es.imim.DisGeNET.network

Class NetworkBuilder

java.lang.Object

es.imim.DisGeNET.network.NetworkBuilder

public class NetworkBuilder
extends Object

Main class for - creating the networks - creating networks with edge attributes - creating additional attributes - handle the progress listeners - retrieve all node names from current net for search - marking nodes from search

Author:

michael

Constructor Summary

Constructors

Constructor and Description
NetworkBuilder()
NetworkBuilder(GuiParameters params)

Method Summary

Modifier and Type	Method and Description
void	addNetCreationListener(NetCreationListener l)
void	buildDiseaseNet(GuiParameters curParams) Generic function to create disease network
void	buildGeneDiseaseNet(GuiParameters curParams) Get the gene/disease net information from the database and call generic function to build net
void	buildGeneNet(GuiParameters curParams) Generic function to create gene network
void	buildNet(List<String> list1, List<String> list2, List<String> nrCommonEntities, String src, GuiParameters params) Builds a new disease-disease or gene-gene network.
void	buildNetWithEdgeAttributes(ArrayList<String> intList, ArrayList<String> disList, ArrayList<String> genList, ArrayList<String> assocList, ArrayList<String> assocTypeList, ArrayList<String> srcList, ArrayList<String> sentenceList, ArrayList<String> pmidsList, ArrayList<String> scoreList, ArrayList<String> eiList, ArrayList<String> elList, GuiParameters params)
void	buildVariantDiseaseNet(GuiParameters curParams) Get the variant/disease net information from the database and call generic function to build net
void	createCyEdgeAttributeColumns(org.cytoscape.model.CyNetwork cyNetwork)
org.cytoscape.model.CyNetwork	createCyNetwork(String name)
void	createNodeAttributeColumns(org.cytoscape.model.CyNetwork cyNetwork)
Map<String,Long>	expandGeneDiseaseNet(GuiParameters curParams, Map<String,Long> nodeMap) Expands the selected gene disease network using the selected nodes as reference.
Map<String,Long>	expandVariantDiseaseNet(GuiParameters curParams, Map<String,Long> nodeMap) Expands the selected variant disease network using the selected nodes as reference.
Database	getDB()
ArrayList<String>	getNodeNamesFromNet() Function to retrieve all node names from currently selected network to be able to search for them.
void	initAdditionalStyleAttributes(GuiParameters<?,?> params) Fills the attribute columns for the different type of networks.
void	removeGenesFromVariantNet() Removes the gene nodes from the variant disease network and updates the view.
void	removeMoodListener(NetCreationListener l)
void	showVariantNetWithGenes() Calls the method to expand a variant disease network and updates the view.

Methods inherited from class java.lang.Object

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

Constructor Detail

NetworkBuilder

public NetworkBuilder()

NetworkBuilder

public NetworkBuilder(GuiParameters params)

Method Detail

getDB

public Database getDB()

createCyNetwork

public org.cytoscape.model.CyNetwork createCyNetwork(String name)

createNodeAttributeColumns

public void createNodeAttributeColumns(org.cytoscape.model.CyNetwork cyNetwork)

createCyEdgeAttributeColumns

public void createCyEdgeAttributeColumns(org.cytoscape.model.CyNetwork cyNetwork)

expandGeneDiseaseNet

public Map<String,Long> expandGeneDiseaseNet(GuiParameters curParams,
                                             Map<String,Long> nodeMap)
                                      throws SQLException,
                                             DisGeNetException

Expands the selected gene disease network using the selected nodes as reference.

Parameters:

curParams - the parameters of the current network.

nodeMap - the nodes that exist in the current network.

Returns:

map containing the existing nodes plus the added ones, with the name as key and the suid as value.

Throws:

DisGeNetException - low level exception with the message for the user.

SQLException - in case of database access error.

expandVariantDiseaseNet

public Map<String,Long> expandVariantDiseaseNet(GuiParameters curParams,
                                                Map<String,Long> nodeMap)
                                         throws SQLException,
                                                DisGeNetException

Expands the selected variant disease network using the selected nodes as reference.

Parameters:

curParams - the parameters of the current network.

nodeMap - the nodes that exist in the current network.

Returns:

map containing the existing nodes plus the added ones, with the name as key and the suid as value.

Throws:

DisGeNetException - low level exception with the error message for the user.

SQLException - in case of database access error.

buildGeneDiseaseNet

public void buildGeneDiseaseNet(GuiParameters curParams)
                         throws DisGeNetException

Get the gene/disease net information from the database and call generic function to build net

Parameters:

curParams - the current parameters of the network.

Throws:

DisGeNetException - low level exception with the message error for the user.

buildVariantDiseaseNet

public void buildVariantDiseaseNet(GuiParameters curParams)
                            throws DisGeNetException,
                                   SQLException

Get the variant/disease net information from the database and call generic function to build net

Parameters:

curParams - the current parameters of the network.

Throws:

DisGeNetException - low level exception with the message error for the user.

SQLException - in case of database access error.

showVariantNetWithGenes

public void showVariantNetWithGenes()
                             throws DisGeNetException,
                                    SQLException

Calls the method to expand a variant disease network and updates the view.

Throws:

DisGeNetException - low level exception with the message error for the user.

SQLException - low level exception with the message error for the user.

removeGenesFromVariantNet

public void removeGenesFromVariantNet()

Removes the gene nodes from the variant disease network and updates the view.

buildDiseaseNet

public void buildDiseaseNet(GuiParameters curParams)
                     throws DisGeNetException

Generic function to create disease network

Parameters:

curParams - the current parameters of the network.

Throws:

DisGeNetException - low level exception with the message error for the user.

buildGeneNet

public void buildGeneNet(GuiParameters curParams)
                  throws DisGeNetException

Generic function to create gene network

Parameters:

curParams - the current parameters of the network.

Throws:

DisGeNetException - low level exception with the message error for the user.

getNodeNamesFromNet

public ArrayList<String> getNodeNamesFromNet()

Function to retrieve all node names from currently selected network to be able to search for them.

Returns:

an arrayList containing the node names.

buildNet

public void buildNet(List<String> list1,
                     List<String> list2,
                     List<String> nrCommonEntities,
                     String src,
                     GuiParameters params)
              throws DisGeNetException

Builds a new disease-disease or gene-gene network.

Parameters:

list1 - list of genes or diseases

list2 - duplication of the first list

src - selected source for the search

params - current params for the network

Throws:

DisGeNetException - low level exception with the error message.

buildNetWithEdgeAttributes

public void buildNetWithEdgeAttributes(ArrayList<String> intList,
                                       ArrayList<String> disList,
                                       ArrayList<String> genList,
                                       ArrayList<String> assocList,
                                       ArrayList<String> assocTypeList,
                                       ArrayList<String> srcList,
                                       ArrayList<String> sentenceList,
                                       ArrayList<String> pmidsList,
                                       ArrayList<String> scoreList,
                                       ArrayList<String> eiList,
                                       ArrayList<String> elList,
                                       GuiParameters params)
                                throws DisGeNetException

Throws:

DisGeNetException

initAdditionalStyleAttributes

public void initAdditionalStyleAttributes(GuiParameters<?,?> params)

Fills the attribute columns for the different type of networks.

Parameters:

params - the parameters given to the network.

addNetCreationListener

public void addNetCreationListener(NetCreationListener l)

removeMoodListener

public void removeMoodListener(NetCreationListener l)