  src | |
 java | |
| cz | |
| vutbr | |
| fit | |
| knot | |
| annotations | |
  app | |
   AppBean.java | Singleton for storing global variables |
| Constants.java | Global constants |
| LastTextModifications.java | Class representing last 3 applied modification sets on a document |
| Localisation.java | Class responsible for localised strings |
| PersistM.java | Persistence manager (database manipulator) |
 TextModification.java | Class representing modification of annotated document text |
| comet | |
| documentLock | |
| LockMaster.java | Class manages documents locks |
| Padlock.java | Class represents the document protection, and provides methods to lock |
| protocolV1 | |
| P1Processor.java | Class which process XML with messages in 4A protocol v 1.x |
| protocolV2_0 | |
| P2Trix | |
| P2BaseTrix.java | Class that represents base trix triple |
| P2EntityAdditionalTrix.java | Class that represents entity additional attribute trix triple |
| P2EntityTrix.java | Class that represents entity trix triple |
| P2LinkedTrix.java | Class that represents linked trix triple |
| P2NestedTrix.java | Class that represents nested trix triple |
| P2SimpleTrix.java | Class that represents simple trix triple |
| P2AnnotationProcessor.java | Class which parses and process XML with messages with annotations for protocol version 2 |
| P2AnnotBaseProcessor.java | Abstract class provides a parser for the annotation of protocol version 2 |
| P2AnnotTypeProcessor.java | Class which parses and process XML with messages with types for protocol version 2 |
| P2Constants.java | Constants for protocol version 2 |
| P2MessagesCreator.java | Class provides methods for transforming objects to messages |
| P2Processor.java | Class which process XML with messages in 4A protocol v 2.0 |
| P2SuggestionProcessor.java | Class which process messages related to suggestions in protocol v 2.0 |
| AnnotCometServlet.java | Servlet for communication with clients (annotation editors) |
| AnnotServerModule.java | Interface for server module |
| DrupAuthServlet.java | Servlet which allows Drupal CMS to send informations about it's users |
| EditorSession.java | Informations about client session |
| Flier.java | Flier with informations for comet handlers |
| GetAnnotServlet.java | Servlet which makes available annotations |
| GetDocServlet.java | Servlet which makes available annotated copies of documents |
| Linearizer.java | Utility functions for document linearization |
| MessageProcessor.java | Static class which parses and process XML with messages |
| Persister.java | Static class which persists data to the database |
| RequestInfo.java | Processed informations about client request |
| ResponseCreator.java | Class that creates responses and persists data |
| SessionCleaner.java | Class that provides cleaning of unactive sessions (basic version, not final) |
| SubscribedSource.java | Subscribed source of annotations |
| SuggestionLogEntry.java | Suggested annotation with informations about suggestion |
| Util.java | Utility class (manipulates RFC 3339 dates and contains other utility methods) |
| document | |
| DocumentUpdate.java | Update of document using TextModifications |
| DocumentUpdateHelper.java | Document update helper which contains methods necessary to provide modification process |
| Pair.java | Contains Java equivalent of C++ Pair or C# Tupple |
| documentCloner | |
| AnnotCloneItem.java | Class representing annotations for clone list item |
| CloneParams.java | Class representing paramethers for document cloning |
| DocClonerServer.java | Class representing approved document clone server |
| DocumentClone.java | Class provides document clonning with new content, iniciated from NLP |
| DocumentClonerServlet.java | Servlet for communication with NLP server (for document clonning) |
| entity | |
| attribute | |
| AnyAnnotationAttribute.java | Class representing attribute of type AnyAnnotation |
| AttributeManager.java | Attribute manager provides a way how to create new attributes |
| BaseAttribute.java | Base class representing attribute of annotation |
| BinaryAttribute.java | Class representing attribute of type Binary |
| BooleanAttribute.java | Class representing attribute of type Boolean |
| DateAttribute.java | Class representing attribute of type Date |
| DateTimeAttribute.java | Class representing attribute of type DateTime |
| DecimalAttribute.java | Class representing attribute of type Decimal |
| DurationAttribute.java | Class representing attribute of type Duration |
| EntityAdditionalAttribute.java | Class representing additional attribute of entity in annotation attribute |
| EntityAttribute.java | Class representing vocabulary entity attribute |
| GeoPointAttribute.java | Class representing attribute of type GeoPoint and class representing GeoPoint |
| ImageAttribute.java | Class representing attribute of type Image |
| IntegerAttribute.java | Class representing attribute of type Integer |
| LinkedAnnotationAttribute.java | Class representing attribute of type AnnotationLink |
| NestedAnnotationAttribute.java | Class representing attribute of type NestedAnnotation |
| PersonAttribute.java | Class representing attribute of type Person |
| StringAttribute.java | Class representing attribute of type String. Also provides functions for other string based attributes such as ImageUri, URI, .. |
| StructuredAttribute.java | Abstract class representing more complex attribute |
