es.imim.DisGeNET.database

Interface Database

All Superinterfaces:

Remote, Serializable

All Known Implementing Classes:

DatabaseImpl

public interface Database
extends Remote, Serializable

Author:

mrautschka

Method Summary

Modifier and Type	Method and Description
ArrayList<String>	getAssociatedDiseases(String geneId, String src, GuiParameters curParams)
ArrayList<String>	getAssociatedDiseases(String geneId, String src, String assocType, GuiParameters curParams)
ArrayList<String>	getAssociatedGeneNames(String diseaseId, String source, String associationType, GuiParameters curParams)
Map<String,String>	getAssociatedGenesToVariants(List<String> genes)
HashMap<String,HashMap<String,String>>	getDiseaseAttributes(GuiParameters curParams)
HashMap<String,String>	getDiseaseClassForAllDiseases(GuiParameters curParams)
HashMap<String,String>	getDiseaseClassForAllGenes(String source, GuiParameters curParams)
String	getDiseaseClassId(String diseaseClassName, GuiParameters curParams)
String	getDiseaseIdWildCardGDA(String diseaseName, GuiParameters curParams)
ArrayList<String>	getDiseaseList(GuiParameters curParams)
ArrayList<String>	getDiseaseListVariant(GuiParameters params)
HashMap<String,ArrayList<String>>	getDiseaseProjectionBySrc(GuiParameters curParams)
Map<String,List<String>>	getDiseasesAssociatedToGenes(GuiParameters params)
HashMap<String,String>	getEdgeAttributes(String assocId, GuiParameters curParams)
HashMap<String,HashMap<String,String>>	getGeneAttributes(GuiParameters curParams)
ArrayList<String>	getGeneDiseaseList(GuiParameters curParams)
HashMap<String,ArrayList<String>>	getGeneDiseaseNetworkBySrc(GuiParameters curParams)
String	getGeneId(String geneName)
ArrayList<String>	getGeneIdList(GuiParameters params)
String	getGeneIdWildCardGda(String geneName, GuiParameters params)
ArrayList<String>	getGeneList(GuiParameters curParams)
ArrayList<String>	getGeneListVariant(GuiParameters params)
HashMap<String,ArrayList<String>>	getGeneProjectionBySrc(GuiParameters curParams)
HashMap<String,ArrayList<String>>	getVariantDiseaseNetworkBySrc(GuiParameters curParams)
ArrayList<String>	getVariantList(GuiParameters curParams)
ResultSet	runQuery(String query)

Method Detail

getAssociatedDiseases

ArrayList<String> getAssociatedDiseases(String geneId,
                                        String src,
                                        GuiParameters curParams)

getAssociatedDiseases

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

getGeneId

String getGeneId(String geneName)

getGeneIdWildCardGda

String getGeneIdWildCardGda(String geneName,
                            GuiParameters params)

getGeneAttributes

HashMap<String,HashMap<String,String>> getGeneAttributes(GuiParameters curParams)
                                                  throws DisGeNetException

Throws:

DisGeNetException

getEdgeAttributes

HashMap<String,String> getEdgeAttributes(String assocId,
                                         GuiParameters curParams)

getGeneProjectionBySrc

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

getGeneList

ArrayList<String> getGeneList(GuiParameters curParams)
                       throws SQLException

Throws:

SQLException

getVariantList

ArrayList<String> getVariantList(GuiParameters curParams)

getDiseaseAttributes

HashMap<String,HashMap<String,String>> getDiseaseAttributes(GuiParameters curParams)
                                                     throws DisGeNetException

Throws:

DisGeNetException

getDiseaseClassForAllDiseases

HashMap<String,String> getDiseaseClassForAllDiseases(GuiParameters curParams)

getDiseaseClassForAllGenes

HashMap<String,String> getDiseaseClassForAllGenes(String source,
                                                  GuiParameters curParams)

getDiseaseClassId

String getDiseaseClassId(String diseaseClassName,
                         GuiParameters curParams)

getDiseaseIdWildCardGDA

String getDiseaseIdWildCardGDA(String diseaseName,
                               GuiParameters curParams)

getDiseaseProjectionBySrc

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

getAssociatedGeneNames

ArrayList<String> getAssociatedGeneNames(String diseaseId,
                                         String source,
                                         String associationType,
                                         GuiParameters curParams)

getDiseaseList

ArrayList<String> getDiseaseList(GuiParameters curParams)

getGeneDiseaseList

ArrayList<String> getGeneDiseaseList(GuiParameters curParams)

getGeneDiseaseNetworkBySrc

HashMap<String,ArrayList<String>> getGeneDiseaseNetworkBySrc(GuiParameters curParams)
                                                      throws DisGeNetException

Throws:

DisGeNetException

runQuery

ResultSet runQuery(String query)

getGeneIdList

ArrayList<String> getGeneIdList(GuiParameters params)

getDiseaseListVariant

ArrayList<String> getDiseaseListVariant(GuiParameters params)

getGeneListVariant

ArrayList<String> getGeneListVariant(GuiParameters params)

getVariantDiseaseNetworkBySrc

HashMap<String,ArrayList<String>> getVariantDiseaseNetworkBySrc(GuiParameters curParams)
                                                         throws DisGeNetException

Throws:

DisGeNetException

getAssociatedGenesToVariants

Map<String,String> getAssociatedGenesToVariants(List<String> genes)
                                         throws SQLException

Throws:

SQLException

getDiseasesAssociatedToGenes

Map<String,List<String>> getDiseasesAssociatedToGenes(GuiParameters params)
                                               throws DisGeNetException

Throws:

DisGeNetException