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A

acc - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
 
addAdditionalField(String, String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
 
addCrossReferenceValue(String, String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
Add a new cross-reference key/value to the corss-references list
addCrossReferenceValue(String, Set<String>) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
Add a new cross-reference key/value to the corss-references list
addDate(Date) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
 
addDate(String, String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
 
addDefaultPublicationDate() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.DatesType
 
addEntry(Entry) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entries
 
AdditionalFields - Class in uk.ac.ebi.ddi.xml.validator.parser.model
Java class for additional_fieldsType complex type.
AdditionalFields() - Constructor for class uk.ac.ebi.ddi.xml.validator.parser.model.AdditionalFields
 
additionalFields - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
 
afterMarshal(Object) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.ObjectClassListener
 
authors - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
 

B

beforeMarshal(Object) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.ObjectClassListener
 
BiologicalDatabases - Enum in uk.ac.ebi.ddi.xml.validator.utils
This code is licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
boost - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry.Name
 
boost - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.Field
 
boost - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.Reference
 

C

close() - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
close() - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.OmicsDataMarshaller
 
close() - Method in class uk.ac.ebi.ddi.xml.validator.parser.OmicsXMLFile
Close the Reader
containsPublicationDate() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.DatesType
 
containsValue(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.CrossReferences
 
createAdditionalFields() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.ObjectFactory
 
createCrossReferences() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.ObjectFactory
 
createDatabase() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.ObjectFactory
 
createDatabase(Database) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.ObjectFactory
 
createDate() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.ObjectFactory
 
createDatesType() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.ObjectFactory
 
createEntries() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.ObjectFactory
 
createEntry() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.ObjectFactory
 
createEntryName() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.ObjectFactory
 
createField() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.ObjectFactory
 
createReference() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.ObjectFactory
 
CrossReferences - Class in uk.ac.ebi.ddi.xml.validator.parser.model
Java class for cross_referencesType complex type.
CrossReferences() - Constructor for class uk.ac.ebi.ddi.xml.validator.parser.model.CrossReferences
 
crossReferences - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
 

D

Database - Class in uk.ac.ebi.ddi.xml.validator.parser.model
Java class for databaseType complex type.
Database() - Constructor for class uk.ac.ebi.ddi.xml.validator.parser.model.Database
 
DataElement - Enum in uk.ac.ebi.ddi.xml.validator.parser.model
 
DataObject - Class in uk.ac.ebi.ddi.xml.validator.parser.model
 
DataObject() - Constructor for class uk.ac.ebi.ddi.xml.validator.parser.model.DataObject
 
DatasetType - Enum in uk.ac.ebi.ddi.xml.validator.utils
This code is licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
Date - Class in uk.ac.ebi.ddi.xml.validator.parser.model
Java class for dateType complex type.
Date() - Constructor for class uk.ac.ebi.ddi.xml.validator.parser.model.Date
Default constructor
Date(String, String) - Constructor for class uk.ac.ebi.ddi.xml.validator.parser.model.Date
Constructor with both parameters
date - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.DatesType
 
dates - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
 
DatesType - Class in uk.ac.ebi.ddi.xml.validator.parser.model
Java class for datesType complex type.
DatesType() - Constructor for class uk.ac.ebi.ddi.xml.validator.parser.model.DatesType
 
dbkey - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.Reference
 
dbname - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.Reference
 
DDIException - Exception in uk.ac.ebi.ddi.xml.validator.exception
 
DDIException() - Constructor for exception uk.ac.ebi.ddi.xml.validator.exception.DDIException
 
DDIException(String) - Constructor for exception uk.ac.ebi.ddi.xml.validator.exception.DDIException
 
DDIException(String, Throwable) - Constructor for exception uk.ac.ebi.ddi.xml.validator.exception.DDIException
 
DDIException(Throwable) - Constructor for exception uk.ac.ebi.ddi.xml.validator.exception.DDIException
 
DDIException(String, Throwable, boolean, boolean) - Constructor for exception uk.ac.ebi.ddi.xml.validator.exception.DDIException
 
description - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.Database
 
description - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
 
description - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.SummaryDatabase
 

