public class BiographUtils extends Graph
Modifier and Type | Field and Description |
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static boolean |
mapSignOfConservationCoeffs |
allGraphs, countGraphs, EdgeHash, Edges, globalComment, metaNodes, name, NodeHash, NodeIndexHash, Nodes, selectedIds, startId, useIDsForOutput, writeHangingNodes
Constructor and Description |
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BiographUtils() |
Modifier and Type | Method and Description |
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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 |
convertReactionNetworkIntoEntityNetwork(Graph reactionNetwork) |
static Graph |
ExcludeIntermediateNodes(Graph gri,
java.util.Vector v,
boolean firstPass) |
static java.util.Vector<java.lang.String> |
extractProteinNamesFromNodeName(java.lang.String id) |
static java.util.Vector<java.lang.String> |
extractProteinNamesFromNodeNames(java.util.Vector<Node> nodes) |
static Graph |
ExtractReactionNetwork(Graph gr)
From arbitrary interface extract standard Reaction Network interface
|
static java.util.Vector<Node> |
findReactionRegulators(Graph reactionNetwork,
java.util.Set<java.lang.String> reactionIds,
java.lang.String[] typesOfRegulations) |
static java.util.Vector<Node> |
findReactionRegulators(Graph reactionNetwork,
java.lang.String reid,
java.lang.String[] typesOfRegulations) |
static int |
getEdgeSign(Edge e) |
static java.util.Vector<java.lang.String> |
getListOfEntityNamesFromId(java.lang.String id) |
static Graph |
getMaterialComponentForEntityName(Graph graph,
java.lang.String name)
Extract a material component subgraph
|
static java.util.HashMap |
getNeighborhoodSets(Graph network,
java.util.Vector<java.lang.String> selected,
boolean goUpstream,
boolean goDownstream,
int searchRadius,
int minimumNumberOfGenes,
boolean takeFromHUGOatt) |
static java.util.Vector<Node> |
getNodeFirstNeighbors(Graph graph,
Node node,
boolean goUpstream,
boolean goDownstream) |
static java.util.Vector<java.lang.String> |
getNodeNamesFromAnAttribute(java.util.Vector<Node> nodes,
java.lang.String attname) |
static java.util.Vector<Node> |
getNodeNeighbors(Graph graph,
Node node,
boolean goUpstream,
boolean goDownstream,
int searchRadius) |
static int |
getPathSign(Graph graph,
java.lang.String sourceNodeId) |
static int |
getPathSign(Path path) |
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 Graph |
LinearizeNetwork(Graph gri) |
static void |
main(java.lang.String[] args) |
static Graph |
mapClassesToNodeProps(Graph gr) |
static Graph |
MergeNetworkAndFilter(java.util.Vector<Graph> graphs,
float pourcentage) |
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.
|
addConnections, addConnectionsAlongSequence, addEdge, addEdgeIdUnique, addEdges, addMetanodeConnections, addNode, addNodes, addNodesFromEdges, assignEdgeIds, calcNodesInOut, correct, createIndexNodeHash, edgesConnectingSubGraphs, getCreateEdge, getCreateNode, getEdge, getEdge, getEdgeByLabel, getEdgeIndex, getHangingNodes, getIncidenceMatrix, getNode, getNodeByLabel, getNodeIndex, getNodesByLabelInclusion, getSelectedNodes, identicalEdges, identicalNodes, identicalTo, includesEdges, includesNodes, includesNodesPercentage, intersection, makeCopy, makeEdgeDoubleSense, printGraphList, recreateNodeEdgeHash, removeEdge, removeNode, removeNodes, removeObsoleteEdges, saveAsCytoscapeGML, saveAsCytoscapeSif, saveAsCytoscapeXGMML, subtractNodes, toString
public static void main(java.lang.String[] args)
public static Graph ShowMonoMolecularReactionsAsEdges(Graph gri)
gri
- public static Graph ExcludeIntermediateNodes(Graph gri, java.util.Vector v, boolean firstPass)
public static int getEdgeSign(Edge e)
public static Graph getSubGraphByLabelInclusions(Graph gri, java.lang.String label)
gri
- label
- public static Graph getMaterialComponentForEntityName(Graph graph, java.lang.String name)
public static java.util.Vector<java.lang.String> getListOfEntityNamesFromId(java.lang.String id)
public static java.util.Vector calcAllMaterialComponents(Graph gri)
gri
- public static Graph inclusionGraph(java.util.Vector graphs)
graphs
- public static java.util.Vector readConservationLaws(Graph gr, java.lang.String fn, boolean useSpeciesIDs)
gr
- fn
- useSpeciesIDs
- public static boolean isNumber(java.lang.String s)
public static Graph addCommonReactions(Graph gr, Graph grglobal)
gr
- grglobal
- public static void printSpeciesReactions(Graph gr)
public static Graph CollapseMetaNodes(Graph global, boolean showIntersections, boolean nodeIntersectionView)
public static Graph ExtractReactionNetwork(Graph gr)
gr
- public static void RemoveNodesOfType(Graph gr, java.lang.String substringAttName, java.lang.String substringAttValue)
substringAttName
- substringAttValue
- public static int getPathSign(Path path)
public static int getPathSign(Graph graph, java.lang.String sourceNodeId)
public static java.util.HashMap getNeighborhoodSets(Graph network, java.util.Vector<java.lang.String> selected, boolean goUpstream, boolean goDownstream, int searchRadius, int minimumNumberOfGenes, boolean takeFromHUGOatt)
public static java.util.Vector<java.lang.String> getNodeNamesFromAnAttribute(java.util.Vector<Node> nodes, java.lang.String attname)
public static java.util.Vector<Node> getNodeNeighbors(Graph graph, Node node, boolean goUpstream, boolean goDownstream, int searchRadius)
public static java.util.Vector<Node> getNodeFirstNeighbors(Graph graph, Node node, boolean goUpstream, boolean goDownstream)
public static java.util.Vector<java.lang.String> extractProteinNamesFromNodeNames(java.util.Vector<Node> nodes)
public static java.util.Vector<java.lang.String> extractProteinNamesFromNodeName(java.lang.String id)
public static Graph MergeNetworkAndFilter(java.util.Vector<Graph> graphs, float pourcentage)
public static Graph convertReactionNetworkIntoEntityNetwork(Graph reactionNetwork)
public static java.util.Vector<Node> findReactionRegulators(Graph reactionNetwork, java.lang.String reid, java.lang.String[] typesOfRegulations)