A B C D E F G H I L M N P R S T U V X 

A

a - Variable in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkVariable.VarConnection
The existence flags for original document.
addChildA(HierarchyNetworkComponent) - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkComponent
Adds a sub-component (below in hierarchy) as it is defined in the original version.
addChildB(HierarchyNetworkComponent) - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkComponent
Adds a sub-component (below in hierarchy) as it is defined in the modified version.
addConnection(NodeConnection) - Method in class de.unirostock.sems.bives.algorithm.SimpleConnectionManager
Adds a new connection unless connection exists.
addConnectionA(HierarchyNetworkVariable) - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkVariable
Adds a connection as defined in the original document.
addConnectionB(HierarchyNetworkVariable) - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkVariable
Adds a connection as defined in the modified document.
addHeader(String) - Method in class de.unirostock.sems.bives.markup.MarkupDocument
Adds a header.
addInputA(ReactionNetworkSubstance, SBOTerm) - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkReaction
Add a reactant of this reaction in its original version.
addInputB(ReactionNetworkSubstance, SBOTerm) - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkReaction
Add a reactant of this reaction in its modified version.
addModA(ReactionNetworkSubstance, SBOTerm) - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkReaction
Adds the modifier of this reaction in its original version.
addModB(ReactionNetworkSubstance, SBOTerm) - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkReaction
Add a modifier of this reaction in its modified version.
addOutputA(ReactionNetworkSubstance, SBOTerm) - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkReaction
Add a product of this reaction in its original version.
addOutputB(ReactionNetworkSubstance, SBOTerm) - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkReaction
Add a product of this reaction in its modified version.
addSection(MarkupSection) - Method in class de.unirostock.sems.bives.markup.MarkupDocument
Adds a section.
addSubElements(MarkupElement) - Method in class de.unirostock.sems.bives.markup.MarkupElement
Adds a sub-element.
addValue(String) - Method in class de.unirostock.sems.bives.markup.MarkupElement
Adds an entry to this element.
addValue(MarkupElement) - Method in class de.unirostock.sems.bives.markup.MarkupSection
Adds an element to this section.
addVariable(HierarchyNetworkVariable) - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkComponent
Adds a variable.
addWeight(double) - Method in class de.unirostock.sems.bives.algorithm.NodeConnection
 
addWeightToAllConnections(double) - Method in class de.unirostock.sems.bives.algorithm.SimpleConnectionManager
Add weight to all connections.
addXhtml(TreeNode) - Method in class de.unirostock.sems.bives.ds.Xhtml
Adds an XHTML subtree.
attribute(String) - Static method in class de.unirostock.sems.bives.markup.MarkupDocument
Highlights an attribute.

B

b - Variable in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkVariable.VarConnection
The existence flags for modified document.
BivesConnectionException - Exception in de.unirostock.sems.bives.exception
The Class BivesConnectionException signaling node-connection problems.
BivesConnectionException(String) - Constructor for exception de.unirostock.sems.bives.exception.BivesConnectionException
Instantiates a new bives connection exception.
BivesDocumentConsistencyException - Exception in de.unirostock.sems.bives.exception
The Class BivesDocumentConsistencyException signaling inconsistencies.
BivesDocumentConsistencyException(String) - Constructor for exception de.unirostock.sems.bives.exception.BivesDocumentConsistencyException
Instantiates a new bives document consistency exception.
BivesException - Exception in de.unirostock.sems.bives.exception
The Class BivesException representing problems that occurred in BiVeS.
BivesException(String) - Constructor for exception de.unirostock.sems.bives.exception.BivesException
Instantiates a new BiVeS exception.
BivesFlattenException - Exception in de.unirostock.sems.bives.exception
The Class BivesFlattenException signaling problems while flattening a document.
BivesFlattenException(String) - Constructor for exception de.unirostock.sems.bives.exception.BivesFlattenException
Instantiates a new bives flatten exception.
BivesImportException - Exception in de.unirostock.sems.bives.exception
The Class BivesImportException signaling errors while importing documents.
BivesImportException(String, Exception) - Constructor for exception de.unirostock.sems.bives.exception.BivesImportException
Instantiates a new bives import exception.
BivesLogicalException - Exception in de.unirostock.sems.bives.exception
The Class BivesLogicalException signaling logical errors.
BivesLogicalException(String) - Constructor for exception de.unirostock.sems.bives.exception.BivesLogicalException
Instantiates a new bives logical exception.
BivesNetworkingException - Exception in de.unirostock.sems.bives.exception
The Class BivesNetworkingException signaling network errors.
BivesNetworkingException(String) - Constructor for exception de.unirostock.sems.bives.exception.BivesNetworkingException
Instantiates a new bives networking exception.
BivesTools - Class in de.unirostock.sems.bives.tools
The Class BivesTools providing some utils for document comparison.
BivesTools() - Constructor for class de.unirostock.sems.bives.tools.BivesTools
 
BivesUnsupportedException - Exception in de.unirostock.sems.bives.exception
The Class BivesUnsupportedException for not (yet) supported operations.
BivesUnsupportedException(String) - Constructor for exception de.unirostock.sems.bives.exception.BivesUnsupportedException
Instantiates a new unsupported exception.

C

conMgmt - Variable in class de.unirostock.sems.bives.algorithm.Connector
The connection manager, holding node-mappings.
conMgmt - Variable in class de.unirostock.sems.bives.algorithm.Interpreter
The connection manager.
conMgmt - Variable in class de.unirostock.sems.bives.algorithm.Producer
The connection manager.
connect() - Method in class de.unirostock.sems.bives.algorithm.Connector
Inherit to search for connections.
connect() - Method in class de.unirostock.sems.bives.algorithm.general.IdConnector
 
connect() - Method in class de.unirostock.sems.bives.algorithm.general.LabelConnector
Deprecated.
 
connect() - Method in class de.unirostock.sems.bives.algorithm.general.XyDiffConnector
 
