public class TriTyperGenotypeData extends Object
| Constructor and Description |
|---|
TriTyperGenotypeData() |
TriTyperGenotypeData(String loc) |
| Modifier and Type | Method and Description |
|---|---|
SNPLoader |
createSNPLoader() |
Byte |
getChr(int s) |
int |
getChrPos(int s) |
String |
getDosageFileName() |
String |
getGenotypeFileName() |
Integer |
getIndividualId(String key) |
String[] |
getIndividuals() |
gnu.trove.map.hash.TObjectIntHashMap<String> |
getIndividualToId() |
Boolean[] |
getIsCase() |
Boolean[] |
getIsFemale() |
Boolean[] |
getIsIncluded() |
SNP |
getSNPObject(int d) |
String[] |
getSNPs() |
gnu.trove.map.hash.TObjectIntHashMap<String> |
getSnpToSNPId() |
void |
load(String loc) |
void |
setDosageFileName(String dosageFileName) |
void |
setGenotypeFileName(String genotypeFileName) |
void |
setIndividualToId(gnu.trove.map.hash.TObjectIntHashMap<String> individualToId) |
void |
setIsCase(Boolean[] isCase) |
void |
setIsFemale(Boolean[] isFemale) |
void |
setIsIncluded(Boolean[] isIncluded) |
void |
setSNPs(String[] SNPs) |
void |
setSnpToSNPObject(gnu.trove.map.hash.TObjectIntHashMap<String> snpToSNPObject) |
public TriTyperGenotypeData(String loc) throws IOException
IOExceptionpublic TriTyperGenotypeData()
public final void load(String loc) throws IOException
IOExceptionpublic Boolean[] getIsFemale()
public void setIsFemale(Boolean[] isFemale)
isFemale - the isFemale to setpublic Boolean[] getIsCase()
public void setIsCase(Boolean[] isCase)
isCase - the isCase to setpublic Boolean[] getIsIncluded()
public void setIsIncluded(Boolean[] isIncluded)
isIncluded - the isIncluded to setpublic gnu.trove.map.hash.TObjectIntHashMap<String> getIndividualToId()
public void setIndividualToId(gnu.trove.map.hash.TObjectIntHashMap<String> individualToId)
individualToId - the individualToId to setpublic gnu.trove.map.hash.TObjectIntHashMap<String> getSnpToSNPId()
public void setSnpToSNPObject(gnu.trove.map.hash.TObjectIntHashMap<String> snpToSNPObject)
snpToSNPObject - the snpToSNPObject to setpublic String getGenotypeFileName()
public void setGenotypeFileName(String genotypeFileName)
genotypeFileName - the genotypeFileName to setpublic String getDosageFileName()
public void setDosageFileName(String dosageFileName)
dosageFileName - the dosageFileName to setpublic String[] getSNPs()
public void setSNPs(String[] SNPs)
SNPs - the SNPs to setpublic String[] getIndividuals()
public Byte getChr(int s)
public int getChrPos(int s)
public SNP getSNPObject(int d)
public SNPLoader createSNPLoader() throws IOException
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