cyTransFinder

Class Network

java.lang.Object

cyTransFinder.Network

public class Network
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
protected CyActivator	CY_ACTIVATOR
protected Document	document
protected org.cytoscape.model.CyNetwork	myNet
protected String	Organism
protected String	SERVICETYPE

Constructor Summary

Constructors

Constructor and Description
Network(org.cytoscape.model.CyNetwork network, CyActivator activator)

Method Summary

Modifier and Type	Method and Description
protected void	addEdge(org.cytoscape.model.CyNode nodeFrom, org.cytoscape.model.CyNode nodeTo, String Type, String Activation, String CODE) Used for enhancing with protein, since in this case we use CyNode instead od String NodeID.
protected void	addEdgePrepare(String nodeFromDB, String nodeToDB, String TYPE, String ACTIVATION, String DBID, String CODE)
protected org.cytoscape.model.CyNode	addGene(String GENESYMBOL, String GENEID, String TYPE)
protected org.cytoscape.model.CyNode	addGeneID(String GENEID, String TYPE)
protected org.cytoscape.model.CyNode	addIntronicMirna(String MIRNAID, String CHROMOSOME, String BASE_START, String BASE_STOP, String mirnaType)
protected org.cytoscape.model.CyNode	addNode(String KEGGID, String REACTOMEID, String GENESYMBOL, String X, String Y, String SHAPE, String ALIAS, String TYPE, String COMPONENT, String PATHWAYCODE, String GENEID)
protected org.cytoscape.model.CyNode	addNodeProtein(String PROTEINID, String PROTEINSYMBOL, String PROTEINACCESSION, String PROTEINISOFORMS)
protected org.cytoscape.model.CyNode	addSourceMirna(String MIRNAID)
protected String	getGeneId(String colname, Object value)
protected String	getGeneSymbol(String colname, Object value)
protected Set<org.cytoscape.model.CyNode>	getNodesWithTwoValue(String COLNAME1, Object VALUE1, String COLNAME2, Object VALUE2)
protected Set<org.cytoscape.model.CyNode>	getNodesWithValue(String colname, Object value)
protected org.cytoscape.model.CyNode	getNodeWithID(String colname, Object value)
void	loadNetwork(File FILE, String EXTENSION, String FILE_MEANING, MyCytoPanel myCytoPanel)
protected void	mergeDuplicatesNodes(String FIELD, String CONTENT, String MATCHING_FIELD)
protected void	prepareTables()
protected void	removeDuppedEdges()
protected void	removeTypeNodes(String FIELD, String CONTENT)
protected void	setNetworkProperties(String viewname)

Methods inherited from class java.lang.Object

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

Field Detail

document

protected Document document

myNet

protected org.cytoscape.model.CyNetwork myNet

Organism

protected String Organism

CY_ACTIVATOR

protected CyActivator CY_ACTIVATOR

SERVICETYPE

protected String SERVICETYPE

Constructor Detail

Network

public Network(org.cytoscape.model.CyNetwork network,
               CyActivator activator)

Method Detail

prepareTables

protected void prepareTables()

loadNetwork

public void loadNetwork(File FILE,
                        String EXTENSION,
                        String FILE_MEANING,
                        MyCytoPanel myCytoPanel)
                 throws IOException,
                        XPathExpressionException

Throws:

IOException

XPathExpressionException

addNode

protected org.cytoscape.model.CyNode addNode(String KEGGID,
                                             String REACTOMEID,
                                             String GENESYMBOL,
                                             String X,
                                             String Y,
                                             String SHAPE,
                                             String ALIAS,
                                             String TYPE,
                                             String COMPONENT,
                                             String PATHWAYCODE,
                                             String GENEID)
                                      throws IOException

Throws:

IOException

addGene

protected org.cytoscape.model.CyNode addGene(String GENESYMBOL,
                                             String GENEID,
                                             String TYPE)
                                      throws IOException

Throws:

IOException

addGeneID

protected org.cytoscape.model.CyNode addGeneID(String GENEID,
                                               String TYPE)
                                        throws IOException

Throws:

IOException

addEdgePrepare

protected void addEdgePrepare(String nodeFromDB,
                              String nodeToDB,
                              String TYPE,
                              String ACTIVATION,
                              String DBID,
                              String CODE)

addNodeProtein

protected org.cytoscape.model.CyNode addNodeProtein(String PROTEINID,
                                                    String PROTEINSYMBOL,
                                                    String PROTEINACCESSION,
                                                    String PROTEINISOFORMS)

addIntronicMirna

protected org.cytoscape.model.CyNode addIntronicMirna(String MIRNAID,
                                                      String CHROMOSOME,
                                                      String BASE_START,
                                                      String BASE_STOP,
                                                      String mirnaType)

addSourceMirna

protected org.cytoscape.model.CyNode addSourceMirna(String MIRNAID)

addEdge

protected void addEdge(org.cytoscape.model.CyNode nodeFrom,
                       org.cytoscape.model.CyNode nodeTo,
                       String Type,
                       String Activation,
                       String CODE)

Used for enhancing with protein, since in this case we use CyNode instead od String NodeID. TODO: transform the previous function "addEdge" according to this one

Parameters:

nodeFrom -

nodeTo -

Type -

Activation -

getNodesWithTwoValue

protected Set<org.cytoscape.model.CyNode> getNodesWithTwoValue(String COLNAME1,
                                                               Object VALUE1,
                                                               String COLNAME2,
                                                               Object VALUE2)

getNodesWithValue

protected Set<org.cytoscape.model.CyNode> getNodesWithValue(String colname,
                                                            Object value)

removeTypeNodes

protected void removeTypeNodes(String FIELD,
                               String CONTENT)

mergeDuplicatesNodes

protected void mergeDuplicatesNodes(String FIELD,
                                    String CONTENT,
                                    String MATCHING_FIELD)

getNodeWithID

protected org.cytoscape.model.CyNode getNodeWithID(String colname,
                                                   Object value)

setNetworkProperties

protected void setNetworkProperties(String viewname)

getGeneSymbol

protected String getGeneSymbol(String colname,
                               Object value)

getGeneId

protected String getGeneId(String colname,
                           Object value)

removeDuppedEdges

protected void removeDuppedEdges()