E

emptyElements - Variable in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.MarshallerFactory
 
entries - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.Database
 
Entries - Class in uk.ac.ebi.ddi.xml.validator.parser.model
Java class for entriesType complex type.
Entries() - Constructor for class uk.ac.ebi.ddi.xml.validator.parser.model.Entries
Default constructor
Entries(List<Entry>) - Constructor for class uk.ac.ebi.ddi.xml.validator.parser.model.Entries
Constructor with all the entries by default
entry - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.Entries
 
Entry - Class in uk.ac.ebi.ddi.xml.validator.parser.model
Java class for entryType complex type.
Entry() - Constructor for class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
 
Entry.Name - Class in uk.ac.ebi.ddi.xml.validator.parser.model
Java class for anonymous complex type.
ENTRY_NOT_FOUND - Static variable in class uk.ac.ebi.ddi.xml.validator.utils.Utils
 
entryCount - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.Database
 
entryCount - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.SummaryDatabase
 
equals(Object) - Method in class uk.ac.ebi.ddi.xml.validator.utils.Tuple
 
ERROR - Static variable in class uk.ac.ebi.ddi.xml.validator.utils.Utils
 
escapeCharacters(String) - Static method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLUtilities
Substitutes all illegal characters in the given string by the value of EscapingXMLUtilities.SUBSTITUTE.
EscapingXMLStreamWriter - Class in uk.ac.ebi.ddi.xml.validator.parser.marshaller
Delegating XMLStreamWriter that filters out UTF-8 characters that are illegal in XML.
EscapingXMLStreamWriter(XMLStreamWriter) - Constructor for class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
EscapingXMLUtilities - Class in uk.ac.ebi.ddi.xml.validator.parser.marshaller
 

F

field - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.AdditionalFields
 
Field - Class in uk.ac.ebi.ddi.xml.validator.parser.model
Java class for fieldType complex type.
Field() - Constructor for class uk.ac.ebi.ddi.xml.validator.parser.model.Field
 
flush() - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 

G

generateSummaryReport(Map<File, List<Tuple>>, PrintStream, String) - Static method in class uk.ac.ebi.ddi.xml.validator.cli.ValidatorCLI
 
getAcc() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
Gets the value of the acc property.
getAdditionalFields() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
Gets the value of the additionalFields property.
getAdditionalFieldValue(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
 
getAdditionalFieldValues(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
Return of a key all the values in the Entry fot the given key
getAllEntries() - Method in class uk.ac.ebi.ddi.xml.validator.parser.OmicsXMLFile
 
getAuthors() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
Gets the value of the authors property.
getBoost() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry.Name
Gets the value of the boost property.
getBoost() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Field
Gets the value of the boost property.
getBoost() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Reference
Gets the value of the boost property.
getClassType() - Method in enum uk.ac.ebi.ddi.xml.validator.parser.model.DataElement
 
getCrossReferenceFieldValue(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
Return a list of values for specific cross-reference database
getCrossReferences() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
Gets the value of the crossReferences property.
getDatabaseName() - Method in class uk.ac.ebi.ddi.xml.validator.parser.OmicsXMLFile
 
getDate() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.DatesType
Gets the value of the date property.
getDateByKey(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.DatesType
 
getDates() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
Gets the value of the dates property.
getDbkey() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Reference
Gets the value of the dbkey property.
getDbname() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Reference
Gets the value of the dbname property.
getDescription() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Database
Gets the value of the description property.
getDescription() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
Gets the value of the description property.
getDescription() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.SummaryDatabase
 
getDescription() - Method in class uk.ac.ebi.ddi.xml.validator.parser.OmicsXMLFile
 
getDescription() - Method in enum uk.ac.ebi.ddi.xml.validator.utils.DatasetType
 
getEntries() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Database
Gets the value of the entries property.
getEntry() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entries
Gets the value of the entry property.
getEntryById(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.OmicsXMLFile
This function return the information of an element using the the id in the XML, for example PXD00001
getEntryByIndex(Integer) - Method in class uk.ac.ebi.ddi.xml.validator.parser.OmicsXMLFile
THis function return an entry using the index element in the file for example first element (index = 0), second element (index = 1)
getEntryCount() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Database
Gets the value of the entryCount property.
getEntryCount() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.SummaryDatabase
 
