All Classes
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All Classes Interface Summary Class Summary Exception Summary Class Description BivesConnectionException The Class BivesConnectionException signaling node-connection problems.BivesDocumentConsistencyException The Class BivesDocumentConsistencyException signaling inconsistencies.BivesException The Class BivesException representing problems that occurred in BiVeS.BivesFlattenException The Class BivesFlattenException signaling problems while flattening a document.BivesImportException The Class BivesImportException signaling errors while importing documents.BivesLogicalException The Class BivesLogicalException signaling logical errors.BivesNetworkingException The Class BivesNetworkingException signaling network errors.BivesTools The Class BivesTools providing some utils for document comparison.BivesUnsupportedException The Class BivesUnsupportedException for not (yet) supported operations.Connector The Class Connector, intended to find node-correspondences between two trees.DefaultDiffAnnotator Diff The Class Diff, the central object if it comes to the comparison of XML documents.DiffAnnotator The abstract class DiffAnnotator is the central item in the patch annotation infrastructure.DiffReporter GraphEntity GraphProducer The Class GraphProducer to produce graphs from models.GraphTranslator The Class GraphTranslator, abstract parent to convert the internal graph representation to (un)common graph formats.GraphTranslatorDot The Class GraphTranslatorDot to translate internal graph structures into DOT format.GraphTranslatorGraphML The Class GraphTranslatorGraphML to translate internal graph structures into GraphML.GraphTranslatorJson The Class GraphTranslatorJson to translate internal graph structures into JSON format.GraphTranslatorSbgnJson The class GraphTranslatorSbgnJson translates the internal graph structure into a JSON which is SBGN PD sufficient.HierarchyNetwork The Class HierarchyNetwork representing a graphical hierarchy network, intended to visualize CellML hierarchical dependencies.HierarchyNetworkComponent The Class HierarchyNetworkComponent representing a component of a HierarchyNetwork.HierarchyNetworkEntity The Class HierarchyNetworkEntity.HierarchyNetworkVariable The Class HierarchyNetworkVariable representing a variable of a HierarchyNetwork.IdConnector Connector to connect nodes with same id.Interpreter LabelConnector Deprecated. Markup The Interface Markup for objects who are able to report their contents to a markup document.MarkupDocument The Class MarkupDocument representing a generic document that can be encoded in different formats using Typesetters.MarkupElement The Class MarkupElement representing an element in a MarkupDocument.MarkupSection The Class MarkupSection representing a section in a MarkupDocument.MathML The Class MathML to host MathML trees.ModelDocument The Class ModelDocument representing a document encoding for a model.ModelValidator The abstract class ModelValidator will serve as parent for ML validators.NodeConnection Patch The Class Patch storing all operations necessary to transfer one document into another.PatchProducer The Class PatchProducer producing patches..Producer The Class Producer produces different kind of output.RDF The Class RDF representing an RDF subtree.RDFDescription The Class RDFDescription representing an rdf:Description element.ReactionNetwork The Class ReactionNetwork representing a reaction network.ReactionNetworkCompartment The Class ReactionNetworkCompartment representing a compartment in a reaction network.ReactionNetworkEntity The Class ReactionNetworkEntity representing an entity in a reaction network.ReactionNetworkReaction The Class ReactionNetworkReaction representing a reaction in a reaction network.ReactionNetworkSubstance The Class ReactionNetworkSubstance representing a substance in a reaction network.ReactionNetworkSubstanceRef The Class ReactionNetworkSubstanceRef representing a reference to aReactionNetworkSubstance
.RegularDiff The Class RegularDiff to compare two regular XML documents.SBOTerm The Class SBOTerm representing a link into the Systems Biology Ontology.SimpleConnectionManager Single The Class Single, providing an API to extract some information about single XML files.Typesetting The Class Typesetting to convert markup documents to certain formats.TypesettingHTML The Class TypesettingHTML to typeset reports in HTML format.TypesettingMarkDown The Class TypesettingMarkDown to typeset reports in MarkDown format.TypesettingReStructuredText The Class TypesettingReStructuredText to typeset reports in ReStructuredText.Xhtml The Class Xhtml representing a sequence of XHTML subtrees.XyDiffConnector The Class XyDiffConnector to map nodes as described in Cobena2002.