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A

addSimulationDescription(GraphSedmlDocument) - Method in class de.unirostock.sems.m2cat.graph.GraphModelDocument
Adds the simulation description.

B

BASE_URL - Static variable in class de.unirostock.sems.m2cat.web.WebSite
The base url.

C

content - Variable in class de.unirostock.sems.m2cat.graph.GraphDbManager.Response
The content.
COOKIE_LIFETIME - Static variable in class de.unirostock.sems.m2cat.web.CookieManager
how long do we want to store the users information?
CookieManager - Class in de.unirostock.sems.m2cat.web
The Class CookieManager.
CookieManager(HttpServletRequest, HttpServletResponse) - Constructor for class de.unirostock.sems.m2cat.web.CookieManager
Instantiates a new cookie manager.
createCombineArchive(File, String, User) - Method in class de.unirostock.sems.m2cat.graph.GraphModelDocument
Creates an combine archive of this model.
CYPHER - Static variable in class de.unirostock.sems.m2cat.graph.GraphDbManager
 
cypher(String, JSONObject) - Static method in class de.unirostock.sems.m2cat.graph.GraphDbManager
Cypher.

D

data - Variable in class de.unirostock.sems.m2cat.graph.GraphNode
The data.
DB_ENTRY_EDGE_END - Static variable in class de.unirostock.sems.m2cat.graph.GraphNode
The Constant DB_ENTRY_EDGE_END.
DB_ENTRY_EDGE_START - Static variable in class de.unirostock.sems.m2cat.graph.GraphNode
The Constant DB_ENTRY_EDGE_START.
DB_ENTRY_EDGE_TYPE - Static variable in class de.unirostock.sems.m2cat.graph.GraphNode
The Constant DB_ENTRY_EDGE_TYPE.
DB_ENTRY_NODE_LABELS - Static variable in class de.unirostock.sems.m2cat.graph.GraphNode
The Constant DB_ENTRY_NODE_LABELS.
DB_ENTRY_NODE_PROPERTIES - Static variable in class de.unirostock.sems.m2cat.graph.GraphNode
The Constant DB_ENTRY_NODE_PROPERTIES.
DB_ENTRY_NODE_SELF - Static variable in class de.unirostock.sems.m2cat.graph.GraphNode
The Constant DB_ENTRY_NODE_SELF.
dbEntry - Variable in class de.unirostock.sems.m2cat.graph.GraphNode
r/o entry received from db, might be null if this entry wasn't obtained from db.
de.unirostock.sems.m2cat - package de.unirostock.sems.m2cat
 
de.unirostock.sems.m2cat.graph - package de.unirostock.sems.m2cat.graph
 
de.unirostock.sems.m2cat.meth - package de.unirostock.sems.m2cat.meth
 
de.unirostock.sems.m2cat.web - package de.unirostock.sems.m2cat.web
 
delete(String) - Static method in class de.unirostock.sems.m2cat.graph.GraphDbManager
Delete.
dir - Variable in class de.unirostock.sems.m2cat.meth.Resource
The directory in archive.
DIR_DATA - Static variable in class de.unirostock.sems.m2cat.meth.Resource
The Constant DIR_DATA representing the directory containing data.
DIR_DOC - Static variable in class de.unirostock.sems.m2cat.meth.Resource
The Constant DIR_DOC representing the directory containing documentation, e.g.
DIR_MODEL - Static variable in class de.unirostock.sems.m2cat.meth.Resource
The Constant DIR_MODEL representing the directory containing the models.
doGet(HttpServletRequest, HttpServletResponse) - Method in class de.unirostock.sems.m2cat.web.WebSite
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class de.unirostock.sems.m2cat.web.WebSite
 

F

f - Variable in class de.unirostock.sems.m2cat.meth.Resource
The f.
findAssociatedSimulations(GraphModelDocument) - Method in class de.unirostock.sems.m2cat.meth.Searcher
Find associated simulations.