getEntryCount() - Method in class uk.ac.ebi.ddi.xml.validator.parser.OmicsXMLFile
 
getEntryIds() - Method in class uk.ac.ebi.ddi.xml.validator.parser.OmicsXMLFile
Return all the entry Ids from the XML
getField() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.AdditionalFields
Gets the value of the field property.
getFullName() - Method in enum uk.ac.ebi.ddi.xml.validator.utils.BiologicalDatabases
 
getFullName() - Method in enum uk.ac.ebi.ddi.xml.validator.utils.OmicsType
 
getHid() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.DataObject
 
getId() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
Gets the value of the id property.
getInstance() - Static method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.MarshallerFactory
 
getInstance() - Static method in class uk.ac.ebi.ddi.xml.validator.parser.unmarshaller.OmicsUnmarshallerFactory
 
getKey() - Method in class uk.ac.ebi.ddi.xml.validator.utils.Tuple
 
getKeywords() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
Gets the value of the keywords property.
getName() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Database
Gets the value of the name property.
getName() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
Gets the value of the name property.
getName() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Field
Gets the value of the name property.
getName() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.SummaryDatabase
 
getName() - Method in class uk.ac.ebi.ddi.xml.validator.parser.OmicsXMLFile
 
getName() - Method in enum uk.ac.ebi.ddi.xml.validator.utils.BiologicalDatabases
 
getName() - Method in enum uk.ac.ebi.ddi.xml.validator.utils.DatasetType
 
getName() - Method in enum uk.ac.ebi.ddi.xml.validator.utils.OmicsType
 
getNamespaceContext() - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
getOmicsType(String) - Static method in enum uk.ac.ebi.ddi.xml.validator.utils.OmicsType
 
getParentType() - Method in enum uk.ac.ebi.ddi.xml.validator.utils.DatasetType
 
getParentType() - Method in enum uk.ac.ebi.ddi.xml.validator.utils.OmicsType
 
getPrefix(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
getProperty(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
getQNameForClass(Class<? extends IDataObject>) - Static method in class uk.ac.ebi.ddi.xml.validator.parser.model.ModelConstants
 
getRef() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.CrossReferences
Gets the value of the ref property.
getRelease() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Database
Gets the value of the release property.
getRelease() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.SummaryDatabase
 
getRelease() - Method in class uk.ac.ebi.ddi.xml.validator.parser.OmicsXMLFile
 
getReleaseDate() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Database
Gets the value of the releaseDate property.
getReleaseDate() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.SummaryDatabase
 
getReleaseDate() - Method in class uk.ac.ebi.ddi.xml.validator.parser.OmicsXMLFile
 
getRepository() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
 
getType() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Date
Gets the value of the type property.
getValue() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Date
Gets the value of the value property.
getValue() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry.Name
Gets the value of the value property.
getValue() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Field
Gets the value of the value property.
getValue() - Method in class uk.ac.ebi.ddi.xml.validator.utils.Tuple
 
getXpath() - Method in enum uk.ac.ebi.ddi.xml.validator.parser.model.DataElement
 
getXpaths() - Static method in enum uk.ac.ebi.ddi.xml.validator.parser.model.DataElement
 

H

hasFileHeader(File) - Static method in class uk.ac.ebi.ddi.xml.validator.parser.OmicsXMLFile
 
hashCode() - Method in class uk.ac.ebi.ddi.xml.validator.utils.Tuple
 
hid - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.DataObject
 

I

id - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
 
IDataObject - Interface in uk.ac.ebi.ddi.xml.validator.parser.model
 
initializeMarshaller() - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.MarshallerFactory
 
initializeUnmarshaller() - Method in class uk.ac.ebi.ddi.xml.validator.parser.unmarshaller.OmicsUnmarshallerFactory
 
isEmpty() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.AdditionalFields
 
isEmpty() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.CrossReferences
 
isEmpty() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.DatesType
 
isSchemaValid(File) - Static method in class uk.ac.ebi.ddi.xml.validator.parser.OmicsXMLFile
 

