Index (molgenis-core 1.21.1 API)

A B C D E F G H I J K L M N O P R S T U V W X Z

A

add(E) - Method in class org.molgenis.util.HugeSet
addAll(Collection<? extends E>) - Method in class org.molgenis.util.HugeSet
addDataset(Dataset) - Method in class org.molgenis.model.elements.Processor: Deprecated.
addEntity(String) - Method in class org.molgenis.model.elements.View
addEntity(Entity) - Method in class org.molgenis.model.jaxb.Model
addEntity(Entity) - Method in class org.molgenis.model.jaxb.Module
addErrorMessage(ErrorMessageResponse.ErrorMessage) - Method in class org.molgenis.util.ErrorMessageResponse
addErrorMessages(List<ErrorMessageResponse.ErrorMessage>) - Method in class org.molgenis.util.ErrorMessageResponse
addField(Field) - Method in class org.molgenis.model.elements.Entity: Adds the given field to the list of fields associated with this entity.
addField(Integer, Field) - Method in class org.molgenis.model.elements.Entity: Adds the given field to the list of fields associated with this entity.
addField(String) - Method in class org.molgenis.model.elements.Index: Adds the field-name to the list of fields.
addField(Field) - Method in class org.molgenis.model.jaxb.Entity
addIndex(Index) - Method in class org.molgenis.model.elements.Entity: Adds the given index to the list of indices associated with this entity.
addInterfaces(Model) - Static method in class org.molgenis.model.MolgenisModelValidator: Add interfaces as artificial entities to the model
addKey(String, String) - Method in class org.molgenis.model.elements.Entity: Adds the given field to the key-list.
addKey(List<String>, boolean, String) - Method in class org.molgenis.model.elements.Entity: Adds the given list of fields to the key-list.
addModule(Module) - Method in class org.molgenis.model.jaxb.Model
addParameter(Parameter) - Method in class org.molgenis.model.elements.Method
addReference(Field) - Method in class org.molgenis.model.elements.Entity
addRule(MethodQuery.Rule) - Method in class org.molgenis.model.elements.MethodQuery
addType(FieldType) - Static method in class org.molgenis.MolgenisFieldTypes
addTypeFieldInSubclasses(Model) - Static method in class org.molgenis.model.MolgenisModelValidator: In each entity of an entity subclass hierarchy a 'type' field is added to enable filtering.
addUpgrade(MolgenisUpgrade) - Method in interface org.molgenis.framework.MolgenisUpgradeService
addXrefLabelsToEntities(Model) - Static method in class org.molgenis.model.MolgenisModelValidator
afterPropertiesSet() - Method in class org.molgenis.util.GsonFactoryBean
allPossibleXrefLabels() - Method in class org.molgenis.model.elements.Field
ApplicationContextProvider - Class in org.molgenis.util: Can be used by legacy classes to get a reference to the application context
ApplicationContextProvider() - Constructor for class org.molgenis.util.ApplicationContextProvider
assign(Object, Object) - Method in class org.molgenis.util.cmdline.FieldAssign: Deprecated.

This method applies the given value to the field in the given object.
AsyncJavaMailSender - Class in org.molgenis.util: Asynchronous mail sender
AsyncJavaMailSender() - Constructor for class org.molgenis.util.AsyncJavaMailSender
authorizable - Variable in class org.molgenis.MolgenisOptions
AutoGson - Annotation Type in org.molgenis.gson: Annotation to allow Gson to construct @AutoValue annotated classes
AutoValueTypeAdapterFactory - Class in org.molgenis.gson
AutoValueTypeAdapterFactory() - Constructor for class org.molgenis.gson.AutoValueTypeAdapterFactory
AutowiringSpringBeanJobFactory - Class in org.molgenis.scheduler: Autowire Quartz jobs, constructor autowiring not possible.
AutowiringSpringBeanJobFactory() - Constructor for class org.molgenis.scheduler.AutowiringSpringBeanJobFactory

B

BaseHttpMessageConverter<T> - Class in org.molgenis.util
BaseHttpMessageConverter() - Constructor for class org.molgenis.util.BaseHttpMessageConverter
BaseHttpMessageConverter(MediaType...) - Constructor for class org.molgenis.util.BaseHttpMessageConverter
BaseHttpMessageConverter(MediaType) - Constructor for class org.molgenis.util.BaseHttpMessageConverter
block_webspiders - Variable in class org.molgenis.MolgenisOptions
BOOL - Static variable in class org.molgenis.MolgenisFieldTypes
BoolField - Class in org.molgenis.fieldtypes
BoolField() - Constructor for class org.molgenis.fieldtypes.BoolField

C

canRead(Class<?>, MediaType) - Method in class org.molgenis.util.GsonHttpMessageConverter
canWrite(Class<?>, MediaType) - Method in class org.molgenis.util.GsonHttpMessageConverter
CATEGORICAL - Static variable in class org.molgenis.MolgenisFieldTypes
CATEGORICAL_MREF - Static variable in class org.molgenis.MolgenisFieldTypes
CategoricalField - Class in org.molgenis.fieldtypes
CategoricalField() - Constructor for class org.molgenis.fieldtypes.CategoricalField
CategoricalMrefField - Class in org.molgenis.fieldtypes
CategoricalMrefField() - Constructor for class org.molgenis.fieldtypes.CategoricalMrefField
CLASS_PER_TABLE - Static variable in class org.molgenis.MolgenisOptions
clear() - Method in class org.molgenis.util.HugeMap
clear() - Method in class org.molgenis.util.HugeSet
close() - Method in interface org.molgenis.util.CloseableIterator
close() - Method in class org.molgenis.util.HugeMap
close() - Method in class org.molgenis.util.HugeSet
close() - Method in class org.molgenis.util.Ssh
CloseableIterator<E> - Interface in org.molgenis.util: Iterator that closes a resource if the decorated iterator is exhausted.
CmdLineException - Exception in org.molgenis.util.cmdline: The general exception-class for the command-line parser.
CmdLineException(String) - Constructor for exception org.molgenis.util.cmdline.CmdLineException: Standard constructor accepting a string containing the message.
CmdLineParser - Class in org.molgenis.util.cmdline: This class defines the commandline options parser.
CmdLineParser(Object) - Constructor for class org.molgenis.util.cmdline.CmdLineParser: Standard constructor where the options-object and the description are set.
CommandLineOnlyConfiguration - Annotation Type in org.molgenis
COMPOUND - Static variable in class org.molgenis.MolgenisFieldTypes
CompoundField - Class in org.molgenis.fieldtypes: Compound field type is a field type for attributes consisting of multiple attributes
CompoundField() - Constructor for class org.molgenis.fieldtypes.CompoundField
compress(List<File>, File, ZipUtils.DirectoryStructure) - Static method in class org.molgenis.util.ZipUtils
contains(Object) - Method in class org.molgenis.util.HugeSet
containsAll(Collection<?>) - Method in class org.molgenis.util.HugeSet
containsKey(Object) - Method in class org.molgenis.util.HugeMap
containsValue(Object) - Method in class org.molgenis.util.HugeMap
convert(Object) - Method in class org.molgenis.fieldtypes.BoolField
convert(Object) - Method in class org.molgenis.fieldtypes.CompoundField
convert(Object) - Method in class org.molgenis.fieldtypes.DateField
convert(Object) - Method in class org.molgenis.fieldtypes.DatetimeField
convert(Object) - Method in class org.molgenis.fieldtypes.DecimalField
convert(Object) - Method in class org.molgenis.fieldtypes.EnumField
convert(Object) - Method in class org.molgenis.fieldtypes.FieldType
convert(Object) - Method in class org.molgenis.fieldtypes.IntField
convert(Object) - Method in class org.molgenis.fieldtypes.LongField
convert(Object) - Method in class org.molgenis.fieldtypes.MrefField
convert(Object) - Method in class org.molgenis.fieldtypes.StringField
convert(Object) - Method in class org.molgenis.fieldtypes.TextField
convert(Object) - Method in class org.molgenis.fieldtypes.XrefField
convertToString() - Static method in class org.molgenis.Version: string representation of the version
copyDecoratorsToSubclass(Model) - Static method in class org.molgenis.model.MolgenisModelValidator
copyDefaultXrefLabels(Model) - Static method in class org.molgenis.model.MolgenisModelValidator: Default xref labels can come from: - the xref_entity (or one of its superclasses)
copyFieldsToSubclassToEnforceConstraints(Model) - Static method in class org.molgenis.model.MolgenisModelValidator: Copy fields to subclasses (redundantly) so this field can be part of an extra constraint.
correctXrefCaseSensitivity(Model) - Static method in class org.molgenis.model.MolgenisModelValidator: test for case sensitivity
CountryCodes - Class in org.molgenis.util: ISO 3166-2 country codes
CountryCodes() - Constructor for class org.molgenis.util.CountryCodes
create(Gson, TypeToken<T>) - Method in class org.molgenis.gson.AutoValueTypeAdapterFactory
createJobInstance(TriggerFiredBundle) - Method in class org.molgenis.scheduler.AutowiringSpringBeanJobFactory
createLinkTablesForMrefs(Model, MolgenisOptions) - Static method in class org.molgenis.model.MolgenisModelValidator: Add link tables for many to many relationships A link table entity will have the name of [from_entity]_[to_entity] A link table has two xrefs to the from/to entity respectively The column names are those of the respective fields In case of a self reference, the second column name is '_self'
CRON_REGEX - Static variable in class org.molgenis.fieldtypes.StringField

D

DatabaseModelExtractor - Class in org.molgenis.model: Tool to create molgenis_db.xml from an existing database
DatabaseModelExtractor() - Constructor for class org.molgenis.model.DatabaseModelExtractor
Dataset - Class in org.molgenis.model.elements
Dataset(String, String) - Constructor for class org.molgenis.model.elements.Dataset
DATE - Static variable in class org.molgenis.MolgenisFieldTypes
DateField - Class in org.molgenis.fieldtypes
DateField() - Constructor for class org.molgenis.fieldtypes.DateField
DATEFORMAT_DATE - Static variable in class org.molgenis.util.MolgenisDateFormat
DATEFORMAT_DATETIME - Static variable in class org.molgenis.util.MolgenisDateFormat
DATEFORMAT_DATETIME_SIMPLE - Static variable in class org.molgenis.util.MolgenisDateFormat
DATETIME - Static variable in class org.molgenis.MolgenisFieldTypes
DatetimeField - Class in org.molgenis.fieldtypes
DatetimeField() - Constructor for class org.molgenis.fieldtypes.DatetimeField
db_filepath - Variable in class org.molgenis.MolgenisOptions: Path where file attachments (<field type="file" ...
DBSchema - Class in org.molgenis.model.elements: Definition of the base-class for objects in the database schema.
DBSchema(String, DBSchema, Model) - Constructor for class org.molgenis.model.elements.DBSchema: The standard constructor, which links the object in the tree (with the parent parameter).
DECIMAL - Static variable in class org.molgenis.MolgenisFieldTypes
DecimalField - Class in org.molgenis.fieldtypes
DecimalField() - Constructor for class org.molgenis.fieldtypes.DecimalField
decorator_overriders - Variable in class org.molgenis.MolgenisOptions: Class folder with overrides for decorators
DEFAULT_CHARSET - Static variable in class org.molgenis.util.BaseHttpMessageConverter
DEFAULT_ESCAPE_CHAR - Static variable in class org.molgenis.util.ListEscapeUtils
DEFAULT_SEPARATOR - Static variable in class org.molgenis.util.ListEscapeUtils
delete_generated_folder - Variable in class org.molgenis.MolgenisOptions
disable_decorators - Variable in class org.molgenis.MolgenisOptions
downloadFile(String, File) - Method in class org.molgenis.util.Ssh: Download remote file to local file via scp
downloadFile(String) - Method in class org.molgenis.util.Ssh
downloadFileIntoString(String) - Method in class org.molgenis.util.Ssh

E

EMAIL - Static variable in class org.molgenis.MolgenisFieldTypes
EmailField - Class in org.molgenis.fieldtypes
EmailField() - Constructor for class org.molgenis.fieldtypes.EmailField
entities - Variable in class org.molgenis.model.elements.View
Entity - Class in org.molgenis.model.elements: Describes a database-entity (or table).
Entity(String, DBSchema) - Constructor for class org.molgenis.model.elements.Entity: Default constructor.
Entity(String, String, DBSchema) - Constructor for class org.molgenis.model.elements.Entity: Default constructor.
Entity(String, String, DBSchema, boolean) - Constructor for class org.molgenis.model.elements.Entity: Default constructor.
entity - Variable in class org.molgenis.model.elements.MethodQuery
Entity - Class in org.molgenis.model.jaxb
Entity() - Constructor for class org.molgenis.model.jaxb.Entity
EntityImportedEvent - Class in org.molgenis.util: Spring application event that is published when a entity was imported
EntityImportedEvent(Object, String, Object) - Constructor for class org.molgenis.util.EntityImportedEvent
entrySet() - Method in class org.molgenis.util.HugeMap
ENUM - Static variable in class org.molgenis.MolgenisFieldTypes
EnumField - Class in org.molgenis.fieldtypes
EnumField() - Constructor for class org.molgenis.fieldtypes.EnumField
equals(Object) - Method in class org.molgenis.fieldtypes.FieldType
equals(Object) - Method in class org.molgenis.framework.ui.MolgenisPlugin
equals(Object) - Method in class org.molgenis.model.elements.Entity: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class org.molgenis.model.elements.Field: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class org.molgenis.model.elements.Index: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class org.molgenis.model.elements.Parameter: Indicates whether some other object is "equal to" this one.
equals(Object) - Method in class org.molgenis.model.elements.Unique
equals(Object) - Method in class org.molgenis.util.ErrorMessageResponse
equals(Object) - Method in class org.molgenis.util.ErrorMessageResponse.ErrorMessage
equals(Object) - Method in class org.molgenis.util.Pair
ErrorMessage(String) - Constructor for class org.molgenis.util.ErrorMessageResponse.ErrorMessage
ErrorMessage(String, Integer) - Constructor for class org.molgenis.util.ErrorMessageResponse.ErrorMessage
ErrorMessageResponse - Class in org.molgenis.util
ErrorMessageResponse() - Constructor for class org.molgenis.util.ErrorMessageResponse
ErrorMessageResponse(ErrorMessageResponse.ErrorMessage) - Constructor for class org.molgenis.util.ErrorMessageResponse
ErrorMessageResponse(List<ErrorMessageResponse.ErrorMessage>) - Constructor for class org.molgenis.util.ErrorMessageResponse
ErrorMessageResponse.ErrorMessage - Class in org.molgenis.util
exclude_system - Variable in class org.molgenis.MolgenisOptions: Advanced option: skip entities marked as 'system="true"'
executeCommand(String) - Method in class org.molgenis.util.Ssh
executeCommand(String, int) - Method in class org.molgenis.util.Ssh: Execute one command and wait for the result to return

F

f - Variable in class org.molgenis.fieldtypes.FieldType: For xref purposes we sometimes need a handle of the field this type was defined as part of.
Field - Class in org.molgenis.model.elements: Describes a field in an entity.
Field(Entity, String, FieldType) - Constructor for class org.molgenis.model.elements.Field
Field(Entity, FieldType, String, String, boolean, boolean, boolean, String, String) - Constructor for class org.molgenis.model.elements.Field: Standard constructor, which sets all the common variables for a field.
Field(String) - Constructor for class org.molgenis.model.elements.Field
Field(Entity, FieldType, String, String, boolean, boolean, boolean, String) - Constructor for class org.molgenis.model.elements.Field: Standard constructor, which sets all the common variables for a field.
Field(Field) - Constructor for class org.molgenis.model.elements.Field: copy-constructor
field - Variable in class org.molgenis.model.elements.MethodQuery.Rule
Field - Class in org.molgenis.model.jaxb
Field() - Constructor for class org.molgenis.model.jaxb.Field
Field.Type - Enum in org.molgenis.model.jaxb: Description of the different types of a field.
FieldAssign - Class in org.molgenis.util.cmdline: Deprecated.
FieldAssign(Field) - Constructor for class org.molgenis.util.cmdline.FieldAssign: Deprecated.

