Index (BiVeS-Core 1.9.2 API)

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.
addAnnotation(Property, RDFNode) - Method in class de.unirostock.sems.bives.algorithm.NodeConnection: Adds an annotation describing this node connection.
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.
ALLOW_DIFFERENT_IDS - Static variable in class de.unirostock.sems.bives.api.Diff: Are mappings of nodes with different ids allowed? At the first glimpse that might sound stupid, but ids are generally arbitrary and say nothing valuable about the entities.
allowDifferentIds - Variable in class de.unirostock.sems.bives.algorithm.Connector: Are mappings of nodes with different ids allowed? see Diff.ALLOW_DIFFERENT_IDS
annotateDeletion(TreeNode, Element, ChangeFactory) - Method in class de.unirostock.sems.bives.algorithm.DiffAnnotator: Annotate a deletion.
annotateDeletion(TreeNode, Element, ChangeFactory) - Method in class de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
annotateInsertion(TreeNode, Element, ChangeFactory) - Method in class de.unirostock.sems.bives.algorithm.DiffAnnotator: Annotate an insertion.
annotateInsertion(TreeNode, Element, ChangeFactory) - Method in class de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
annotateMove(TreeNode, TreeNode, Element, ChangeFactory, boolean) - Method in class de.unirostock.sems.bives.algorithm.DiffAnnotator: Annotate a move.
annotateMove(TreeNode, TreeNode, Element, ChangeFactory, boolean) - Method in class de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
annotatePatch(String, ChangeFactory) - Method in class de.unirostock.sems.bives.algorithm.DiffAnnotator: Annotate the Patch itself with information about the software used to create this .
annotatePatch(String, ChangeFactory) - Method in class de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
annotatePatch() - Method in class de.unirostock.sems.bives.ds.Patch: Annotate the whole patch.
annotateUpdateAttribute(TreeNode, TreeNode, String, Element, ChangeFactory) - Method in class de.unirostock.sems.bives.algorithm.DiffAnnotator: Annotate an update of an attribute value.
annotateUpdateAttribute(TreeNode, TreeNode, String, Element, ChangeFactory) - Method in class de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
annotateUpdateText(TextNode, TextNode, Element, ChangeFactory) - Method in class de.unirostock.sems.bives.algorithm.DiffAnnotator: Annotate an update of a text node.
annotateUpdateText(TextNode, TextNode, Element, ChangeFactory) - Method in class de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
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