connections - Variable in class de.unirostock.sems.bives.api.Diff
The connections.
Connector - Class in de.unirostock.sems.bives.algorithm
The Class Connector, intended to find node-correspondences between two trees.
Connector(TreeDocument, TreeDocument) - Constructor for class de.unirostock.sems.bives.algorithm.Connector
Instantiates a new connector.
createInhibitor() - Static method in class de.unirostock.sems.bives.ds.ontology.SBOTerm
Creates a dummy inhibitor.
createStimulator() - Static method in class de.unirostock.sems.bives.ds.ontology.SBOTerm
Creates a dummy stimulator.
CSS_CLASS_ATTRIBUTE - Static variable in class de.unirostock.sems.bives.markup.Typesetting
The Constant CSS_CLASS_ATTRIBUTE.
CSS_CLASS_DELETE - Static variable in class de.unirostock.sems.bives.markup.Typesetting
The Constant CSS_CLASS_DELETE.
CSS_CLASS_INSERT - Static variable in class de.unirostock.sems.bives.markup.Typesetting
The Constant CSS_CLASS_INSERT.
CSS_CLASS_MATH - Static variable in class de.unirostock.sems.bives.markup.Typesetting
The Constant CSS_CLASS_MATH.
CSS_CLASS_MATH_MODIFIED - Static variable in class de.unirostock.sems.bives.markup.Typesetting
The Constant CSS_CLASS_MATH_MODIFIED.
CSS_CLASS_MATH_ORIGINAL - Static variable in class de.unirostock.sems.bives.markup.Typesetting
The Constant CSS_CLASS_MATH_ORIGINAL.
CSS_CLASS_MOVE - Static variable in class de.unirostock.sems.bives.markup.Typesetting
The Constant CSS_CLASS_MOVE.
CSS_CLASS_TABLE_LEFT_COLUMN - Static variable in class de.unirostock.sems.bives.markup.Typesetting
The Constant CSS_CLASS_TABLE_LEFT_COLUMN.
CSS_CLASS_TABLE_RIGHT_COLUMN - Static variable in class de.unirostock.sems.bives.markup.Typesetting
The Constant CSS_CLASS_TABLE_RIGHT_COLUMN.
CSS_CLASS_UPDATE - Static variable in class de.unirostock.sems.bives.markup.Typesetting
The Constant CSS_CLASS_UPDATE.

D

de.unirostock.sems.bives.algorithm - package de.unirostock.sems.bives.algorithm
 
de.unirostock.sems.bives.algorithm.general - package de.unirostock.sems.bives.algorithm.general
 
de.unirostock.sems.bives.api - package de.unirostock.sems.bives.api
 
de.unirostock.sems.bives.ds - package de.unirostock.sems.bives.ds
 
de.unirostock.sems.bives.ds.graph - package de.unirostock.sems.bives.ds.graph
 
de.unirostock.sems.bives.ds.hn - package de.unirostock.sems.bives.ds.hn
 
de.unirostock.sems.bives.ds.ontology - package de.unirostock.sems.bives.ds.ontology
 
de.unirostock.sems.bives.ds.rdf - package de.unirostock.sems.bives.ds.rdf
 
de.unirostock.sems.bives.ds.rn - package de.unirostock.sems.bives.ds.rn
 
de.unirostock.sems.bives.exception - package de.unirostock.sems.bives.exception
 
de.unirostock.sems.bives.markup - package de.unirostock.sems.bives.markup
 
de.unirostock.sems.bives.tools - package de.unirostock.sems.bives.tools
 
DELETE - Static variable in interface de.unirostock.sems.bives.ds.GraphEntity
The flag for DELETEd entities.
delete(String) - Static method in class de.unirostock.sems.bives.markup.MarkupDocument
Highlights a delete.
deleteMatchedNodes(List<TreeNode>) - Method in class de.unirostock.sems.bives.algorithm.SimpleConnectionManager
Delete nodes of a vector which have connections.
deleteNode(TreeNode, int) - Method in class de.unirostock.sems.bives.ds.Patch
Delete a single node.
deleteSubtree(TreeNode, int) - Method in class de.unirostock.sems.bives.ds.Patch
Mark a whole subtree as deleted.
Diff - Class in de.unirostock.sems.bives.api
The Class Diff, the central object if it comes to the comparison of XML documents.
Diff(File, File) - Constructor for class de.unirostock.sems.bives.api.Diff
Instantiates a new diff object in order to compare two documents stored in files fileA and fileB.
Diff(String, String) - Constructor for class de.unirostock.sems.bives.api.Diff
Instantiates a new diff object in order to compare two documents stored in strings docA and docB.
Diff(TreeDocument, TreeDocument) - Constructor for class de.unirostock.sems.bives.api.Diff
Instantiates a new diff object in order to compare two tree documents.
DiffReporter - Interface in de.unirostock.sems.bives.algorithm
 
doc - Variable in class de.unirostock.sems.bives.ds.ModelDocument
The document storing this model.
docA - Variable in class de.unirostock.sems.bives.algorithm.Connector
The original document.
docA - Variable in class de.unirostock.sems.bives.algorithm.Interpreter
The original document.
docA - Variable in class de.unirostock.sems.bives.algorithm.Producer
The original version.
docA - Variable in class de.unirostock.sems.bives.ds.rn.ReactionNetworkEntity
The original document.
docB - Variable in class de.unirostock.sems.bives.algorithm.Connector
The modified document.
docB - Variable in class de.unirostock.sems.bives.algorithm.Interpreter
The modified document.
docB - Variable in class de.unirostock.sems.bives.algorithm.Producer
The modified version.
docB - Variable in class de.unirostock.sems.bives.ds.rn.ReactionNetworkEntity
The modified document.
dropConnection(TreeNode) - Method in class de.unirostock.sems.bives.algorithm.SimpleConnectionManager
Drop all connections of a node.
dropConnection(Connection) - Method in class de.unirostock.sems.bives.algorithm.SimpleConnectionManager
Drop a certain connection.

E

error - Variable in class de.unirostock.sems.bives.algorithm.ModelValidator
The error.

F

findConnections() - Method in class de.unirostock.sems.bives.algorithm.Connector
Find connections between nodes of both versions of your document.
flatten() - Method in class de.unirostock.sems.bives.api.Single
Flatten the document.
flatten() - Method in class de.unirostock.sems.bives.ds.ModelDocument
Flatten this document.