J

JAXB_ENCODING_PROPERTY - Static variable in class uk.ac.ebi.ddi.xml.validator.parser.model.ModelConstants
 
JAXB_FORMATTING_PROPERTY - Static variable in class uk.ac.ebi.ddi.xml.validator.parser.model.ModelConstants
 
JAXB_FRAGMENT_PROPERTY - Static variable in class uk.ac.ebi.ddi.xml.validator.parser.model.ModelConstants
 

K

keywords - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
 

M

main(String[]) - Static method in class uk.ac.ebi.ddi.xml.validator.cli.ValidatorCLI
 
marshal(Long) - Method in class uk.ac.ebi.ddi.xml.validator.utils.NonNegativeIntegerAdapter
 
marshall(T) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.OmicsDataMarshaller
 
marshall(T, OutputStream) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.OmicsDataMarshaller
 
marshall(T, Writer) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.OmicsDataMarshaller
 
MarshallerFactory - Class in uk.ac.ebi.ddi.xml.validator.parser.marshaller
 
MODEL_PKG - Static variable in class uk.ac.ebi.ddi.xml.validator.parser.model.ModelConstants
 
ModelConstants - Class in uk.ac.ebi.ddi.xml.validator.parser.model
 
ModelConstants() - Constructor for class uk.ac.ebi.ddi.xml.validator.parser.model.ModelConstants
 

N

name - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.Database
 
name - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
 
Name() - Constructor for class uk.ac.ebi.ddi.xml.validator.parser.model.Entry.Name
 
name - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.Field
 
name - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.SummaryDatabase
 
NonNegativeIntegerAdapter - Class in uk.ac.ebi.ddi.xml.validator.utils
 
NonNegativeIntegerAdapter() - Constructor for class uk.ac.ebi.ddi.xml.validator.utils.NonNegativeIntegerAdapter
 
NOT_FOUND_MESSAGE - Static variable in class uk.ac.ebi.ddi.xml.validator.utils.Utils
 
NOT_FOUND_UPDATED - Static variable in class uk.ac.ebi.ddi.xml.validator.utils.Utils
 

O

ObjectClassListener - Class in uk.ac.ebi.ddi.xml.validator.parser.marshaller
 
ObjectClassListener() - Constructor for class uk.ac.ebi.ddi.xml.validator.parser.marshaller.ObjectClassListener
 
ObjectFactory - Class in uk.ac.ebi.ddi.xml.validator.parser.model
This object contains factory methods for each Java content interface and Java element interface generated in the uk.ac.ebi.ddi.xml.validator.parser.model package.
ObjectFactory() - Constructor for class uk.ac.ebi.ddi.xml.validator.parser.model.ObjectFactory
Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: uk.ac.ebi.ddi.xml.validator.parser.model
OmicsDataMarshaller - Class in uk.ac.ebi.ddi.xml.validator.parser.marshaller
 
OmicsDataMarshaller() - Constructor for class uk.ac.ebi.ddi.xml.validator.parser.marshaller.OmicsDataMarshaller
 
OmicsDataUnmarshaller - Interface in uk.ac.ebi.ddi.xml.validator.parser.unmarshaller
 
OmicsType - Enum in uk.ac.ebi.ddi.xml.validator.utils
This code is licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
OmicsUnmarshallerFactory - Class in uk.ac.ebi.ddi.xml.validator.parser.unmarshaller
 
OmicsXMLFile - Class in uk.ac.ebi.ddi.xml.validator.parser
This class reads an XML file for DDI and generate a set of data structures to handle the underlying data structures, objects IT also provide classes for validation using the DDI Schema, etc.
OmicsXMLFile(File) - Constructor for class uk.ac.ebi.ddi.xml.validator.parser.OmicsXMLFile
 

