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| Packages that use Graph | |
|---|---|
| fr.curie.BiNoM.pathways.analysis.structure | Tools for structural analysis of biological graphs |
| fr.curie.BiNoM.pathways.utils | Utility classes |
| fr.curie.BiNoM.pathways.wrappers | Auxilary containers representing different systems biology formats |
| Uses of Graph in fr.curie.BiNoM.pathways.analysis.structure |
|---|
| Subclasses of Graph in fr.curie.BiNoM.pathways.analysis.structure | |
|---|---|
class |
BiographUtils
Set of functions using specific graph node semantics of BiNoM |
class |
BipartiteGraph
Was supposed to deal with Bi-partite graphs specifically but has not been used yet |
| Methods in fr.curie.BiNoM.pathways.analysis.structure that return Graph | |
|---|---|
static Graph |
BiographUtils.addCommonReactions(Graph gr,
Graph grglobal)
Adds to gr all connecting reactions, found in grglobal |
static Graph |
BiographUtils.CollapseMetaNodes(Graph global,
boolean showIntersections,
boolean nodeIntersectionView)
Calculates modular representation of graph global, using Graph.Metanodes list of subgraphs showIntersections - if true then all metanode intersections will be shown explicitly nodeIntersectionView - if true then all the edges connecting nodes in the intersection will not be shown, but instead for every common node there will be a 'INTERSECT' edge shown |
static Graph |
BiographUtils.ExtractReactionNetwork(Graph gr)
From arbitrary interface extract standard Reaction Network interface |
static Graph |
GraphAlgorithms.GetBiggestGraph(java.util.Vector v)
|
static Graph |
GraphAlgorithms.GetConnectedComponent(Graph graph,
Node n)
|
Graph |
Graph.getHangingNodes()
|
Graph |
Graph.getNodesByLabelInclusion(java.lang.String label)
|
Graph |
Graph.getSelectedNodes()
|
static Graph |
BiographUtils.getSubGraphByLabelInclusions(Graph gri,
java.lang.String label)
Simply extraxts a subgraph with nodes whose name have label as a substring |
static Graph |
BiographUtils.inclusionGraph(java.util.Vector graphs)
Creates a new graph where nodes represent other graphs and edges represent intersections in nodes between these graphs. |
Graph |
Graph.intersection(Graph gr)
|
Graph |
Graph.makeCopy()
|
static Graph |
BiographUtils.mapClassesToNodeProps(Graph gr)
|
static Graph |
BiographUtils.ShowMonoMolecularReactionsAsEdges(Graph gri)
Finds all reactions on the graph gri having only one reactant and one product and no modifiers and substitutes them by edge. |
| Methods in fr.curie.BiNoM.pathways.analysis.structure that return types with arguments of type Graph | |
|---|---|
static java.util.Vector<Graph> |
GraphAlgorithms.CombineIncludedGraphsApprox(java.util.Vector<Graph> graphs,
float thresh)
Clusters graphs with node overlap more than threshold |
static java.util.Vector<Graph> |
GraphAlgorithms.ConnectedComponents(Graph graph)
|
static java.util.Vector<Graph> |
GraphAlgorithms.CycleDecomposition(Graph graph,
int sizeThreshold)
|
static java.util.Vector<Graph> |
GraphAlgorithms.Dijkstra(Graph graph,
Node source,
Node target,
boolean directedGraph,
boolean suboptimal,
double searchRadius)
|
static java.util.Vector<Graph> |
GraphAlgorithms.DijkstraAlgorithm(Graph graph,
Node source,
Node target,
boolean directedGraph,
double searchRadius)
|
static java.util.Vector<Graph> |
GraphAlgorithms.FindAllPaths(Graph graph,
Node source,
java.util.Set<Node> targets,
boolean directedGraph,
double searchRadius)
Note: searchRadius here is the number of edges from source (edge weights are not considered) |
static java.util.Vector<Graph> |
GraphAlgorithms.PruneGraph(Graph graph,
boolean includeInterface)
Graph pruning (eliminataing IN and OUT layers) |
