A B C D E F G H I L M N P R S T U V X
All Classes All Packages
All Classes All Packages
All Classes All Packages
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(MarkupElement) - Method in class de.unirostock.sems.bives.markup.MarkupSection
-
Adds an element to this section.
- addValue(String) - Method in class de.unirostock.sems.bives.markup.MarkupElement
-
Adds an entry to this element.
- 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() - Method in class de.unirostock.sems.bives.ds.Patch
-
Annotate the whole patch.
- 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
- 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) - Constructor for class de.unirostock.sems.bives.algorithm.Connector
-
Instantiates a new connector.
- Connector(TreeDocument, TreeDocument, boolean, boolean, boolean) - 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(String) - Static method in class de.unirostock.sems.bives.markup.MarkupDocument
-
Highlights a delete.
- DELETE - Static variable in interface de.unirostock.sems.bives.ds.GraphEntity
-
The flag for DELETEd entities.
- 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(TreeDocument, TreeDocument) - Constructor for class de.unirostock.sems.bives.api.Diff
-
Instantiates a new diff object in order to compare two tree documents.
- 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.
- 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(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) - 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(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.
- 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(Connection) - Method in class de.unirostock.sems.bives.algorithm.SimpleConnectionManager
-
Drop a certain connection.
- dropConnection(TreeNode) - Method in class de.unirostock.sems.bives.algorithm.SimpleConnectionManager
-
Drop all connections of a node.
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() - 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.
- getCompartment(TreeNode) - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetwork
-
Gets a compartment.
- getCompartments() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetwork
-
Gets the compartments.
- getComponent() - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetworkVariable
-
Gets the component.
- getComponent(TreeNode) - Method in class de.unirostock.sems.bives.ds.hn.HierarchyNetwork
-
Gets a 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() - Method in class de.unirostock.sems.bives.ds.Patch
-
Gets the document containing all changes.
- getDocument(boolean) - 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() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkSubstanceRef
-
Gets the referenced substance.
- getSubstance(TreeNode) - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetwork
-
Gets a 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() - Method in class de.unirostock.sems.bives.algorithm.general.XyDiffConnector
- init(SimpleConnectionManager, TreeDocument, TreeDocument) - Method in class de.unirostock.sems.bives.algorithm.general.PatchProducer
- init(SimpleConnectionManager, TreeDocument, TreeDocument) - Method in class de.unirostock.sems.bives.algorithm.Producer
-
Initializes the producer.
- init(SimpleConnectionManager, TreeDocument, TreeDocument, DiffAnnotator) - Method in class de.unirostock.sems.bives.algorithm.general.PatchProducer
-
Initialise this patch producer providing a diff annotator.
- insert(String) - Static method in class de.unirostock.sems.bives.markup.MarkupDocument
-
Highlights an insert.
- INSERT - Static variable in interface de.unirostock.sems.bives.ds.GraphEntity
-
The flag for INSERTed entities.
- insertNode(DocumentNode, int) - Method in class de.unirostock.sems.bives.ds.Patch
-
Insert a single node.
- insertNode(TreeNode, int) - Method in class de.unirostock.sems.bives.ds.Patch
-
Insert a single node.
- insertSubtree(TreeNode, int) - Method in class de.unirostock.sems.bives.ds.Patch
-
Mark a whole subtree as inserted.
- interprete() - Method in class de.unirostock.sems.bives.algorithm.Interpreter
-
Interprete the connections!
- Interpreter - Class in de.unirostock.sems.bives.algorithm
- Interpreter(SimpleConnectionManager, TreeDocument, TreeDocument) - Constructor for class de.unirostock.sems.bives.algorithm.Interpreter
-
Instantiates a new interpreter.
- intersection(SimpleConnectionManager) - Method in class de.unirostock.sems.bives.algorithm.SimpleConnectionManager
-
Create a ConnectionManager that contains only connections from this ConnectionManager and_another instance.
- isReversible() - Method in class de.unirostock.sems.bives.ds.rn.ReactionNetworkReaction
-
Checks if is reversible.
L
- labelA - Variable in class de.unirostock.sems.bives.ds.rn.ReactionNetworkEntity
-
The labels in original doc.
- labelB - Variable in class de.unirostock.sems.bives.ds.rn.ReactionNetworkEntity
-
The labels in modified doc.
- LabelConnector - Class in de.unirostock.sems.bives.algorithm.general
-
Deprecated.