G

genAttributeMarkupStats(DocumentNode, DocumentNode, MarkupElement) - Static method in class de.unirostock.sems.bives.tools.BivesTools
Generate some Attribute difference report for Markup Documents.
genMathMarkupStats(DocumentNode, DocumentNode, MarkupElement) - Static method in class de.unirostock.sems.bives.tools.BivesTools
Generate some MathML difference report for Markup Documents .
getA() - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkEntity
Gets the original document node.
getA() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkEntity
Gets the original document node.
getAbout() - Method in class de.unirostock.sems.bives.ds.rdf.RDFDescription
Gets the about id.
getB() - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkEntity
Gets the modified document node.
getB() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkEntity
Gets the modified document node.
getBaseUri() - Method in class de.unirostock.sems.bives.ds.ModelDocument
Gets the base URI.
getCompartment(TreeNode) - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetwork
Gets a compartment.
getCompartment() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkReaction
Gets the compartment.
getCompartment() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkSubstance
Gets the compartment.
getCompartments() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetwork
Gets the compartments.
getComponent(TreeNode) - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetwork
Gets a component.
getComponent() - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkVariable
Gets the component.
getComponents() - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetwork
Gets the components.
getConnectionForNode(TreeNode) - Method in class de.unirostock.sems.bives.algorithm.SimpleConnectionManager
Gets the connections for node.
getConnectionOfNodes(TreeNode, TreeNode) - Method in class de.unirostock.sems.bives.algorithm.SimpleConnectionManager
Gets the connection of two certain nodes.
getConnections() - Method in class de.unirostock.sems.bives.algorithm.Connector
Gets the connections.
getConnections() - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkVariable
Gets the connections of this variable to other variables of the hierarchy network.
getCRN() - Method in class de.unirostock.sems.bives.algorithm.GraphProducer
Deprecated.
As of 1.3.3 replaced by GraphProducer.getReactionNetwork()
getCRNDotGraph() - Method in class de.unirostock.sems.bives.api.Diff
Deprecated.
As of 1.3.3 replaced by Diff.getReactionsDotGraph()
getCRNDotGraph() - Method in class de.unirostock.sems.bives.api.Single
Deprecated.
As of 1.3.3 replaced by Single.getReactionsDotGraph()
getCRNGraph(GraphTranslator) - Method in class de.unirostock.sems.bives.api.Diff
getCRNGraph(GraphTranslator) - Method in class de.unirostock.sems.bives.api.Single
getCRNGraphML() - Method in class de.unirostock.sems.bives.api.Diff
Deprecated.
As of 1.3.3 replaced by Diff.getReactionsGraphML()
getCRNGraphML() - Method in class de.unirostock.sems.bives.api.Single
Deprecated.
As of 1.3.3 replaced by Single.getReactionsGraphML()
getCRNJsonGraph() - Method in class de.unirostock.sems.bives.api.Diff
Deprecated.
As of 1.3.3 replaced by Diff.getReactionsJsonGraph()
getCRNJsonGraph() - Method in class de.unirostock.sems.bives.api.Single
Deprecated.
As of 1.3.3 replaced by Single.getReactionsJsonGraph()
getDeletes() - Method in class de.unirostock.sems.bives.ds.Patch
Gets the deletes.
getDescriptions() - Method in class de.unirostock.sems.bives.ds.rdf.RDF
Gets the descriptions.
getDiff() - Method in class de.unirostock.sems.bives.api.Diff
Gets the diff as a string, encoded in XML.
getDocA() - Method in class de.unirostock.sems.bives.algorithm.Connector
Gets the original document.
getDocB() - Method in class de.unirostock.sems.bives.algorithm.Connector
Gets the modified document.
getDocument() - Method in class de.unirostock.sems.bives.algorithm.ModelValidator
Gets the parsed document if it was valid, of null otherwise.
getDocument() - Method in class de.unirostock.sems.bives.ds.Patch
Gets the document containing all changes.
getDocumentNode() - Method in class de.unirostock.sems.bives.ds.MathML
Gets the document node that roots the MathML subtree.
getError() - Method in class de.unirostock.sems.bives.algorithm.ModelValidator
Gets the error the was thrown in case of an invalid document.
getGraphmlDocument() - Method in class de.unirostock.sems.bives.ds.graph.GraphTranslatorGraphML
Gets the graphml document.
getHeader() - Method in class de.unirostock.sems.bives.markup.MarkupDocument
Gets the header.
getHeader() - Method in class de.unirostock.sems.bives.markup.MarkupElement
Gets the header.
getHeader() - Method in class de.unirostock.sems.bives.markup.MarkupSection
Gets the header.
getHeadline() - Method in class de.unirostock.sems.bives.markup.MarkupDocument
Gets the headline.
getHierarchy() - Method in class de.unirostock.sems.bives.algorithm.GraphProducer
Gets the hierarchy network graph.
getHierarchyDotGraph() - Method in class de.unirostock.sems.bives.api.Diff
Returns the component's hierarchy graph encoded in DOT language.
getHierarchyDotGraph() - Method in class de.unirostock.sems.bives.api.RegularDiff
 
getHierarchyDotGraph() - Method in class de.unirostock.sems.bives.api.Single
Returns the component's hierarchy graph encoded in DOT language.
getHierarchyGraph(GraphTranslator) - Method in class de.unirostock.sems.bives.api.Diff
Returns the component's hierarchy graph providing an own graph translator.
getHierarchyGraph(GraphTranslator) - Method in class de.unirostock.sems.bives.api.RegularDiff
 
getHierarchyGraph(GraphTranslator) - Method in class de.unirostock.sems.bives.api.Single
Returns the component's hierarchy graph providing an own graph translator.
getHierarchyGraphML() - Method in class de.unirostock.sems.bives.api.Diff
Returns the component's hierarchy graph encoded in GraphML.
getHierarchyGraphML() - Method in class de.unirostock.sems.bives.api.RegularDiff
 
getHierarchyGraphML() - Method in class de.unirostock.sems.bives.api.Single
Returns the component's hierarchy graph encoded in GraphML.
getHierarchyJsonGraph() - Method in class de.unirostock.sems.bives.api.Diff
Returns the component's hierarchy graph encoded in JSON.
getHierarchyJsonGraph() - Method in class de.unirostock.sems.bives.api.RegularDiff
 
getHierarchyJsonGraph() - Method in class de.unirostock.sems.bives.api.Single
Returns the component's hierarchy graph encoded in JSON.
getHTMLReport() - Method in class de.unirostock.sems.bives.api.Diff
Returns the report encoded in HTML.
getHTMLReport() - Method in class de.unirostock.sems.bives.api.RegularDiff
 
getId() - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkEntity
Gets the id of this entity.
getId() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkEntity
Gets the id of the entity.
getInputs() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkReaction
Gets the reactants.
getInserts() - Method in class de.unirostock.sems.bives.ds.Patch
Gets the inserts.
getJsonGraph() - Method in class de.unirostock.sems.bives.ds.graph.GraphTranslatorJson
Gets the JSON object.
getLabel() - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkEntity
Gets the label of this entity.
getLabel() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkEntity
Gets the label.
getMarkDownReport() - Method in class de.unirostock.sems.bives.api.Diff
Returns the report encoded MarkDown.
getMarkDownReport() - Method in class de.unirostock.sems.bives.api.RegularDiff
 
getModification() - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkComponent
Gets the modification of this entity.
getModification() - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkEntity
Gets the modification of this entity.
getModification() - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkVariable
Gets the modification of this entity.
getModification() - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkVariable.VarConnection
Gets the modification.
getModification() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkEntity
Gets the modification of this entity.
getModification() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkReaction
 
