Package edu.mssm.crover.webservices.rbde

Interface Summary

CustomizedDiagram	Encapsulates all necessary diagram components for storage.
CustomizedDiagram2_0	Encapsulates all necessary diagram components for storage.
DS_PersistenceScheme	Interface to support plugable persistence schemes.

Class Summary

AtEditorNode	Menu node for the attribute editor page.
AttributesInputPage	The servlet returns an HTML page that contains both the Secondary Structure editor and Transmembrane Segments editor as well as the sequence diagram image.
convertFrom1_0
CopySStoTM	Servlet that copies secondary structure annotations to transmembrane segment annotations.
CopyTMtoSS	Servlet that copies transmembrane segment annotations to secondary structure annotations.
CustomizedDiagramImpl1_0	Encapsulates all necessary diagram components for storage.
CustomizedDiagramImpl1_1	Encapsulates all necessary diagram components for storage.
CustomizedDiagramImpl3_0	Encapsulates all necessary diagram components for storage.
CustomizedDiagramImpl5_0	Encapsulates all necessary diagram components for storage.
DiagramAttributesEditor
DiagramAttributesForm
DiagramLibrary	Allow the user to browse available diagrams, Select one and import it for further edition with the service, Save a diagram to the library.
DiagramLibraryNode
DiagramMapProcessing
DiagramMenuBar
DiagramService	Global data and services to help build the Residue-based Diagram web server.
DownloadCustomizedDiagram
DS_PersistenceScheme_JDBC_Impl	JDBCsistence scheme.
DS_UserSession	Stores the information useful for maintaining the complex state of the RbDe web service.
Elipses
FastDiagramMode	Servlet that constructs an HTML page that displays sequence entered in servlet Start.
FastDiagramModeNode	Menu node for the attribute editor page.
GetDiagram
GetDiagramNode
HomeNode
InstanceIterator	Provides information about persistent instances.
InvalidURLError	Servlet that is presented the user tries to link a residue to an invalid URL.
LayoutPicker	Determines which layout option was selected.
LayoutSSEditor	Reads and commits changes to Secondary Structure submitted through HTML form LayoutSSFormDisplay.
LayoutSSFormDisplay	Creates an HTML Element Container that contains a form for editing Secondary Structure annotations (SecondaryStructure_Annotation).
LibraryObjectForm
LibraryObjectFormProcessor
ListDiagrams
ListDiagramsNode
MissingInformation	This servlet handles exceptional cases when a servlet is invoked to perform a treatment and the session does not contain the prerequisites for the treatment.
MutantSubServiceState	Holds the mutant sub-service state.
MutationFilters
MutationNode
Mutations	Allow the user to Query mutation servers Filter the set of mutants Select mutants for further processing
NewLayoutInputEditor	Reads the user-submitted layout file, modifies it so that "<", ">" and "\"" do not get interpreted by the browser, and sends it to be stored.
PredefinedColors
PrintRbDgFile	Builds and returns an SVG document representation of the sequence diagram.
PrintSVG	Servlet that constructs an HTML page that displays sequence entered in servlet Start.
RegistrationDeskNode
ResidueAttributesEditor
ResidueAttributesForm
SaveDiagram
SaveDiagramNode
SecondaryStructureEdit	The servlet returns an HTML page that contains both the Secondary Structure editor and Transmembrane Segments editor as well as the sequence diagram image.
SequenceDiagramGif	Builds and returns a GIF image of the sequence diagram.
SequenceDiagramSVG	Builds and returns a GIF image of the sequence diagram.
SequenceDisplay	Servlet that constructs an HTML page that displays sequence entered in servlet Start.
SequenceInputEditor	Servlet that constructs an HTML page that displays sequence entered in servlet Start.
SequenceNode
SessionError	Builds HTML page that is returned in case of unexpected error with reference back to the Start page.
ShowDiagram	Servlet to build a diagram in one GET connection.
SpacerAdjustment	Allows the adjustment of the spacers.
SSEditor	Reads and commits changes to Secondary Structure submitted through HTML form SSFormDisplay.
SSEditorNode
SSFormDisplay	Creates an HTML Element Container that contains a form for editing Secondary Structure annotations (SecondaryStructure_Annotation).
Start	The Diagram service begins here.
StartNode
StoreDiagram	1/ Starts a guest session if none is available.
StoreNewLayout
SVGDiagram	Builds and returns an SVG document representation of the sequence diagram.
SwissProtSearchURL	Allows to retrieve sequences (AnnotatedBioSequence[]) from SwissProt database.
TMEditor	Reads and commits changes to Transmembrane segments (TM_Annotation)-s submitted through HTML form TMFormDisplay.
TMFormDisplay	Creates an HTML Element Container that contains a form for editing Transmembrane segment annotations (TM_Annotation).
UninitializedSessionError	Servlet that returns an Error warning HTML page with reference to the Start page.
URLTestNode
URLTestPage	Page for testing the URL annotations.
URLTestProcessing	Processes ismap image request from page URLTestPage.
UserColorInputEditor
UserColorInputForm
UserColors
ViewLayout
XMLGenerator	Generates the XML needed to generate an RbDg diagram.

Exception Summary

MissingFormParameterException

Thrown when form editing method does not find expected parameters in the HttpRequest.