G

get(String) - Static method in class de.unirostock.sems.m2cat.graph.GraphDbManager
Gets the.
getArchiveName() - Method in class de.unirostock.sems.m2cat.graph.GraphModelDocument
Gets the archive name.
getCookie(String) - Method in class de.unirostock.sems.m2cat.web.CookieManager
Gets the cookie.
getCookieValue(String) - Method in class de.unirostock.sems.m2cat.web.CookieManager
Gets the value of a cookie.
getCurationResultPic(List<Resource>) - Method in class de.unirostock.sems.m2cat.graph.GraphModelDocument
Gets the reaction network.
getData() - Method in class de.unirostock.sems.m2cat.graph.GraphNode
Gets the data.
getDocId() - Method in class de.unirostock.sems.m2cat.graph.GraphModelDocument
Gets the archive name.
getDocUri() - Method in class de.unirostock.sems.m2cat.graph.GraphModelDocument
Gets the URI to the document.
getFileName() - Method in class de.unirostock.sems.m2cat.graph.GraphModelDocument
Gets the file name.
getFileName() - Method in class de.unirostock.sems.m2cat.graph.GraphSedmlDocument
Gets the file name.
getFileUri() - Method in class de.unirostock.sems.m2cat.graph.GraphNode
Gets the file uri.
getFileUri() - Method in class de.unirostock.sems.m2cat.graph.GraphSedmlDocument
Gets the file uri.
getFirstName() - Method in class de.unirostock.sems.m2cat.web.User
Gets the first name.
getFirstSimulationDescription() - Method in class de.unirostock.sems.m2cat.graph.GraphModelDocument
Gets the first simulation description.
getId() - Method in class de.unirostock.sems.m2cat.graph.GraphNode
Gets the id.
getLabels() - Method in class de.unirostock.sems.m2cat.graph.GraphNode
Gets the labels.
getLastName() - Method in class de.unirostock.sems.m2cat.web.User
Gets the last name.
getMail() - Method in class de.unirostock.sems.m2cat.web.User
Gets the mail.
getModel() - Method in class de.unirostock.sems.m2cat.graph.GraphModelDocument
Gets the model.
getModelId() - Method in class de.unirostock.sems.m2cat.graph.GraphModel
Gets the model id.
getModelName() - Method in class de.unirostock.sems.m2cat.graph.GraphModel
Gets the model name.
getName() - Method in class de.unirostock.sems.m2cat.meth.Resource
Gets the name.
getNodeEntry(String) - Method in class de.unirostock.sems.m2cat.graph.GraphNode
Gets the node entry.
getOrganization() - Method in class de.unirostock.sems.m2cat.web.User
Gets the organization.
getReactionNetworkPic(List<Resource>) - Method in class de.unirostock.sems.m2cat.graph.GraphModelDocument
Gets the reaction network.
getResources() - Method in class de.unirostock.sems.m2cat.graph.GraphModelDocument
Gets the resources.
getRestProperties() - Method in class de.unirostock.sems.m2cat.graph.GraphNode
Gets the rest properties.
getSedml() - Method in class de.unirostock.sems.m2cat.graph.GraphSedmlDocument
Gets the sedml.
getType() - Method in class de.unirostock.sems.m2cat.meth.Resource
Gets the type.
getUrlUserInfo() - Method in class de.unirostock.sems.m2cat.web.User
Gets the user info encoded in base64.
getUserFromUrl(String) - Static method in class de.unirostock.sems.m2cat.web.User
Gets the user from url.
getVcard() - Method in class de.unirostock.sems.m2cat.web.User
Gets the vcard.
GraphDbManager - Class in de.unirostock.sems.m2cat.graph
The Class GraphDbManager.
GraphDbManager() - Constructor for class de.unirostock.sems.m2cat.graph.GraphDbManager
 
