- b - Variable in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkVariable.VarConnection
-
The existence flags for original/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.
- 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
-
- getCRNDotGraph() - Method in class de.unirostock.sems.bives.api.Diff
-
- getCRNDotGraph() - Method in class de.unirostock.sems.bives.api.Single
-
- 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
-
- getCRNGraphML() - Method in class de.unirostock.sems.bives.api.Single
-
- getCRNJsonGraph() - Method in class de.unirostock.sems.bives.api.Diff
-
- getCRNJsonGraph() - Method in class de.unirostock.sems.bives.api.Single
-
- 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
-
- 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 versions A/B.
- modTermB - Variable in class de.unirostock.sems.bives.ds.rn.ReactionNetworkSubstanceRef
-
The optional modification terms in versions A/B.
- 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.
- 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
-
- 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
-
- reportInsert() - Method in interface de.unirostock.sems.bives.algorithm.DiffReporter
-
- reportModification(SimpleConnectionManager, DiffReporter, DiffReporter) - Method in interface de.unirostock.sems.bives.algorithm.DiffReporter
-
- 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.
- 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
-
- 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
-
- SimpleConnectionManager - Class in de.unirostock.sems.bives.algorithm
-
- SimpleConnectionManager(TreeDocument, TreeDocument) - Constructor for class de.unirostock.sems.bives.algorithm.SimpleConnectionManager
-
- 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.