DatabaseImpl (DISGENET-app)

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 and Description

DatabaseImpl()

Constructors
Constructor and Description
`DatabaseImpl()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`ArrayList<String>`	`genNamesToId(List<String> pieces)` Converts a list of gene symbols to their corresponding gene IDs.
`ArrayList<String>`	`genWildCard(String geneName)` Retrieves all the gene IDs associated to one or more given gene string name/s
`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 Detail
  - DatabaseImpl
```
public DatabaseImpl()
```
- Method Detail
  - getInstance
```
public static DatabaseImpl getInstance()
```
  - genWildCard
```
public ArrayList<String> genWildCard(String geneName)
```
    Retrieves all the gene IDs associated to one or more given gene string name/s
    
    Parameters:
    
    geneName - The gene name from a free-text-search-string
    
    Returns:
    
    A list of first 100 NCBI gene IDs
  - 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

Class DatabaseImpl

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

DatabaseImpl

Method Detail

getInstance

genWildCard

getVariantNames

getDiseaseNames

getGeneNames

getGeneId

genNamesToId

getAssociatedGenesToVariants

getDiseasesAssociatedToGenes

getGeneIdList

getGeneList

getVariantList

getDiseaseList

getDiseaseListVariant

getGeneListVariant

getGeneAttributes

getDiseaseAttributes

getVariantAttributes

getGeneProjectionBySrc

getDiseaseProjectionBySrc

getGeneDiseaseNetworkBySrc

getVariantDiseaseNetworkBySrc

main