- LabelConnector(TreeDocument, TreeDocument) - Constructor for class de.unirostock.sems.bives.algorithm.general.LabelConnector
-
Deprecated.Instantiates a new label connector.
M
- mapTrees() - Method in class de.unirostock.sems.bives.api.Diff
-
Map both trees.
- mapTrees(boolean, boolean, boolean) - 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() - Method in interface de.unirostock.sems.bives.markup.Markup
-
Produce some markup presenting the contents of this object.
- Markup - Interface in de.unirostock.sems.bives.markup
-
The Interface Markup for objects who are able to report their contents to a markup document.
- markUpdated(DocumentNode) - Static method in class de.unirostock.sems.bives.tools.BivesTools
-
Mark a document node as updated.
- markUpdated(TextNode) - Static method in class de.unirostock.sems.bives.tools.BivesTools
-
Mark a text 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(NodeConnection) - Constructor for class de.unirostock.sems.bives.algorithm.NodeConnection
-
Instantiates a new connection as a copy of toCopy.
- NodeConnection(TreeNode, TreeNode) - Constructor for class de.unirostock.sems.bives.algorithm.NodeConnection
-
Instantiates a new connection, implicitly setting the weight to 1.
- NodeConnection(TreeNode, TreeNode, double) - Constructor for class de.unirostock.sems.bives.algorithm.NodeConnection
-
Instantiates a new connection, explicitly defining a weight.
P
- parentsConnected(Connection) - Method in class de.unirostock.sems.bives.algorithm.SimpleConnectionManager
-
Check if parents connected.
- Patch - Class in de.unirostock.sems.bives.ds
-
The Class Patch storing all operations necessary to transfer one document into another.
- Patch() - Constructor for class de.unirostock.sems.bives.ds.Patch
-
Instantiates a new patch.
- Patch(boolean) - Constructor for class de.unirostock.sems.bives.ds.Patch
-
Instantiates a new patch specifying the fullDiff flag.
- 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(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, 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(DiffAnnotator) - Constructor for class de.unirostock.sems.bives.ds.Patch
-
Instantiates a new patch specifying.
- Patch(URI) - Constructor for class de.unirostock.sems.bives.ds.Patch
-
Instantiates a new patch specifying the file name of the resulting patch.
- 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_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() - Method in class de.unirostock.sems.bives.algorithm.Producer
-
Produce the output.
- produce(boolean) - Method in class de.unirostock.sems.bives.algorithm.general.PatchProducer
-
Produce the patch.
- 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(TreeDocument, TreeDocument) - Constructor for class de.unirostock.sems.bives.api.RegularDiff
-
Instantiates a new regular diff object in order to compare two tree 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.
- 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() - Method in class de.unirostock.sems.bives.ds.ontology.SBOTerm
-
Resolve this modifier.
- resolveModifier(String) - Static method in class de.unirostock.sems.bives.ds.ontology.SBOTerm
-
Resolve a 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(SimpleConnectionManager) - Constructor for class de.unirostock.sems.bives.algorithm.SimpleConnectionManager
-
Instantiates a new connection manager as a copy of toCopy.
- SimpleConnectionManager(TreeDocument, TreeDocument) - Constructor for class de.unirostock.sems.bives.algorithm.SimpleConnectionManager
-
Instantiates a new simple connection manager.
- 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(TreeDocument) - Constructor for class de.unirostock.sems.bives.api.Single
-
Instantiates a new single object.
- 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.
- 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(HierarchyNetwork) - Method in class de.unirostock.sems.bives.ds.graph.GraphTranslator
-
Translate a hierarchy network.
- 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(HierarchyNetwork) - Method in class de.unirostock.sems.bives.ds.graph.GraphTranslatorJson
- translate(HierarchyNetwork) - Method in class de.unirostock.sems.bives.ds.graph.GraphTranslatorSbgnJson
- translate(ReactionNetwork) - Method in class de.unirostock.sems.bives.ds.graph.GraphTranslator
-
Translate a reaction network.
- translate(ReactionNetwork) - Method in class de.unirostock.sems.bives.ds.graph.GraphTranslatorDot
- 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(ReactionNetwork) - 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(Connector) - 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(TreeDocument, TreeDocument) - Constructor for class de.unirostock.sems.bives.algorithm.general.XyDiffConnector
-
Instantiates a new XyDiffConnector.
- XyDiffConnector(TreeDocument, TreeDocument, boolean, boolean, boolean) - Constructor for class de.unirostock.sems.bives.algorithm.general.XyDiffConnector
-
Instantiates a new XyDiffConnector.
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