fr.curie.BiNoM.pathways.analysis.structure
Class BiographUtils

java.lang.Object
  fr.curie.BiNoM.pathways.analysis.structure.Graph
      fr.curie.BiNoM.pathways.analysis.structure.BiographUtils

public class BiographUtils
extends Graph

Set of functions using specific graph node semantics of BiNoM

Field Summary

static boolean

mapSignOfConservationCoeffs

Fields inherited from class fr.curie.BiNoM.pathways.analysis.structure.Graph

allGraphs, countGraphs, EdgeHash, Edges, globalComment, metaNodes, name, NodeHash, NodeIndexHash, Nodes, selectedIds, startId, useIDsForOutput, writeHangingNodes

Constructor Summary

BiographUtils()

Method Summary

static Graph	addCommonReactions(Graph gr, Graph grglobal) Adds to gr all connecting reactions, found in grglobal
static java.util.Vector	calcAllMaterialComponents(Graph gri) For every protein name, creates a subgraph with all its modifications, complexes, locations
static Graph	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	ExtractReactionNetwork(Graph gr) From arbitrary interface extract standard Reaction Network interface
static Graph	getSubGraphByLabelInclusions(Graph gri, java.lang.String label) Simply extraxts a subgraph with nodes whose name have label as a substring
static Graph	inclusionGraph(java.util.Vector graphs) Creates a new graph where nodes represent other graphs and edges represent intersections in nodes between these graphs.
static boolean	isNumber(java.lang.String s)
static void	main(java.lang.String[] args)
static Graph	mapClassesToNodeProps(Graph gr)
static void	printSpeciesReactions(Graph gr)
static java.util.Vector	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?)
static void	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	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 inherited from class fr.curie.BiNoM.pathways.analysis.structure.Graph

addConnections, addEdge, addEdgeIdUnique, addEdges, addMetanodeConnections, addNode, addNodes, addNodesFromEdges, assignEdgeIds, calcNodesInOut, createIndexNodeHash, edgesConnectingSubGraphs, getCreateEdge, getCreateNode, getEdge, getEdge, getEdgeByLabel, getEdgeIndex, getHangingNodes, getNode, getNodeByLabel, getNodeIndex, getNodesByLabelInclusion, getSelectedNodes, identicalNodes, includesNodes, includesNodesPercentage, intersection, makeCopy, makeEdgeDoubleSense, printGraphList, removeNode, removeNodes, removeObsoleteEdges, saveAsCytoscapeGML, saveAsCytoscapeSif, saveAsCytoscapeXGMML, subtractNodes

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

mapSignOfConservationCoeffs

public static boolean mapSignOfConservationCoeffs

Constructor Detail

BiographUtils

public BiographUtils()

Method Detail

main

public static void main(java.lang.String[] args)

ShowMonoMolecularReactionsAsEdges

public static Graph 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. The type of the edge is guessed from any reaction Attribute, having "EFFECT" substring in its name (like "TRANSPATH_EFFECT:"). If the attribute's value contains 'activation' or 'inhibition' substring (or some others), the corresponding edge sign is assigned

Parameters:

gri -

Returns:

getSubGraphByLabelInclusions

public static Graph getSubGraphByLabelInclusions(Graph gri,
                                                 java.lang.String label)

Simply extraxts a subgraph with nodes whose name have label as a substring

Parameters:

gri -

label -

Returns:

calcAllMaterialComponents

public static java.util.Vector calcAllMaterialComponents(Graph gri)

For every protein name, creates a subgraph with all its modifications, complexes, locations

Parameters:

gri -

Returns:

inclusionGraph

public static Graph inclusionGraph(java.util.Vector graphs)

Creates a new graph where nodes represent other graphs and edges represent intersections in nodes between these graphs.

Parameters:

graphs -

Returns:

mapClassesToNodeProps

public static Graph mapClassesToNodeProps(Graph gr)

readConservationLaws

public static java.util.Vector 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?)

Parameters:

gr -

fn -

useSpeciesIDs -

Returns:

list of subgraphs

isNumber

public static boolean isNumber(java.lang.String s)

addCommonReactions

public static Graph addCommonReactions(Graph gr,
                                       Graph grglobal)

Adds to gr all connecting reactions, found in grglobal

Parameters:

gr -

grglobal -

Returns:

printSpeciesReactions

public static void printSpeciesReactions(Graph gr)

CollapseMetaNodes

public static Graph 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

ExtractReactionNetwork

public static Graph ExtractReactionNetwork(Graph gr)

From arbitrary interface extract standard Reaction Network interface

Parameters:

gr -

Returns:

RemoveNodesOfType

public static void 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

Parameters:

substringAttName -

substringAttValue -