...
FieldType - Class in org.molgenis.fieldtypes: Definition of a MOLGENIS field type.
FieldType() - Constructor for class org.molgenis.fieldtypes.FieldType
FieldWithXrefLabel - Class in org.molgenis.model.elements: Helper class to deal with xref_label fields.
FieldWithXrefLabel(Field) - Constructor for class org.molgenis.model.elements.FieldWithXrefLabel
FILE - Static variable in class org.molgenis.MolgenisFieldTypes
FileField - Class in org.molgenis.fieldtypes
FileField() - Constructor for class org.molgenis.fieldtypes.FileField
FileUploadUtils - Class in org.molgenis.util
FileUploadUtils() - Constructor for class org.molgenis.util.FileUploadUtils
finalize() - Method in class org.molgenis.util.Ssh
findEntity(String) - Method in class org.molgenis.model.jaxb.Model: find entity across local entities, and the ones contained in modules
findField(String) - Method in class org.molgenis.model.elements.Model
findModuleNameForEntity(String) - Method in class org.molgenis.model.jaxb.Model
findRemoveEntity(String) - Method in class org.molgenis.model.jaxb.Model: Find and remove an entity from either root or a module.
firstToUpper(String) - Static method in class org.molgenis.model.elements.Field: Convert string with first character to uppercase.
Form - Class in org.molgenis.model.elements
Form(String, UISchema) - Constructor for class org.molgenis.model.elements.Form
Form.SortOrder - Enum in org.molgenis.model.elements
Form.ViewType - Enum in org.molgenis.model.elements
format_type - Variable in enum org.molgenis.model.jaxb.Field.Type
forward(int, String, int) - Method in class org.molgenis.util.Ssh
fromSafeUrlString(String) - Static method in class org.molgenis.util.HtmlTools: Helper function to convert an URL-safe string (passed from eg.
fromSafeUrlStringO_b_f(String) - Static method in class org.molgenis.util.HtmlTools: Helper function to convert an URL-safe string (passed from eg.