getModification() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkSubstanceRef
Gets the modification.
getModifiers() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkReaction
Gets the modifiers.
getModTerm() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkSubstanceRef
Gets the modifier term.
getMoves() - Method in class de.unirostock.sems.bives.ds.Patch
Gets the moves.
getNextCompartmentID() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetwork
Gets the next compartment id.
getNextComponentID() - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetwork
Gets the next component id.
getNextReactionID() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetwork
Gets the next reaction id.
getNextSubstanceID() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetwork
Gets the next substance id.
getNextVariableID() - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetwork
Gets the next variable id.
getNode() - Method in class de.unirostock.sems.bives.ds.rdf.RDF
Gets the node.
getNode() - Method in class de.unirostock.sems.bives.ds.rdf.RDFDescription
Gets the node.
getNumAttributeChanges() - Method in class de.unirostock.sems.bives.ds.Patch
Gets the number of attribute changes.
getNumDeletes() - Method in class de.unirostock.sems.bives.ds.Patch
Gets the number of stored delete operations.
getNumInserts() - Method in class de.unirostock.sems.bives.ds.Patch
Gets the number of stored insert operations.
getNumMoves() - Method in class de.unirostock.sems.bives.ds.Patch
Gets the number of stored move operations.
getNumNodeChanges() - Method in class de.unirostock.sems.bives.ds.Patch
Gets the number of node changes.
getNumTextChanges() - Method in class de.unirostock.sems.bives.ds.Patch
Gets the number of text changes.
getNumUpdates() - Method in class de.unirostock.sems.bives.ds.Patch
Gets the number of stored update operations.
getOutputs() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkReaction
Gets the products.
getParentA() - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkComponent
Gets the parent component as it is defined in the original version.
getParentB() - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkComponent
Gets the parent component as it is defined in the modified version.
getPartnerOf(TreeNode) - Method in class de.unirostock.sems.bives.algorithm.NodeConnection
 
getPatch() - Method in class de.unirostock.sems.bives.algorithm.general.PatchProducer
Gets the patch.
getPatch() - Method in class de.unirostock.sems.bives.api.Diff
Gets the patch object.
getReaction(TreeNode) - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetwork
Gets a reaction.
getReactionNetwork() - Method in class de.unirostock.sems.bives.algorithm.GraphProducer
Gets the reaction network graph.
getReactions() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetwork
Gets the reactions.
getReactionsDotGraph() - Method in class de.unirostock.sems.bives.api.Diff
Returns the graph of the reaction network encoded in DOT language.
getReactionsDotGraph() - Method in class de.unirostock.sems.bives.api.RegularDiff
 
getReactionsDotGraph() - Method in class de.unirostock.sems.bives.api.Single
Returns the graph of the reaction network encoded in DOT language.
getReactionsGraph(GraphTranslator) - Method in class de.unirostock.sems.bives.api.Diff
Returns the graph of the reaction network providing an own graph translator.
getReactionsGraph(GraphTranslator) - Method in class de.unirostock.sems.bives.api.RegularDiff
 
getReactionsGraph(GraphTranslator) - Method in class de.unirostock.sems.bives.api.Single
Returns the graph of the reaction network providing an own graph translator.
getReactionsGraphML() - Method in class de.unirostock.sems.bives.api.Diff
Returns the graph of the reaction network encoded in GraphML.
getReactionsGraphML() - Method in class de.unirostock.sems.bives.api.RegularDiff
 
getReactionsGraphML() - Method in class de.unirostock.sems.bives.api.Single
Returns the graph of the reaction network encoded in GraphML.
getReactionsJsonGraph() - Method in class de.unirostock.sems.bives.api.Diff
Returns the graph of the reaction network encoded in JSON.
getReactionsJsonGraph() - Method in class de.unirostock.sems.bives.api.RegularDiff
 
getReactionsJsonGraph() - Method in class de.unirostock.sems.bives.api.Single
Returns the graph of the reaction network encoded in JSON.
getReport(Typesetting) - Method in class de.unirostock.sems.bives.api.Diff
Returns the report providing an on markup processor.
getReport(Typesetting) - Method in class de.unirostock.sems.bives.api.RegularDiff
 
getReStructuredTextReport() - Method in class de.unirostock.sems.bives.api.Diff
Returns the report encoded in ReStructured text.
getReStructuredTextReport() - Method in class de.unirostock.sems.bives.api.RegularDiff
 
getSBO() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkReaction
Gets the sbo.
getSBO() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkSubstance
Gets the SBOTerm describing this substance.
getSBO() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkSubstanceRef
Gets the SBOTerm.
getSBOTerm() - Method in class de.unirostock.sems.bives.ds.ontology.SBOTerm
Gets the SBO term stored in here.
getSections() - Method in class de.unirostock.sems.bives.markup.MarkupDocument
Gets the sections.
getSubElements() - Method in class de.unirostock.sems.bives.markup.MarkupElement
Gets the sub-elements.
getSubstance(TreeNode) - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetwork
Gets a substance.
getSubstance() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkSubstanceRef
Gets the referenced substance.
getSubstances() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetwork
Gets the substances.
getTreeA() - Method in class de.unirostock.sems.bives.algorithm.NodeConnection
Gets the corresponding node in tree a.
getTreeB() - Method in class de.unirostock.sems.bives.algorithm.NodeConnection
Gets the corresponding node in tree b.
getTreeDocument() - Method in class de.unirostock.sems.bives.ds.ModelDocument
Gets the tree document.
getUnmatched(TreeNode, List<TreeNode>) - Method in class de.unirostock.sems.bives.algorithm.SimpleConnectionManager
Gets the unmatched nodes in a subtree.
getUpdates() - Method in class de.unirostock.sems.bives.ds.Patch
Gets the updates.
getValues() - Method in class de.unirostock.sems.bives.markup.MarkupElement
Gets the entries stored in this element.
getValues() - Method in class de.unirostock.sems.bives.markup.MarkupSection
Gets the elements.
getVariable(TreeNode) - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetwork
Gets a variable.
getVariables() - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetwork
Gets the variables.
getVariables() - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkComponent
Gets the variables hosted in this component.
getWeight() - Method in class de.unirostock.sems.bives.algorithm.NodeConnection
 
GraphEntity - Interface in de.unirostock.sems.bives.ds
 
GraphProducer - Class in de.unirostock.sems.bives.algorithm
The Class GraphProducer to produce graphs from models.
GraphProducer(boolean) - Constructor for class de.unirostock.sems.bives.algorithm.GraphProducer
Instantiates a new graph producer.
GraphTranslator - Class in de.unirostock.sems.bives.ds.graph
The Class GraphTranslator, abstract parent to convert the internal graph representation to (un)common graph formats.
GraphTranslator() - Constructor for class de.unirostock.sems.bives.ds.graph.GraphTranslator
 
GraphTranslatorDot - Class in de.unirostock.sems.bives.ds.graph
The Class GraphTranslatorDot to translate internal graph structures into DOT format.
GraphTranslatorDot() - Constructor for class de.unirostock.sems.bives.ds.graph.GraphTranslatorDot
Instantiates a new graph translator for DOT conversion.
GraphTranslatorGraphML - Class in de.unirostock.sems.bives.ds.graph
The Class GraphTranslatorGraphML to translate internal graph structures into GraphML.
GraphTranslatorGraphML() - Constructor for class de.unirostock.sems.bives.ds.graph.GraphTranslatorGraphML
 
