uk.ac.ebi.intact.application.hierarchView.business.graph
Class InteractionNetwork

java.lang.Object
  |
  +--java.util.AbstractMap
        |
        +--java.util.HashMap
              |
              +--uk.ac.ebi.intact.simpleGraph.BasicGraph
                    |
                    +--uk.ac.ebi.intact.simpleGraph.Graph
                          |
                          +--uk.ac.ebi.intact.application.hierarchView.business.graph.InteractionNetwork

All Implemented Interfaces:

BasicGraphI, java.lang.Cloneable, GraphI, java.util.Map, java.io.Serializable

public class InteractionNetwork

extends Graph

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class java.util.Map

java.util.Map.Entry

Field Summary

static int

DEFAULT_MAX_CENTRAL_PROTEIN

Constructor Summary

InteractionNetwork(Interactor aCentralProtein)
Constructor

Method Summary

void	addCentralProtein(Node node)
void	addCriteria(CriteriaBean aCriteria) Add a new criteria to the interaction network
Node	addNode(Interactor anInteractor) add the initialization part to the super class method
java.lang.String	exportBioLayout() Create a String giving informations for the bioLayout EMBL software the informations are just pairwise of protein label.
java.lang.String	exportTlp() Create a String giving informations for the Tulip treatment the informations are : - the number of nodes, - the whole of the edges and nodes associeted for each edge, - the label of each node.
void	fusion(InteractionNetwork network) Fusion a interaction network to the current one. For each edge of the new network we check if it exists in the current one. If the edge already exists : continue. If not, we check if the two Nodes of the edge already exists in the current network : if the node exists, update the edge with its reference if not add it to the current network finally we add the up-to-date edge to the current network
java.util.ArrayList	getCentralInteractors()
Interactor	getCentralProtein()
java.lang.String	getCentralProteinAC()
java.util.ArrayList	getCentralProteins()
java.util.ArrayList	getCriteria()
int	getCurrentCentralProteinCount()
ImageDimension	getImageDimension() Return the object ImageDimension which correspond to the graph
static int	getMaxCentralProtein()
java.util.ArrayList	getOrderedNodes() return a list of nodes ordered
java.lang.String[]	importDataToImage(java.lang.String dataTlp) Send a String to Tulip to calculate coordinates Enter the obtained coordinates in the graph.
void	init() Initialization of the interaction network Record the nodes in a list which allows to keep an order ...
void	initNodeDisplay(NodeI aNode) initialisation of one Node about its color, its visible attribute
void	initNodes() Allow to put the default color and default visibility for each protein of the interaction network
void	resetCriteria() remove all existing criteria from the interaction network
int	sizeEdges() Return the number of edge
int	sizeNodes() Return the number of node

Methods inherited from class uk.ac.ebi.intact.simpleGraph.Graph

addEdge, addNode, addVisited, getEdges, getNodes, isVisited, toString

Methods inherited from class uk.ac.ebi.intact.simpleGraph.BasicGraph

getId, getLabel, setId, setLabel

Methods inherited from class java.util.HashMap

clear, clone, containsKey, containsValue, entrySet, get, isEmpty, keySet, put, putAll, remove, size, values

Methods inherited from class java.util.AbstractMap

equals, hashCode

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface uk.ac.ebi.intact.simpleGraph.BasicGraphI

getId, getLabel, setId, setLabel

Methods inherited from interface java.util.Map

clear, containsKey, containsValue, entrySet, equals, get, hashCode, isEmpty, keySet, put, putAll, remove, size, values

Field Detail

DEFAULT_MAX_CENTRAL_PROTEIN

public static final int DEFAULT_MAX_CENTRAL_PROTEIN

See Also:

Constant Field Values

Constructor Detail

InteractionNetwork

public InteractionNetwork(Interactor aCentralProtein)

Constructor

Method Detail

getMaxCentralProtein

public static int getMaxCentralProtein()

getCurrentCentralProteinCount

public int getCurrentCentralProteinCount()

getCentralProteinAC

public java.lang.String getCentralProteinAC()

getCentralProtein

public Interactor getCentralProtein()

addCentralProtein

public void addCentralProtein(Node node)

getCentralProteins

public java.util.ArrayList getCentralProteins()

getCentralInteractors

public java.util.ArrayList getCentralInteractors()

getCriteria

public java.util.ArrayList getCriteria()

addCriteria

public void addCriteria(CriteriaBean aCriteria)

Add a new criteria to the interaction network

Parameters:

aCriteria - the criteria to add if it doesn't exist in the collection already

resetCriteria

public void resetCriteria()

remove all existing criteria from the interaction network

init

public void init()

Initialization of the interaction network Record the nodes in a list which allows to keep an order ...

addNode

public Node addNode(Interactor anInteractor)

add the initialization part to the super class method

Specified by:

addNode in interface GraphI

Overrides:

addNode in class Graph

Parameters:

anInteractor - the interactor to add in the graph

Returns:

the created Node

getOrderedNodes

public java.util.ArrayList getOrderedNodes()

return a list of nodes ordered

initNodes

public void initNodes()

Allow to put the default color and default visibility for each protein of the interaction network

initNodeDisplay

public void initNodeDisplay(NodeI aNode)

initialisation of one Node about its color, its visible attribute

Parameters:

aNode - the node to update

sizeNodes

public int sizeNodes()

Return the number of node

Returns:

the number of nodes

sizeEdges

public int sizeEdges()

Return the number of edge

Returns:

the number of edge

getImageDimension

public ImageDimension getImageDimension()

Return the object ImageDimension which correspond to the graph

Returns:

an object ImageDimension

exportTlp

public java.lang.String exportTlp()

Create a String giving informations for the Tulip treatment the informations are : - the number of nodes, - the whole of the edges and nodes associeted for each edge, - the label of each node.

Returns:

an object String

exportBioLayout

public java.lang.String exportBioLayout()

Create a String giving informations for the bioLayout EMBL software the informations are just pairwise of protein label.

Returns:

an object String

importDataToImage

public java.lang.String[] importDataToImage(java.lang.String dataTlp)
                                     throws java.rmi.RemoteException

Send a String to Tulip to calculate coordinates Enter the obtained coordinates in the graph.

Parameters:

dataTlp - The obtained String by the exportTlp() method

Returns:

an array of error message or null if no error occurs.

java.rmi.RemoteException

fusion

public void fusion(InteractionNetwork network)

Fusion a interaction network to the current one.
For each edge of the new network we check if it exists in the current one.
If the edge already exists : continue.
If not, we check if the two Nodes of the edge already exists in the current network :

if the node exists, update the edge with its reference
if not add it to the current network

finally we add the up-to-date edge to the current network

Parameters:

network - the interaction network we want to fusioned to the current one.