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

Methods

Modifier and Type	Method and Description
void	addNetCreationListener(NetCreationListener l)
ArrayList<String>	buildDiseaseNet(GuiParameters curParams) Generic function to create disease network
ArrayList<String>	buildGeneDiseaseNet(GuiParameters curParams) Get the gene/disease net information from the database and call generic function to build net
ArrayList<String>	buildGeneNet(GuiParameters curParams) Generic function to create gene network
void	buildNet(ArrayList<String> list1, ArrayList<String> list2, String src, GuiParameters params)
void	buildNetWithEdgeAttributes(ArrayList<String> disList, ArrayList<String> genList, ArrayList<String> list3, ArrayList<String> assocTypeList, ArrayList<String> srcList, ArrayList<String> sentenceList, ArrayList<String> pmidsList, ArrayList<String> scoreList, GuiParameters params)
ArrayList<String>	buildVariantDiseaseNet(GuiParameters curParams) Get the variant/disease net information from the database and call generic function to build net
void	expandGeneDiseaseNet(GuiParameters curParams, ArrayList<String> ids, boolean expand, boolean foreignNet)
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)
void	markNodes(String field, String keyword)
void	removeMoodListener(NetCreationListener l)

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()

expandGeneDiseaseNet

public void expandGeneDiseaseNet(GuiParameters curParams,
                        ArrayList<String> ids,
                        boolean expand,
                        boolean foreignNet)
                          throws SQLException,
                                 ClassNotFoundException

Parameters:

ids -

expand -

foreignNet -

Throws:

ClassNotFoundException

SQLException

buildGeneDiseaseNet

public ArrayList<String> buildGeneDiseaseNet(GuiParameters curParams)
                                      throws DisGeNetException,
                                             ClassNotFoundException,
                                             SQLException

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

Parameters:

curParams -

Returns:

Throws:

SQLException

ClassNotFoundException

Exception

DisGeNetException

buildVariantDiseaseNet

public ArrayList<String> buildVariantDiseaseNet(GuiParameters curParams)
                                         throws DisGeNetException,
                                                ClassNotFoundException,
                                                SQLException

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

Parameters:

curParams -

Returns:

Throws:

DisGeNetException

ClassNotFoundException

SQLException

buildDiseaseNet

public ArrayList<String> buildDiseaseNet(GuiParameters curParams)
                                  throws Exception

Generic function to create disease network

Parameters:

curParams -

Returns:

Throws:

Exception

buildGeneNet

public ArrayList<String> buildGeneNet(GuiParameters curParams)
                               throws Exception

Generic function to create gene network

Parameters:

curParams -

Returns:

Throws:

Exception

getNodeNamesFromNet

public ArrayList<String> getNodeNamesFromNet()

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

Returns:

buildNet

public void buildNet(ArrayList<String> list1,
            ArrayList<String> list2,
            String src,
            GuiParameters params)
              throws SQLException,
                     ClassNotFoundException

Throws:

SQLException

ClassNotFoundException

buildNetWithEdgeAttributes

public void buildNetWithEdgeAttributes(ArrayList<String> disList,
                              ArrayList<String> genList,
                              ArrayList<String> list3,
                              ArrayList<String> assocTypeList,
                              ArrayList<String> srcList,
                              ArrayList<String> sentenceList,
                              ArrayList<String> pmidsList,
                              ArrayList<String> scoreList,
                              GuiParameters params)
                                throws SQLException,
                                       ClassNotFoundException

Throws:

SQLException

ClassNotFoundException

markNodes

public void markNodes(String field,
             String keyword)

initAdditionalStyleAttributes

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

addNetCreationListener

public void addNetCreationListener(NetCreationListener l)

removeMoodListener

public void removeMoodListener(NetCreationListener l)