G

generate_db - Variable in class org.molgenis.MolgenisOptions
generate_entityio - Variable in class org.molgenis.MolgenisOptions
generate_jpa - Variable in class org.molgenis.MolgenisOptions
generate_jpa_repository_source - Variable in class org.molgenis.MolgenisOptions
generate_model - Variable in class org.molgenis.MolgenisOptions
generate_persistence - Variable in class org.molgenis.MolgenisOptions
generate_tests - Variable in class org.molgenis.MolgenisOptions
get(Field) - Static method in class org.molgenis.MolgenisFieldTypes
get() - Static method in class org.molgenis.util.CountryCodes
get(String) - Static method in class org.molgenis.util.CountryCodes
get(Object) - Method in class org.molgenis.util.HugeMap
get() - Method in class org.molgenis.util.Property: Returns the value of the property.
get(String) - Method in class org.molgenis.util.SimpleTree
get(String) - Method in interface org.molgenis.util.Tree: Retrieve a subtree by name.
getA() - Method in class org.molgenis.util.Pair: Returns the pointer to the first object.
getAddFields() - Method in class org.molgenis.model.elements.Entity
getAllAddFields() - Method in class org.molgenis.model.elements.Entity
getAllAncestors() - Method in class org.molgenis.model.elements.Entity
getAllChildren() - Method in class org.molgenis.util.SimpleTree
getAllChildren(boolean) - Method in class org.molgenis.util.SimpleTree: sort in order of dependency
getAllChildren() - Method in interface org.molgenis.util.Tree: Get the children, and their children, etc.
getAllChildren(boolean) - Method in interface org.molgenis.util.Tree: Get all children, optional including self
getAllDescendants() - Method in class org.molgenis.model.elements.Entity
getAllField(String) - Method in class org.molgenis.model.elements.Entity: Returns the field with the given name from entity or any of its parents.
getAllFields() - Method in class org.molgenis.model.elements.Entity
getAllFields() - Method in class org.molgenis.model.elements.View
getAllFieldsOf(FieldType) - Method in class org.molgenis.model.elements.Entity
getAllFieldsOf(String) - Method in class org.molgenis.model.elements.Entity
getAllForms() - Method in class org.molgenis.model.elements.UISchema
getAllImplements() - Method in class org.molgenis.model.elements.Entity
getAllIndices() - Method in class org.molgenis.model.elements.Entity
getAllKeys() - Method in class org.molgenis.model.elements.Entity
getAllLocalFields() - Method in class org.molgenis.model.elements.Entity: Returns a vector with all the fields that are actualy located in this entity.
getAllocationSize() - Method in class org.molgenis.model.elements.Entity
getAllowedOperators() - Method in class org.molgenis.fieldtypes.DateField
getAllowedOperators() - Method in class org.molgenis.fieldtypes.DatetimeField
getAllowedOperators() - Method in class org.molgenis.fieldtypes.DecimalField
getAllowedOperators() - Method in class org.molgenis.fieldtypes.FieldType
getAllowedOperators() - Method in class org.molgenis.fieldtypes.IntField
getAllowedOperators() - Method in class org.molgenis.fieldtypes.LongField
getAllUniqueGroups() - Method in class org.molgenis.model.elements.UISchema
getAllUpdateFields() - Method in class org.molgenis.model.elements.Entity
getAncestor() - Method in class org.molgenis.model.elements.Entity
getAnnotations() - Method in class org.molgenis.model.elements.Field
getApplicationContext() - Static method in class org.molgenis.util.ApplicationContextProvider
getAuto() - Method in class org.molgenis.model.jaxb.Field
getB() - Method in class org.molgenis.util.Pair: Returns the pointer to the second object.
getBaseURI() - Method in class org.molgenis.util.SchemaLoader.LSInputImpl
getBytes(String) - Static method in class org.molgenis.util.ResourceUtils
getBytes(Class<?>, String) - Static method in class org.molgenis.util.ResourceUtils
getByteStream() - Method in class org.molgenis.util.SchemaLoader.LSInputImpl
getCanonicalClassName() - Method in class org.molgenis.model.elements.UISchema
getCertifiedText() - Method in class org.molgenis.util.SchemaLoader.LSInputImpl
getCharacterStream() - Method in class org.molgenis.util.SchemaLoader.LSInputImpl
getCharset(HttpHeaders) - Method in class org.molgenis.util.BaseHttpMessageConverter
getChild(String) - Method in class org.molgenis.util.SimpleTree
getChild(String) - Method in interface org.molgenis.util.Tree: Get a subtree by name.
getChildren() - Method in class org.molgenis.util.SimpleTree
getChildren() - Method in interface org.molgenis.util.Tree: Get the children of this element.
getClassName() - Method in class org.molgenis.model.elements.UISchema
getCode() - Method in class org.molgenis.util.ErrorMessageResponse.ErrorMessage
getCol() - Method in class org.molgenis.model.elements.Matrix
getColEntity() - Method in class org.molgenis.model.elements.Matrix: Return the Entity that contains the labels for the columns.
getColEntityName() - Method in class org.molgenis.model.elements.Matrix
getCommands() - Method in class org.molgenis.model.elements.Form
getCompactView() - Method in class org.molgenis.model.elements.Form
getCompleteSchema() - Method in class org.molgenis.model.elements.UISchema
getConcreteEntities() - Method in class org.molgenis.model.elements.Model
getContainer() - Method in class org.molgenis.model.elements.Matrix
getContainerEntity() - Method in class org.molgenis.model.elements.Matrix: Return the Entity that contains the container
getContent() - Method in class org.molgenis.model.elements.Matrix
getContentEntity() - Method in class org.molgenis.model.elements.Matrix
getCppJavaPropertyType() - Method in class org.molgenis.fieldtypes.BoolField
getCppJavaPropertyType() - Method in class org.molgenis.fieldtypes.CompoundField
getCppJavaPropertyType() - Method in class org.molgenis.fieldtypes.DateField
getCppJavaPropertyType() - Method in class org.molgenis.fieldtypes.DatetimeField
getCppJavaPropertyType() - Method in class org.molgenis.fieldtypes.DecimalField
getCppJavaPropertyType() - Method in class org.molgenis.fieldtypes.EnumField
getCppJavaPropertyType() - Method in class org.molgenis.fieldtypes.FieldType
getCppJavaPropertyType() - Method in class org.molgenis.fieldtypes.IntField
getCppJavaPropertyType() - Method in class org.molgenis.fieldtypes.LongField
getCppJavaPropertyType() - Method in class org.molgenis.fieldtypes.MrefField
getCppJavaPropertyType() - Method in class org.molgenis.fieldtypes.StringField
getCppJavaPropertyType() - Method in class org.molgenis.fieldtypes.TextField
getCppJavaPropertyType() - Method in class org.molgenis.fieldtypes.XrefField
getCppPropertyType() - Method in class org.molgenis.fieldtypes.BoolField
getCppPropertyType() - Method in class org.molgenis.fieldtypes.CompoundField
getCppPropertyType() - Method in class org.molgenis.fieldtypes.DateField
getCppPropertyType() - Method in class org.molgenis.fieldtypes.DatetimeField
getCppPropertyType() - Method in class org.molgenis.fieldtypes.DecimalField
getCppPropertyType() - Method in class org.molgenis.fieldtypes.EnumField
getCppPropertyType() - Method in class org.molgenis.fieldtypes.FieldType: Product the Java type of this field type.
getCppPropertyType() - Method in class org.molgenis.fieldtypes.IntField
getCppPropertyType() - Method in class org.molgenis.fieldtypes.LongField
getCppPropertyType() - Method in class org.molgenis.fieldtypes.MrefField
getCppPropertyType() - Method in class org.molgenis.fieldtypes.StringField
getCppPropertyType() - Method in class org.molgenis.fieldtypes.TextField
getCppPropertyType() - Method in class org.molgenis.fieldtypes.XrefField
getDatabase() - Method in class org.molgenis.model.elements.Model
getDatasets() - Method in class org.molgenis.model.elements.Processor: Deprecated.
getDateFormat() - Static method in class org.molgenis.util.MolgenisDateFormat
getDateTimeFormat() - Static method in class org.molgenis.util.MolgenisDateFormat
getDateTimeFormatSimple() - Static method in class org.molgenis.util.MolgenisDateFormat
getDBDescription() - Method in class org.molgenis.model.elements.Model
getDbFilepath() - Method in class org.molgenis.MolgenisOptions
getDecorator() - Method in class org.molgenis.model.elements.Entity
getDecorator() - Method in class org.molgenis.model.jaxb.Entity
getDefaultCode() - Method in class org.molgenis.model.elements.Field
getDefaultValue() - Method in class org.molgenis.model.elements.Field: Returns the value the database should set for the field when there is no value set.
getDefaultValue() - Method in class org.molgenis.model.elements.Parameter: Returns the value the database should set for the field when there is no value set.
getDefaultValue() - Method in class org.molgenis.model.jaxb.Field
getDependencies() - Method in class org.molgenis.model.elements.Entity
getDescendants() - Method in class org.molgenis.model.elements.Entity: Get the subclasses of this entity.
getDescription() - Method in class org.molgenis.model.elements.Entity: Returns the description of the entity.
getDescription() - Method in class org.molgenis.model.elements.Field: Returns the description of the entity.
getDescription() - Method in class org.molgenis.model.elements.Form: Getter/setter for optional description for the selected form screen
getDescription() - Method in class org.molgenis.model.elements.Method
getDescription() - Method in class org.molgenis.model.elements.Module
getDescription() - Method in class org.molgenis.model.elements.Parameter: Returns the description of the entity.
getDescription() - Method in class org.molgenis.model.elements.Unique
getDescription() - Method in class org.molgenis.model.elements.View
getDescription() - Method in class org.molgenis.model.jaxb.Entity
getDescription() - Method in class org.molgenis.model.jaxb.Field
getEmbedchildfield() - Method in class org.molgenis.model.elements.Form
getEmbedchildname() - Method in class org.molgenis.model.elements.Form
getEmbedfields() - Method in class org.molgenis.model.elements.Form
getEmbedkeyfield() - Method in class org.molgenis.model.elements.Form
getEmbedparentfield() - Method in class org.molgenis.model.elements.Form
getEmbedparentname() - Method in class org.molgenis.model.elements.Form
getEncoding() - Method in class org.molgenis.util.SchemaLoader.LSInputImpl
getEntities() - Method in class org.molgenis.model.elements.Model
getEntities(boolean, boolean) - Method in class org.molgenis.model.elements.Model
getEntities(boolean) - Method in class org.molgenis.model.elements.Model
getEntities() - Method in class org.molgenis.model.elements.Module
getEntities() - Method in class org.molgenis.model.elements.View
getEntities() - Method in class org.molgenis.model.jaxb.Model
getEntities() - Method in class org.molgenis.model.jaxb.Module
getEntity() - Method in class org.molgenis.model.elements.Dataset
getEntity() - Method in class org.molgenis.model.elements.Field
getEntity() - Method in class org.molgenis.model.elements.Form
getEntity() - Method in class org.molgenis.model.elements.MethodQuery
getEntity(String) - Method in class org.molgenis.model.elements.Model
getEntity() - Method in class org.molgenis.model.elements.Parameter
getEntity() - Method in class org.molgenis.model.elements.Plugin
getEntity() - Method in class org.molgenis.model.elements.Tree
getEntity() - Method in class org.molgenis.model.elements.Unique: Returns the associated entity.
getEntity(String) - Method in class org.molgenis.model.jaxb.Model
getEntity(String) - Method in class org.molgenis.model.jaxb.Module
getEntityByName(String) - Method in class org.molgenis.fieldtypes.FieldType: Get an entity from the field type (only works if the field type is linked to a Field instance).
getEntityId() - Method in class org.molgenis.util.EntityImportedEvent
getEntityName() - Method in class org.molgenis.util.EntityImportedEvent
getEnumOptions() - Method in class org.molgenis.fieldtypes.EnumField
getEnumOptions() - Method in class org.molgenis.model.elements.Field
getEnumOptions() - Method in class org.molgenis.model.elements.Parameter
getEnumoptions() - Method in class org.molgenis.model.jaxb.Field
getEnumType() - Method in class org.molgenis.fieldtypes.BoolField
getEnumType() - Method in class org.molgenis.fieldtypes.CategoricalField
getEnumType() - Method in class org.molgenis.fieldtypes.CategoricalMrefField
getEnumType() - Method in class org.molgenis.fieldtypes.CompoundField
getEnumType() - Method in class org.molgenis.fieldtypes.DateField
getEnumType() - Method in class org.molgenis.fieldtypes.DatetimeField
getEnumType() - Method in class org.molgenis.fieldtypes.DecimalField
getEnumType() - Method in class org.molgenis.fieldtypes.EmailField
getEnumType() - Method in class org.molgenis.fieldtypes.EnumField
getEnumType() - Method in class org.molgenis.fieldtypes.FieldType
getEnumType() - Method in class org.molgenis.fieldtypes.FileField
getEnumType() - Method in class org.molgenis.fieldtypes.HtmlField
getEnumType() - Method in class org.molgenis.fieldtypes.HyperlinkField
getEnumType() - Method in class org.molgenis.fieldtypes.IntField
getEnumType() - Method in class org.molgenis.fieldtypes.LongField
getEnumType() - Method in class org.molgenis.fieldtypes.MrefField
getEnumType() - Method in class org.molgenis.fieldtypes.ScriptField
getEnumType() - Method in class org.molgenis.fieldtypes.StringField
getEnumType() - Method in class org.molgenis.fieldtypes.TextField
getEnumType() - Method in class org.molgenis.fieldtypes.XrefField
getErrors() - Method in class org.molgenis.util.ErrorMessageResponse
getExtends() - Method in class org.molgenis.model.jaxb.Entity
getField(String, boolean, boolean, boolean) - Method in class org.molgenis.model.elements.Entity: Returns the field with the given name.
getField(String) - Method in class org.molgenis.model.elements.Entity
getField() - Method in class org.molgenis.model.elements.MethodQuery.Rule
getField(String) - Method in class org.molgenis.model.jaxb.Entity
getFieldRecusive(String) - Method in class org.molgenis.model.elements.Entity
getFields() - Method in class org.molgenis.model.elements.Entity: Returns a vector with all the fields associated with this entity.
getFields(boolean, boolean, boolean, boolean) - Method in class org.molgenis.model.elements.Entity: Returns a vector with all the fields associated with this entity.
getFields(boolean, boolean, boolean) - Method in class org.molgenis.model.elements.Entity
getFields() - Method in class org.molgenis.model.elements.Index: Returns a vector with all the field-names this index indexes.
getFields() - Method in interface org.molgenis.model.elements.Record
getFields() - Method in class org.molgenis.model.elements.Unique: Returns a list of all the fields that make up this unique.
getFields() - Method in class org.molgenis.model.elements.View
getFields() - Method in class org.molgenis.model.jaxb.Entity
getFields() - Method in class org.molgenis.model.jaxb.Unique
getFieldsOf(FieldType) - Method in class org.molgenis.model.elements.Entity: Returns a vector with all the fields associated with this entity and are of the given type.
getFieldType(Field) - Method in class org.molgenis.fieldtypes.FieldType: Get the field type from a field.
getFile(String) - Static method in class org.molgenis.util.ResourceUtils
getFile(Class<?>, String) - Static method in class org.molgenis.util.ResourceUtils
getFilterfield() - Method in class org.molgenis.model.elements.Field
getFilterfield() - Method in class org.molgenis.model.elements.Form
getFiltertype() - Method in class org.molgenis.model.elements.Field
getFiltertype() - Method in class org.molgenis.model.elements.Form
getFiltervalue() - Method in class org.molgenis.model.elements.Field
getFiltervalue() - Method in class org.molgenis.model.elements.Form
getFingerprint(String) - Method in class org.molgenis.util.ResourceFingerprintRegistry
getFingerprint(Class<?>, String) - Method in class org.molgenis.util.ResourceFingerprintRegistry
getFlavor() - Method in class org.molgenis.model.elements.Plugin
getFormatString() - Method in class org.molgenis.fieldtypes.BoolField
getFormatString() - Method in class org.molgenis.fieldtypes.CompoundField
getFormatString() - Method in class org.molgenis.fieldtypes.DateField
getFormatString() - Method in class org.molgenis.fieldtypes.DatetimeField
getFormatString() - Method in class org.molgenis.fieldtypes.DecimalField
getFormatString() - Method in class org.molgenis.fieldtypes.EnumField
getFormatString() - Method in class org.molgenis.fieldtypes.FieldType: Get the format string, e.g.
getFormatString() - Method in class org.molgenis.fieldtypes.IntField
getFormatString() - Method in class org.molgenis.fieldtypes.LongField
getFormatString() - Method in class org.molgenis.fieldtypes.MrefField
getFormatString() - Method in class org.molgenis.fieldtypes.StringField
getFormatString() - Method in class org.molgenis.fieldtypes.TextField
getFormatString() - Method in class org.molgenis.fieldtypes.XrefField
getFormatString() - Method in class org.molgenis.model.elements.Field
getForms() - Method in class org.molgenis.model.elements.UISchema
getFromVersion() - Method in class org.molgenis.framework.MolgenisUpgrade
getFullUri() - Method in class org.molgenis.framework.ui.MolgenisPlugin
getGroup() - Method in class org.molgenis.model.elements.UISchema
getGroupRead() - Method in class org.molgenis.model.elements.UISchema
getHeader() - Method in class org.molgenis.model.elements.Form: Getter/setter for optional custom header for the selected form screen
getHideFields() - Method in class org.molgenis.model.elements.Form
getHost() - Method in class org.molgenis.util.Ssh
getHsqlType() - Method in class org.molgenis.fieldtypes.BoolField
getHsqlType() - Method in class org.molgenis.fieldtypes.CompoundField
getHsqlType() - Method in class org.molgenis.fieldtypes.DateField
getHsqlType() - Method in class org.molgenis.fieldtypes.DatetimeField
getHsqlType() - Method in class org.molgenis.fieldtypes.DecimalField
getHsqlType() - Method in class org.molgenis.fieldtypes.EnumField
getHsqlType() - Method in class org.molgenis.fieldtypes.FieldType: Produce a valid hsql snippet indicating the mysql type.
getHsqlType() - Method in class org.molgenis.fieldtypes.IntField
getHsqlType() - Method in class org.molgenis.fieldtypes.LongField
getHsqlType() - Method in class org.molgenis.fieldtypes.MrefField
getHsqlType() - Method in class org.molgenis.fieldtypes.StringField
getHsqlType() - Method in class org.molgenis.fieldtypes.TextField
getHsqlType() - Method in class org.molgenis.fieldtypes.XrefField
getId() - Method in class org.molgenis.framework.ui.MolgenisPlugin
getIdField() - Method in class org.molgenis.model.elements.Tree
getImplementedFields() - Method in class org.molgenis.model.elements.Entity: Get fields for this entity as well as from the interfaces it implements.
getImplementedFieldsOf(FieldType) - Method in class org.molgenis.model.elements.Entity
getImplementedFieldsOf(String) - Method in class org.molgenis.model.elements.Entity
getImplements() - Method in class org.molgenis.model.elements.Entity
getImplements() - Method in class org.molgenis.model.jaxb.Entity
getImplementsNames() - Method in class org.molgenis.model.elements.Entity
getIndex(String) - Method in class org.molgenis.model.elements.Entity: Returns the index with the given name.
getIndices() - Method in class org.molgenis.model.elements.Entity: Returns a vector with all the indices associated with this entity.
getInheritedFields() - Method in class org.molgenis.model.elements.Entity
getInputStream() - Method in class org.molgenis.util.SchemaLoader.LSInputImpl
getJavaAssignment(String) - Method in class org.molgenis.fieldtypes.BoolField
getJavaAssignment(String) - Method in class org.molgenis.fieldtypes.CompoundField
getJavaAssignment(String) - Method in class org.molgenis.fieldtypes.DateField
getJavaAssignment(String) - Method in class org.molgenis.fieldtypes.DatetimeField
getJavaAssignment(String) - Method in class org.molgenis.fieldtypes.DecimalField
getJavaAssignment(String) - Method in class org.molgenis.fieldtypes.EnumField
getJavaAssignment(String) - Method in class org.molgenis.fieldtypes.FieldType: Produce a valid Java snippet to set a value for field.
getJavaAssignment(String) - Method in class org.molgenis.fieldtypes.IntField
getJavaAssignment(String) - Method in class org.molgenis.fieldtypes.LongField
getJavaAssignment(String) - Method in class org.molgenis.fieldtypes.MrefField
getJavaAssignment(String) - Method in class org.molgenis.fieldtypes.StringField
getJavaAssignment(String) - Method in class org.molgenis.fieldtypes.TextField
getJavaAssignment(String) - Method in class org.molgenis.fieldtypes.XrefField
getJavaPropertyDefault() - Method in class org.molgenis.fieldtypes.BoolField
getJavaPropertyDefault() - Method in class org.molgenis.fieldtypes.CompoundField
getJavaPropertyDefault() - Method in class org.molgenis.fieldtypes.DateField
getJavaPropertyDefault() - Method in class org.molgenis.fieldtypes.DatetimeField
getJavaPropertyDefault() - Method in class org.molgenis.fieldtypes.DecimalField
getJavaPropertyDefault() - Method in class org.molgenis.fieldtypes.EnumField
getJavaPropertyDefault() - Method in class org.molgenis.fieldtypes.FieldType: Produce a valid Java snippet to set the default of a field, using the 'getDefault' function of that field.
getJavaPropertyDefault() - Method in class org.molgenis.fieldtypes.IntField
getJavaPropertyDefault() - Method in class org.molgenis.fieldtypes.LongField
getJavaPropertyDefault() - Method in class org.molgenis.fieldtypes.MrefField
getJavaPropertyDefault() - Method in class org.molgenis.fieldtypes.StringField
getJavaPropertyDefault() - Method in class org.molgenis.fieldtypes.TextField
getJavaPropertyDefault() - Method in class org.molgenis.fieldtypes.XrefField
getJavaPropertyType() - Method in class org.molgenis.fieldtypes.BoolField
getJavaPropertyType() - Method in class org.molgenis.fieldtypes.CompoundField
getJavaPropertyType() - Method in class org.molgenis.fieldtypes.DateField
getJavaPropertyType() - Method in class org.molgenis.fieldtypes.DatetimeField
getJavaPropertyType() - Method in class org.molgenis.fieldtypes.DecimalField
getJavaPropertyType() - Method in class org.molgenis.fieldtypes.EnumField
getJavaPropertyType() - Method in class org.molgenis.fieldtypes.FieldType: Product the Java type of this field type.
getJavaPropertyType() - Method in class org.molgenis.fieldtypes.IntField
getJavaPropertyType() - Method in class org.molgenis.fieldtypes.LongField
getJavaPropertyType() - Method in class org.molgenis.fieldtypes.MrefField
getJavaPropertyType() - Method in class org.molgenis.fieldtypes.StringField
getJavaPropertyType() - Method in class org.molgenis.fieldtypes.TextField
getJavaPropertyType() - Method in class org.molgenis.fieldtypes.XrefField
getJavaSetterType() - Method in class org.molgenis.fieldtypes.CompoundField