CARE_ABOUT_NAMES - Static variable in class de.unirostock.sems.bives.api.Diff: Do we care about names? Should we treat names differently? They often provide more information than other attributes.
careAboutNames - Variable in class de.unirostock.sems.bives.algorithm.Connector: Do we care about names? see Diff.CARE_ABOUT_NAMES
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, boolean, boolean, boolean) - Constructor for class de.unirostock.sems.bives.algorithm.Connector: Instantiates a new connector.
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_SUPP - Static variable in class de.unirostock.sems.bives.markup.Typesetting: The Constant CSS_CLASS_DELETE.
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
DefaultDiffAnnotator - Class in de.unirostock.sems.bives.algorithm.general
DefaultDiffAnnotator() - Constructor for class de.unirostock.sems.bives.algorithm.general.DefaultDiffAnnotator
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.
Diff(File, File, DiffAnnotator) - 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, DiffAnnotator) - 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, DiffAnnotator) - Constructor for class de.unirostock.sems.bives.api.Diff: Instantiates a new diff object in order to compare two tree documents.
DiffAnnotator - Class in de.unirostock.sems.bives.algorithm: The abstract class DiffAnnotator is the central item in the patch annotation infrastructure.
DiffAnnotator() - Constructor for class de.unirostock.sems.bives.algorithm.DiffAnnotator
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.
flagInvisibleModification() - Method in class de.unirostock.sems.bives.markup.MarkupElement: Set a flag indicating that this element has modifications which are not visible in the markup 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.
getAnnotationDocumentXml() - Method in class de.unirostock.sems.bives.ds.Patch: Gets the annotation document encoded in XML.
getAnnotations() - Method in class de.unirostock.sems.bives.algorithm.general.PatchProducer: Gets the annotations of the patch.
getAnnotations() - Method in class de.unirostock.sems.bives.algorithm.NodeConnection: Gets the annotations of this mapping.
getAnnotations() - Method in class de.unirostock.sems.bives.ds.Patch: Gets the actual annotations.
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.
getBivesVersion() - Static method in class de.unirostock.sems.bives.tools.BivesTools: Returns the bives version that is currently running.
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: Deprecated.
As of 1.3.3 replaced by Diff.getReactionsGraph(de.unirostock.sems.bives.ds.graph.GraphTranslator)
getCRNGraph(GraphTranslator) - Method in class de.unirostock.sems.bives.api.Single: Deprecated.
As of 1.3.3 replaced by Single.getReactionsGraph(de.unirostock.sems.bives.ds.graph.GraphTranslator)
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.
getDiff(boolean) - Method in class de.unirostock.sems.bives.api.Diff: Gets the differences encoded in an XML string
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(boolean) - Method in class de.unirostock.sems.bives.ds.Patch: Gets the document containing all changes.
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.
getDocumentNode() - Method in class de.unirostock.sems.bives.ds.Xhtml: Gets the corresponding document node.
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.
getJsonGraph() - Method in class de.unirostock.sems.bives.ds.graph.GraphTranslatorSbgnJson: 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.
getNumAnnotations() - Method in class de.unirostock.sems.bives.ds.Patch: Gets the number of annotations for the differences in this patch.
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.
getReactionsSbgnJsonGraph() - Method in class de.unirostock.sems.bives.api.Diff: Returns the graph of the reaction network encoded in an SBGN-JSON format.
getReactionsSbgnJsonGraph() - Method in class de.unirostock.sems.bives.api.RegularDiff
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
GraphTranslatorSbgnJson - Class in de.unirostock.sems.bives.ds.graph: The class GraphTranslatorSbgnJson translates the internal graph structure into a JSON which is SBGN PD sufficient.
GraphTranslatorSbgnJson() - Constructor for class de.unirostock.sems.bives.ds.graph.GraphTranslatorSbgnJson

