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See:
Description
| Interface Summary | |
|---|---|
| IGraphMetaphor | interface for graph metaphor, which describe the mapping of the presentation layer of the graph and the content of the pathways. |
| IGraphProcessor | change the graph struture, while IGraphMetaphor only change the graph attribute |
| MyJGraphModelAdapter.ICellFactory | Creates the JGraph cells that reflect the respective JGraphT elements. |
| VersionListener | |
| Class Summary | |
|---|---|
| AbstractGraphMetaphor | abstract graph metaphor containing common utility functions and default behaviors. |
| AbstractGraphProcessor | |
| AbstractVersionGraphMetaphor | special metaphor for version graph |
| AdjacencyGraphWalker | specialized graph walker which walk throigh all adjacecy interaction nodes in the graph model in each pass |
| AlignmentMetaphor | given the alignment, metaphor the current graph view |
| CategoryEncoder | |
| CategoryLayoutAlgorithm | |
| CategoryMetaphor | metaphor of pathway categroy graph |
| ChemicalReactionMetaphor | flux analysis on this collect all valid edges collect all valid interaction nodes (including hidden transport node) get the component graph or subsystem pop up dialog with table which displays the sub-system (in combobox) and corresponding interaction, and rates field, and freedom hint (require user continue input) set up the linear equation system and solve it metaphor the sub-system with the solution |
| ComparativeMetaphor | in the case of multiple pathways in a preview window. |
| CompositionGraphModel | contain the nodes of the current graph. |
| CompositionRelationMetaphor | use normal location metaphor and color the and relation as red, or relation as blue |
| DefaultGraphMetaphor | interface for graph metaphor, which describe the mapping of the presentation layer of the graph and the content of the pathways. |
| EditingLayoutAlgorithm | support the general network layout based on the node id |
| EditingMetaphor | follow the FCMetaphor but never look at the database. |
| FCMetaphor | default metaphor (nodeType = RNA) maps to (shape = rectangular) (nodeType = Protein) maps to (shape = diamond) (nodeType = Compound) maps to (shape = ecclipse) (location = cytosol) maps to (node fill color = 0xFFFFCC) (location = mitochondria*) maps to (node fill color = pink) (location = microbody) maps to (node fill color = grey) (location = plastid*) maps to (node fill color = green) (location = apoplast) maps to (node fill color = 0x6699FF) (location = nucleus) maps to (node outline color = yellow) (location = thylakoids*) maps to (node outline color = green) (edgeType = Catalysis) maps to (line thickness = medium) (edgeType = Catalysis) maps to (line color = blue) (edgeType = Enzymatic) maps to (line thickness = medium) (edgeType = OR) maps to (line thickness = medium-narrow) (edgeType = OR) maps to (line color = yellow) (edgeType = Regulation/Positive regulation) maps to (line color = green) (edgeType = Regulation/Positive regulation) maps to (line thickness = medium-narrow) (edgeType = Regulation/Negative regulation) maps to (line color = red) (edgeType = Regulation/Negative regulation) maps to (line thickness = medium-narrow) (certainty = indirect evidence) maps to (line type = dash-dot) (certainty = several line*) maps to (line type = dotted) (certainty = wild hypo*) maps to (line type = dotted) |
| GlobalGraphWalker | specialized walker which walk throgh the all interaction node in the graph model in each pass |
| GraphValidity | store the information of the graph validity |
| GraphWalker | facility to traverse the graph, and run the interaction node |
| HierachyLayoutAlgorithm | hierachical layout. |
| InputEncoder | input graph encoder |
| InputLayoutAlgorithm | input graph layout |
| IsomorphismMetaphor | special metaphor for subgraph isomorphism |
| JCategoryGraph | |
| JGraphEncoder | create Dot format file to describe the graph data in memory. |
| JInputGraph | |
| JMetaphorGraph | extend the JGraph by applying the metaphor description based on the content of the pathway |
| MetaphorTypeInformation | obviously checking the edge type can be extended to any interaction inforation of specified edge, thus we need a wrapper of all information |
| MultiNodeCell | define my cell for my view |
| MultiPathwayModel | this pathway model is used for displaying combination of multiple pathway. |
| MultiVertexView | implement a special vertex view and renderer which can use two background color. |
| MultiVertexView.MultiVertexRenderer | customized the renderer to use two background colors for one node |
| MyJGraphModelAdapter | |
| MyTreeAlgorithm | copy from JGraph, modified for pathway category. |
| NetworkEditHelper | helper function for NetworkEditForm |
| NetworkEncoder | encode the network in editing |
| PathwayElementMetaphor | metaphor for selected element. |
| PathwayModel | special graph model, which only add interaction nodes, and automatically add entitywithlocation nodes and edges related to these nodes |
| RandomLayoutAlgorithm | |
| RelationObject | |
| RemoveBridgeNodes | |
| RemoveCompositionNodes | the only difference with remove RemoveSelectedNodes is not connect the upstream nodes with downstream nodes |
| RemoveSelectedNodes | |
| SearchInteractionTypeMetaphor | |
| SearchNameMetaphor | |
| ValidityMetaphor | highlight the nodes and edges that have problems |
| VersionEncoder | create Dot format file to describe the graph data in memory. |
| VersionGraph | extend the JGraph by applying the metaphor description based on the content of the pathway XXX (cancelled) may we need a different but same feature class for version editor only. |
| VersionGraphMetaphor | get the version graph metaphor, by default, simple black on white |
| VersionGraphModel | hold the version graph model through jgrapht |
| VersionyLayoutAlgorithm | hierachical layout. |
new graph model for metnet pathways
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