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java.lang.Objectfr.umlv.gramofone.graphs.MyGraph
public class MyGraph
Manage the network (and the connected component of a graph are considered as MyGraphs too)
| Field Summary | |
|---|---|
protected static int |
IDEDGE
|
| Constructor Summary | |
|---|---|
MyGraph(CyNetwork networkBrut,
MyPattern pattern,
Homologies homologies,
int NDel,
int NIns,
GMTask task)
Create a new MyGraph to manage the cytoscape network |
|
MyGraph(int n,
int m,
MyPattern motif,
int Ndel,
int Nins)
Create a new random network with n nodes and m edges. |
|
| Method Summary | |
|---|---|
java.util.List<CyNode> |
computeNeighbours(java.util.List<CyNode> nodes)
Return a list with CyNode wich are connected to nodes in the list nodes |
java.util.Set<java.lang.Integer> |
getColors(int node)
Get the colors associated to this node |
java.util.LinkedList<MyGraph> |
getConnectedComponent()
Get the list of connected components |
Edges |
getEdgeObject()
|
java.util.HashSet<Edge> |
getEdges()
Get a set with edges of the MyGraph |
int |
getNdel()
Return the number of deletions allowed (updated after the apriori deletions) |
java.util.Set<java.lang.Integer> |
getNeighbors(int v)
Get the neighbors of the node v in the MyGraph |
CyNetwork |
getNetwork()
get the cynetwork of the MyGraph |
int |
getNins()
Return the number of insertions allowed |
java.util.List<java.lang.Integer> |
getNodes()
Return the list of nodes id in the graph |
java.util.Set<java.lang.Integer> |
getNodesOfThisColors(int color)
return a set with all nodes with the color color |
java.util.HashSet<java.lang.Integer> |
getNodesWithoutColors()
Get a set of nodes without colors in the MyGraph after the coloring |
CyNetwork |
getOriginalNetwork()
|
MyPattern |
getPattern()
Get the motif |
java.util.Set<java.lang.Integer> |
getPatternColorful()
Get only different colors of the pattern |
java.util.Set<java.lang.String> |
getPreviouslyDeletedProteins()
Get the set of proteins deleted before the computation (if there got no homologous in the network) |
int |
getSize()
Return the number of nodes in the MyGraph |
SubGraphResult |
model2SubGraph(int[] model,
java.lang.Number score,
Constraints constraints)
From the result of the pseudoBoolean resolution, extract the corresponding subgraph in Cytoscape |
java.lang.String |
toString()
|
| Methods inherited from class java.lang.Object |
|---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
| Field Detail |
|---|
protected static int IDEDGE
| Constructor Detail |
|---|
public MyGraph(int n,
int m,
MyPattern motif,
int Ndel,
int Nins)
n - nb of nodes in the random networkm - nb of edges in the random networkmotif - pattern to searchNdel - maximum number of deletionsNins - maximum number of insertions
public MyGraph(CyNetwork networkBrut,
MyPattern pattern,
Homologies homologies,
int NDel,
int NIns,
GMTask task)
networkBrut - networkpattern - motif to searchhomologies - homologies between proteinsNDel - maximum number of deletionsNIns - maximum number of insertionstask - Cytoscape task| Method Detail |
|---|
public java.util.List<java.lang.Integer> getNodes()
public int getSize()
public java.util.Set<java.lang.Integer> getPatternColorful()
public java.util.Set<java.lang.Integer> getNodesOfThisColors(int color)
color -
public java.util.Set<java.lang.Integer> getColors(int node)
node - graph node
public java.util.HashSet<Edge> getEdges()
public java.util.Set<java.lang.Integer> getNeighbors(int v)
v -
public java.util.Set<java.lang.String> getPreviouslyDeletedProteins()
public Edges getEdgeObject()
public int getNdel()
public int getNins()
public CyNetwork getNetwork()
public CyNetwork getOriginalNetwork()
public java.util.LinkedList<MyGraph> getConnectedComponent()
public java.util.HashSet<java.lang.Integer> getNodesWithoutColors()
public MyPattern getPattern()
public java.util.List<CyNode> computeNeighbours(java.util.List<CyNode> nodes)
nodes -
public SubGraphResult model2SubGraph(int[] model,
java.lang.Number score,
Constraints constraints)
model - the assignation of variables in PseudoBooleanscore - the score of the resolutionconstraints -
public java.lang.String toString()
toString in class java.lang.Object
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