H

hasInvisibleModifications() - Method in class de.unirostock.sems.bives.markup.MarkupElement: Does this element have modifications which are not visible in the markup document?.
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.
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(SimpleConnectionManager, TreeDocument, TreeDocument, DiffAnnotator) - Method in class de.unirostock.sems.bives.algorithm.general.PatchProducer: Initialise this patch producer providing a diff annotator.
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(boolean, boolean, boolean) - Method in class de.unirostock.sems.bives.api.Diff: Map both trees.
mapTrees() - Method in class de.unirostock.sems.bives.api.Diff: Map both trees.
mapTrees(boolean, boolean, boolean) - Method in class de.unirostock.sems.bives.api.RegularDiff
markDeleted(DocumentNode) - Static method in class de.unirostock.sems.bives.tools.BivesTools: Mark a document node as deleted.
markInserted(DocumentNode) - Static method in class de.unirostock.sems.bives.tools.BivesTools: Mark a document node as inserted.
markMoved(DocumentNode) - Static method in class de.unirostock.sems.bives.tools.BivesTools: Mark a document node as moved.
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.
markUpdated(TextNode) - Static method in class de.unirostock.sems.bives.tools.BivesTools: Mark a text node as updated.
markUpdated(DocumentNode) - Static method in class de.unirostock.sems.bives.tools.BivesTools: Mark a document node as updated.
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.
MAX_ATTR_DIST - Static variable in class de.unirostock.sems.bives.algorithm.general.XyDiffConnector
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.
nodeAssign(TreeNode, TreeNode) - Method in class de.unirostock.sems.bives.algorithm.Connector: Assign two nodes to each other, as long as they don't have a connection.
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(URI, DiffAnnotator) - Constructor for class de.unirostock.sems.bives.ds.Patch: Instantiates a new patch specifying the file name of the resulting patch and an annotator to annotate the differences.
Patch(DiffAnnotator) - Constructor for class de.unirostock.sems.bives.ds.Patch: Instantiates a new patch specifying.
Patch(boolean, URI, DiffAnnotator) - Constructor for class de.unirostock.sems.bives.ds.Patch: Instantiates a new patch specifying the fullDiff flag, the file name of the resulting patch, and an annotator to annotate the differences.
Patch(boolean, DiffAnnotator) - Constructor for class de.unirostock.sems.bives.ds.Patch: Instantiates a new patch specifying the fullDiff flag and an annotator to annotate the differences.
Patch(URI) - Constructor for class de.unirostock.sems.bives.ds.Patch: Instantiates a new patch specifying the file name of the resulting patch.
Patch() - Constructor for class de.unirostock.sems.bives.ds.Patch: Instantiates a new patch.
Patch(boolean, URI) - Constructor for class de.unirostock.sems.bives.ds.Patch: Instantiates a new patch specifying the fullDiff flag and the file name of the resulting patch.
Patch(boolean) - Constructor for class de.unirostock.sems.bives.ds.Patch: Instantiates a new patch specifying the fullDiff flag.
PATCH_FILE_NAME - Static variable in class de.unirostock.sems.bives.ds.Patch: The default file name of the path.
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(boolean) - Method in class de.unirostock.sems.bives.algorithm.general.PatchProducer: Produce the patch.
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.
replaceSupplementals(String, String, String) - Static method in class de.unirostock.sems.bives.markup.MarkupDocument: Replaces supplementary information.
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.
reportDelete(MarkupElement) - Method in class de.unirostock.sems.bives.ds.Xhtml: Report this object as deleted.
reportInsert() - Method in interface de.unirostock.sems.bives.algorithm.DiffReporter: Report an insert.
reportInsert(MarkupElement) - Method in class de.unirostock.sems.bives.ds.Xhtml: Report this object as inserted.
reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in interface de.unirostock.sems.bives.algorithm.DiffReporter: Report as a modification.
reportModification(SimpleConnectionManager, Xhtml, Xhtml, MarkupElement) - Method in class de.unirostock.sems.bives.ds.Xhtml: Report a modification between to Xhtml objects.
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.
setInvisibleModifications(boolean) - Method in class de.unirostock.sems.bives.markup.MarkupElement: Does this element have modifications which are not visible in the markup document?.
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.
setXhtml(DocumentNode) - Method in class de.unirostock.sems.bives.ds.Xhtml: Adds an XHTML subtree.
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.
STRICTER_NAMES - Static variable in class de.unirostock.sems.bives.api.Diff: Should we handle names very strictly? Go for this option if you're sure that you're names are very similar.
stricterNames - Variable in class de.unirostock.sems.bives.algorithm.Connector: Should we handle names very strictly? see Diff.STRICTER_NAMES
subst - Variable in class de.unirostock.sems.bives.ds.rn.ReactionNetworkSubstanceRef: The substance.
supplemental(String) - Static method in class de.unirostock.sems.bives.markup.MarkupDocument: Highlights supplementary information.
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
translate(ReactionNetwork) - Method in class de.unirostock.sems.bives.ds.graph.GraphTranslatorSbgnJson
translate(HierarchyNetwork) - Method in class de.unirostock.sems.bives.ds.graph.GraphTranslatorSbgnJson
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(NodeConnection, 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.
VarConnection(boolean, boolean) - Constructor for class de.unirostock.sems.bives.ds.hn.HierarchyNetworkVariable.VarConnection: Instantiates a new connection to another variable.

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, boolean, boolean, boolean) - Constructor for class de.unirostock.sems.bives.algorithm.general.XyDiffConnector: Instantiates a new XyDiffConnector.
XyDiffConnector(TreeDocument, TreeDocument) - Constructor for class de.unirostock.sems.bives.algorithm.general.XyDiffConnector: Instantiates a new XyDiffConnector.
XyDiffConnector(Connector, boolean, boolean, boolean) - 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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