GraphDbManager.Response - Class in de.unirostock.sems.m2cat.graph
The Class Response.
GraphModel - Class in de.unirostock.sems.m2cat.graph
 
GraphModel(JSONObject) - Constructor for class de.unirostock.sems.m2cat.graph.GraphModel
The Constructor.
GraphModelDocument - Class in de.unirostock.sems.m2cat.graph
The Class GraphDocument.
GraphModelDocument(JSONObject, GraphModel) - Constructor for class de.unirostock.sems.m2cat.graph.GraphModelDocument
The Constructor.
GraphNode - Class in de.unirostock.sems.m2cat.graph
The Class GraphNode.
GraphNode(JSONObject) - Constructor for class de.unirostock.sems.m2cat.graph.GraphNode
The Constructor.
GraphSedml - Class in de.unirostock.sems.m2cat.graph
 
GraphSedml(JSONObject) - Constructor for class de.unirostock.sems.m2cat.graph.GraphSedml
The Constructor.
GraphSedmlDocument - Class in de.unirostock.sems.m2cat.graph
The Class GraphDocument.
GraphSedmlDocument(JSONObject, GraphSedml) - Constructor for class de.unirostock.sems.m2cat.graph.GraphSedmlDocument
The Constructor.

H

hasDbErr() - Method in class de.unirostock.sems.m2cat.meth.Searcher
Checks for a DB err.

I

init(ServletConfig) - Method in class de.unirostock.sems.m2cat.web.WebSite
 
isCellML() - Method in class de.unirostock.sems.m2cat.graph.GraphModelDocument
Checks if is cell ml.
isSimulationDescription() - Method in class de.unirostock.sems.m2cat.graph.GraphModelDocument
Checks if is simulation description.
isValid() - Method in class de.unirostock.sems.m2cat.web.User
Checks if is valid.

L

loadSettingsFromContext(ServletContext) - Static method in class de.unirostock.sems.m2cat.web.WebSite
Load settings from context.
location - Variable in class de.unirostock.sems.m2cat.graph.GraphDbManager.Response
The location.

M

Main - Class in de.unirostock.sems.m2cat
 
Main() - Constructor for class de.unirostock.sems.m2cat.Main
 
main(String[]) - Static method in class de.unirostock.sems.m2cat.Main
The main method.
main(String[]) - Static method in class de.unirostock.sems.m2cat.meth.Searcher
The main method.

N

name - Variable in class de.unirostock.sems.m2cat.meth.Resource
The name.
NL - Static variable in class de.unirostock.sems.m2cat.Main
 
note - Variable in class de.unirostock.sems.m2cat.meth.Resource
The note.

P

parseSearchResponse(GraphDbManager.Response) - Method in class de.unirostock.sems.m2cat.meth.Searcher
Parses the search response.
parseSedmlResponse(GraphDbManager.Response, GraphModelDocument) - Method in class de.unirostock.sems.m2cat.meth.Searcher
Parses the search response.
post(String, String) - Static method in class de.unirostock.sems.m2cat.graph.GraphDbManager
Post.
put(String, String) - Static method in class de.unirostock.sems.m2cat.graph.GraphDbManager
Put.

R

readResponse(ClientResponse) - Static method in class de.unirostock.sems.m2cat.graph.GraphDbManager
Read response.
Resource - Class in de.unirostock.sems.m2cat.meth
The Class Resource.
Resource(String, String, String, File, String) - Constructor for class de.unirostock.sems.m2cat.meth.Resource
The Constructor.
Response(URI, String, int) - Constructor for class de.unirostock.sems.m2cat.graph.GraphDbManager.Response
The Constructor.
retrieveAdditionalResources() - Method in class de.unirostock.sems.m2cat.graph.GraphModelDocument
Gets the additional resources.
retrieveModelFiles() - Method in class de.unirostock.sems.m2cat.graph.GraphModelDocument
Retrieve model file.
retrieveModelFiles() - Method in class de.unirostock.sems.m2cat.graph.GraphSedmlDocument
Retrieve sedml file.
retrieveResources(GraphModelDocument) - Method in class de.unirostock.sems.m2cat.meth.Searcher
Gets the further resources.
ROOT_URI - Static variable in class de.unirostock.sems.m2cat.graph.GraphDbManager
 