GraphTranslatorJson - Class in de.unirostock.sems.bives.ds.graph
The Class GraphTranslatorJson to translate internal graph structures into JSON format.
GraphTranslatorJson() - Constructor for class de.unirostock.sems.bives.ds.graph.GraphTranslatorJson
 

H

HierarchyNetwork - Class in de.unirostock.sems.bives.ds.hn
The Class HierarchyNetwork representing a graphical hierarchy network, intended to visualize CellML hierarchical dependencies.
HierarchyNetwork() - Constructor for class de.unirostock.sems.bives.ds.hn.HierarchyNetwork
Instantiates a new hierarchy network.
HierarchyNetworkComponent - Class in de.unirostock.sems.bives.ds.hn
The Class HierarchyNetworkComponent representing a component of a HierarchyNetwork.
HierarchyNetworkComponent(HierarchyNetwork, String, String, DocumentNode, DocumentNode) - Constructor for class de.unirostock.sems.bives.ds.hn.HierarchyNetworkComponent
Instantiates a new hierarchy network component.
HierarchyNetworkEntity - Class in de.unirostock.sems.bives.ds.hn
The Class HierarchyNetworkEntity.
HierarchyNetworkEntity(String, String, String, DocumentNode, DocumentNode) - Constructor for class de.unirostock.sems.bives.ds.hn.HierarchyNetworkEntity
Instantiates a new hierarchy network entity.
HierarchyNetworkVariable - Class in de.unirostock.sems.bives.ds.hn
The Class HierarchyNetworkVariable representing a variable of a HierarchyNetwork.
HierarchyNetworkVariable(HierarchyNetwork, String, String, DocumentNode, DocumentNode, HierarchyNetworkComponent, HierarchyNetworkComponent) - Constructor for class de.unirostock.sems.bives.ds.hn.HierarchyNetworkVariable
Instantiates a new hierarchy network variable.
HierarchyNetworkVariable.VarConnection - Class in de.unirostock.sems.bives.ds.hn
The Class VarConnection representing a connection of two variables.
HierarchyNetworkVariable.VarConnection(boolean, boolean) - Constructor for class de.unirostock.sems.bives.ds.hn.HierarchyNetworkVariable.VarConnection
Instantiates a new connection to another variable.
highlight(String) - Static method in class de.unirostock.sems.bives.markup.MarkupDocument
Highlights a string, e.g.
hn - Variable in class de.unirostock.sems.bives.algorithm.GraphProducer
The hierarchy network.

I

id - Variable in class de.unirostock.sems.bives.ds.rn.ReactionNetworkEntity
The id of this entity.
IdConnector - Class in de.unirostock.sems.bives.algorithm.general
Connector to connect nodes with same id.
IdConnector(TreeDocument, TreeDocument, boolean) - Constructor for class de.unirostock.sems.bives.algorithm.general.IdConnector
Instantiates a new XyDiffConnector.
init() - Method in class de.unirostock.sems.bives.algorithm.Connector
Initializes the extension.
init() - Method in class de.unirostock.sems.bives.algorithm.general.IdConnector
 
init() - Method in class de.unirostock.sems.bives.algorithm.general.LabelConnector
Deprecated.
 
init(SimpleConnectionManager, TreeDocument, TreeDocument) - Method in class de.unirostock.sems.bives.algorithm.general.PatchProducer
 
init() - Method in class de.unirostock.sems.bives.algorithm.general.XyDiffConnector
 
init(SimpleConnectionManager, TreeDocument, TreeDocument) - Method in class de.unirostock.sems.bives.algorithm.Producer
Initializes the producer.
INSERT - Static variable in interface de.unirostock.sems.bives.ds.GraphEntity
The flag for INSERTed entities.
insert(String) - Static method in class de.unirostock.sems.bives.markup.MarkupDocument
Highlights an insert.
insertNode(TreeNode, int) - Method in class de.unirostock.sems.bives.ds.Patch
Insert a single node.
insertNode(DocumentNode, int) - Method in class de.unirostock.sems.bives.ds.Patch
Insert a single node.
insertSubtree(TreeNode, int) - Method in class de.unirostock.sems.bives.ds.Patch
Mark a whole subtree as inserted.
interprete() - Method in class de.unirostock.sems.bives.algorithm.Interpreter
Interprete the connections!
Interpreter - Class in de.unirostock.sems.bives.algorithm
 
Interpreter(SimpleConnectionManager, TreeDocument, TreeDocument) - Constructor for class de.unirostock.sems.bives.algorithm.Interpreter
Instantiates a new interpreter.
intersection(SimpleConnectionManager) - Method in class de.unirostock.sems.bives.algorithm.SimpleConnectionManager
Create a ConnectionManager that contains only connections from this ConnectionManager and_another instance.
isReversible() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkReaction
Checks if is reversible.

L

labelA - Variable in class de.unirostock.sems.bives.ds.rn.ReactionNetworkEntity
The labels in original doc.
labelB - Variable in class de.unirostock.sems.bives.ds.rn.ReactionNetworkEntity
The labels in modified doc.
LabelConnector - Class in de.unirostock.sems.bives.algorithm.general
Deprecated.
LabelConnector(TreeDocument, TreeDocument) - Constructor for class de.unirostock.sems.bives.algorithm.general.LabelConnector
Deprecated.
Instantiates a new label connector.

M

mapTrees() - Method in class de.unirostock.sems.bives.api.Diff
Map both trees.
mapTrees() - Method in class de.unirostock.sems.bives.api.RegularDiff
 
Markup - Interface in de.unirostock.sems.bives.markup
The Interface Markup for objects who are able to report their contents to a markup document.
markup() - Method in interface de.unirostock.sems.bives.markup.Markup
Produce some markup presenting the contents of this object.
MarkupDocument - Class in de.unirostock.sems.bives.markup
The Class MarkupDocument representing a generic document that can be encoded in different formats using Typesetters.
MarkupDocument(String) - Constructor for class de.unirostock.sems.bives.markup.MarkupDocument
Instantiates a new markup document.
MarkupElement - Class in de.unirostock.sems.bives.markup
The Class MarkupElement representing an element in a MarkupDocument.
MarkupElement(String) - Constructor for class de.unirostock.sems.bives.markup.MarkupElement
Instantiates a new markup element.
MarkupSection - Class in de.unirostock.sems.bives.markup
The Class MarkupSection representing a section in a MarkupDocument.
MarkupSection(String) - Constructor for class de.unirostock.sems.bives.markup.MarkupSection
Instantiates a new markup section.
math(String) - Static method in class de.unirostock.sems.bives.markup.MarkupDocument
Container for unchanged math.
math(String, boolean) - Static method in class de.unirostock.sems.bives.markup.MarkupDocument
Container for modified math.
MathML - Class in de.unirostock.sems.bives.ds
The Class MathML to host MathML trees.
MathML(DocumentNode) - Constructor for class de.unirostock.sems.bives.ds.MathML
Instantiates a new MathML object.
MOD_INHIBITOR - Static variable in class de.unirostock.sems.bives.ds.ontology.SBOTerm
The string defining an INHIBITOR.
MOD_NONE - Static variable in class de.unirostock.sems.bives.ds.ontology.SBOTerm
The string defining no modification at all.
MOD_STIMULATOR - Static variable in class de.unirostock.sems.bives.ds.ontology.SBOTerm
The string defining a STIMULATOR.
MOD_UNKNOWN - Static variable in class de.unirostock.sems.bives.ds.ontology.SBOTerm
The string defining an UNKNOWN modifier.
ModelDocument - Class in de.unirostock.sems.bives.ds
The Class ModelDocument representing a document encoding for a model.
ModelDocument(TreeDocument) - Constructor for class de.unirostock.sems.bives.ds.ModelDocument
Instantiates a new model document.
ModelValidator - Class in de.unirostock.sems.bives.algorithm
The abstract class ModelValidator will serve as parent for ML validators.
ModelValidator() - Constructor for class de.unirostock.sems.bives.algorithm.ModelValidator
 