| TextAttribute.java | Class representing attribute of type Text |
| TimeAttribute.java | Class representing attribute of type Time |
| UriAttribute.java | Class representing attribute of type URI |
| Annotation.java | Class representing annotation |
| AnnotDocument.java | Class representing annotated copy of document |
| AnnotType.java | Class representing type of annotation |
| AnnotTypeAttr.java | Class representing attribute of type of annotation |
| DefaultSettings.java | Class representing parameter of default user settings |
| DrupAuthServer.java | Class representing approved drupal authentization server |
| Fragment.java | Class representing annotated fragment |
| ServerSetting.java | |
| Settings.java | Class representing parameter of user settings |
| Source.java | Class representing source of subscription |
| StoredDocument.java | Class representing stored document |
| Subscription.java | Class representing subscription |
| TypeAttrOnto.java | Class representing attribute of unknown type of annotation |
| User.java | Class representing user |
| UserGroup.java | Class representing user group |
| fragmentUpdater | |
| compareMethods | |
| CompareMethod.java | Generic abstract class for compare methods |
| ExactMethod.java | Exact compare method |
| LevenshteinMethod.java | Compare class using Levenshtein approximate string matching method |
| MetaphoneMethod.java | Compare class using Metaphone approximate string matching method |
| SoundexMethod.java | Compare class using Soundex approximate string matching method |
| nodeIterators | |
| BidirectionallyUnNestNodeIterator.java | Node iterator which is gradually unnesting |
| NodeIterator.java | Generic class for node iterators |
| RecursiveNodeIterator.java | Recursive node iterator |
| SequenceNodeIterator.java | Sequence node iterator |
| XPathNodeIterator.java | Exact XPath node iterator |
| Comparator.java | Class consisting of traversing method and compare method |
| Matcher.java | Class for matcher consisting of comparator and node iterator |
| MatcherProvider.java | Class providing access to available matchers |
| MatcherWrapper.java | Wrapper class for matcher |
| UpdatableFragment.java | Class for XML document fragment |
| XPathHelper.java | Helper class with util XPath methods |
| modules | |
| SECDictionaryInterface | |
| SECDInterfaceModule.java | Class provides connection of SEC Dictionary module with server |
| SECDInterfaceThread.java | Class forwards queries from anotation client to the NLP server and and creates a message for annotation client with the results from the NLP server |
| StoryscopeInterface | |
| SavedMessage.java | Class represent message that belongs to the StoryScope and it was saved because StoryScope was not available |
| StoryScope.java | Class representing StoryScope for needs of Storyscope Interface |
| StoryscopeInterfaceModule.java | Class provides connection of Storyscope Interface module with server |
| StoryscopeInterfaceSender.java | Class represent thread of Storyscope Interface that sends messages to StoryScopes |
| SubscribedItem.java | Class representing item of subscripted or unsubscripted sources list |
| suggestionManager | |
| alternative | |
| AltEntityAdditionalAttribute.java | Class representing additional attribute of entity in alternative attribute |
| Alternative.java | Class representing alternative of suggestion |
| AlternativeAttribute.java | Class representing attribute of alternative of suggestion |
| AlternativeFragment.java | Class representing fragment for suggestion alternative |
| AlternativeManager.java | Class for manipulation with alternatives of suggestions |
| AltLinkedAttribute.java | Class representing attribute of type AnnotationLink for purpose of alternative |
| SecAttribute.java | Interface for SugBaseAttribute and AlternativeAttribuge |
| SecFragment.java | Interface for SuggestionFragment and AlternativeFragment |
| SecSuggestion.java | Interface for Suggestion and Alternative |
| attributes | |
| SugAnyAttribute.java | Class representing attribute of type AnyAnnotation for prupose of suggestion |
| SugAttributeManager.java | Suggestion attribute manager provides a way how to create new attributes |
| SugBaseAttribute.java | Class representing attribute of suggestion |
| SugBinaryAttribute.java | Class representing attribute of type Binary for prupose of suggestion |
| SugBooleanAttribute.java | Class representing attribute of type Boolean for prupose of suggestion |
| SugDateAttribute.java | Class representing attribute of type Date for prupose of suggestion |
| SugDateTimeAttribute.java | Class representing attribute of type DateTime prupose of suggestion |
| SugDecimalAttribute.java | Class representing attribute of type Decimal for prupose of suggestion |
| SugDurationAttribute.java | Class representing attribute of type Duration for prupose of suggestion |
| SugEntityAdditionalAttribute.java | Class representing additional attribute of entity in suggestion attribute |
| SugEntityAttribute.java | Class representing vocabulary entity attribute for prupose of suggestion |
| SugGeoPointAttribute.java | Class representing attribute of type GeoPoint and class representing GeoPoint |
| SugImageAttribute.java | Class representing attribute of type Image for pruposes of suggestion |
| SugIntegerAttribute.java | Class representing attribute of type Integer for prupose of suggestion |
| SugLinkedAttribute.java | Class representing attribute of type AnnotationLink for prupose of suggestion |