getJavaSetterType() - Method in class org.molgenis.fieldtypes.DateField
getJavaSetterType() - Method in class org.molgenis.fieldtypes.DatetimeField
getJavaSetterType() - Method in class org.molgenis.fieldtypes.FieldType
getJavaSetterType() - Method in class org.molgenis.fieldtypes.IntField
getJavaSetterType() - Method in class org.molgenis.fieldtypes.MrefField
getJavaSetterType() - Method in class org.molgenis.fieldtypes.XrefField
getJavaType() - Method in class org.molgenis.fieldtypes.BoolField
getJavaType() - Method in class org.molgenis.fieldtypes.CompoundField
getJavaType() - Method in class org.molgenis.fieldtypes.DateField
getJavaType() - Method in class org.molgenis.fieldtypes.DatetimeField
getJavaType() - Method in class org.molgenis.fieldtypes.DecimalField
getJavaType() - Method in class org.molgenis.fieldtypes.EnumField
getJavaType() - Method in class org.molgenis.fieldtypes.FieldType: Produce the Java class corresponding to the value
getJavaType() - Method in class org.molgenis.fieldtypes.IntField
getJavaType() - Method in class org.molgenis.fieldtypes.LongField
getJavaType() - Method in class org.molgenis.fieldtypes.MrefField
getJavaType() - Method in class org.molgenis.fieldtypes.StringField
getJavaType() - Method in class org.molgenis.fieldtypes.TextField
getJavaType() - Method in class org.molgenis.fieldtypes.XrefField
getJpaCascade() - Method in class org.molgenis.model.elements.Field
getKey(int) - Method in class org.molgenis.model.elements.Entity: Returns the key at the given index.
getKeyFields(int) - Method in class org.molgenis.model.elements.Entity: Returns a list of the fields that make up the key at the given index.
getKeys() - Method in class org.molgenis.model.elements.Entity: Returns a list with all the keys.
getLabel() - Method in class org.molgenis.model.elements.Entity: Returns the label of this entity.
getLabel() - Method in class org.molgenis.model.elements.Field: This method returns the label of this field.
getLabel() - Method in class org.molgenis.model.elements.Model
getLabel() - Method in class org.molgenis.model.elements.Module
getLabel() - Method in class org.molgenis.model.elements.Parameter: This method returns the label of this field.
getLabel() - Method in interface org.molgenis.model.elements.Record
getLabel() - Method in class org.molgenis.model.elements.UISchema
getLabel() - Method in class org.molgenis.model.elements.View
getLabel() - Method in class org.molgenis.model.jaxb.Entity
getLabel() - Method in class org.molgenis.model.jaxb.Field
getLabel() - Method in class org.molgenis.model.jaxb.Model
getLabel() - Method in class org.molgenis.util.ValueLabel: Retrieve the label
getLabelField() - Method in class org.molgenis.model.elements.Tree
getLength() - Method in class org.molgenis.model.elements.Field
getLength() - Method in class org.molgenis.model.jaxb.Field
getLimit() - Method in class org.molgenis.model.elements.Form
getLocalFields() - Method in class org.molgenis.model.elements.Entity: Returns a vector with all the fields that are actualy located in this entity.
getMatrices() - Method in class org.molgenis.model.elements.Model
getMaxLength() - Method in class org.molgenis.fieldtypes.BoolField
getMaxLength() - Method in class org.molgenis.fieldtypes.CompoundField
getMaxLength() - Method in class org.molgenis.fieldtypes.DateField
getMaxLength() - Method in class org.molgenis.fieldtypes.DatetimeField
getMaxLength() - Method in class org.molgenis.fieldtypes.DecimalField
getMaxLength() - Method in class org.molgenis.fieldtypes.EnumField
getMaxLength() - Method in class org.molgenis.fieldtypes.FieldType: Returns the maximum number of characters for this field type or null if not applicable
getMaxLength() - Method in class org.molgenis.fieldtypes.IntField
getMaxLength() - Method in class org.molgenis.fieldtypes.LongField
getMaxLength() - Method in class org.molgenis.fieldtypes.MrefField
getMaxLength() - Method in class org.molgenis.fieldtypes.StringField
getMaxLength() - Method in class org.molgenis.fieldtypes.TextField
getMaxLength() - Method in class org.molgenis.fieldtypes.XrefField
getMaxRange() - Method in class org.molgenis.model.elements.Field
getMenus() - Method in class org.molgenis.model.elements.UISchema
getMessage() - Method in class org.molgenis.util.ErrorMessageResponse.ErrorMessage
getMethods() - Method in class org.molgenis.model.elements.Model
getMethodSchema() - Method in class org.molgenis.model.elements.Model
getMinRange() - Method in class org.molgenis.model.elements.Field
getModel() - Method in class org.molgenis.model.elements.DBSchema
getModel() - Method in class org.molgenis.model.elements.Entity
getModelDatabase() - Method in class org.molgenis.MolgenisOptions
getModule() - Method in class org.molgenis.model.elements.Entity
getModule(String) - Method in class org.molgenis.model.jaxb.Model
getModules() - Method in class org.molgenis.model.elements.DBSchema
getModules() - Method in class org.molgenis.model.elements.Model
getModules() - Method in class org.molgenis.model.jaxb.Model
getMolgenis_properties() - Method in class org.molgenis.MolgenisOptions
getMrefLocalid() - Method in class org.molgenis.model.elements.Field
getMrefLocalid() - Method in class org.molgenis.model.jaxb.Field
getMrefName() - Method in class org.molgenis.model.elements.Field: Gets the name of the link-table when this field is a XREF_MULTIPLE.
getMrefName() - Method in class org.molgenis.model.jaxb.Field
getMrefRemoteid() - Method in class org.molgenis.model.elements.Field
getMrefRemoteid() - Method in class org.molgenis.model.jaxb.Field
getMysqlType() - Method in class org.molgenis.fieldtypes.BoolField
getMysqlType() - Method in class org.molgenis.fieldtypes.CompoundField
getMysqlType() - Method in class org.molgenis.fieldtypes.DateField
getMysqlType() - Method in class org.molgenis.fieldtypes.DatetimeField
getMysqlType() - Method in class org.molgenis.fieldtypes.DecimalField
getMysqlType() - Method in class org.molgenis.fieldtypes.EnumField
getMysqlType() - Method in class org.molgenis.fieldtypes.FieldType: Produce a valid mysql snippet indicating the mysql type.
getMysqlType() - Method in class org.molgenis.fieldtypes.IntField
getMysqlType() - Method in class org.molgenis.fieldtypes.LongField
getMysqlType() - Method in class org.molgenis.fieldtypes.MrefField
getMysqlType() - Method in class org.molgenis.fieldtypes.StringField
getMysqlType() - Method in class org.molgenis.fieldtypes.TextField
getMysqlType() - Method in class org.molgenis.fieldtypes.XrefField
getName() - Method in class org.molgenis.framework.ui.MolgenisPlugin
getName() - Method in class org.molgenis.model.elements.Dataset
getName() - Method in class org.molgenis.model.elements.Field: This method returns the name of this field.
getName() - Method in class org.molgenis.model.elements.Index: Returns the name of the index.
getName() - Method in class org.molgenis.model.elements.Model
getName() - Method in class org.molgenis.model.elements.Module
getName() - Method in class org.molgenis.model.elements.Parameter: This method returns the name of this field.
getName() - Method in interface org.molgenis.model.elements.Record
getName() - Method in class org.molgenis.model.jaxb.Entity
getName() - Method in class org.molgenis.model.jaxb.Field
getName() - Method in class org.molgenis.model.jaxb.Model
getName() - Method in class org.molgenis.model.jaxb.Module
getName() - Method in class org.molgenis.model.jaxb.Screen
getName() - Method in class org.molgenis.util.SimpleTree
getName() - Method in interface org.molgenis.util.Tree: Retrieve the unique name of this tree element.
getNamespace() - Method in class org.molgenis.model.elements.Entity
getNamespace() - Method in class org.molgenis.model.elements.UISchema
getNillable() - Method in class org.molgenis.model.jaxb.Field
getNonSystemFields(boolean) - Method in class org.molgenis.model.elements.Entity: Returns all the fields belonging to this entity, which have not set the system-property.
getNrEntities() - Method in class org.molgenis.model.elements.View
getNumberOfMrefTo(Entity) - Method in class org.molgenis.model.elements.Entity
getNumberOfMrefTo(Entity, Field) - Method in class org.molgenis.model.elements.Entity
getNumberOfReferencesTo(Entity) - Method in class org.molgenis.model.elements.Entity
getNumberOfReferencesTo(Entity, Field) - Method in class org.molgenis.model.elements.Entity
getNumberOfReferencesTo(Entity) - Method in class org.molgenis.model.elements.Model
getObject() - Method in class org.molgenis.util.GsonFactoryBean: Return the created Gson instance.
getObjectRelationalMapping() - Method in class org.molgenis.MolgenisOptions
getObjectType() - Method in class org.molgenis.util.GsonFactoryBean
getOperator() - Method in class org.molgenis.model.elements.MethodQuery.Rule
getOptionsAsMap() - Method in class org.molgenis.MolgenisOptions: Get the options as a map, used in the UsedMolgenisOptionsGen.ftl template
getOptionsLowercase() - Static method in enum org.molgenis.MolgenisFieldTypes.FieldTypeEnum
getOracleType() - Method in class org.molgenis.fieldtypes.BoolField
getOracleType() - Method in class org.molgenis.fieldtypes.CompoundField
getOracleType() - Method in class org.molgenis.fieldtypes.DateField
getOracleType() - Method in class org.molgenis.fieldtypes.DatetimeField
getOracleType() - Method in class org.molgenis.fieldtypes.DecimalField
getOracleType() - Method in class org.molgenis.fieldtypes.EnumField
getOracleType() - Method in class org.molgenis.fieldtypes.FieldType
getOracleType() - Method in class org.molgenis.fieldtypes.IntField
getOracleType() - Method in class org.molgenis.fieldtypes.LongField
getOracleType() - Method in class org.molgenis.fieldtypes.MrefField
getOracleType() - Method in class org.molgenis.fieldtypes.StringField
getOracleType() - Method in class org.molgenis.fieldtypes.TextField
getOracleType() - Method in class org.molgenis.fieldtypes.XrefField
getOrder() - Method in class org.molgenis.framework.db.WebAppDatabasePopulator
getOriginalFileName(Part) - Static method in class org.molgenis.util.FileUploadUtils: Get the filename of an uploaded file
getOutputDoc() - Method in class org.molgenis.MolgenisOptions
getOutputHand() - Method in class org.molgenis.MolgenisOptions
getOutputSql() - Method in class org.molgenis.MolgenisOptions
getOutputSrc() - Method in class org.molgenis.MolgenisOptions
getOutputWeb() - Method in class org.molgenis.MolgenisOptions
getPackageName() - Method in class org.molgenis.model.elements.UISchema
getParameter() - Method in class org.molgenis.model.elements.MethodQuery.Rule
getParameters() - Method in class org.molgenis.model.elements.Method
getParent() - Method in class org.molgenis.model.elements.Field: Deprecated.
getParent() - Method in class org.molgenis.model.elements.Parameter: Deprecated.
getParent() - Method in class org.molgenis.util.SimpleTree
getParent() - Method in interface org.molgenis.util.Tree: Retrieve the parent node of current element.
getParentField() - Method in class org.molgenis.model.elements.Tree
getParents() - Method in class org.molgenis.model.elements.Entity: Returns all the parents of this entity.
getParents() - Method in interface org.molgenis.model.elements.Record
getParents() - Method in class org.molgenis.model.elements.View
getPassword() - Method in class org.molgenis.util.Ssh
getPath() - Method in class org.molgenis.MolgenisOptions
getPath(String) - Method in class org.molgenis.util.SimpleTree
getPath(String) - Method in interface org.molgenis.util.Tree: Translate the path of this subtree as a separated string.
getPathName() - Method in class org.molgenis.model.elements.UISchema
getPlugin(String) - Method in interface org.molgenis.framework.ui.MolgenisPluginRegistry
getPlugin(String) - Method in class org.molgenis.framework.ui.MolgenisPluginRegistryImpl
getPluginMethod(String) - Static method in enum org.molgenis.model.elements.Plugin.Flavor
getPlugins() - Method in class org.molgenis.model.elements.UISchema
getPluginType() - Method in class org.molgenis.model.elements.Plugin
getPort() - Method in class org.molgenis.util.Ssh
getPosition() - Method in class org.molgenis.model.elements.Menu
getPosition(String) - Static method in enum org.molgenis.model.elements.Menu.Position
getPRDescription() - Method in class org.molgenis.model.elements.Model
getPrimaryKey() - Method in class org.molgenis.model.elements.Entity
getPublicId() - Method in class org.molgenis.util.SchemaLoader.LSInputImpl
getQuery() - Method in class org.molgenis.model.elements.Method
getReadOnly() - Method in class org.molgenis.model.elements.Form
getReadOnly() - Method in class org.molgenis.model.elements.Plugin
getReadOnly() - Method in class org.molgenis.model.elements.Tree
getReadonly() - Method in class org.molgenis.model.jaxb.Field
getRecord() - Method in class org.molgenis.model.elements.Form
getRecord(String) - Method in class org.molgenis.model.elements.Model
getRecord() - Method in class org.molgenis.model.elements.Plugin
getRecord() - Method in class org.molgenis.model.elements.Tree
getReferences() - Method in class org.molgenis.model.elements.Entity
getRemoteFields() - Method in class org.molgenis.model.elements.Entity: Returns a vector with all the fields that are located in other tables, but belong to this entity (xref_multiple).
getReturnType() - Method in class org.molgenis.model.elements.Method
getRoot() - Method in class org.molgenis.util.SimpleTree
getRoot() - Method in interface org.molgenis.util.Tree: Get the root element of this tree.
getRootAncestor() - Method in class org.molgenis.model.elements.Entity: Returns the root of the entity hierarchy this entity belongs to.
getRootEntities() - Method in class org.molgenis.model.elements.Model: Get entities that are NOT in modules (and are NOT mrefs).
getRow() - Method in class org.molgenis.model.elements.Matrix
getRowEntity() - Method in class org.molgenis.model.elements.Matrix: Return the Entity that contains the labels for the rows.
getRowEntityName() - Method in class org.molgenis.model.elements.Matrix
getRules() - Method in class org.molgenis.model.elements.MethodQuery
getSchema() - Method in class org.molgenis.util.SchemaLoader
getScreens() - Method in class org.molgenis.model.jaxb.Model
getSerialVersionUID() - Static method in class org.molgenis.model.elements.DBSchema
getSortby() - Method in class org.molgenis.model.elements.Form
getSortorder() - Method in class org.molgenis.model.elements.Form
getSqlName() - Method in class org.molgenis.model.elements.Field
getSrc() - Method in class org.molgenis.model.elements.Import
getStdErr() - Method in class org.molgenis.util.SshResult
getStdOut() - Method in class org.molgenis.util.SshResult
getString(String) - Static method in class org.molgenis.util.ResourceUtils
getString(Class<?>, String) - Static method in class org.molgenis.util.ResourceUtils
getString(Class<?>, String, Charset) - Static method in class org.molgenis.util.ResourceUtils
getStringData() - Method in class org.molgenis.util.SchemaLoader.LSInputImpl
getStringValue() - Method in class org.molgenis.util.SimpleTree
getSystemFields(boolean) - Method in class org.molgenis.model.elements.Entity
getSystemId() - Method in class org.molgenis.util.SchemaLoader.LSInputImpl
getTableName() - Method in class org.molgenis.model.elements.Field
getToVersion() - Method in class org.molgenis.framework.MolgenisUpgrade
getTreeElements() - Method in class org.molgenis.util.SimpleTree
getTreeElements() - Method in interface org.molgenis.util.Tree: Retrieve all tree elements as map.
getTrees() - Method in class org.molgenis.model.elements.UISchema
getType() - Method in class org.molgenis.model.elements.Field: This method returns the type of this field.
getType() - Method in class org.molgenis.model.elements.Form
getType() - Method in class org.molgenis.model.elements.Menu
getType() - Method in class org.molgenis.model.elements.Parameter: This method returns the type of this field.
getType(String) - Static method in enum org.molgenis.model.elements.Parameter.Type: With this method the enumeration-type can be found based on the given string.
getType() - Method in class org.molgenis.model.elements.Plugin
getType() - Method in class org.molgenis.model.elements.Tree
getType() - Method in class org.molgenis.model.elements.UISchema
getType() - Method in class org.molgenis.model.jaxb.Field
getType(int) - Static method in enum org.molgenis.model.jaxb.Field.Type: With this method the enumeration-type can be found based on the given int conforming to java.sql.Types
getType(String) - Static method in enum org.molgenis.model.jaxb.Field.Type: With this method the enumeration-type can be found based on the given string.
getType(String) - Static method in class org.molgenis.MolgenisFieldTypes
getType() - Method in class org.molgenis.util.GsonHttpMessageConverter
getTypeBySqlTypesCode(int) - Static method in class org.molgenis.MolgenisFieldTypes
getTypedValue(String) - Method in class org.molgenis.fieldtypes.BoolField
getTypedValue(String) - Method in class org.molgenis.fieldtypes.CompoundField
getTypedValue(String) - Method in class org.molgenis.fieldtypes.DateField
getTypedValue(String) - Method in class org.molgenis.fieldtypes.DatetimeField
getTypedValue(String) - Method in class org.molgenis.fieldtypes.DecimalField
getTypedValue(String) - Method in class org.molgenis.fieldtypes.EnumField
getTypedValue(String) - Method in class org.molgenis.fieldtypes.FieldType
getTypedValue(String) - Method in class org.molgenis.fieldtypes.IntField
getTypedValue(String) - Method in class org.molgenis.fieldtypes.LongField
getTypedValue(String) - Method in class org.molgenis.fieldtypes.MrefField
getTypedValue(String) - Method in class org.molgenis.fieldtypes.StringField
getTypedValue(String) - Method in class org.molgenis.fieldtypes.TextField
getTypedValue(String) - Method in class org.molgenis.fieldtypes.XrefField
getUIDescription() - Method in class org.molgenis.model.elements.Model
getUnique() - Method in class org.molgenis.model.jaxb.Field
getUniqueKeysWithoutPk() - Method in class org.molgenis.model.elements.Entity
getUniques() - Method in class org.molgenis.model.jaxb.Entity
getUrl() - Method in class org.molgenis.framework.ui.MolgenisPlugin
getUserData() - Method in class org.molgenis.model.elements.Field
getUserData() - Method in class org.molgenis.model.elements.Parameter
getUserFields() - Method in class org.molgenis.model.elements.Entity
getUserinterface() - Method in class org.molgenis.model.elements.Model
getUsername() - Method in class org.molgenis.util.Ssh
getValue() - Method in enum org.molgenis.model.elements.Form.ViewType
getValue() - Method in enum org.molgenis.model.elements.Tree.ViewType
getValue() - Method in class org.molgenis.util.SimpleTree
getValue() - Method in interface org.molgenis.util.Tree: Retrieve the value of this node/leaf
getValue() - Method in class org.molgenis.util.ValueLabel: Retrieve the value
getVarCharLength() - Method in class org.molgenis.model.elements.Field: When this field is of type Type.VARCHAR, this method returns the maximum length the varchar can be.
getVarCharLength() - Method in class org.molgenis.model.elements.Parameter: When this field is of type Type.VARCHAR, this method returns the maximum length the varchar can be.
getVelocityName() - Method in class org.molgenis.model.elements.UISchema
getVersion() - Method in class org.molgenis.model.jaxb.Model
getViews() - Method in class org.molgenis.model.elements.Model
getViewType() - Method in class org.molgenis.model.elements.Form
getXrefEntity() - Method in class org.molgenis.model.elements.Field: Returns the name of the entity this field is referencing to.
getXrefEntity() - Method in class org.molgenis.model.jaxb.Field
getXrefEntityName() - Method in class org.molgenis.model.elements.Field
getXrefField() - Method in class org.molgenis.model.elements.Field: Returns the name of the field of the entity this field is referencing to.
getXrefField() - Method in class org.molgenis.model.jaxb.Field
getXrefFieldName() - Method in class org.molgenis.model.elements.Field
getXRefFields() - Method in class org.molgenis.model.elements.Entity
getXrefLabel() - Method in class org.molgenis.model.jaxb.Field
getXrefLabelNames() - Method in class org.molgenis.model.elements.Field: Returns the label of this reference.
getXrefLabelPath(String) - Method in class org.molgenis.model.elements.Field
getXrefLabelPath() - Method in class org.molgenis.model.elements.FieldWithXrefLabel
getXrefLabels() - Method in class org.molgenis.model.elements.Entity
getXrefLabels() - Method in class org.molgenis.model.elements.Field
getXrefLabelsTemp() - Method in class org.molgenis.model.elements.Field
getXrefLabelTree() - Method in class org.molgenis.model.elements.Field: Return a tree wich describes the path to xref labels.
getXrefLabelTree(boolean) - Method in class org.molgenis.model.elements.Field
getXrefLabelTree(List<String>, SimpleTree<?>) - Method in class org.molgenis.model.elements.Field: Creates a tree with leafs that match labels and nodes that match entities.
getXrefLabelTree(List<String>, SimpleTree<?>, boolean) - Method in class org.molgenis.model.elements.Field: Creates a tree with leafs that match labels and nodes that match entities.
getXrefLookupFields() - Method in class org.molgenis.model.elements.Entity
getXRefName() - Method in class org.molgenis.model.jaxb.Field
getXRefsFor(Entity, List<Entity>) - Method in class org.molgenis.model.elements.View
getXsdType() - Method in class org.molgenis.fieldtypes.BoolField
getXsdType() - Method in class org.molgenis.fieldtypes.CompoundField
getXsdType() - Method in class org.molgenis.fieldtypes.DateField
getXsdType() - Method in class org.molgenis.fieldtypes.DatetimeField
getXsdType() - Method in class org.molgenis.fieldtypes.DecimalField
getXsdType() - Method in class org.molgenis.fieldtypes.EnumField
getXsdType() - Method in class org.molgenis.fieldtypes.FieldType: Produce valid XSD type
getXsdType() - Method in class org.molgenis.fieldtypes.IntField
getXsdType() - Method in class org.molgenis.fieldtypes.LongField
getXsdType() - Method in class org.molgenis.fieldtypes.MrefField
getXsdType() - Method in class org.molgenis.fieldtypes.StringField
getXsdType() - Method in class org.molgenis.fieldtypes.TextField
getXsdType() - Method in class org.molgenis.fieldtypes.XrefField
GsonFactoryBean - Class in org.molgenis.util: A FactoryBean for creating a Google Gson 2.x Gson instance.
GsonFactoryBean() - Constructor for class org.molgenis.util.GsonFactoryBean
GsonHttpMessageConverter - Class in org.molgenis.util: Converts objects to json string and vica versa If logging is set to debug it will print the incoming and outgoing json strings
GsonHttpMessageConverter(Gson) - Constructor for class org.molgenis.util.GsonHttpMessageConverter: Construct a new GsonHttpMessageConverter.