R

ref - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.CrossReferences
 
Reference - Class in uk.ac.ebi.ddi.xml.validator.parser.model
Java class for refType complex type.
Reference() - Constructor for class uk.ac.ebi.ddi.xml.validator.parser.model.Reference
 
release - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.Database
 
release - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.SummaryDatabase
 
releaseDate - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.Database
 
releaseDate - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.SummaryDatabase
 
removeCrossReferences(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
 
REPORT_SPACE - Static variable in class uk.ac.ebi.ddi.xml.validator.utils.Utils
 

S

setAcc(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
Sets the value of the acc property.
setAdditionalFields(AdditionalFields) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
Sets the value of the additionalFields property.
setAuthors(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
Sets the value of the authors property.
setBoost(Float) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry.Name
Sets the value of the boost property.
setBoost(Float) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Field
Sets the value of the boost property.
setBoost(Float) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Reference
Sets the value of the boost property.
setCrossReferences(CrossReferences) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
Sets the value of the crossReferences property.
setCrossReferences(List<Reference>) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
 
setDatabaseName(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.OmicsXMLFile
 
setDates(DatesType) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
Sets the value of the dates property.
setDbkey(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Reference
Sets the value of the dbkey property.
setDbname(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Reference
Sets the value of the dbname property.
setDefaultNamespace(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
setDescription(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Database
Sets the value of the description property.
setDescription(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
Sets the value of the description property.
setDescription(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.SummaryDatabase
 
setDescription(String) - Method in enum uk.ac.ebi.ddi.xml.validator.utils.DatasetType
 
setEntries(Entries) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Database
Sets the value of the entries property.
setEntries(List<Entry>) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Database
 
setEntryCount(Integer) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Database
Sets the value of the entryCount property.
setEntryCount(Integer) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.SummaryDatabase
 
setField(List<Field>) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.AdditionalFields
 
setFullName(String) - Method in enum uk.ac.ebi.ddi.xml.validator.utils.BiologicalDatabases
 
setFullName(String) - Method in enum uk.ac.ebi.ddi.xml.validator.utils.OmicsType
 
setId(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
Sets the value of the id property.
setKey(K) - Method in class uk.ac.ebi.ddi.xml.validator.utils.Tuple
 
setKeywords(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
Sets the value of the keywords property.
setName(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Database
Sets the value of the name property.
setName(Entry.Name) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
Sets the value of the name property.
setName(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
 
setName(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Field
Sets the value of the name property.
setName(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.SummaryDatabase
 
setName(String) - Method in enum uk.ac.ebi.ddi.xml.validator.utils.BiologicalDatabases
 
setName(String) - Method in enum uk.ac.ebi.ddi.xml.validator.utils.DatasetType
 
setName(String) - Method in enum uk.ac.ebi.ddi.xml.validator.utils.OmicsType
 
setNamespaceContext(NamespaceContext) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
setParentType(DatasetType) - Method in enum uk.ac.ebi.ddi.xml.validator.utils.DatasetType
 
setParentType(OmicsType[]) - Method in enum uk.ac.ebi.ddi.xml.validator.utils.OmicsType
 
setPrefix(String, String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
setRef(List<Reference>) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.CrossReferences
 
setRelease(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Database
Sets the value of the release property.
setRelease(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.SummaryDatabase
 
setReleaseDate(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Database
Sets the value of the releaseDate property.
setReleaseDate(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.SummaryDatabase
 
setType(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Date
Sets the value of the type property.
setValue(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Date
Sets the value of the value property.
setValue(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry.Name
Sets the value of the value property.
setValue(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Field
Sets the value of the value property.
setValue(V) - Method in class uk.ac.ebi.ddi.xml.validator.utils.Tuple
 
SUBSTITUTE - Static variable in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLUtilities
 
SummaryDatabase - Class in uk.ac.ebi.ddi.xml.validator.parser.model
 
SummaryDatabase() - Constructor for class uk.ac.ebi.ddi.xml.validator.parser.model.SummaryDatabase
 
SummaryDatabase(String, String, String, String, Integer) - Constructor for class uk.ac.ebi.ddi.xml.validator.parser.model.SummaryDatabase
 

