umcg.genetica.io.gwascatalog

Class GWASCatalog

java.lang.Object

umcg.genetica.io.gwascatalog.GWASCatalog

public class GWASCatalog
extends Object

Author:

harmjan

Constructor Summary

Constructors

Constructor and Description
GWASCatalog()
GWASCatalog(String gwasCatalogLoc)
GWASCatalog(String gwasCatalogLoc, double pvaluethreshold)

Method Summary

Modifier and Type	Method and Description
HashSet<GWASTrait>	getFullTraitsForCertainSnps(String key)
HashSet<GWASLocus>	getLoci()
GWASLocus[]	getLociForCertainKey(String key)
HashMap<String,GWASLocus>	getLocusToObj()
HashSet<String>	getMappedGenesForCertainKey(String key)
HashMap<String,GWASPublication>	getPublicationToObj()
HashSet<String>	getReportedGenesForCertainKey(String key)
HashSet<GWASSNP>	getSnps()
GWASSNP[]	getSnpsArray()
GWASSNP[]	getSNPsForTraitContainingKey(String key)
HashMap<String,GWASSNP>	getSnpToObj()
GWASTrait[]	getTraits()
GWASTrait[]	getTraitsForCertainKey(String key)
HashSet<String>	getTraitsForCertainSnps(String key)
HashMap<String,GWASTrait>	getTraitToObj()
void	read(String calatogloc)
void	setLoci(HashSet<GWASLocus> loci)
void	setLocusToObj(HashMap<String,GWASLocus> locusToObj)
void	setPublicationToObj(HashMap<String,GWASPublication> publicationToObj)
void	setSnps(HashSet<GWASSNP> snps)
void	setSnpToObj(HashMap<String,GWASSNP> snpToObj)
void	setTraits(HashSet<GWASTrait> traits)
void	setTraitToObj(HashMap<String,GWASTrait> traitToObj)

Methods inherited from class java.lang.Object

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

Constructor Detail

GWASCatalog

public GWASCatalog()

GWASCatalog

public GWASCatalog(String gwasCatalogLoc)
            throws IOException

Throws:

IOException

GWASCatalog

public GWASCatalog(String gwasCatalogLoc,
                   double pvaluethreshold)
            throws IOException

Throws:

IOException

Method Detail

read

public void read(String calatogloc)
          throws IOException

Throws:

IOException

getTraits

public GWASTrait[] getTraits()

getLoci

public HashSet<GWASLocus> getLoci()

Returns:

the loci

setLoci

public void setLoci(HashSet<GWASLocus> loci)

Parameters:

loci - the loci to set

getSnps

public HashSet<GWASSNP> getSnps()

Returns:

the snps

setSnps

public void setSnps(HashSet<GWASSNP> snps)

Parameters:

snps - the snps to set

setTraits

public void setTraits(HashSet<GWASTrait> traits)

Parameters:

traits - the traits to set

getPublicationToObj

public HashMap<String,GWASPublication> getPublicationToObj()

Returns:

the publicationToObj

setPublicationToObj

public void setPublicationToObj(HashMap<String,GWASPublication> publicationToObj)

Parameters:

publicationToObj - the publicationToObj to set

getSnpToObj

public HashMap<String,GWASSNP> getSnpToObj()

Returns:

the snpToObj

setSnpToObj

public void setSnpToObj(HashMap<String,GWASSNP> snpToObj)

Parameters:

snpToObj - the snpToObj to set

getLocusToObj

public HashMap<String,GWASLocus> getLocusToObj()

Returns:

the locusToObj

setLocusToObj

public void setLocusToObj(HashMap<String,GWASLocus> locusToObj)

Parameters:

locusToObj - the locusToObj to set

getTraitToObj

public HashMap<String,GWASTrait> getTraitToObj()

Returns:

the traitToObj

setTraitToObj

public void setTraitToObj(HashMap<String,GWASTrait> traitToObj)

Parameters:

traitToObj - the traitToObj to set

getSnpsArray

public GWASSNP[] getSnpsArray()

getSNPsForTraitContainingKey

public GWASSNP[] getSNPsForTraitContainingKey(String key)

getTraitsForCertainKey

public GWASTrait[] getTraitsForCertainKey(String key)

getLociForCertainKey

public GWASLocus[] getLociForCertainKey(String key)

getReportedGenesForCertainKey

public HashSet<String> getReportedGenesForCertainKey(String key)

getMappedGenesForCertainKey

public HashSet<String> getMappedGenesForCertainKey(String key)

getTraitsForCertainSnps

public HashSet<String> getTraitsForCertainSnps(String key)

getFullTraitsForCertainSnps

public HashSet<GWASTrait> getFullTraitsForCertainSnps(String key)