static java.util.Vector<Graph> |
GraphAlgorithms.StronglyConnectedComponentsTarjan(Graph graph,
int minimumComponentSize)
|
| Methods in fr.curie.BiNoM.pathways.analysis.structure with parameters of type Graph | |
|---|---|
static Graph |
BiographUtils.addCommonReactions(Graph gr,
Graph grglobal)
Adds to gr all connecting reactions, found in grglobal |
void |
Graph.addConnections(Graph gr)
|
void |
Graph.addEdges(Graph gr)
|
void |
Graph.addMetanodeConnections(Graph gr,
boolean nodeIntersectionView,
boolean showIntersections)
|
void |
Graph.addNodes(Graph gr)
|
static java.util.Vector |
BiographUtils.calcAllMaterialComponents(Graph gri)
For every protein name, creates a subgraph with all its modifications, complexes, locations |
static Graph |
BiographUtils.CollapseMetaNodes(Graph global,
boolean showIntersections,
boolean nodeIntersectionView)
Calculates modular representation of graph global, using Graph.Metanodes list of subgraphs showIntersections - if true then all metanode intersections will be shown explicitly nodeIntersectionView - if true then all the edges connecting nodes in the intersection will not be shown, but instead for every common node there will be a 'INTERSECT' edge shown |
static java.util.Vector<Graph> |
GraphAlgorithms.ConnectedComponents(Graph graph)
|
static java.util.Vector<Graph> |
GraphAlgorithms.CycleDecomposition(Graph graph,
int sizeThreshold)
|
static java.util.Vector<Graph> |
GraphAlgorithms.Dijkstra(Graph graph,
Node source,
Node target,
boolean directedGraph,
boolean suboptimal,
double searchRadius)
|
static java.util.Vector<Graph> |
GraphAlgorithms.DijkstraAlgorithm(Graph graph,
Node source,
Node target,
boolean directedGraph,
double searchRadius)
|
static void |
GraphAlgorithms.DijkstraProcedure(Graph graph,
int isource,
int iend,
double[] d,
java.util.Vector<java.util.Vector<java.lang.Integer>> previous,
boolean directedGraph,
double searchRadius)
Principal Dijkstra procedure 2 for each vertex v in V[G] // Initializations 3 d[v] := infinity // Unknown distance function from s to v 4 previous[v] := undefined 5 d[s] := 0 // Distance from s to s 6 S := empty set // Set of all visited vertices 7 Q := V[G] // Set of all unvisited vertices 8 while Q is not an empty set // The algorithm itself 9 u := Extract_Min(Q) // Remove best vertex from priority queue 10 S := S union {u} // Mark it 'visited' 11 for each edge (u,v) outgoing from u 12 if d[u] + w(u,v) < d[v] // Relax (u,v) 13 d[v] := d[u] + w(u,v) 14 previous[v] := u |
java.util.Vector |
Graph.edgesConnectingSubGraphs(Graph meta1,
Graph meta2,
Graph grglobal,
boolean nodeIntersectionView)
|
static Graph |
BiographUtils.ExtractReactionNetwork(Graph gr)
From arbitrary interface extract standard Reaction Network interface |
static java.util.Vector<Graph> |
GraphAlgorithms.FindAllPaths(Graph graph,
Node source,
java.util.Set<Node> targets,
boolean directedGraph,
double searchRadius)
Note: searchRadius here is the number of edges from source (edge weights are not considered) |
static java.util.Set<java.lang.String> |
StructureAnalysisUtils.findPaths(Graph network,
java.util.Vector<java.lang.String> sources,
java.util.Vector<java.lang.String> targets,
StructureAnalysisUtils.Option options)
|
static Graph |
GraphAlgorithms.GetConnectedComponent(Graph graph,
Node n)
|
static Graph |
BiographUtils.getSubGraphByLabelInclusions(Graph gri,
java.lang.String label)
Simply extraxts a subgraph with nodes whose name have label as a substring |
boolean |
Graph.identicalNodes(Graph gr)
|
java.util.Vector |
Graph.includesNodes(Graph gr)
|
float |
Graph.includesNodesPercentage(Graph gr)
|
Graph |
Graph.intersection(Graph gr)
|