| SugNestedAttribute.java | Class representing attribute of type NestedAnnotation for peupose of suggestion |
| SugPersonAttribute.java | Class representing attribute of type Person for peupose of suggestion |
| SugStringAttribute.java | Class representing attribute of type String for prupose of suggestion. Also provides functions for other string based attributes such as ImageUri, URI, .. |
| SugStructuredAttribute.java | Abstract class representing more complex attribute of suggestion |
| SugTextAttribute.java | Class representing attribute of type Text for prupose of suggestion |
| SugTimeAttribute.java | Class representing attribute of type Time for prupose of suggestion |
| SugUriAttribute.java | Class representing attribute of type URI for prupose of suggestion |
| AnnotSugPair.java | Class holds pair of suggestion and corresponding anntation |
| NERInterface.java | Interface for call of external program (deamon) with NER |
| SECAPIConn.java | Class implementing functions for communication with remote SEC API |
| SECAPIInterface.java | Interface for call of SEC API (locally as a daemon) |
| SecApiReqTypeDef.java | |
| SECAPISuggestionTranslator.java | |
| SECTypesTranslator.java | |
| Suggestion.java | Class representing suggestion of annotation |
| SuggestionFeedback.java | Class represents database entitiy that holds information about group suggestion feedback |
| SuggestionFragment.java | Class representing suggested annotation fragment |
| SuggestionManager.java | Methods for translating output from SEC API to the Suggestion objects |
| SuggestionManagerModule.java | Class implements module for suggestiong of annotations |
| SugPersister.java | Static class which persists data to the database |
| CoreFuncModule.java | Document, annotations and types manipulation functionality |
| PersonsModule.java | Operations with persons (users of this server) and with user groups |
| textModifications | |
| TextModificationsXMLUnitProvider.java | TextModification provider |
 web | |
| AttrO.java | Backbean for page with attributes from ontology |
| ATypes.java | Backbean for page with types of annotations |
| CloneServerMain.java | Backbean for page with administration of document cloner approved servers |
| Documents.java | Backbean for page with administration of uploaded documents |
| DrupAuthServerMain.java | Backbean for page with administration of drupal authorization servers |
| EditAT.java | Backbean for adding, editing and deleting of types of annotations |
| EditATA.java | Backbean for managing attributes of types of annotations |
| EditDocumentCloneServer.java | Backbean of pages for managing document clonner approved servers |
| EditDrupAuthServer.java | Backbean of pages for managing drupal authorization approved servers |
| EditServerSetting.java | Backbean for pages for editing of server settings |
| EditStoryScope.java | Backbean for pages for adding, editing and deleting of StoryScopes |
| EditSubscriptions.java | Backbean for pages for adding, editing and deleting of StoryScope's subscriptions |
| EditTAO.java | Backbean for managing attributes from ontology |
| EditUG.java | Backbean for adding, editing and deleting of user group |
| EditUser.java | Backbean for adding, editing and deleting of users |
| EditUserASSetting.java | Backbean for pages for adding, editing and deleting of user annotation style settings |
| EditUserDefaultASSetting.java | Backbean for pages for adding, editing and deleting of default annotation style settings for new users |
| EditUserDefaultSetting.java | Backbean for pages for adding, editing and deleting of simple user default settings |
| EditUserSetting.java | Backbean for pages for adding, editing and deleting of simple user settings |
| GetDocumentServlet.java | Servlet which makes available uploaded documents |
| Index.java | Backbean for index page |
| Login.java | Backbean for login page |
| Menu.java | Backbean for template.xhtml, class for menu handling |
| MessageProvider.java | Class for getting localized messages from message bundle |
| OWLVisitorForRestrictionData.java | Class collect information about restrictions |
| RenameTypes.java | Backbean for page for batch renaming of types of annotations |
| SelectAT.java | Backbean for page with selection of type of annotation |
| ServerSettings.java | Class representing parameter of server settings |
| SessionManager.java | Class for manipulating with session |
| SetServerURI.java | Backbean for page for setting of server URI |
| StoryscopesMain.java | Backbean for page with administration of StoryScopes |
| Subscriptions.java | Backbean for page with administration of subscriptions |
| TextsFromOWLConstants.java | Class with constants for ontology import |
| TypeSelect.java | Backbean for page with selection of annotation type |
| UploadDocument.java | Backbean for page for uploading documents |
| UploadOntology.java | Backbean for page for uploading ontology |
| UserDefaultSettings.java | Backbean for page with list of default settings for new user |
| UserGroups.java | Backbean for page with administration of user groups |
| UserGroupSelectionForUser.java | Backbean for page with selection of user groups |
| Users.java | Backbean for page with administration of users |
| UserSelectionForGroup.java | Backbean for page with selection of user |
| UserSettings.java | Backbean for page with list of user settings |
| WebSession.java | Class for handling session variables in the web |
1.8.6 