H

hasAncestor() - Method in class org.molgenis.model.elements.Entity
hasChildren() - Method in class org.molgenis.util.SimpleTree
hasChildren() - Method in interface org.molgenis.util.Tree: Retrieve wether this Tree has children
hasDescendants() - Method in class org.molgenis.model.elements.Entity
hasFilter() - Method in class org.molgenis.model.elements.Field
hashCode() - Method in class org.molgenis.fieldtypes.FieldType
hashCode() - Method in class org.molgenis.framework.ui.MolgenisPlugin
hashCode() - Method in class org.molgenis.model.elements.Entity: Returns a hash code value for the Entity.
hashCode() - Method in class org.molgenis.model.elements.Field: Returns a hash code value for the Field.
hashCode() - Method in class org.molgenis.model.elements.Index: Returns a hash code value for the Field.
hashCode() - Method in class org.molgenis.model.elements.Parameter: Returns a hash code value for the Field.
hashCode() - Method in class org.molgenis.model.elements.Unique
hashCode() - Method in class org.molgenis.util.ErrorMessageResponse.ErrorMessage
hashCode() - Method in class org.molgenis.util.ErrorMessageResponse
hashCode() - Method in class org.molgenis.util.Pair
hasImplements() - Method in class org.molgenis.model.elements.Entity
hasParent() - Method in class org.molgenis.util.SimpleTree
hasParent() - Method in interface org.molgenis.util.Tree: Retrieve wether this Tree has a parent
hasSuperclassField(String) - Method in class org.molgenis.model.elements.Entity
hasXRefs() - Method in class org.molgenis.model.elements.Entity
hasXRefs() - Method in interface org.molgenis.model.elements.Record
hasXRefs() - Method in class org.molgenis.model.elements.View
HIERARCHY_PER_TABLE - Static variable in class org.molgenis.MolgenisOptions
HSQL_KEYWORDS - Static variable in class org.molgenis.model.ReservedKeywords
HTML - Static variable in class org.molgenis.MolgenisFieldTypes
HtmlField - Class in org.molgenis.fieldtypes
HtmlField() - Constructor for class org.molgenis.fieldtypes.HtmlField
HtmlTools - Class in org.molgenis.util: Helper functions for HTML interaction
HtmlTools() - Constructor for class org.molgenis.util.HtmlTools
HugeMap<K,V> - Class in org.molgenis.util
HugeMap() - Constructor for class org.molgenis.util.HugeMap
HugeSet<E> - Class in org.molgenis.util: Set that can contain a huge amount of data by storing it on disk.
HugeSet() - Constructor for class org.molgenis.util.HugeSet
HYPERLINK - Static variable in class org.molgenis.MolgenisFieldTypes
HyperlinkField - Class in org.molgenis.fieldtypes
HyperlinkField() - Constructor for class org.molgenis.fieldtypes.HyperlinkField

I

ImageField - Class in org.molgenis.fieldtypes
ImageField() - Constructor for class org.molgenis.fieldtypes.ImageField
Import - Class in org.molgenis.model.elements: Import model
Import() - Constructor for class org.molgenis.model.elements.Import
import_model_database - Variable in class org.molgenis.MolgenisOptions: relative paths to the data model XML files, objects in these files are used only, not generated
Index - Class in org.molgenis.model.elements: This class describes a single index-field.
Index(String) - Constructor for class org.molgenis.model.elements.Index: Default constructor, which sets the name of the index.
InstallCert - Class in org.molgenis.util
InstallCert() - Constructor for class org.molgenis.util.InstallCert
INT - Static variable in class org.molgenis.MolgenisFieldTypes
IntField - Class in org.molgenis.fieldtypes
IntField() - Constructor for class org.molgenis.fieldtypes.IntField
isAbstract() - Method in class org.molgenis.model.elements.Entity: Returns whether this entry is abstract
isAbstract() - Method in class org.molgenis.model.jaxb.Entity
isAggregateable() - Method in class org.molgenis.model.elements.Field
isAncestor(String) - Method in class org.molgenis.model.elements.Entity
isAssociation() - Method in class org.molgenis.model.elements.Entity
isAuto() - Method in class org.molgenis.model.elements.Field: Returns whether this field is auto-assigned by the database.
isCyclic() - Method in class org.molgenis.model.elements.Field
isDatabasePopulated() - Method in interface org.molgenis.framework.db.WebAppDatabasePopulatorService
isDisable_decorators() - Method in class org.molgenis.MolgenisOptions
isEditable() - Method in class org.molgenis.util.Property: Returns true when the set-method of this property can be called and false otherwise.
isEmbedchild() - Method in class org.molgenis.model.elements.Form
isEmbedparent() - Method in class org.molgenis.model.elements.Form
isEmpty() - Method in class org.molgenis.util.HugeMap
isEmpty() - Method in class org.molgenis.util.HugeSet
isEnum() - Method in class org.molgenis.model.elements.Field: Returns whether this field has enum options.
isExcludeSystem() - Method in class org.molgenis.MolgenisOptions
isFilter() - Method in class org.molgenis.model.elements.Form
isHidden() - Method in class org.molgenis.model.elements.Field
isImported() - Method in class org.molgenis.model.elements.Entity
isLocal() - Method in class org.molgenis.model.elements.Field: Returns whether this field is locally available in the table, or whether it is located in another table (for example link-table).
isMRef() - Method in class org.molgenis.model.elements.Field: Returns whether this field is a mref.
isNillable() - Method in class org.molgenis.model.elements.Field: Returns whether this field can be NULL in the database.
isNillable() - Method in class org.molgenis.model.elements.Parameter: Returns whether this field can be NULL in the database.
isParent(String) - Method in class org.molgenis.model.elements.Entity
isReadOnly() - Method in class org.molgenis.model.elements.Field: Returns whether this field is read-only in the database.
isRootAncestor() - Method in class org.molgenis.model.elements.Entity: Returns whether this entry has NO parent AND whether it has children' removed.
isSingleton() - Method in class org.molgenis.util.GsonFactoryBean
isSubclass() - Method in class org.molgenis.model.elements.Unique
isSystem() - Method in class org.molgenis.model.elements.Entity: Returns whether this entity is system-specific.
isSystem() - Method in class org.molgenis.model.elements.Field: Returns whether this field is a system-field.
isUnique() - Method in class org.molgenis.model.elements.Field: If this a unique field? If this field is part of a compound key it will return false
isXRef() - Method in class org.molgenis.model.elements.Field: Returns whether this field is a xref.
isXrefCascade() - Method in class org.molgenis.model.elements.Field
iterator() - Method in class org.molgenis.framework.ui.MolgenisPluginRegistryImpl
iterator() - Method in class org.molgenis.util.HugeSet

J

JAVA_KEYWORDS - Static variable in class org.molgenis.model.ReservedKeywords
JAVASCRIPT_KEYWORDS - Static variable in class org.molgenis.model.ReservedKeywords
jpa_use_sequence - Variable in class org.molgenis.MolgenisOptions

K

keySet() - Method in class org.molgenis.util.HugeMap

L

LENGTH_NOT_SET - Static variable in class org.molgenis.model.elements.Parameter: Fixed value used for determining the not-set value for the varchar.
LinkableTree<T extends Tree<T>> - Class in org.molgenis.util: Implementation of a simple tree
LinkableTree(String, T, String) - Constructor for class org.molgenis.util.LinkableTree: Construct a new Tree
ListEscapeUtils - Class in org.molgenis.util
LONG - Static variable in class org.molgenis.MolgenisFieldTypes
LongField - Class in org.molgenis.fieldtypes
LongField() - Constructor for class org.molgenis.fieldtypes.LongField
LSInputImpl(String, String, InputStream) - Constructor for class org.molgenis.util.SchemaLoader.LSInputImpl