MODIFIED - Static variable in interface de.unirostock.sems.bives.ds.GraphEntity
The flag for MODIFIED entities.
modTermA - Variable in class de.unirostock.sems.bives.ds.rn.ReactionNetworkSubstanceRef
The optional modification terms in original doc.
modTermB - Variable in class de.unirostock.sems.bives.ds.rn.ReactionNetworkSubstanceRef
The optional modification terms in modified doc.
modToString(int) - Static method in class de.unirostock.sems.bives.ds.rn.ReactionNetwork
Convert a modification to a string representation.
multiply() - Static method in class de.unirostock.sems.bives.markup.MarkupDocument
Produces a multiply symbol.

N

NL_HTML - Static variable in class de.unirostock.sems.bives.markup.Typesetting
represents a new line in HTML files.
NL_TXT - Static variable in class de.unirostock.sems.bives.markup.Typesetting
represents the system specific new line character.
NL_XHTML - Static variable in class de.unirostock.sems.bives.markup.Typesetting
represents a new line in XHTML files.
NodeConnection - Class in de.unirostock.sems.bives.algorithm
 
NodeConnection(TreeNode, TreeNode) - Constructor for class de.unirostock.sems.bives.algorithm.NodeConnection
Instantiates a new connection, implicitly setting the weight to 1.
NodeConnection(NodeConnection) - Constructor for class de.unirostock.sems.bives.algorithm.NodeConnection
Instantiates a new connection as a copy of toCopy.
NodeConnection(TreeNode, TreeNode, double) - Constructor for class de.unirostock.sems.bives.algorithm.NodeConnection
Instantiates a new connection, explicitly defining a weight.

P

parentsConnected(Connection) - Method in class de.unirostock.sems.bives.algorithm.SimpleConnectionManager
Check if parents connected.
Patch - Class in de.unirostock.sems.bives.ds
The Class Patch storing all operations necessary to transfer one document into another.
Patch() - Constructor for class de.unirostock.sems.bives.ds.Patch
Instantiates a new patch.
Patch(boolean) - Constructor for class de.unirostock.sems.bives.ds.Patch
Instantiates a new patch.
PatchProducer - Class in de.unirostock.sems.bives.algorithm.general
The Class PatchProducer producing patches..
PatchProducer() - Constructor for class de.unirostock.sems.bives.algorithm.general.PatchProducer
 
produce() - Method in class de.unirostock.sems.bives.algorithm.general.PatchProducer
 
produce() - Method in class de.unirostock.sems.bives.algorithm.Producer
Produce the output.
produceHierarchyGraph() - Method in class de.unirostock.sems.bives.algorithm.GraphProducer
Produce hierarchy graph.
Producer - Class in de.unirostock.sems.bives.algorithm
The Class Producer produces different kind of output.
Producer() - Constructor for class de.unirostock.sems.bives.algorithm.Producer
 
produceReactionNetwork() - Method in class de.unirostock.sems.bives.algorithm.GraphProducer
Produce the reaction network.

