public class NetworkBuilder extends Object
Constructor and Description |
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NetworkBuilder() |
NetworkBuilder(GuiParameters params) |
Modifier and Type | Method and Description |
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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,
ArrayList<String> yearList,
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.
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Map<String,Long> |
expandVariantDiseaseNet(GuiParameters curParams,
Map<String,Long> nodeMap)
Expands the selected variant disease network using the selected nodes as reference.
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Database |
getDB() |
ArrayList<String> |
getNodeNamesFromNet()
Function to retrieve all node names from currently selected network to be
able to search for them.
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void |
initAdditionalStyleAttributes(GuiParameters<?,?> params)
Fills the attribute columns for the different type of networks.
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void |
removeGenesFromVariantNet()
Removes the gene nodes from the variant disease network and updates the view.
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void |
removeMoodListener(NetCreationListener l) |
void |
showVariantNetWithGenes()
Calls the method to expand a variant disease network and updates the view.
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public NetworkBuilder()
public NetworkBuilder(GuiParameters params)
public Database getDB()
public org.cytoscape.model.CyNetwork createCyNetwork(String name)
public void createNodeAttributeColumns(org.cytoscape.model.CyNetwork cyNetwork)
public void createCyEdgeAttributeColumns(org.cytoscape.model.CyNetwork cyNetwork)
public Map<String,Long> expandGeneDiseaseNet(GuiParameters curParams, Map<String,Long> nodeMap) throws SQLException, DisGeNetException
curParams
- the parameters of the current network.nodeMap
- the nodes that exist in the current network.DisGeNetException
- low level exception with the message for the user.SQLException
- in case of database access error.public Map<String,Long> expandVariantDiseaseNet(GuiParameters curParams, Map<String,Long> nodeMap) throws SQLException, DisGeNetException
curParams
- the parameters of the current network.nodeMap
- the nodes that exist in the current network.DisGeNetException
- low level exception with the error message for the user.SQLException
- in case of database access error.public void buildGeneDiseaseNet(GuiParameters curParams) throws DisGeNetException
curParams
- the current parameters of the network.DisGeNetException
- low level exception with the message error for the user.public void buildVariantDiseaseNet(GuiParameters curParams) throws DisGeNetException, SQLException
curParams
- the current parameters of the network.DisGeNetException
- low level exception with the message error for the user.SQLException
- in case of database access error.public void showVariantNetWithGenes() throws DisGeNetException, SQLException
DisGeNetException
- low level exception with the message error for the user.SQLException
- low level exception with the message error for the user.public void removeGenesFromVariantNet()
public void buildDiseaseNet(GuiParameters curParams) throws DisGeNetException
curParams
- the current parameters of the network.DisGeNetException
- low level exception with the message error for the user.public void buildGeneNet(GuiParameters curParams) throws DisGeNetException
curParams
- the current parameters of the network.DisGeNetException
- low level exception with the message error for the user.public ArrayList<String> getNodeNamesFromNet()
public void buildNet(List<String> list1, List<String> list2, List<String> nrCommonEntities, String src, GuiParameters params) throws DisGeNetException
list1
- list of genes or diseaseslist2
- duplication of the first listsrc
- selected source for the searchnrCommonEntities
- number of entities in commonparams
- current params for the networkDisGeNetException
- low level exception with the error message.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, ArrayList<String> yearList, GuiParameters params) throws DisGeNetException
DisGeNetException
public void initAdditionalStyleAttributes(GuiParameters<?,?> params)
params
- the parameters given to the network.public void addNetCreationListener(NetCreationListener l)
public void removeMoodListener(NetCreationListener l)
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