M

main(String[]) - Static method in class org.molgenis.model.DatabaseModelExtractor
main(String[]) - Static method in class org.molgenis.util.InstallCert
MAINTENANCE - Static variable in class org.molgenis.Version: The maintenance part of the version, which is changed for bug-fixes
MAJOR - Static variable in class org.molgenis.Version: The major part of the version, which is changed for major interface changes
Matrix - Class in org.molgenis.model.elements
Matrix(String, DBSchema) - Constructor for class org.molgenis.model.elements.Matrix
Menu - Class in org.molgenis.model.elements: Describes a menu-element in the user-interface.
Menu(String, UISchema) - Constructor for class org.molgenis.model.elements.Menu
Menu - Class in org.molgenis.model.jaxb
Menu() - Constructor for class org.molgenis.model.jaxb.Menu
Menu.Position - Enum in org.molgenis.model.elements
Method - Class in org.molgenis.model.elements: Describes an exposable method in the molgenis framework.
Method(String, MethodSchema) - Constructor for class org.molgenis.model.elements.Method
MethodQuery - Class in org.molgenis.model.elements
MethodQuery(String) - Constructor for class org.molgenis.model.elements.MethodQuery
MethodQuery.Rule - Class in org.molgenis.model.elements
MethodSchema - Class in org.molgenis.model.elements: A method-schema describes a number of methods, which can be exposed with something like webservices.
MethodSchema(String, MethodSchema) - Constructor for class org.molgenis.model.elements.MethodSchema
MINOR - Static variable in class org.molgenis.Version: The minor part of the version, which is changed when interfaces have been added
Model - Class in org.molgenis.model.elements
Model(String) - Constructor for class org.molgenis.model.elements.Model
Model - Class in org.molgenis.model.jaxb
Model() - Constructor for class org.molgenis.model.jaxb.Model
model_database - Variable in class org.molgenis.MolgenisOptions: relative paths to the data model XML files.
Module - Class in org.molgenis.model.elements: Annotation classes.
Module(String, Model) - Constructor for class org.molgenis.model.elements.Module
Module - Class in org.molgenis.model.jaxb
Module() - Constructor for class org.molgenis.model.jaxb.Module
MOLGENIS_KEYWORDS - Static variable in class org.molgenis.model.ReservedKeywords
MolgenisDateFormat - Class in org.molgenis.util
MolgenisDateFormat() - Constructor for class org.molgenis.util.MolgenisDateFormat
MolgenisFieldTypes - Class in org.molgenis: Singleton class that holds all known field types in MOLGENIS.
MolgenisFieldTypes() - Constructor for class org.molgenis.MolgenisFieldTypes
MolgenisFieldTypes.FieldTypeEnum - Enum in org.molgenis
MolgenisModel - Class in org.molgenis.model
MolgenisModel() - Constructor for class org.molgenis.model.MolgenisModel
MolgenisModelException - Exception in org.molgenis.model
MolgenisModelException(String) - Constructor for exception org.molgenis.model.MolgenisModelException
MolgenisModelParser - Class in org.molgenis.model: TODO: refactor: spread over multiple files.
MolgenisModelParser() - Constructor for class org.molgenis.model.MolgenisModelParser
MolgenisModelValidator - Class in org.molgenis.model
MolgenisModelValidator() - Constructor for class org.molgenis.model.MolgenisModelValidator
MolgenisOptions - Class in org.molgenis: Option to parameterize the Molgenis and the org.molgenis.framework.server.MolgenisServer
MolgenisOptions() - Constructor for class org.molgenis.MolgenisOptions: Initialize with the defaults
MolgenisOptions(Properties) - Constructor for class org.molgenis.MolgenisOptions: Initialize options from properties object
MolgenisPlugin - Class in org.molgenis.framework.ui
MolgenisPlugin(String, String, String, String) - Constructor for class org.molgenis.framework.ui.MolgenisPlugin
MolgenisPluginFactory - Interface in org.molgenis.framework.ui
MolgenisPluginRegistry - Interface in org.molgenis.framework.ui
MolgenisPluginRegistryImpl - Class in org.molgenis.framework.ui
MolgenisPluginRegistryImpl() - Constructor for class org.molgenis.framework.ui.MolgenisPluginRegistryImpl
MolgenisUpgrade - Class in org.molgenis.framework: Base class for Molgenis upgrade steps.
MolgenisUpgrade(int, int) - Constructor for class org.molgenis.framework.MolgenisUpgrade
MolgenisUpgradeService - Interface in org.molgenis.framework
moveMrefsFromInterfaceAndCopyToSubclass(Model) - Static method in class org.molgenis.model.MolgenisModelValidator: As mrefs are a linking table between to other tables, interfaces cannot be part of mrefs (as they don't have a linking table).
MREF - Static variable in class org.molgenis.MolgenisFieldTypes
MrefField - Class in org.molgenis.fieldtypes: Many to many reference.
MrefField() - Constructor for class org.molgenis.fieldtypes.MrefField
MultimapCollectors - Class in org.molgenis.util.stream: Collectors that collect to Multimap.
MultimapCollectors() - Constructor for class org.molgenis.util.stream.MultimapCollectors
MYSQL_KEYWORDS - Static variable in class org.molgenis.model.ReservedKeywords

N

name - Variable in class org.molgenis.util.SimpleTree: Unique name of this element

O

object_relational_mapping - Variable in class org.molgenis.MolgenisOptions: Advanced option: Type of object relational mapping.
onApplicationEvent(ContextRefreshedEvent) - Method in class org.molgenis.framework.db.WebAppDatabasePopulator
operator - Variable in class org.molgenis.model.elements.MethodQuery.Rule
Option - Annotation Type in org.molgenis.util.cmdline: This annotation type helps to describe a single commandline option.
Option.Param - Enum in org.molgenis.util.cmdline
Option.Type - Enum in org.molgenis.util.cmdline: Describes the different types a command-line option can be.
OptionsClass - Annotation Type in org.molgenis.util.cmdline: Option class ? Another kind of option
ORACLE_KEYWORDS - Static variable in class org.molgenis.model.ReservedKeywords
org.molgenis - package org.molgenis: MOLGENIS generative platform for life sciences having framework, generators, models and util.
org.molgenis.fieldtypes - package org.molgenis.fieldtypes: Helper functions for each field type.
org.molgenis.framework - package org.molgenis.framework
org.molgenis.framework.db - package org.molgenis.framework.db
org.molgenis.framework.ui - package org.molgenis.framework.ui
org.molgenis.gson - package org.molgenis.gson
org.molgenis.model - package org.molgenis.model: MOLGENIS meta model parser.
org.molgenis.model.elements - package org.molgenis.model.elements: Currently known model elements like 'entity' and 'field'.
org.molgenis.model.jaxb - package org.molgenis.model.jaxb: Jaxb implementation of subset of model elements.
org.molgenis.scheduler - package org.molgenis.scheduler
org.molgenis.util - package org.molgenis.util: MOLGENIS supporting utilities
org.molgenis.util.cmdline - package org.molgenis.util.cmdline
org.molgenis.util.stream - package org.molgenis.util.stream
output_dir - Variable in class org.molgenis.MolgenisOptions
output_doc - Variable in class org.molgenis.MolgenisOptions: Source directory for generated doc
output_hand - Variable in class org.molgenis.MolgenisOptions: Source directory for handwritten java
output_sql - Variable in class org.molgenis.MolgenisOptions: Source directory for generated sql
output_src - Variable in class org.molgenis.MolgenisOptions: Source directory for generated java
output_web - Variable in class org.molgenis.MolgenisOptions: Source directory for web content

P

Pair<T,T2> - Class in org.molgenis.util: Generic pair to link two objects together.
Pair() - Constructor for class org.molgenis.util.Pair: Standard constructor, which initializes the two values to null.
Pair(T, T2) - Constructor for class org.molgenis.util.Pair: Specific constructor, which initializes the two values to the two values passed as parameters.
parameter - Variable in class org.molgenis.model.elements.MethodQuery.Rule
Parameter - Class in org.molgenis.model.elements: Describes a field in an entity.
Parameter(Method, Parameter.Type) - Constructor for class org.molgenis.model.elements.Parameter: Constructor specifically meant for constructing a return-type.
Parameter(Method, Parameter.Type, String, String, boolean, String) - Constructor for class org.molgenis.model.elements.Parameter: Standard constructor, which sets all the common variables for a field.
Parameter.Type - Enum in org.molgenis.model.elements: Description of the different types of a field.
parentName - Variable in class org.molgenis.util.SimpleTree: parent.name (or null if root element)
parse(String) - Static method in enum org.molgenis.model.elements.Form.SortOrder
parse(MolgenisOptions) - Static method in class org.molgenis.model.MolgenisModel
parse(Properties) - Static method in class org.molgenis.model.MolgenisModel
parse(String[]) - Method in class org.molgenis.util.cmdline.CmdLineParser: With this function the parser is invoked for the command-line options.
parse(Properties) - Method in class org.molgenis.util.cmdline.CmdLineParser: With this function the parser is invoked for the properties.
parseDbSchema(String) - Static method in class org.molgenis.model.MolgenisModelParser: Simple parse an xml string
parseDbSchema(ArrayList<String>) - Static method in class org.molgenis.model.MolgenisModelParser
parseDbSchema(ArrayList<String>, String) - Static method in class org.molgenis.model.MolgenisModelParser
parseEntity(Model, Element) - Static method in class org.molgenis.model.MolgenisModelParser
parseField(Entity, Element) - Static method in class org.molgenis.model.MolgenisModelParser
parseMatrix(Model, Element) - Static method in class org.molgenis.model.MolgenisModelParser
parseMethod(Model, Element) - Static method in class org.molgenis.model.MolgenisModelParser
parseModule(Model, Element) - Static method in class org.molgenis.model.MolgenisModelParser
parseParameter(Method, Element) - Static method in class org.molgenis.model.MolgenisModelParser
parseQuery(Model, Method, Element) - Static method in class org.molgenis.model.MolgenisModelParser
parseQueryRule(Model, MethodQuery, Element) - Static method in class org.molgenis.model.MolgenisModelParser
parseReturnType(Model, Method, Element) - Static method in class org.molgenis.model.MolgenisModelParser
parseView(Model, Element) - Static method in class org.molgenis.model.MolgenisModelParser
parseViewType(String) - Static method in enum org.molgenis.model.elements.Form.ViewType
parseViewType(String) - Static method in enum org.molgenis.model.elements.Tree.ViewType
path - Variable in class org.molgenis.MolgenisOptions
PATTERN_CSS - Static variable in class org.molgenis.framework.ui.ResourcePathPatterns
PATTERN_FONTS - Static variable in class org.molgenis.framework.ui.ResourcePathPatterns
PATTERN_IMG - Static variable in class org.molgenis.framework.ui.ResourcePathPatterns
PATTERN_JS - Static variable in class org.molgenis.framework.ui.ResourcePathPatterns
Plugin - Class in org.molgenis.model.elements
Plugin(String, UISchema, String) - Constructor for class org.molgenis.model.elements.Plugin
Plugin.Flavor - Enum in org.molgenis.model.elements
populateDatabase() - Method in interface org.molgenis.framework.db.WebAppDatabasePopulatorService
PRIMARY_KEY - Static variable in class org.molgenis.model.elements.Entity: Convenience variable for retrieving the primary key from the keys
printOptions() - Method in class org.molgenis.util.cmdline.CmdLineParser
printUsage(PrintStream, String) - Method in class org.molgenis.util.cmdline.CmdLineParser: With this method the usage description can be printed to a print-stream.
Processor - Class in org.molgenis.model.elements: Deprecated.
Processor(String, PRSchema) - Constructor for class org.molgenis.model.elements.Processor: Deprecated.
Property<GaType> - Class in org.molgenis.util: Implementation of a property.
Property(GaType) - Constructor for class org.molgenis.util.Property: Default constructor which sets the property-value to the given value and the editable-flag to true.
Property(GaType, boolean) - Constructor for class org.molgenis.util.Property: Default constructor which sets the property-value to the given value and the editable-flag to given value.
PRSchema - Class in org.molgenis.model.elements: Deprecated.
PRSchema(String, PRSchema) - Constructor for class org.molgenis.model.elements.PRSchema: Deprecated.
put(K, V) - Method in class org.molgenis.util.HugeMap
putAll(Map<? extends K, ? extends V>) - Method in class org.molgenis.util.HugeMap

R

readInternal(Class<?>, HttpInputMessage) - Method in class org.molgenis.util.GsonHttpMessageConverter
Record - Interface in org.molgenis.model.elements: This interface describes the functionality for a Record.
registerPlugin(MolgenisPlugin) - Method in interface org.molgenis.framework.ui.MolgenisPluginRegistry
registerPlugin(MolgenisPlugin) - Method in class org.molgenis.framework.ui.MolgenisPluginRegistryImpl
registerPluginFactory(MolgenisPluginFactory) - Method in interface org.molgenis.framework.ui.MolgenisPluginRegistry
registerPluginFactory(MolgenisPluginFactory) - Method in class org.molgenis.framework.ui.MolgenisPluginRegistryImpl
registerTypeAdapterFactory(TypeAdapterFactory) - Method in class org.molgenis.util.GsonFactoryBean
registerTypeHierarchyAdapter(Class<?>, Object) - Method in class org.molgenis.util.GsonFactoryBean
remove(Object) - Method in class org.molgenis.util.HugeMap
remove(Object) - Method in class org.molgenis.util.HugeSet
remove() - Method in class org.molgenis.util.SimpleTree
removeAll(Collection<?>) - Method in class org.molgenis.util.HugeSet
removeField(Field) - Method in class org.molgenis.model.elements.Entity
removeField(int) - Method in class org.molgenis.model.jaxb.Entity
removeModule(String) - Method in class org.molgenis.model.jaxb.Model: Remove module, and return the index of the module that came before this one in the list (for GUI select purposes).
Report - Class in org.molgenis.model.elements
Report(String) - Constructor for class org.molgenis.model.elements.Report
ReservedKeywords - Class in org.molgenis.model: Collection of reserved keywords used by different languages.
ReservedKeywords() - Constructor for class org.molgenis.model.ReservedKeywords
resolveResource(String, String, String, String, String) - Method in class org.molgenis.util.SchemaLoader
ResourceFingerprintRegistry - Class in org.molgenis.util
ResourceFingerprintRegistry() - Constructor for class org.molgenis.util.ResourceFingerprintRegistry
ResourcePathPatterns - Class in org.molgenis.framework.ui
ResourceUtils - Class in org.molgenis.util
retainAll(Collection<?>) - Method in class org.molgenis.util.HugeSet
Rule(String, String, String) - Constructor for class org.molgenis.model.elements.MethodQuery.Rule
rules - Variable in class org.molgenis.model.elements.MethodQuery

