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

A

add(E) - Method in class org.molgenis.util.HugeSet

addAll(Collection<? extends E>) - Method in class org.molgenis.util.HugeSet

addErrorMessage(ErrorMessageResponse.ErrorMessage) - Method in class org.molgenis.util.ErrorMessageResponse

addErrorMessages(List<ErrorMessageResponse.ErrorMessage>) - Method in class org.molgenis.util.ErrorMessageResponse

addUpgrade(MolgenisUpgrade) - Method in interface org.molgenis.framework.MolgenisUpgradeService

afterPropertiesSet() - Method in class org.molgenis.util.GsonFactoryBean

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

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

C

canRead(Class<?>, MediaType) - Method in class org.molgenis.util.GsonHttpMessageConverter

canWrite(Class<?>, MediaType) - Method in class org.molgenis.util.GsonHttpMessageConverter

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

CloseableIterator<E> - Interface in org.molgenis.util

Iterator that closes a resource if the decorated iterator is exhausted.

CommandLineOnlyConfiguration - Annotation Type in org.molgenis

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

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

CRON_REGEX - Static variable in class org.molgenis.util.RegexUtils

D

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

E

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

equals(Object) - Method in class org.molgenis.framework.ui.MolgenisPlugin

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

F

FileUploadUtils - Class in org.molgenis.util

FileUploadUtils() - Constructor for class org.molgenis.util.FileUploadUtils

G

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

getA() - Method in class org.molgenis.util.Pair

Returns the pointer to the first object.

getApplicationContext() - Static method in class org.molgenis.util.ApplicationContextProvider

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

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

getCode() - Method in class org.molgenis.util.ErrorMessageResponse.ErrorMessage

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

getEncoding() - Method in class org.molgenis.util.SchemaLoader.LSInputImpl

getErrors() - Method in class org.molgenis.util.ErrorMessageResponse

getFile(String) - Static method in class org.molgenis.util.ResourceUtils

getFile(Class<?>, String) - Static method in class org.molgenis.util.ResourceUtils

getFingerprint(String) - Method in class org.molgenis.util.ResourceFingerprintRegistry

getFingerprint(Class<?>, String) - Method in class org.molgenis.util.ResourceFingerprintRegistry

getFromVersion() - Method in class org.molgenis.framework.MolgenisUpgrade

getFullUri() - Method in class org.molgenis.framework.ui.MolgenisPlugin

getId() - Method in class org.molgenis.framework.ui.MolgenisPlugin

getInputStream() - Method in class org.molgenis.util.SchemaLoader.LSInputImpl

getLabel() - Method in class org.molgenis.util.ValueLabel

Retrieve the label

getMessage() - Method in class org.molgenis.util.ErrorMessageResponse.ErrorMessage

getName() - Method in class org.molgenis.framework.ui.MolgenisPlugin

getObject() - Method in class org.molgenis.util.GsonFactoryBean

Return the created Gson instance.

getObjectType() - Method in class org.molgenis.util.GsonFactoryBean

getOriginalFileName(Part) - Static method in class org.molgenis.util.FileUploadUtils

Get the filename of an uploaded file

getPlugin(String) - Method in interface org.molgenis.framework.ui.MolgenisPluginRegistry

getPlugin(String) - Method in class org.molgenis.framework.ui.MolgenisPluginRegistryImpl

getPublicId() - Method in class org.molgenis.util.SchemaLoader.LSInputImpl

getSchema() - Method in class org.molgenis.util.SchemaLoader

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

getSystemId() - Method in class org.molgenis.util.SchemaLoader.LSInputImpl

getToVersion() - Method in class org.molgenis.framework.MolgenisUpgrade

getType() - Method in class org.molgenis.util.GsonHttpMessageConverter

getUrl() - Method in class org.molgenis.framework.ui.MolgenisPlugin

getValue() - Method in class org.molgenis.util.ValueLabel

Retrieve the value

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

hashCode() - Method in class org.molgenis.framework.ui.MolgenisPlugin

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

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

I

isDatabasePopulated() - Method in interface org.molgenis.framework.db.WebAppDatabasePopulatorService

