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| Interface Summary | |
|---|---|
| AlignmentAlgorithm | define the interface of pathway alignment, following the way like metaphor and process |
| HistoryBlockunit | get the version information |
| IMetnetBlockUnit | general node in the graph |
| MultiPathwayElementNode | interface for multi-pathway graph element node |
| MultiPathwayGraph | a pathway graph containing several pathways based on the alignment information, we do not use Super- to prevent confusing |
| PathwayAlignment | alignment data structure |
| PathwayElementNode | hold the data of the element in a version of pathway |
| PathwayGraph | |
| Class Summary | |
|---|---|
| AbbreviationObject | |
| AbstractMultiPathwayElementNode | pathway element nodes which holds multiple element nodes from different pathway graphs. |
| AbstractPathwayElementNode | pathway element node. |
| AlignmentObject | used to store the information of alignment over the network |
| AtGeneSearchLocusObject | get all information for locus id |
| BidiMultiHashMap | bidirectional multi-singlekey <->multi-singlevalue mapping |
| Candidate | |
| CategoryNode | store the node in category graph |
| ChebiObject | chebi info data object. |
| ChebiOntologyName | |
| CommentObject | |
| EntityNode | |
| GoTermID | contain the term and id in one object |
| GroupObject | |
| HistoryBlockunitImpl | an implementationo of the historyblockunit for version check |
| HistoryInformation | contain the history information, such as the blockid, recordid for undelete, name if deleted and other information for display |
| InputNode | use to store the input graph node data while adapt to the display requirement of JGraph |
| InteractionInformation | dummy display for interaction selector |
| InteractionNode | |
| InteractionObject | similarf to AtGeneSearchObject and ChebiObject, store the information for tooltips in the pathway preview |
| InteractionStructure | define the comparable property of interactions |
| MetnetBlockUnit | general node in the graph |
| MetnetInteraction | interaction nodes in the graph, should handle catalysis secifically |
| MetnetLiveEntity | entitywithlocation node in the graph |
| MetnetPathway | abstract pathway node in the graph, which should be invisible and not connect to other nodes, otherwise cause layout problem |
| MultiEntityNode | entity node in multiple pathway graph which holds multi entity node from multiple pathways. |
| MultiInteractionNode | interaction node for multiple pathway. |
| MultiPathwayGraphImpl | implementation of multi-pathway graph |
| MyVersionGraph | a simple graph structure supporting transfering over network. |
| MyVersionNode | a simple node graph support transfering over network. |
| NameSource | |
| PathwayA | |
| PathwayAlignmentImpl | implementation of alignment |
| PathwayGraphImpl | a simple pathway graph to detect the structure change. |
| PathwayObject | store basic pathway information for pathway selector |
| ReferenceObject | |
| RelationMap | |
| SoybeanHomology | store the soybean homology information |
| SynonymObject | |
| TairReferenceObject | |
| TrivialMetabolite | contains the information of trivial metabolites that have highly connections |
| ZEdge | used to store edge control points for remotelly layout |
| ZVertex | used to store the vertex position for layout remotelly |
| Exception Summary | |
|---|---|
| NoSuchNodeException | special exception for pathway structure |
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