S

saveToTempFile(Part) - Static method in class org.molgenis.util.FileUploadUtils: Saves an uploaded file to a tempfile with prefix 'molgenis-', keeps the original file extension
saveToTempFolder(Part) - Static method in class org.molgenis.util.FileUploadUtils: Save an Uploaded file to the temp folder keeping it original name
SchedulerConfig - Class in org.molgenis.scheduler: Configure a scheduler factory based on a Quartz scheduler with jobs supporting autowiring.
SchedulerConfig() - Constructor for class org.molgenis.scheduler.SchedulerConfig
schedulerFactoryBean() - Method in class org.molgenis.scheduler.SchedulerConfig
SchemaLoader - Class in org.molgenis.util: Compiles a xsd.
SchemaLoader(String) - Constructor for class org.molgenis.util.SchemaLoader
SchemaLoader(InputStream) - Constructor for class org.molgenis.util.SchemaLoader
SchemaLoader.LSInputImpl - Class in org.molgenis.util
Screen - Class in org.molgenis.model.jaxb
Screen() - Constructor for class org.molgenis.model.jaxb.Screen
SCRIPT - Static variable in class org.molgenis.MolgenisFieldTypes
ScriptField - Class in org.molgenis.fieldtypes
ScriptField() - Constructor for class org.molgenis.fieldtypes.ScriptField
send(MimeMessage) - Method in class org.molgenis.util.AsyncJavaMailSender
send(MimeMessage[]) - Method in class org.molgenis.util.AsyncJavaMailSender
send(MimeMessagePreparator) - Method in class org.molgenis.util.AsyncJavaMailSender
send(MimeMessagePreparator[]) - Method in class org.molgenis.util.AsyncJavaMailSender
send(SimpleMailMessage) - Method in class org.molgenis.util.AsyncJavaMailSender
send(SimpleMailMessage[]) - Method in class org.molgenis.util.AsyncJavaMailSender
set(GaType) - Method in class org.molgenis.util.Property: Sets the given value as the new value for the property.
setA(T) - Method in class org.molgenis.util.Pair: Sets the first object
setAbstract(boolean) - Method in class org.molgenis.model.elements.Entity
setAbstract(Boolean) - Method in class org.molgenis.model.jaxb.Entity
setAggregateable(boolean) - Method in class org.molgenis.model.elements.Field
setAllocationSize(Integer) - Method in class org.molgenis.model.elements.Entity
setAnnotations(String) - Method in class org.molgenis.model.elements.Field
setApplicationContext(ApplicationContext) - Method in class org.molgenis.scheduler.AutowiringSpringBeanJobFactory
setApplicationContext(ApplicationContext) - Method in class org.molgenis.util.ApplicationContextProvider
setAssociation(boolean) - Method in class org.molgenis.model.elements.Entity
setAuto(boolean) - Method in class org.molgenis.model.elements.Field
setAuto(Boolean) - Method in class org.molgenis.model.jaxb.Field
setB(T2) - Method in class org.molgenis.util.Pair: Sets the second object
setBaseURI(String) - Method in class org.molgenis.util.SchemaLoader.LSInputImpl
setByteStream(InputStream) - Method in class org.molgenis.util.SchemaLoader.LSInputImpl
setCertifiedText(boolean) - Method in class org.molgenis.util.SchemaLoader.LSInputImpl
setCharacterStream(Reader) - Method in class org.molgenis.util.SchemaLoader.LSInputImpl
setCol(String) - Method in class org.molgenis.model.elements.Matrix
setColEntityName(String) - Method in class org.molgenis.model.elements.Matrix
setCommands(List<String>) - Method in class org.molgenis.model.elements.Form
setCompactView(List<String>) - Method in class org.molgenis.model.elements.Form
setContainer(String) - Method in class org.molgenis.model.elements.Matrix
setContent(String) - Method in class org.molgenis.model.elements.Matrix
setContentEntity(String) - Method in class org.molgenis.model.elements.Matrix
setDateFormatPattern(String) - Method in class org.molgenis.util.GsonFactoryBean: Define the date/time format with a SimpleDateFormat-style pattern.
setDBDescription(String) - Method in class org.molgenis.model.elements.Model
setDbFilepath(String) - Method in class org.molgenis.MolgenisOptions
setDecorator(String) - Method in class org.molgenis.model.elements.Entity
setDecorator(String) - Method in class org.molgenis.model.jaxb.Entity
setDefaultCode(String) - Method in class org.molgenis.model.elements.Field
setDefaultValue(String) - Method in class org.molgenis.model.elements.Field
setDefaultValue(String) - Method in class org.molgenis.model.jaxb.Field
setDescription(String) - Method in class org.molgenis.model.elements.Entity: Sets the description of this entity.
setDescription(String) - Method in class org.molgenis.model.elements.Field: Sets the description of this entity.
setDescription(String) - Method in class org.molgenis.model.elements.Form
setDescription(String) - Method in class org.molgenis.model.elements.Method
setDescription(String) - Method in class org.molgenis.model.elements.Module
setDescription(String) - Method in class org.molgenis.model.elements.Parameter: Sets the description of this entity.
setDescription(String) - Method in class org.molgenis.model.elements.Unique
setDescription(String) - Method in class org.molgenis.model.elements.View
setDescription(String) - Method in class org.molgenis.model.jaxb.Entity
setDescription(String) - Method in class org.molgenis.model.jaxb.Field
setDisable_decorators(boolean) - Method in class org.molgenis.MolgenisOptions
setDisableHtmlEscaping(boolean) - Method in class org.molgenis.util.GsonFactoryBean: Whether to use the GsonBuilder.disableHtmlEscaping() when writing JSON.
setEmbedchild(boolean) - Method in class org.molgenis.model.elements.Form
setEmbedchildfield(String) - Method in class org.molgenis.model.elements.Form
setEmbedchildname(String) - Method in class org.molgenis.model.elements.Form
setEmbedfields(String) - Method in class org.molgenis.model.elements.Form
setEmbedkeyfield(String) - Method in class org.molgenis.model.elements.Form
setEmbedparent(boolean) - Method in class org.molgenis.model.elements.Form
setEmbedparentfield(String) - Method in class org.molgenis.model.elements.Form
setEmbedparentname(String) - Method in class org.molgenis.model.elements.Form
setEncoding(String) - Method in class org.molgenis.util.SchemaLoader.LSInputImpl
setEntities(List<Entity>) - Method in class org.molgenis.model.elements.Module
setEntities(List<Entity>) - Method in class org.molgenis.model.jaxb.Model
setEntities(List<Entity>) - Method in class org.molgenis.model.jaxb.Module
setEntity(String) - Method in class org.molgenis.model.elements.Dataset
setEntity(Entity) - Method in class org.molgenis.model.elements.Field
setEntity(Entity) - Method in class org.molgenis.model.elements.Form
setEntity(Entity) - Method in class org.molgenis.model.elements.Plugin
setEntity(Entity) - Method in class org.molgenis.model.elements.Tree
setEntity(Entity) - Method in class org.molgenis.model.elements.Unique
setEnumOptions(List<String>) - Method in class org.molgenis.fieldtypes.EnumField
setEnumOptions(Vector<String>) - Method in class org.molgenis.model.elements.Field
setEnumOptions(List<String>) - Method in class org.molgenis.model.elements.Parameter
setEnumoptions(String) - Method in class org.molgenis.model.jaxb.Field
setExcludeSystem(boolean) - Method in class org.molgenis.MolgenisOptions
setExtends(String) - Method in class org.molgenis.model.jaxb.Entity
setField(Field) - Method in class org.molgenis.fieldtypes.FieldType
setFields(List<Field>) - Method in class org.molgenis.model.jaxb.Entity
setFields(String) - Method in class org.molgenis.model.jaxb.Unique
setFilter(boolean) - Method in class org.molgenis.model.elements.Field
setFilter(boolean) - Method in class org.molgenis.model.elements.Form
setFilterfield(String) - Method in class org.molgenis.model.elements.Field
setFilterfield(String) - Method in class org.molgenis.model.elements.Form
setFiltertype(String) - Method in class org.molgenis.model.elements.Field
setFiltertype(String) - Method in class org.molgenis.model.elements.Form
setFiltervalue(String) - Method in class org.molgenis.model.elements.Field
setFiltervalue(String) - Method in class org.molgenis.model.elements.Form
setGenerateTests(boolean) - Method in class org.molgenis.MolgenisOptions
setGroup(String) - Method in class org.molgenis.model.elements.UISchema
setGroupRead(String) - Method in class org.molgenis.model.elements.UISchema
setHeader(String) - Method in class org.molgenis.model.elements.Form
setHidden(boolean) - Method in class org.molgenis.model.elements.Field
setHideFields(List<String>) - Method in class org.molgenis.model.elements.Form
setHost(String) - Method in class org.molgenis.util.Ssh
setIdField(String) - Method in class org.molgenis.model.elements.Tree
setImplements(String...) - Method in class org.molgenis.model.elements.Entity
setImplements(Vector<String>) - Method in class org.molgenis.model.elements.Entity
setImplements(String) - Method in class org.molgenis.model.jaxb.Entity
setImported(boolean) - Method in class org.molgenis.model.elements.Entity
setInputStream(BufferedInputStream) - Method in class org.molgenis.util.SchemaLoader.LSInputImpl
setJpaCascade(String) - Method in class org.molgenis.model.elements.Field
setLabel(String) - Method in class org.molgenis.model.elements.Entity: Set the label of this entity.
setLabel(String) - Method in class org.molgenis.model.elements.Field
setLabel(String) - Method in class org.molgenis.model.elements.Model
setLabel(String) - Method in class org.molgenis.model.elements.Module
setLabel(String) - Method in class org.molgenis.model.elements.UISchema
setLabel(String) - Method in class org.molgenis.model.jaxb.Entity
setLabel(String) - Method in class org.molgenis.model.jaxb.Field
setLabel(String) - Method in class org.molgenis.model.jaxb.Model
setLabel(String) - Method in class org.molgenis.util.ValueLabel: Set the label
setLabelField(String) - Method in class org.molgenis.model.elements.Tree
setLength(Integer) - Method in class org.molgenis.model.jaxb.Field
setLimit(int) - Method in class org.molgenis.model.elements.Form
setMaxRange(Long) - Method in class org.molgenis.model.elements.Field
setMinRange(Long) - Method in class org.molgenis.model.elements.Field
setModel(Model) - Method in class org.molgenis.model.elements.DBSchema
setModelDatabase(ArrayList<String>) - Method in class org.molgenis.MolgenisOptions
setModelDatabase(String) - Method in class org.molgenis.MolgenisOptions
setModule(Module) - Method in class org.molgenis.model.elements.Entity
setModules(List<Module>) - Method in class org.molgenis.model.elements.DBSchema
setModules(List<Module>) - Method in class org.molgenis.model.jaxb.Model
setMolgenis_properties(String) - Method in class org.molgenis.MolgenisOptions
setMrefLocalid(String) - Method in class org.molgenis.model.elements.Field
setMrefLocalid(String) - Method in class org.molgenis.model.jaxb.Field
setMrefName(String) - Method in class org.molgenis.model.elements.Field: Sets the name of the link-table when this field is a XREF_MULTIPLE.
setMrefName(String) - Method in class org.molgenis.model.jaxb.Field
setMrefRemoteid(String) - Method in class org.molgenis.model.elements.Field
setMrefRemoteid(String) - Method in class org.molgenis.model.jaxb.Field
setName(String) - Method in class org.molgenis.model.elements.Dataset
setName(String) - Method in class org.molgenis.model.elements.Field
setName(String) - Method in class org.molgenis.model.elements.Model
setName(String) - Method in class org.molgenis.model.elements.Module
setName(String) - Method in class org.molgenis.model.jaxb.Entity
setName(String) - Method in class org.molgenis.model.jaxb.Field
setName(String) - Method in class org.molgenis.model.jaxb.Model
setName(String) - Method in class org.molgenis.model.jaxb.Module
setName(String) - Method in class org.molgenis.model.jaxb.Screen
setName(String) - Method in class org.molgenis.util.SimpleTree
setName(String, String) - Method in class org.molgenis.util.SimpleTree
setNamespace(String) - Method in class org.molgenis.model.elements.Entity
setNamespace(String) - Method in class org.molgenis.model.elements.UISchema
setNillable(boolean) - Method in class org.molgenis.model.elements.Field
setNillable(Boolean) - Method in class org.molgenis.model.jaxb.Field
setObjectRelationalMapping(String) - Method in class org.molgenis.MolgenisOptions
setOutputDoc(String) - Method in class org.molgenis.MolgenisOptions
setOutputHand(String) - Method in class org.molgenis.MolgenisOptions
setOutputSql(String) - Method in class org.molgenis.MolgenisOptions
setOutputSrc(String) - Method in class org.molgenis.MolgenisOptions
setOutputWeb(String) - Method in class org.molgenis.MolgenisOptions
setParent(T) - Method in class org.molgenis.util.SimpleTree
setParent(T) - Method in interface org.molgenis.util.Tree: Set the parent of current element (and move the children accordingly).
setParentField(String) - Method in class org.molgenis.model.elements.Tree
setParents(Vector<String>) - Method in class org.molgenis.model.elements.Entity: With this method all the parents of this entity can be set in one call.
setParents(String[]) - Method in class org.molgenis.model.elements.Entity
setPassword(String) - Method in class org.molgenis.util.Ssh
setPath(String) - Method in class org.molgenis.MolgenisOptions
setPluginMethod(Plugin.Flavor) - Method in class org.molgenis.model.elements.Plugin
setPluginType(String) - Method in class org.molgenis.model.elements.Plugin
setPort(int) - Method in class org.molgenis.util.Ssh
setPosition(Menu.Position) - Method in class org.molgenis.model.elements.Menu
setPRDescription(String) - Method in class org.molgenis.model.elements.Model
setPrefixJson(boolean) - Method in class org.molgenis.util.GsonHttpMessageConverter: Indicates whether the JSON output by this view should be prefixed with "{} &&".
setPrettyPrinting(boolean) - Method in class org.molgenis.util.GsonFactoryBean: Whether to use the GsonBuilder.setPrettyPrinting() when writing JSON.
setPublicId(String) - Method in class org.molgenis.util.SchemaLoader.LSInputImpl
setQuery(MethodQuery) - Method in class org.molgenis.model.elements.Method
setReadonly(boolean) - Method in class org.molgenis.model.elements.Field
setReadOnly(boolean) - Method in class org.molgenis.model.elements.Form
setReadOnly(boolean) - Method in class org.molgenis.model.elements.Plugin
setReadOnly(boolean) - Method in class org.molgenis.model.elements.Tree
setReadonly(Boolean) - Method in class org.molgenis.model.jaxb.Field
setRecord(Record) - Method in class org.molgenis.model.elements.Form
setRecord(Record) - Method in class org.molgenis.model.elements.Plugin
setRecord(Record) - Method in class org.molgenis.model.elements.Tree
setReturnType(Entity) - Method in class org.molgenis.model.elements.Method
setRow(String) - Method in class org.molgenis.model.elements.Matrix
setRowEntityName(String) - Method in class org.molgenis.model.elements.Matrix
setScreens(List<Screen>) - Method in class org.molgenis.model.jaxb.Model
setSerializeNulls(boolean) - Method in class org.molgenis.util.GsonFactoryBean: Whether to use the GsonBuilder.serializeNulls() option when writing JSON.
setSortby(String) - Method in class org.molgenis.model.elements.Form
setSortorder(Form.SortOrder) - Method in class org.molgenis.model.elements.Form
setSrc(String) - Method in class org.molgenis.model.elements.Import
setStdErr(String) - Method in class org.molgenis.util.SshResult
setStdOut(String) - Method in class org.molgenis.util.SshResult
setStringData(String) - Method in class org.molgenis.util.SchemaLoader.LSInputImpl
setSubclass(boolean) - Method in class org.molgenis.model.elements.Unique
setSystem(boolean) - Method in class org.molgenis.model.elements.Entity
setSystem(boolean) - Method in class org.molgenis.model.elements.Field: With this set-function the system-property can be set.
setSystemId(String) - Method in class org.molgenis.util.SchemaLoader.LSInputImpl
setTableName(String) - Method in class org.molgenis.model.elements.Field
setType(FieldType) - Method in class org.molgenis.model.elements.Field
setType(Parameter.Type) - Method in class org.molgenis.model.elements.Parameter
setType(Field.Type) - Method in class org.molgenis.model.jaxb.Field
setType(Type) - Method in class org.molgenis.util.GsonHttpMessageConverter
setUIDescription(String) - Method in class org.molgenis.model.elements.Model
setUnique(Boolean) - Method in class org.molgenis.model.jaxb.Field
setUniques(List<Unique>) - Method in class org.molgenis.model.jaxb.Entity
setUserData(Object) - Method in class org.molgenis.model.elements.Field
setUserData(Object) - Method in class org.molgenis.model.elements.Parameter
setUsername(String) - Method in class org.molgenis.util.Ssh
setValue(Object) - Method in class org.molgenis.util.SimpleTree
setValue(Object) - Method in interface org.molgenis.util.Tree: Set the value of this node/leaf
setValue(Object) - Method in class org.molgenis.util.ValueLabel: Set the value
setVarCharLength(int) - Method in class org.molgenis.model.elements.Field: When this field is of type Type.VARCHAR, this method sets the maximum length the varchar can be.
setVarCharLength(int) - Method in class org.molgenis.model.elements.Parameter: When this field is of type Type.VARCHAR, this method sets the maximum length the varchar can be.
setVersion(String) - Method in class org.molgenis.model.jaxb.Model
setViewType(Form.ViewType) - Method in class org.molgenis.model.elements.Form
setXrefCascade(boolean) - Method in class org.molgenis.model.elements.Field
setXRefEntity(String) - Method in class org.molgenis.model.elements.Field
setXrefEntity(String) - Method in class org.molgenis.model.jaxb.Field
setXrefField(String) - Method in class org.molgenis.model.elements.Field
setXrefField(String) - Method in class org.molgenis.model.jaxb.Field
setXrefLabel(String) - Method in class org.molgenis.model.jaxb.Field
setXrefLabelNames(List<String>) - Method in class org.molgenis.model.elements.Field
setXrefLabelPath(String) - Method in class org.molgenis.model.elements.FieldWithXrefLabel
setXrefLabels(List<String>) - Method in class org.molgenis.model.elements.Entity
setXrefLookupFields(List<String>) - Method in class org.molgenis.model.elements.Entity
setXRefName(String) - Method in class org.molgenis.model.jaxb.Field
setXRefVariables(String, String, List<String>) - Method in class org.molgenis.model.elements.Field: With this method all the additional information for this xref-field can be set.
SimpleTree<T extends Tree> - Class in org.molgenis.util: Implementation of a simple tree
SimpleTree(String, T) - Constructor for class org.molgenis.util.SimpleTree: Construct a new Tree
size() - Method in class org.molgenis.util.HugeMap
size() - Method in class org.molgenis.util.HugeSet
sortEntitiesByDependency(List<Entity>, Model) - Static method in class org.molgenis.model.MolgenisModel
Ssh - Class in org.molgenis.util: Wrapper arround ssh.
Ssh(String, String, String) - Constructor for class org.molgenis.util.Ssh
Ssh(String, String, String, int) - Constructor for class org.molgenis.util.Ssh
Ssh(String, String, String, int, String, String, String, int) - Constructor for class org.molgenis.util.Ssh
SshResult - Class in org.molgenis.util
SshResult(String, String) - Constructor for class org.molgenis.util.SshResult
STRING - Static variable in class org.molgenis.MolgenisFieldTypes
StringField - Class in org.molgenis.fieldtypes
StringField() - Constructor for class org.molgenis.fieldtypes.StringField
SUBCLASS_PER_TABLE - Static variable in class org.molgenis.MolgenisOptions
supports(Class<?>) - Method in class org.molgenis.util.GsonHttpMessageConverter

