es.imim.DisGeNET.database

Class DatabaseImpl

java.lang.Object

es.imim.DisGeNET.database.DatabaseImpl

All Implemented Interfaces:

Database, Serializable, Remote

public class DatabaseImpl
extends Object
implements Database

Class implements all queries to create networks

Author:

anna

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
DatabaseImpl()

Method Summary

Methods

Modifier and Type	Method and Description
ArrayList<String>	getAssociatedDiseases(String geneId, String src, GuiParameters params)
ArrayList<String>	getAssociatedDiseases(String geneId, String src, String assocType, GuiParameters params)
ArrayList<String>	getAssociatedGeneNames(String diseaseId, String src, String assocType, GuiParameters params)
HashMap<String,HashMap<String,String>>	getDiseaseAttributes(GuiParameters params)
HashMap<String,String>	getDiseaseClassForAllDiseases(GuiParameters params)
HashMap<String,String>	getDiseaseClassForAllGenes(String source, GuiParameters params)
String	getDiseaseClassId(String diseaseClassName, GuiParameters params)
String	getDiseaseId(String diseaseName, GuiParameters params)
String	getDiseaseIdWildCard(String diseaseName, GuiParameters params)
ArrayList<String>	getDiseaseList(GuiParameters curParams)
ArrayList<String>	getDiseaseListVariant(GuiParameters curParams)
HashMap<String,ArrayList<String>>	getDiseaseProjectionBySrc(GuiParameters curParams)
HashMap<String,String>	getEdgeAttributes(String assocId, GuiParameters params)
HashMap<String,ArrayList<String>>	getExpandedGeneDiseaseNetwork(GuiParameters curParams, ArrayList<String> ids)
HashMap<String,HashMap<String,String>>	getGeneAttributes(GuiParameters curParams)
HashMap<String,String>	getGeneAttributes(String geneId, GuiParameters params)
ArrayList<String>	getGeneDiseaseList(GuiParameters curParams)
HashMap<String,ArrayList<String>>	getGeneDiseaseNetworkBySrc(GuiParameters curParams)
String	getGeneId(String geneName, GuiParameters params)
ArrayList<String>	getGeneIdList(GuiParameters params)
String	getGeneIdWildCard(String geneName, GuiParameters params)
ArrayList<String>	getGeneList(GuiParameters curParams)
HashMap<String,ArrayList<String>>	getGeneProjectionBySrc(GuiParameters curParams)
static DatabaseImpl	getInstance()
DatabaseManager	getManager()
ArrayList<String>	getVariantAssociatedDiseases(String variantId, String src, String assocType, GuiParameters params)
HashMap<String,HashMap<String,String>>	getVariantAttributes(GuiParameters curParams)
HashMap<String,ArrayList<String>>	getVariantDiseaseNetworkBySrc(GuiParameters curParams)
String	getVariantIdWildCard(String variantId, GuiParameters params)
ArrayList<String>	getVariantList(GuiParameters curParams)
ResultSet	runQuery(String query)

Methods inherited from class java.lang.Object

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

Constructor Detail

DatabaseImpl

public DatabaseImpl()

Method Detail

getManager

public DatabaseManager getManager()

getInstance

public static DatabaseImpl getInstance()

getAssociatedDiseases

public ArrayList<String> getAssociatedDiseases(String geneId,
                                      String src,
                                      GuiParameters params)

Specified by:

getAssociatedDiseases in interface Database

getAssociatedDiseases

public ArrayList<String> getAssociatedDiseases(String geneId,
                                      String src,
                                      String assocType,
                                      GuiParameters params)

Specified by:

getAssociatedDiseases in interface Database

getVariantAssociatedDiseases

public ArrayList<String> getVariantAssociatedDiseases(String variantId,
                                             String src,
                                             String assocType,
                                             GuiParameters params)

getAssociatedGeneNames

public ArrayList<String> getAssociatedGeneNames(String diseaseId,
                                       String src,
                                       String assocType,
                                       GuiParameters params)

Specified by:

getAssociatedGeneNames in interface Database

getDiseaseAttributes

public HashMap<String,HashMap<String,String>> getDiseaseAttributes(GuiParameters params)