S

search(String) - Method in class de.unirostock.sems.m2cat.meth.Searcher
Search.
Searcher - Class in de.unirostock.sems.m2cat.meth
Hello world!
Searcher() - Constructor for class de.unirostock.sems.m2cat.meth.Searcher
Instantiates a new searcher.
searchForAnnotation(String) - Method in class de.unirostock.sems.m2cat.meth.Searcher
Search for annotation.
searchForAuthor(String) - Method in class de.unirostock.sems.m2cat.meth.Searcher
Search for author.
searchForId(int) - Method in class de.unirostock.sems.m2cat.meth.Searcher
Search.
searchForModelId(int) - Method in class de.unirostock.sems.m2cat.meth.Searcher
Search for model id.
setCookie(Cookie) - Method in class de.unirostock.sems.m2cat.web.CookieManager
Sets the cookie.
status - Variable in class de.unirostock.sems.m2cat.graph.GraphDbManager.Response
The status.
STORAGE - Static variable in class de.unirostock.sems.m2cat.web.WebSite
The storage.

T

toString() - Method in class de.unirostock.sems.m2cat.graph.GraphDbManager.Response
 
toString() - Method in class de.unirostock.sems.m2cat.graph.GraphModel
 
toString() - Method in class de.unirostock.sems.m2cat.graph.GraphModelDocument
 
toString() - Method in class de.unirostock.sems.m2cat.graph.GraphSedml
 
toString() - Method in class de.unirostock.sems.m2cat.graph.GraphSedmlDocument
 
toString() - Method in class de.unirostock.sems.m2cat.meth.Resource
 
type - Variable in class de.unirostock.sems.m2cat.meth.Resource
The type.
TYPE_AUTHOR - Static variable in class de.unirostock.sems.m2cat.graph.GraphNode
The Constant TYPE_AUTHOR.
TYPE_BIBENTRY - Static variable in class de.unirostock.sems.m2cat.graph.GraphNode
The Constant TYPE_BIBENTRY.
TYPE_COMMENT - Static variable in class de.unirostock.sems.m2cat.graph.GraphNode
The Constant TYPE_COMMENT.
TYPE_FILE - Static variable in class de.unirostock.sems.m2cat.graph.GraphNode
The Constant TYPE_FILE.
TYPE_INSTALLATION - Static variable in class de.unirostock.sems.m2cat.graph.GraphNode
The Constant TYPE_INSTALLATION.
TYPE_PLATFORM - Static variable in class de.unirostock.sems.m2cat.graph.GraphNode
The Constant TYPE_PLATFORM.
TYPE_POST - Static variable in class de.unirostock.sems.m2cat.graph.GraphNode
The Constant TYPE_POST.
TYPE_PUBLISHER - Static variable in class de.unirostock.sems.m2cat.graph.GraphNode
The Constant TYPE_PUBLISHER.
TYPE_REGISTERED - Static variable in class de.unirostock.sems.m2cat.graph.GraphNode
The Constant TYPE_REGISTERED.
TYPE_TAG - Static variable in class de.unirostock.sems.m2cat.graph.GraphNode
The Constant TYPE_TAG.
TYPE_USER - Static variable in class de.unirostock.sems.m2cat.graph.GraphNode
The Constant TYPE_USER.

U

User - Class in de.unirostock.sems.m2cat.web
The Class User.
User(String, String, String, String) - Constructor for class de.unirostock.sems.m2cat.web.User
Instantiates a new user.

W

WebSite - Class in de.unirostock.sems.m2cat.web
 
WebSite() - Constructor for class de.unirostock.sems.m2cat.web.WebSite
 
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