T

tag - Variable in enum org.molgenis.model.elements.Parameter.Type: The string-representation of the enumeration-type.
tag - Variable in enum org.molgenis.model.jaxb.Field.Type: The string-representation of the enumeration-type.
TESTING - Static variable in class org.molgenis.Version: Flag to indicate that this is a testing release
TEXT - Static variable in class org.molgenis.MolgenisFieldTypes
TextField - Class in org.molgenis.fieldtypes
TextField() - Constructor for class org.molgenis.fieldtypes.TextField
THRESHOLD - Static variable in class org.molgenis.util.HugeMap
THRESHOLD - Static variable in class org.molgenis.util.HugeSet
toArray() - Method in class org.molgenis.util.HugeSet
toArray(T[]) - Method in class org.molgenis.util.HugeSet
toArrayListMultimap(Function<E, K>, Function<E, V>) - Static method in class org.molgenis.util.stream.MultimapCollectors
toCsv(List<String>) - Method in class org.molgenis.fieldtypes.FieldType: Convert a list of string to comma separated values.
toCsv(List<String>) - Method in class org.molgenis.model.elements.Field: Convert a list of string to comma separated values.
toLinkedHashMultimap() - Static method in class org.molgenis.util.stream.MultimapCollectors
toList(String) - Static method in class org.molgenis.util.ListEscapeUtils
toList(String, char) - Static method in class org.molgenis.util.ListEscapeUtils
toList(String, char, char) - Static method in class org.molgenis.util.ListEscapeUtils
toMultimap(Supplier<A>, Function<E, K>, Function<E, V>) - Static method in class org.molgenis.util.stream.MultimapCollectors
toMultimap(Supplier<A>) - Static method in class org.molgenis.util.stream.MultimapCollectors
toSafeUrlString(String) - Static method in class org.molgenis.util.HtmlTools: Helper function to convert any string into URL-safe encoding.
toSafeUrlStringO_b_f(String) - Static method in class org.molgenis.util.HtmlTools: Helper function to convert any string into URL-safe encoding.
toSafeUrlStringObv(String) - Static method in class org.molgenis.util.HtmlTools: Helper function to convert any string into URL-safe encoding.
toString() - Method in class org.molgenis.fieldtypes.FieldType: The string value of this type, e.g.
toString() - Method in class org.molgenis.model.elements.Dataset
toString() - Method in class org.molgenis.model.elements.Entity: Returns a string representation of the Entity.
toString() - Method in class org.molgenis.model.elements.Field: Returns a string representation of the Field.
toString() - Method in class org.molgenis.model.elements.Form
toString() - Method in class org.molgenis.model.elements.Index: Returns a string representation of the Index.
toString() - Method in class org.molgenis.model.elements.Matrix
toString() - Method in enum org.molgenis.model.elements.Menu.Position
toString() - Method in class org.molgenis.model.elements.Menu
toString() - Method in class org.molgenis.model.elements.Method
toString() - Method in class org.molgenis.model.elements.Model
toString() - Method in class org.molgenis.model.elements.Parameter: Returns a string representation of the Field.
toString() - Method in enum org.molgenis.model.elements.Plugin.Flavor
toString() - Method in class org.molgenis.model.elements.Plugin
toString() - Method in class org.molgenis.model.elements.Processor: Deprecated.
toString() - Method in class org.molgenis.model.elements.Unique
toString() - Method in enum org.molgenis.model.jaxb.Field.Type
toString() - Method in class org.molgenis.MolgenisOptions
toString(Object) - Method in class org.molgenis.util.cmdline.CmdLineParser: Pretty print the options.
toString(List<?>) - Static method in class org.molgenis.util.ListEscapeUtils
toString(List<?>, char) - Static method in class org.molgenis.util.ListEscapeUtils
toString(List<?>, char, char) - Static method in class org.molgenis.util.ListEscapeUtils
toString() - Method in class org.molgenis.util.Pair
toString(boolean) - Method in class org.molgenis.util.SimpleTree
toString(boolean, int) - Method in class org.molgenis.util.SimpleTree
toString() - Method in class org.molgenis.util.SimpleTree
toString() - Method in interface org.molgenis.util.Tree: Print the tree.
toString(boolean, int) - Method in interface org.molgenis.util.Tree: Pretty print the (sub)tree, but only a certain levels
toString() - Method in class org.molgenis.util.ValueLabel
Tree - Class in org.molgenis.model.elements
Tree(String, UISchema, String, String, String) - Constructor for class org.molgenis.model.elements.Tree
Tree<T> - Interface in org.molgenis.util: A tree with uniquely named nodes.
Tree.ViewType - Enum in org.molgenis.model.elements
treeElements - Variable in class org.molgenis.util.SimpleTree: map of tree elements (ordered)
TYPE_FIELD - Static variable in class org.molgenis.model.elements.Field

U

UISchema - Class in org.molgenis.model.elements: Definition of the base-class for objects in the user interface schema.
UISchema(String, UISchema) - Constructor for class org.molgenis.model.elements.UISchema: The standard constructor, which links the object in the tree (with the parent parameter).
Unique - Class in org.molgenis.model.elements: This class describes a unique (combination of) field(s) associated with entity.
Unique(Entity, String, boolean, String) - Constructor for class org.molgenis.model.elements.Unique: Constructor, which sets the associated entity and a single field as the unique.
Unique(Unique) - Constructor for class org.molgenis.model.elements.Unique: Copy constructor
Unique(Entity, List<String>, boolean, String) - Constructor for class org.molgenis.model.elements.Unique: Constructor, which sets the associated entity and the list of fields as the unique.
Unique - Class in org.molgenis.model.jaxb
Unique() - Constructor for class org.molgenis.model.jaxb.Unique
upgrade() - Method in class org.molgenis.framework.MolgenisUpgrade
upgrade() - Method in interface org.molgenis.framework.MolgenisUpgradeService
uploadFile(File, String) - Method in class org.molgenis.util.Ssh: Download remote file to local file via scp
uploadStringToFile(String, String) - Method in class org.molgenis.util.Ssh: Upload string to remote file.
uploadStringToFile(String, String, String) - Method in class org.molgenis.util.Ssh: Upload a string using scp, with seperate directory and file parameters.

V

validate(Model, MolgenisOptions) - Static method in class org.molgenis.model.MolgenisModelValidator
validateExtendsAndImplements(Model) - Static method in class org.molgenis.model.MolgenisModelValidator: Validate extends and implements relationships: Do superclasses actually exist Do 'implements' refer to abstract superclasses (interfaces) Do 'extends' refer to non-abstract superclasses Copy primary key to subclass to form parent/child relationships
validateForeignKeys(Model) - Static method in class org.molgenis.model.MolgenisModelValidator: Validate foreign key relationships: Do the xref_field and xref_label refer to fields actually exist Is the entity refered to non-abstract Does the xref_field refer to a unique field (i.e.
validateHideFields(Model) - Static method in class org.molgenis.model.MolgenisModelValidator
validateKeys(Model) - Static method in class org.molgenis.model.MolgenisModelValidator: Validate the unique constraints Do unique field names refer to existing fields? Is there a unique column id + unique label?
validateNamesAndReservedWords(Model, MolgenisOptions) - Static method in class org.molgenis.model.MolgenisModelValidator
validateNameSize(Model, MolgenisOptions) - Static method in class org.molgenis.model.MolgenisModelValidator
validateOveride(Model) - Static method in class org.molgenis.model.MolgenisModelValidator: Subclasses can override fields of superclasses.
validatePrimaryKeys(Model) - Static method in class org.molgenis.model.MolgenisModelValidator
validateViews(Model) - Static method in class org.molgenis.model.MolgenisModelValidator: Check if the view objects are an aggregate of known entities.
ValueLabel - Class in org.molgenis.util: Specific pair to link String label to Object.
ValueLabel() - Constructor for class org.molgenis.util.ValueLabel: Construct a new ValueLabel
ValueLabel(Object, String) - Constructor for class org.molgenis.util.ValueLabel: Construct a new ValueLabel
valueOf(String) - Static method in enum org.molgenis.model.elements.Form.SortOrder: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.molgenis.model.elements.Form.ViewType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.molgenis.model.elements.Menu.Position: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.molgenis.model.elements.Parameter.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.molgenis.model.elements.Plugin.Flavor: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.molgenis.model.elements.Tree.ViewType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.molgenis.model.jaxb.Field.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.molgenis.MolgenisFieldTypes.FieldTypeEnum: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.molgenis.util.cmdline.Option.Param: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.molgenis.util.cmdline.Option.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.molgenis.util.ZipUtils.DirectoryStructure: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.molgenis.model.elements.Form.SortOrder: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.molgenis.model.elements.Form.ViewType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.molgenis.model.elements.Menu.Position: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.molgenis.model.elements.Parameter.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.molgenis.model.elements.Plugin.Flavor: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.molgenis.model.elements.Tree.ViewType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.molgenis.model.jaxb.Field.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.molgenis.MolgenisFieldTypes.FieldTypeEnum: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.molgenis.util.cmdline.Option.Param: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.molgenis.util.cmdline.Option.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Method in class org.molgenis.util.HugeMap
values() - Static method in enum org.molgenis.util.ZipUtils.DirectoryStructure: Returns an array containing the constants of this enum type, in the order they are declared.
Version - Class in org.molgenis: Version counter for the invengine package.
Version() - Constructor for class org.molgenis.Version
View - Class in org.molgenis.model.elements: This class describes an updatable view, which shows two or more entities.
View(String, String, DBSchema) - Constructor for class org.molgenis.model.elements.View

W

WebAppDatabasePopulator - Class in org.molgenis.framework.db
WebAppDatabasePopulator(WebAppDatabasePopulatorService) - Constructor for class org.molgenis.framework.db.WebAppDatabasePopulator
WebAppDatabasePopulatorService - Interface in org.molgenis.framework.db
writeInternal(Object, HttpOutputMessage) - Method in class org.molgenis.util.GsonHttpMessageConverter

X

XREF - Static variable in class org.molgenis.MolgenisFieldTypes
XrefField - Class in org.molgenis.fieldtypes
XrefField() - Constructor for class org.molgenis.fieldtypes.XrefField

Z

ZipUtils - Class in org.molgenis.util
ZipUtils() - Constructor for class org.molgenis.util.ZipUtils
ZipUtils.DirectoryStructure - Enum in org.molgenis.util

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