType

Sets the value of the message property.

setMessage(String) - Method in class org.biopax.validator.jaxb.ErrorType

Sets the value of the message property.

setModelSerialized(String) - Method in class org.biopax.validator.jaxb.Validation

Sets the value of the modelSerialized property.

setNormalize(boolean) - Method in class org.biopax.validator.jaxb.Validation

Sets the value of the normalize property.

setNotFixedCases(int) - Method in class org.biopax.validator.jaxb.ErrorType

Sets the value of the notFixedCases property.

setNotFixedErrors(int) - Method in class org.biopax.validator.jaxb.Validation

Sets the value of the notFixedErrors property.

setNotFixedProblems(int) - Method in class org.biopax.validator.jaxb.Validation

Sets the value of the notFixedProblems property.

setObject(String) - Method in class org.biopax.validator.jaxb.ErrorCaseType

Sets the value of the object property.

setReportedBy(String) - Method in class org.biopax.validator.jaxb.ErrorCaseType

Sets the value of the reportedBy property.

setSummary(String) - Method in class org.biopax.validator.jaxb.Validation

Sets the value of the summary property.

setThreshold(Behavior) - Method in class org.biopax.validator.jaxb.Validation

Sets the value of the threshold property.

setTotalCases(int) - Method in class org.biopax.validator.jaxb.ErrorType

Sets the value of the totalCases property.

setTotalProblemsFound(int) - Method in class org.biopax.validator.jaxb.Validation

Sets the value of the totalProblemsFound property.

setType(Behavior) - Method in class org.biopax.validator.jaxb.ErrorType

Sets the value of the type property.

setUrl(String) - Method in class org.biopax.validator.BiopaxValidatorClient

summary - Variable in class org.biopax.validator.jaxb.Validation

T

threshold - Variable in class org.biopax.validator.jaxb.Validation

totalCases - Variable in class org.biopax.validator.jaxb.ErrorType

totalProblemsFound - Variable in class org.biopax.validator.jaxb.Validation

type - Variable in class org.biopax.validator.jaxb.ErrorType

U

unmarshal(String) - Static method in class org.biopax.validator.BiopaxValidatorClient

V

validate(boolean, boolean, BiopaxValidatorClient.RetFormat, Behavior, Integer, String, File[], OutputStream) - Method in class org.biopax.validator.BiopaxValidatorClient

Checks a BioPAX OWL file(s) or resource using the online BioPAX Validator and prints the results to the output stream.

Validation - Class in org.biopax.validator.jaxb

Java class for Validation complex type.

Validation() - Constructor for class org.biopax.validator.jaxb.Validation

validationResult - Variable in class org.biopax.validator.jaxb.ValidatorResponse

ValidatorResponse - Class in org.biopax.validator.jaxb

Java class for ValidatorResponse complex type.

ValidatorResponse() - Constructor for class org.biopax.validator.jaxb.ValidatorResponse

value() - Method in enum org.biopax.validator.jaxb.Behavior

value() - Method in enum org.biopax.validator.jaxb.Category

valueOf(String) - Static method in enum org.biopax.validator.BiopaxValidatorClient.RetFormat

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

valueOf(String) - Static method in enum org.biopax.validator.jaxb.Behavior

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

valueOf(String) - Static method in enum org.biopax.validator.jaxb.Category

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

values() - Static method in enum org.biopax.validator.BiopaxValidatorClient.RetFormat

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

values() - Static method in enum org.biopax.validator.jaxb.Behavior

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

values() - Static method in enum org.biopax.validator.jaxb.Category

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

B C D E F G I M N O R S T U V