idare.sbmlannotator.internal.gpr

Class GPRManager

java.lang.Object

idare.sbmlannotator.internal.gpr.GPRManager

public class GPRManager
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static String	GENE_BASE
static String	PROTEIN_BASE

Constructor Summary

Constructors

Constructor and Description
GPRManager(IDARESettingsManager ism)

Method Summary

Modifier and Type	Method and Description
GPRAssociation	associateGenesToProtein(Protein p, Set<Gene> genes)
Gene	getGene(HashMap<String,String> databaseids)
Gene	getGene(String genename)
GPRAssociation	getGPRAssoc(Protein p)
Protein	getProtein(GPRAssociation assoc)
Protein	getProtein(HashMap<String,String> databaseids)
Protein	getProtein(String Proteinname)
Set<Gene>	getProteinBuildingGenes(Protein p)
Set<Protein>	getProteins(Collection<GPRAssociation> assocs)
Protein	getSingleGeneProtein(Gene g)
Gene	getUnassociatedGene(String name)
Protein	getUnassociatedProtein(String name)
void	updateGenedbs(Gene g, HashMap<String,String> databaseids)
void	updateProteindbs(Protein p, HashMap<String,String> databaseids)

Methods inherited from class java.lang.Object

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

Field Detail

PROTEIN_BASE

public static String PROTEIN_BASE

GENE_BASE

public static String GENE_BASE

Constructor Detail

GPRManager

public GPRManager(IDARESettingsManager ism)

Method Detail

associateGenesToProtein

public GPRAssociation associateGenesToProtein(Protein p,
                                              Set<Gene> genes)

getSingleGeneProtein

public Protein getSingleGeneProtein(Gene g)

getProteinBuildingGenes

public Set<Gene> getProteinBuildingGenes(Protein p)

getGene

public Gene getGene(String genename)

getGPRAssoc

public GPRAssociation getGPRAssoc(Protein p)

getProtein

public Protein getProtein(GPRAssociation assoc)

getProteins

public Set<Protein> getProteins(Collection<GPRAssociation> assocs)

getProtein

public Protein getProtein(String Proteinname)

getGene

public Gene getGene(HashMap<String,String> databaseids)

getUnassociatedProtein

public Protein getUnassociatedProtein(String name)

getUnassociatedGene

public Gene getUnassociatedGene(String name)

getProtein

public Protein getProtein(HashMap<String,String> databaseids)

updateGenedbs

public void updateGenedbs(Gene g,
                          HashMap<String,String> databaseids)

updateProteindbs

public void updateProteindbs(Protein p,
                             HashMap<String,String> databaseids)