Package 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

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
DatabaseImpl()

Method Summary

Modifier and Type	Method	Description
ArrayList<String>	genNamesToId(List<String> pieces)	Converts a list of gene symbols to their corresponding gene IDs.
Map<String,String>	getAssociatedGenesToVariants(List<String> genes)	Returns a map with the gene ID for each gene symbol of the provided list
HashMap<String,HashMap<String,String>>	getDiseaseAttributes(GuiParameters curParams)
ArrayList<String>	getDiseaseList(GuiParameters curParams)	Case in gene-dis panel
ArrayList<String>	getDiseaseListVariant(GuiParameters curParams)	Case in var-dis panel
ArrayList<String>	getDiseaseNames(String diseaseName)
HashMap<String,ArrayList<String>>	getDiseaseProjectionBySrc(GuiParameters curParams)
ArrayList<String>	getDiseasesAssociatedToGenes(GuiParameters curParams)
HashMap<String,HashMap<String,String>>	getGeneAttributes(GuiParameters curParams)
HashMap<String,ArrayList<String>>	getGeneDiseaseNetworkBySrc(GuiParameters curParams)
String	getGeneId(String geneName)	Converts a symbol of gene to their corresponding gene ID.
ArrayList<String>	getGeneIdList(GuiParameters curParams)	Case in gen-dis panel
ArrayList<String>	getGeneList(GuiParameters curParams)	Case in gene-dis panel
ArrayList<String>	getGeneListVariant(GuiParameters curParams)	Case in var-dis panel
ArrayList<String>	getGeneNames(String geneName)
HashMap<String,ArrayList<String>>	getGeneProjectionBySrc(GuiParameters curParams)
static DatabaseImpl	getInstance()
HashMap<String,HashMap<String,String>>	getVariantAttributes(GuiParameters curParams)
HashMap<String,ArrayList<String>>	getVariantDiseaseNetworkBySrc(GuiParameters curParams)
ArrayList<String>	getVariantList(GuiParameters curParams)	Case in var-dis panel
ArrayList<String>	getVariantNames(String variantName)
static void	main(String[] args)

Methods inherited from class java.lang.Object

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

Constructor Details

DatabaseImpl

public DatabaseImpl()

Method Details

getInstance

public static DatabaseImpl getInstance()

getVariantNames

public ArrayList<String> getVariantNames(String variantName)

getDiseaseNames

public ArrayList<String> getDiseaseNames(String diseaseName)

getGeneNames

public ArrayList<String> getGeneNames(String geneName)

getGeneId

public String getGeneId(String geneName)

Converts a symbol of gene to their corresponding gene ID.

Specified by:

getGeneId in interface Database

Parameters:

geneName - symbol of the gene

Returns:

the gene ID corresponding to the input gene symbol name.

genNamesToId

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

Converts a list of gene symbols to their corresponding gene IDs.

Parameters:

pieces - A list of symbols of gene

Returns:

A list of gene IDs for the input gene symbols

getAssociatedGenesToVariants

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

Returns a map with the gene ID for each gene symbol of the provided list

Specified by:

getAssociatedGenesToVariants in interface Database

Parameters:

genes - List of gene symbols

Returns:

a map with the gene ID for each gene symbol of the provided list

getDiseasesAssociatedToGenes

public ArrayList<String> getDiseasesAssociatedToGenes(GuiParameters curParams)

Specified by:

getDiseasesAssociatedToGenes in interface Database

getGeneIdList

public ArrayList<String> getGeneIdList(GuiParameters curParams)

Case in gen-dis panel

Specified by:

getGeneIdList in interface Database

Parameters:

curParams - GuiParamaeters

Returns:

the gene ids related to provided params.

getGeneList

public ArrayList<String> getGeneList(GuiParameters curParams)

Case in gene-dis panel

Specified by:

getGeneList in interface Database

Parameters:

curParams - GuiParamaeters

Returns:

the gene symbols related to provided params.

getVariantList

public ArrayList<String> getVariantList(GuiParameters curParams)

Case in var-dis panel

Specified by:

getVariantList in interface Database

Parameters:

curParams - GuiParamaeters

Returns:

the variant ids related to provided params.

getDiseaseList

public ArrayList<String> getDiseaseList(GuiParameters curParams)

Case in gene-dis panel

Specified by:

getDiseaseList in interface Database

Parameters:

curParams - GuiParamaeters

Returns:

the disease ids related to provided params.

getDiseaseListVariant

public ArrayList<String> getDiseaseListVariant(GuiParameters curParams)

Case in var-dis panel

Specified by:

getDiseaseListVariant in interface Database

Parameters:

curParams - GuiParamaeters

Returns:

the disease ids related to provided params.

getGeneListVariant

public ArrayList<String> getGeneListVariant(GuiParameters curParams)

Case in var-dis panel

Specified by:

getGeneListVariant in interface Database

Parameters:

curParams - GuiParameters

Returns:

the gene ids related to provided params.

getGeneAttributes

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

Specified by:

getGeneAttributes in interface Database

getDiseaseAttributes

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

Specified by:

getDiseaseAttributes in interface Database

getVariantAttributes

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

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

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

main

public static void main(String[] args)
                 throws DisGeNetException

Throws:

DisGeNetException