Specified by:

getDiseaseAttributes in interface Database

getDiseaseClassForAllDiseases

public HashMap<String,String> getDiseaseClassForAllDiseases(GuiParameters params)

Specified by:

getDiseaseClassForAllDiseases in interface Database

getDiseaseClassForAllGenes

public HashMap<String,String> getDiseaseClassForAllGenes(String source,
                                                GuiParameters params)

Specified by:

getDiseaseClassForAllGenes in interface Database

getDiseaseClassId

public String getDiseaseClassId(String diseaseClassName,
                       GuiParameters params)

Specified by:

getDiseaseClassId in interface Database

getGeneList

public ArrayList<String> getGeneList(GuiParameters curParams)

Specified by:

getGeneList in interface Database

getGeneDiseaseList

public ArrayList<String> getGeneDiseaseList(GuiParameters curParams)

Specified by:

getGeneDiseaseList in interface Database

getDiseaseList

public ArrayList<String> getDiseaseList(GuiParameters curParams)

Specified by:

getDiseaseList in interface Database

getVariantList

public ArrayList<String> getVariantList(GuiParameters curParams)

Specified by:

getVariantList in interface Database

getDiseaseListVariant

public ArrayList<String> getDiseaseListVariant(GuiParameters curParams)

Specified by:

getDiseaseListVariant in interface Database

getGeneIdWildCard

public String getGeneIdWildCard(String geneName,
                       GuiParameters params)

Specified by:

getGeneIdWildCard in interface Database

getGeneId

public String getGeneId(String geneName,
               GuiParameters params)

Specified by:

getGeneId in interface Database

getGeneIdList

public ArrayList<String> getGeneIdList(GuiParameters params)

Specified by:

getGeneIdList in interface Database

getDiseaseIdWildCard

public String getDiseaseIdWildCard(String diseaseName,
                          GuiParameters params)

Specified by:

getDiseaseIdWildCard in interface Database

getDiseaseId

public String getDiseaseId(String diseaseName,
                  GuiParameters params)

Specified by:

getDiseaseId in interface Database

getVariantIdWildCard

public String getVariantIdWildCard(String variantId,
                          GuiParameters params)

getGeneAttributes

public HashMap<String,HashMap<String,String>> getGeneAttributes(GuiParameters curParams)

Specified by:

getGeneAttributes in interface Database

getGeneAttributes

public HashMap<String,String> getGeneAttributes(String geneId,
                                       GuiParameters params)

Specified by:

getGeneAttributes in interface Database

getVariantAttributes

public HashMap<String,HashMap<String,String>> getVariantAttributes(GuiParameters curParams)

getGeneDiseaseNetworkBySrc

public HashMap<String,ArrayList<String>> getGeneDiseaseNetworkBySrc(GuiParameters curParams)

Specified by:

getGeneDiseaseNetworkBySrc in interface Database

getVariantDiseaseNetworkBySrc

public HashMap<String,ArrayList<String>> getVariantDiseaseNetworkBySrc(GuiParameters curParams)

Specified by:

getVariantDiseaseNetworkBySrc in interface Database

getGeneProjectionBySrc

public HashMap<String,ArrayList<String>> getGeneProjectionBySrc(GuiParameters curParams)

Specified by:

getGeneProjectionBySrc in interface Database

getDiseaseProjectionBySrc

public HashMap<String,ArrayList<String>> getDiseaseProjectionBySrc(GuiParameters curParams)

Specified by:

getDiseaseProjectionBySrc in interface Database

getEdgeAttributes

public HashMap<String,String> getEdgeAttributes(String assocId,
                                       GuiParameters params)

Specified by:

getEdgeAttributes in interface Database

runQuery

public ResultSet runQuery(String query)

Specified by:

runQuery in interface Database

getExpandedGeneDiseaseNetwork

public HashMap<String,ArrayList<String>> getExpandedGeneDiseaseNetwork(GuiParameters curParams,
                                                              ArrayList<String> ids)

Specified by:

getExpandedGeneDiseaseNetwork in interface Database