public class DatabaseImpl extends Object implements Database
Constructor and Description |
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DatabaseImpl() |
public DatabaseManager getManager()
public static DatabaseImpl getInstance()
public ArrayList<String> getAssociatedDiseases(String geneId, String src, GuiParameters params)
getAssociatedDiseases
in interface Database
public ArrayList<String> getAssociatedDiseases(String geneId, String src, String assocType, GuiParameters params)
getAssociatedDiseases
in interface Database
public List<String> getVariantAssociatedDiseases(String variantId, String src, String assocType, GuiParameters params)
public ArrayList<String> getAssociatedGeneNames(String diseaseId, String src, String assocType, GuiParameters params)
getAssociatedGeneNames
in interface Database
public HashMap<String,String> getDiseaseClassForAllDiseases(GuiParameters params)
getDiseaseClassForAllDiseases
in interface Database
public HashMap<String,String> getDiseaseClassForAllGenes(String source, GuiParameters params)
getDiseaseClassForAllGenes
in interface Database
public String getDiseaseClassId(String diseaseClassName, GuiParameters params)
getDiseaseClassId
in interface Database
public ArrayList<String> getGeneList(GuiParameters curParams) throws SQLException
getGeneList
in interface Database
SQLException
public ArrayList<String> getDiseaseList(GuiParameters curParams)
getDiseaseList
in interface Database
public ArrayList<String> getVariantList(GuiParameters curParams)
getVariantList
in interface Database
public ArrayList<String> getDiseaseListVariant(GuiParameters curParams)
getDiseaseListVariant
in interface Database
public ArrayList<String> getGeneListVariant(GuiParameters curParams)
getGeneListVariant
in interface Database
public String getGeneIdWildCardGda(String geneName, GuiParameters params)
getGeneIdWildCardGda
in interface Database
public String getGeneIdWildCardVda(String geneName, GuiParameters params)
public ArrayList<String> getGeneIdList(GuiParameters params)
getGeneIdList
in interface Database
public String getDiseaseIdWildCardGDA(String diseaseName, GuiParameters params)
getDiseaseIdWildCardGDA
in interface Database
public String getDiseaseIdWildCardVDA(String diseaseName, GuiParameters params)
public String getVariantIdWildCard(String variantId, GuiParameters params)
public HashMap<String,HashMap<String,String>> getDiseaseAttributes(GuiParameters params) throws DisGeNetException
getDiseaseAttributes
in interface Database
DisGeNetException
public HashMap<String,HashMap<String,String>> getGeneAttributes(GuiParameters curParams) throws DisGeNetException
getGeneAttributes
in interface Database
DisGeNetException
public HashMap<String,HashMap<String,String>> getVariantAttributes(GuiParameters curParams)
public HashMap<String,ArrayList<String>> getGeneDiseaseNetworkBySrc(GuiParameters curParams) throws DisGeNetException
getGeneDiseaseNetworkBySrc
in interface Database
DisGeNetException
public Map<String,String> getAssociatedGenesToVariants(List<String> genes) throws SQLException
getAssociatedGenesToVariants
in interface Database
SQLException
public HashMap<String,ArrayList<String>> getVariantDiseaseNetworkBySrc(GuiParameters curParams) throws DisGeNetException
getVariantDiseaseNetworkBySrc
in interface Database
DisGeNetException
public HashMap<String,ArrayList<String>> getGeneProjectionBySrc(GuiParameters curParams)
getGeneProjectionBySrc
in interface Database
public HashMap<String,ArrayList<String>> getDiseaseProjectionBySrc(GuiParameters curParams)
getDiseaseProjectionBySrc
in interface Database
public HashMap<String,String> getEdgeAttributes(String assocId, GuiParameters params)
getEdgeAttributes
in interface Database
public Map<String,List<String>> getDiseasesAssociatedToGenes(GuiParameters params) throws DisGeNetException
getDiseasesAssociatedToGenes
in interface Database
DisGeNetException
public String multipleSearchParams(Set<String> pieces)
pieces
- the search fieldspublic ArrayList<String> genNamesToId(List<String> pieces)
pieces
- List containing all the gene names as strings.public ArrayList<String> getGeneDiseaseList(GuiParameters curParams)
getGeneDiseaseList
in interface Database
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