Package es.imim.DISGENET.network
Class NetworkBuilder
java.lang.Object
es.imim.DISGENET.network.NetworkBuilder
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptionvoid
void
buildDiseaseNet(GuiParameters curParams)
Generic function to create disease networkvoid
buildGeneDiseaseNet(GuiParameters curParams)
Get the gene/disease net information from the database and call generic function to build netvoid
buildGeneNet(GuiParameters curParams)
Generic function to create gene networkvoid
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> scoreList, ArrayList<String> eiList, ArrayList<String> yearList, ArrayList<String> yearFinalList, GuiParameters params)
void
buildVariantDiseaseNet(GuiParameters curParams)
Get the variant/disease net information from the database and call generic function to build netvoid
createCyEdgeAttributeColumns(org.cytoscape.model.CyNetwork cyNetwork)
org.cytoscape.model.CyNetwork
createCyNetwork(String name)
void
createNodeAttributeColumns(org.cytoscape.model.CyNetwork cyNetwork)
expandGeneDiseaseNet(GuiParameters curParams, Map<String,Long> nodeMap)
Expands the selected gene disease network using the selected nodes as reference.expandVariantDiseaseNet(GuiParameters curParams, Map<String,Long> nodeMap)
Expands the selected variant disease network using the selected nodes as reference.getDB()
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
Removes the gene nodes from the variant disease network and updates the view.void
void
Calls the method to expand a variant disease network and updates the view.
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Constructor Details
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NetworkBuilder
public NetworkBuilder() -
NetworkBuilder
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Method Details
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getDB
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createCyNetwork
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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, DisGeNetExceptionExpands 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.
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expandVariantDiseaseNet
public Map<String,Long> expandVariantDiseaseNet(GuiParameters curParams, Map<String,Long> nodeMap) throws SQLException, DisGeNetExceptionExpands 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.
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buildGeneDiseaseNet
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.
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buildVariantDiseaseNet
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.
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showVariantNetWithGenes
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.
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removeGenesFromVariantNet
public void removeGenesFromVariantNet()Removes the gene nodes from the variant disease network and updates the view. -
buildDiseaseNet
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.
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buildGeneNet
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.
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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.
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buildNet
public void buildNet(List<String> list1, List<String> list2, List<String> nrCommonEntities, String src, GuiParameters params) throws DisGeNetExceptionBuilds a new disease-disease or gene-gene network.- Parameters:
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 network- Throws:
DisGeNetException
- low level exception with the error message.
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buildNetWithEdgeAttributes
public void buildNetWithEdgeAttributes(ArrayList<String> intList, ArrayList<String> disList, ArrayList<String> genList, ArrayList<String> scoreList, ArrayList<String> eiList, ArrayList<String> yearList, ArrayList<String> yearFinalList, GuiParameters params) throws DisGeNetException- Throws:
DisGeNetException
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initAdditionalStyleAttributes
Fills the attribute columns for the different type of networks.- Parameters:
params
- the parameters given to the network.
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addNetCreationListener
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removeMoodListener
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