static Graph |
BiographUtils.mapClassesToNodeProps(Graph gr)
|
static java.util.Vector<java.util.Vector<Edge>> |
GraphAlgorithms.neighboursOfNodeHash(Graph graph,
boolean directedGraph)
Sub-routine for Dijkstra's algorithm Returns vector (of length number of nodes) of vectors of outgoing edges numbers |
static void |
BiographUtils.printSpeciesReactions(Graph gr)
|
static java.util.Vector<Graph> |
GraphAlgorithms.PruneGraph(Graph graph,
boolean includeInterface)
Graph pruning (eliminataing IN and OUT layers) |
static java.util.Vector |
BiographUtils.readConservationLaws(Graph gr,
java.lang.String fn,
boolean useSpeciesIDs)
Reads a file produced by Structural Analysis GUI software in SB Workbench and finds subgraphs, corresponding to the conservation laws (P-invariants?) |
void |
Graph.removeNodes(Graph gr)
|
static void |
BiographUtils.RemoveNodesOfType(Graph gr,
java.lang.String substringAttName,
java.lang.String substringAttValue)
Removes nodes which have an attribute with substringAttName in its name and substringAttValue in its value |
static Graph |
BiographUtils.ShowMonoMolecularReactionsAsEdges(Graph gri)
Finds all reactions on the graph gri having only one reactant and one product and no modifiers and substitutes them by edge. |
static java.util.Vector<Graph> |
GraphAlgorithms.StronglyConnectedComponentsTarjan(Graph graph,
int minimumComponentSize)
|
void |
Graph.subtractNodes(Graph gr)
|
| Method parameters in fr.curie.BiNoM.pathways.analysis.structure with type arguments of type Graph | |
|---|---|
static java.util.Vector<Graph> |
GraphAlgorithms.CombineIncludedGraphsApprox(java.util.Vector<Graph> graphs,
float thresh)
Clusters graphs with node overlap more than threshold |
| Uses of Graph in fr.curie.BiNoM.pathways.utils |
|---|
| Fields in fr.curie.BiNoM.pathways.utils declared as Graph | |
|---|---|
Graph |
BioPAXGraphQueryEngine.database
The index with which the query is performed |
Graph |
BioPAXGraphQueryEngine.databaseCopyForPathAnalysis
Copy of the database to perform index path analysis |
Graph |
GraphXGMMLParser.graph
|
Graph |
BioPAXGraphQuery.input
Input for the query |
Graph |
BioPAXGraphQuery.result
Output of the query |
| Methods in fr.curie.BiNoM.pathways.utils with parameters of type Graph | |
|---|---|
static void |
Utils.CorrectCytoscapeNodeIds(Graph graph)
After reading XGMML files saved by Cytoscape, this function is used to recover the original Node Ids (Cytoscape will put negative numbers for it). |
static com.hp.hpl.jena.ontology.OntModel |
BioPAXUtilities.extractFromModel(com.hp.hpl.jena.rdf.model.Model source,
Graph graph)
|
static com.hp.hpl.jena.ontology.OntModel |
BioPAXUtilities.extractFromModel(com.hp.hpl.jena.rdf.model.Model source,
Graph graph,
java.lang.String namespace,
java.lang.String importString)
From all elements in graph BIOPAX_URI attribute values are used to extract a part of the source |
void |
BioPAXGraphQueryEngine.setDatabase(Graph graph)
Setting the BioPAX index file for performing the query |
| Uses of Graph in fr.curie.BiNoM.pathways.wrappers |
|---|
| Methods in fr.curie.BiNoM.pathways.wrappers that return Graph | |
|---|---|
static Graph |
XGMML.convertXGMMLToGraph(edu.rpi.cs.xgmml.GraphDocument xgr)
Converts GraphDocument to internal BiNoM graph representation (fr.curie.BiNoM.pathways.analysis.structure.Graph) |
| Methods in fr.curie.BiNoM.pathways.wrappers with parameters of type Graph | |
|---|---|
static edu.rpi.cs.xgmml.GraphDocument |
XGMML.convertGraphToXGMML(Graph gr)
Converts internal BiNoM graph representation to GraphDocument |
static void |
XGMML.saveToXGMML(Graph graph,
java.lang.String fn)
|
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