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

Modifier and Type	Method and Description
ArrayList<String>	genNamesToId(List<String> pieces) Searches all the id's for the given gene names
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)
Map<String,String>	getAssociatedGenesToVariants(List<String> genes)
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)
String	getDiseaseIdWildCardGDA(String diseaseName, GuiParameters params)
String	getDiseaseIdWildCardVDA(String diseaseName, GuiParameters params)
ArrayList<String>	getDiseaseList(GuiParameters curParams)
ArrayList<String>	getDiseaseListVariant(GuiParameters curParams)
HashMap<String,ArrayList<String>>	getDiseaseProjectionBySrc(GuiParameters curParams)
Map<String,List<String>>	getDiseasesAssociatedToGenes(GuiParameters params)
HashMap<String,String>	getEdgeAttributes(String assocId, GuiParameters params)
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)
String	getGeneIdWildCardVda(String geneName, GuiParameters params)
ArrayList<String>	getGeneList(GuiParameters curParams)
ArrayList<String>	getGeneListVariant(GuiParameters curParams)
HashMap<String,ArrayList<String>>	getGeneProjectionBySrc(GuiParameters curParams)
static DatabaseImpl	getInstance()
DatabaseManager	getManager()
List<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)
String	multipleSearchParams(Set<String> pieces) Concatenates an array string into a multiple sql format string.
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 List<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

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)
                              throws SQLException

Specified by:

getGeneList in interface Database

Throws:

SQLException

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

getGeneListVariant

public ArrayList<String> getGeneListVariant(GuiParameters curParams)

Specified by:

getGeneListVariant in interface Database

getGeneIdWildCardGda

public String getGeneIdWildCardGda(String geneName,
                                   GuiParameters params)

Specified by:

getGeneIdWildCardGda in interface Database

getGeneIdWildCardVda

public String getGeneIdWildCardVda(String geneName,
                                   GuiParameters params)

getGeneId

public String getGeneId(String geneName)

Specified by:

getGeneId in interface Database

getGeneIdList

public ArrayList<String> getGeneIdList(GuiParameters params)

Specified by:

getGeneIdList in interface Database

getDiseaseIdWildCardGDA

public String getDiseaseIdWildCardGDA(String diseaseName,
                                      GuiParameters params)

Specified by:

getDiseaseIdWildCardGDA in interface Database

getDiseaseIdWildCardVDA

public String getDiseaseIdWildCardVDA(String diseaseName,
                                      GuiParameters params)

getDiseaseId

public String getDiseaseId(String diseaseName)

getVariantIdWildCard

public String getVariantIdWildCard(String variantId,
                                   GuiParameters params)

getDiseaseAttributes

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

Specified by:

getDiseaseAttributes in interface Database

Throws:

DisGeNetException

getGeneAttributes

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

Specified by:

getGeneAttributes in interface Database

Throws:

DisGeNetException

getVariantAttributes

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

getGeneDiseaseNetworkBySrc

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

Specified by:

getGeneDiseaseNetworkBySrc in interface Database

Throws:

DisGeNetException

getAssociatedGenesToVariants

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

Specified by:

getAssociatedGenesToVariants in interface Database

Throws:

SQLException

getVariantDiseaseNetworkBySrc

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

Specified by:

getVariantDiseaseNetworkBySrc in interface Database

Throws:

DisGeNetException

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

getDiseasesAssociatedToGenes

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

Specified by:

getDiseasesAssociatedToGenes in interface Database

Throws:

DisGeNetException

runQuery

public ResultSet runQuery(String query)

Specified by:

runQuery in interface Database

multipleSearchParams

public String multipleSearchParams(Set<String> pieces)

Concatenates an array string into a multiple sql format string.

Parameters:

pieces - the search fields

Returns:

String containing the next format '(item1,item2...)' or '()' in case the arrayList is empty

genNamesToId

public ArrayList<String> genNamesToId(List<String> pieces)

Searches all the id's for the given gene names

Parameters:

pieces - List containing all the gene names as strings.

Returns:

all the found ids for the given names.

getGeneDiseaseList

public ArrayList<String> getGeneDiseaseList(GuiParameters curParams)

Specified by:

getGeneDiseaseList in interface Database