T

toString() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.AdditionalFields
 
toString() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.CrossReferences
 
toString() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Date
 
toString() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry.Name
 
toString() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry
 
toString() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Field
 
toString() - Method in class uk.ac.ebi.ddi.xml.validator.parser.model.Reference
 
Tuple<K,V> - Class in uk.ac.ebi.ddi.xml.validator.utils
 
Tuple(K, V) - Constructor for class uk.ac.ebi.ddi.xml.validator.utils.Tuple
 
type - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.Date
 

U

uk.ac.ebi.ddi.xml.validator.cli - package uk.ac.ebi.ddi.xml.validator.cli
 
uk.ac.ebi.ddi.xml.validator.exception - package uk.ac.ebi.ddi.xml.validator.exception
 
uk.ac.ebi.ddi.xml.validator.parser - package uk.ac.ebi.ddi.xml.validator.parser
 
uk.ac.ebi.ddi.xml.validator.parser.marshaller - package uk.ac.ebi.ddi.xml.validator.parser.marshaller
 
uk.ac.ebi.ddi.xml.validator.parser.model - package uk.ac.ebi.ddi.xml.validator.parser.model
 
uk.ac.ebi.ddi.xml.validator.parser.unmarshaller - package uk.ac.ebi.ddi.xml.validator.parser.unmarshaller
 
uk.ac.ebi.ddi.xml.validator.utils - package uk.ac.ebi.ddi.xml.validator.utils
 
unmarshal(String, DataElement) - Method in interface uk.ac.ebi.ddi.xml.validator.parser.unmarshaller.OmicsDataUnmarshaller
 
unmarshal(String) - Method in class uk.ac.ebi.ddi.xml.validator.utils.NonNegativeIntegerAdapter
 
Utils - Class in uk.ac.ebi.ddi.xml.validator.utils
 
Utils() - Constructor for class uk.ac.ebi.ddi.xml.validator.utils.Utils
 

V

validateDate(String) - Static method in class uk.ac.ebi.ddi.xml.validator.utils.Utils
 
validateSchema(File) - Static method in class uk.ac.ebi.ddi.xml.validator.parser.OmicsXMLFile
Return Error as a Tuple with the Code of the Error and the message.
validateSemantic(File) - Static method in class uk.ac.ebi.ddi.xml.validator.parser.OmicsXMLFile
 
validateSemantic(Entry) - Static method in class uk.ac.ebi.ddi.xml.validator.utils.Utils
 
ValidatorCLI - Class in uk.ac.ebi.ddi.xml.validator.cli
This class allow the user to interact with the library: - Validate files.
ValidatorCLI() - Constructor for class uk.ac.ebi.ddi.xml.validator.cli.ValidatorCLI
 
value - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.Date
 
value - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.Entry.Name
 
value - Variable in class uk.ac.ebi.ddi.xml.validator.parser.model.Field
 
valueOf(String) - Static method in enum uk.ac.ebi.ddi.xml.validator.parser.model.DataElement
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.ebi.ddi.xml.validator.utils.BiologicalDatabases
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.ebi.ddi.xml.validator.utils.DatasetType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum uk.ac.ebi.ddi.xml.validator.utils.OmicsType
Returns the enum constant of this type with the specified name.
values() - Static method in enum uk.ac.ebi.ddi.xml.validator.parser.model.DataElement
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum uk.ac.ebi.ddi.xml.validator.utils.BiologicalDatabases
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum uk.ac.ebi.ddi.xml.validator.utils.DatasetType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum uk.ac.ebi.ddi.xml.validator.utils.OmicsType
Returns an array containing the constants of this enum type, in the order they are declared.

W

WARN - Static variable in class uk.ac.ebi.ddi.xml.validator.utils.Utils
 
writeAttribute(String, String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
writeAttribute(String, String, String, String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
writeAttribute(String, String, String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
writeCData(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
writeCharacters(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
writeCharacters(char[], int, int) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
writeComment(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
writeDefaultNamespace(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
writeDTD(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
writeEmptyElement(String, String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
writeEmptyElement(String, String, String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
writeEmptyElement(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
writeEndDocument() - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
writeEndElement() - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
writeEntityRef(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
writeNamespace(String, String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
writeProcessingInstruction(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
writeProcessingInstruction(String, String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
writeStartDocument() - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
writeStartDocument(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
writeStartDocument(String, String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
writeStartElement(String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
writeStartElement(String, String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
writeStartElement(String, String, String) - Method in class uk.ac.ebi.ddi.xml.validator.parser.marshaller.EscapingXMLStreamWriter
 
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