R

RDF - Class in de.unirostock.sems.bives.ds.rdf
The Class RDF representing an RDF subtree.
RDF(DocumentNode) - Constructor for class de.unirostock.sems.bives.ds.rdf.RDF
Instantiates a new RDF object.
RDFDescription - Class in de.unirostock.sems.bives.ds.rdf
The Class RDFDescription representing an rdf:Description element.
RDFDescription(DocumentNode) - Constructor for class de.unirostock.sems.bives.ds.rdf.RDFDescription
Instantiates a new RDF object.
ReactionNetwork - Class in de.unirostock.sems.bives.ds.rn
The Class ReactionNetwork representing a reaction network.
ReactionNetwork() - Constructor for class de.unirostock.sems.bives.ds.rn.ReactionNetwork
Instantiates a new reaction network.
ReactionNetworkCompartment - Class in de.unirostock.sems.bives.ds.rn
The Class ReactionNetworkCompartment representing a compartment in a reaction network.
ReactionNetworkCompartment(ReactionNetwork, String, String, DocumentNode, DocumentNode) - Constructor for class de.unirostock.sems.bives.ds.rn.ReactionNetworkCompartment
Instantiates a new compartment.
ReactionNetworkEntity - Class in de.unirostock.sems.bives.ds.rn
The Class ReactionNetworkEntity representing an entity in a reaction network.
ReactionNetworkEntity(String, String, String, DocumentNode, DocumentNode) - Constructor for class de.unirostock.sems.bives.ds.rn.ReactionNetworkEntity
Instantiates a new entity.
ReactionNetworkReaction - Class in de.unirostock.sems.bives.ds.rn
The Class ReactionNetworkReaction representing a reaction in a reaction network.
ReactionNetworkReaction(ReactionNetwork, String, String, DocumentNode, DocumentNode, ReactionNetworkCompartment, ReactionNetworkCompartment, boolean) - Constructor for class de.unirostock.sems.bives.ds.rn.ReactionNetworkReaction
Instantiates a new ReactionNetwork reaction.
ReactionNetworkSubstance - Class in de.unirostock.sems.bives.ds.rn
The Class ReactionNetworkSubstance representing a substance in a reaction network.
ReactionNetworkSubstance(ReactionNetwork, String, String, DocumentNode, DocumentNode, ReactionNetworkCompartment, ReactionNetworkCompartment) - Constructor for class de.unirostock.sems.bives.ds.rn.ReactionNetworkSubstance
Instantiates a new substance in a reaction network.
ReactionNetworkSubstanceRef - Class in de.unirostock.sems.bives.ds.rn
The Class ReactionNetworkSubstanceRef representing a reference to a ReactionNetworkSubstance.
ReactionNetworkSubstanceRef(ReactionNetworkSubstance, boolean, boolean, SBOTerm, SBOTerm) - Constructor for class de.unirostock.sems.bives.ds.rn.ReactionNetworkSubstanceRef
Instantiates a new substance reference.
RegularDiff - Class in de.unirostock.sems.bives.api
The Class RegularDiff to compare two regular XML documents.
RegularDiff(File, File) - Constructor for class de.unirostock.sems.bives.api.RegularDiff
Instantiates a new regular diff object in order to compare two documents stored in files fileA and fileB.
RegularDiff(String, String) - Constructor for class de.unirostock.sems.bives.api.RegularDiff
Instantiates a new regular diff object in order to compare two documents stored in strings docA and docB.
RegularDiff(TreeDocument, TreeDocument) - Constructor for class de.unirostock.sems.bives.api.RegularDiff
Instantiates a new regular diff object in order to compare two tree documents.
replaceAllMaths(String, String, String) - Static method in class de.unirostock.sems.bives.markup.MarkupDocument
Replaces all math stuff, doesn't matter if inserted or deleted.
replaceAttributes(String, String, String) - Static method in class de.unirostock.sems.bives.markup.MarkupDocument
Replaces attributes.
replaceDeletes(String, String, String) - Static method in class de.unirostock.sems.bives.markup.MarkupDocument
Replaces deletes.
replaceHighlights(String, String, String) - Static method in class de.unirostock.sems.bives.markup.MarkupDocument
Replaces highlights.
replaceInserts(String, String, String) - Static method in class de.unirostock.sems.bives.markup.MarkupDocument
Replaces inserts.
replaceModifiedMaths(String, String, String) - Static method in class de.unirostock.sems.bives.markup.MarkupDocument
Replaces modified math.
replaceMultiplication(String, String) - Static method in class de.unirostock.sems.bives.markup.MarkupDocument
Replaces multiplication.
replaceOriginalMaths(String, String, String) - Static method in class de.unirostock.sems.bives.markup.MarkupDocument
Replaces original math.
replaceRightArrow(String, String) - Static method in class de.unirostock.sems.bives.markup.MarkupDocument
Replaces right arrow.
replaceUnchangedMaths(String, String, String) - Static method in class de.unirostock.sems.bives.markup.MarkupDocument
Replaces math that hasn't changed.
reportDelete() - Method in interface de.unirostock.sems.bives.algorithm.DiffReporter
Report a delete.
reportInsert() - Method in interface de.unirostock.sems.bives.algorithm.DiffReporter
Report an insert.
reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in interface de.unirostock.sems.bives.algorithm.DiffReporter
Report as a modification.
resolveModifier(String) - Static method in class de.unirostock.sems.bives.ds.ontology.SBOTerm
Resolve a modifier.
resolveModifier() - Method in class de.unirostock.sems.bives.ds.ontology.SBOTerm
Resolve this modifier.
rightArrow() - Static method in class de.unirostock.sems.bives.markup.MarkupDocument
Produces a right arrow.
rn - Variable in class de.unirostock.sems.bives.algorithm.GraphProducer
The reaction network.

S

sameModifier(SBOTerm, SBOTerm) - Static method in class de.unirostock.sems.bives.ds.ontology.SBOTerm
Check if modifiers are equal (in terms of chemical reaction networks).
SBOTerm - Class in de.unirostock.sems.bives.ds.ontology
The Class SBOTerm representing a link into the Systems Biology Ontology.
SBOTerm(String) - Constructor for class de.unirostock.sems.bives.ds.ontology.SBOTerm
Instantiates a new SBO term.
scaleWeight(double) - Method in class de.unirostock.sems.bives.algorithm.NodeConnection
 
scaleWeightOfAllConnections(double) - Method in class de.unirostock.sems.bives.algorithm.SimpleConnectionManager
Scale the weight of all connections.
setAbout(String) - Method in class de.unirostock.sems.bives.ds.rdf.RDFDescription
Sets the about attribute.
setCompartment(TreeNode, ReactionNetworkCompartment) - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetwork
Adds a compartment.
setCompartmentA(ReactionNetworkCompartment) - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkReaction
Sets the compartment in original version.
setCompartmentA(ReactionNetworkCompartment) - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkSubstance
Sets the compartment in original version.
setCompartmentB(ReactionNetworkCompartment) - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkReaction
Sets the compartment in modified version.
setCompartmentB(ReactionNetworkCompartment) - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkSubstance
Sets the compartment in modified version.
setComponent(TreeNode, HierarchyNetworkComponent) - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetwork
Adds a new component to the hierarchy.
setComponentA(HierarchyNetworkComponent) - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkVariable
Sets the component hosting this variable as defined in the original document.
setComponentB(HierarchyNetworkComponent) - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkVariable
Sets the component hosting this variable as defined in the modified document.
setDiff(SimpleConnectionManager) - Method in class de.unirostock.sems.bives.algorithm.SimpleConnectionManager
Create a ConnectionManager that contains only connections from this ConnectionManager which are not included in another instance.
setDocA(DocumentNode) - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkEntity
Sets the document node from the original document.
setDocA(DocumentNode) - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkEntity
Sets the original document node.
setDocB(DocumentNode) - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkEntity
Sets the document node from the modified document.
setDocB(DocumentNode) - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkEntity
Sets the modified document node.
setFlagA(boolean) - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkSubstanceRef
Sets the existence flag for the original version.
setFlagB(boolean) - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkSubstanceRef
Sets the existence flag for the modified version.
setHeader(String) - Method in class de.unirostock.sems.bives.markup.MarkupElement
Sets the header.
setHeader(String) - Method in class de.unirostock.sems.bives.markup.MarkupSection
Sets the header.
setLabelA(String) - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkEntity
Sets the label from the original document.
setLabelA(String) - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkEntity
Sets the original label.
setLabelB(String) - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkEntity
Sets the label from the modified document.
setLabelB(String) - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkEntity
Sets the modified label.
setParentA(HierarchyNetworkComponent) - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkComponent
Sets the parent component (above in hierarchy) as it is defined in the original version.
setParentB(HierarchyNetworkComponent) - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkComponent
Sets the parent component (above in hierarchy) as it is defined in the modified version.
setReaction(TreeNode, ReactionNetworkReaction) - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetwork
Adds a reaction.
setSboA(SBOTerm) - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkSubstanceRef
Sets the SBOTerm as defined in the original version.
setSboB(SBOTerm) - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkSubstanceRef
Sets the SBOTerm as defined in the modified version.
setSingleDocument() - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetwork
Sets the single document flag for non-comparison graphs.
setSingleDocument() - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkEntity
Sets the single document flag.
setSingleDocument() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetwork
Sets the single document flag for non-comparison graphs.
setSingleDocument() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkEntity
Sets the single document flag.
setSingleDocument() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkReaction
Sets the single document flag.
setSingleDocument() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkSubstanceRef
Sets the single document flag.
setSubstance(TreeNode, ReactionNetworkSubstance) - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetwork
Adds a substance.
setVariable(TreeNode, HierarchyNetworkVariable) - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetwork
Adds a new variable.
setWeight(double) - Method in class de.unirostock.sems.bives.algorithm.NodeConnection
 
setWeightOfAllConnections(double) - Method in class de.unirostock.sems.bives.algorithm.SimpleConnectionManager
Sets the weight of all connections.
SimpleConnectionManager - Class in de.unirostock.sems.bives.algorithm
 