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

isEmpty() - Method in class org.molgenis.util.HugeSet

isSingleton() - Method in class org.molgenis.util.GsonFactoryBean

iterator() - Method in class org.molgenis.framework.ui.MolgenisPluginRegistryImpl

iterator() - Method in class org.molgenis.util.HugeSet

K

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

L

ListEscapeUtils - Class in org.molgenis.util

LSInputImpl(String, String, InputStream) - Constructor for class org.molgenis.util.SchemaLoader.LSInputImpl

M

MOLGENIS_KEYWORDS - Static variable in class org.molgenis.MolgenisReservedKeywords

MolgenisDateFormat - Class in org.molgenis.util

MolgenisDateFormat() - Constructor for class org.molgenis.util.MolgenisDateFormat

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

MolgenisReservedKeywords - Class in org.molgenis

Collection of reserved keywords used by MOLGENIS.

MolgenisReservedKeywords() - Constructor for class org.molgenis.MolgenisReservedKeywords

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

MultimapCollectors - Class in org.molgenis.util.stream

Collectors that collect to Multimap.

MultimapCollectors() - Constructor for class org.molgenis.util.stream.MultimapCollectors

O

OptionsClass - Annotation Type in org.molgenis.util.cmdline

Option class ? Another kind of option

org.molgenis - package org.molgenis

MOLGENIS generative platform for life sciences having framework, generators, models and util.

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.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

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.

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

populateDatabase() - Method in interface org.molgenis.framework.db.WebAppDatabasePopulatorService

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

RegexUtils - Class in org.molgenis.util

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

removeAll(Collection<?>) - Method in class org.molgenis.util.HugeSet

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

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

setA(T) - Method in class org.molgenis.util.Pair

Sets the first object

setApplicationContext(ApplicationContext) - Method in class org.molgenis.scheduler.AutowiringSpringBeanJobFactory

setApplicationContext(ApplicationContext) - Method in class org.molgenis.util.ApplicationContextProvider

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

setDateFormatPattern(String) - Method in class org.molgenis.util.GsonFactoryBean

Define the date/time format with a SimpleDateFormat-style pattern.

setDisableHtmlEscaping(boolean) - Method in class org.molgenis.util.GsonFactoryBean

Whether to use the GsonBuilder.disableHtmlEscaping() when writing JSON.

setEncoding(String) - Method in class org.molgenis.util.SchemaLoader.LSInputImpl

setInputStream(BufferedInputStream) - Method in class org.molgenis.util.SchemaLoader.LSInputImpl

setLabel(String) - Method in class org.molgenis.util.ValueLabel

Set the label

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

setSerializeNulls(boolean) - Method in class org.molgenis.util.GsonFactoryBean

Whether to use the GsonBuilder.serializeNulls() option when writing JSON.

setStringData(String) - Method in class org.molgenis.util.SchemaLoader.LSInputImpl

setSystemId(String) - Method in class org.molgenis.util.SchemaLoader.LSInputImpl

setType(Type) - Method in class org.molgenis.util.GsonHttpMessageConverter

setValue(Object) - Method in class org.molgenis.util.ValueLabel

Set the value

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

size() - Method in class org.molgenis.util.HugeSet

supports(Class<?>) - Method in class org.molgenis.util.GsonHttpMessageConverter

T

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

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

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() - Method in class org.molgenis.util.ValueLabel

U

upgrade() - Method in class org.molgenis.framework.MolgenisUpgrade

upgrade() - Method in interface org.molgenis.framework.MolgenisUpgradeService

V

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

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

W

WebAppDatabasePopulatorService - Interface in org.molgenis.framework.db

writeInternal(Object, HttpOutputMessage) - Method in class org.molgenis.util.GsonHttpMessageConverter

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