SimpleConnectionManager(TreeDocument, TreeDocument) - Constructor for class de.unirostock.sems.bives.algorithm.SimpleConnectionManager
Instantiates a new simple connection manager.
SimpleConnectionManager(SimpleConnectionManager) - Constructor for class de.unirostock.sems.bives.algorithm.SimpleConnectionManager
Instantiates a new connection manager as a copy of toCopy.
single - Variable in class de.unirostock.sems.bives.algorithm.GraphProducer
The single flag.
Single - Class in de.unirostock.sems.bives.api
The Class Single, providing an API to extract some information about single XML files.
Single(File) - Constructor for class de.unirostock.sems.bives.api.Single
Instantiates a new single object reading the document from a file.
Single(String) - Constructor for class de.unirostock.sems.bives.api.Single
Instantiates a new single object reading the document from a string.
Single(TreeDocument) - Constructor for class de.unirostock.sems.bives.api.Single
Instantiates a new single object.
singleDoc - Variable in class de.unirostock.sems.bives.ds.rn.ReactionNetworkEntity
The single doc flag if in single-doc-operation-mode.
singleDoc - Variable in class de.unirostock.sems.bives.ds.rn.ReactionNetworkSubstanceRef
The single doc flag if in single-doc-operation-mode.
subst - Variable in class de.unirostock.sems.bives.ds.rn.ReactionNetworkSubstanceRef
The substance.
symDiff(SimpleConnectionManager) - Method in class de.unirostock.sems.bives.algorithm.SimpleConnectionManager
Create a ConnectionManager that contains only connections from this ConnectionManager and another instance and are not included in both managers.

T

toString() - Method in class de.unirostock.sems.bives.algorithm.NodeConnection
 
toString() - Method in class de.unirostock.sems.bives.algorithm.SimpleConnectionManager
 
toString() - Method in class de.unirostock.sems.bives.ds.Xhtml
Prints the sequence of subtrees, all in one string.
translate(ReactionNetwork) - Method in class de.unirostock.sems.bives.ds.graph.GraphTranslator
Translate a reaction network.
translate(HierarchyNetwork) - Method in class de.unirostock.sems.bives.ds.graph.GraphTranslator
Translate a hierarchy network.
translate(ReactionNetwork) - Method in class de.unirostock.sems.bives.ds.graph.GraphTranslatorDot
 
translate(HierarchyNetwork) - Method in class de.unirostock.sems.bives.ds.graph.GraphTranslatorDot
 
translate(HierarchyNetwork) - Method in class de.unirostock.sems.bives.ds.graph.GraphTranslatorGraphML
 
translate(ReactionNetwork) - Method in class de.unirostock.sems.bives.ds.graph.GraphTranslatorGraphML
 
translate(ReactionNetwork) - Method in class de.unirostock.sems.bives.ds.graph.GraphTranslatorJson
 
translate(HierarchyNetwork) - Method in class de.unirostock.sems.bives.ds.graph.GraphTranslatorJson
 
tree - Variable in class de.unirostock.sems.bives.api.Single
The tree.
treeA - Variable in class de.unirostock.sems.bives.api.Diff
The tree corresponding to the former version.
treeB - Variable in class de.unirostock.sems.bives.api.Diff
The tree corresponding to the later version.
typeset(MarkupDocument) - Method in class de.unirostock.sems.bives.markup.Typesetting
convert a markup document using a format-specific make-up.
typeset(MarkupDocument) - Method in class de.unirostock.sems.bives.markup.TypesettingHTML
 
typeset(MarkupDocument) - Method in class de.unirostock.sems.bives.markup.TypesettingMarkDown
 
typeset(MarkupDocument) - Method in class de.unirostock.sems.bives.markup.TypesettingReStructuredText
 
Typesetting - Class in de.unirostock.sems.bives.markup
The Class Typesetting to convert markup documents to certain formats.
Typesetting() - Constructor for class de.unirostock.sems.bives.markup.Typesetting
 
TypesettingHTML - Class in de.unirostock.sems.bives.markup
The Class TypesettingHTML to typeset reports in HTML format.
TypesettingHTML() - Constructor for class de.unirostock.sems.bives.markup.TypesettingHTML
 
TypesettingMarkDown - Class in de.unirostock.sems.bives.markup
The Class TypesettingMarkDown to typeset reports in MarkDown format.
TypesettingMarkDown() - Constructor for class de.unirostock.sems.bives.markup.TypesettingMarkDown
 
TypesettingReStructuredText - Class in de.unirostock.sems.bives.markup
The Class TypesettingReStructuredText to typeset reports in ReStructuredText.
TypesettingReStructuredText() - Constructor for class de.unirostock.sems.bives.markup.TypesettingReStructuredText
 

U

union(SimpleConnectionManager) - Method in class de.unirostock.sems.bives.algorithm.SimpleConnectionManager
Create a ConnectionManager that combines all connections from this ConnectionManager and another instance.
UNMODIFIED - Static variable in interface de.unirostock.sems.bives.ds.GraphEntity
The flag for UNMODIFIED entities.
updateNode(Connection, SimpleConnectionManager) - Method in class de.unirostock.sems.bives.ds.Patch
Update a node.

V

validate(TreeDocument) - Method in class de.unirostock.sems.bives.algorithm.ModelValidator
Validate a document.
validate(File) - Method in class de.unirostock.sems.bives.algorithm.ModelValidator
Validate a document represented as a file.
validate(String) - Method in class de.unirostock.sems.bives.algorithm.ModelValidator
Validate a document represented as a string.
validate(URL) - Method in class de.unirostock.sems.bives.algorithm.ModelValidator
Validate a document downladable from a web server.

X

Xhtml - Class in de.unirostock.sems.bives.ds
The Class Xhtml representing a sequence of XHTML subtrees.
Xhtml() - Constructor for class de.unirostock.sems.bives.ds.Xhtml
Instantiates a new Xhtml object.
XyDiffConnector - Class in de.unirostock.sems.bives.algorithm.general
The Class XyDiffConnector to map nodes as described in Cobena2002.
XyDiffConnector(TreeDocument, TreeDocument) - Constructor for class de.unirostock.sems.bives.algorithm.general.XyDiffConnector
Instantiates a new XyDiffConnector.
XyDiffConnector(Connector) - Constructor for class de.unirostock.sems.bives.algorithm.general.XyDiffConnector
Instantiates a new XyDiffConnector.
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