A B C D E F G H I J L M N O P Q R S T V W X Y 

A

AANOTATION - Static variable in class org.molgenis.omx.xgap.Variant
 
AAPOSITION - Static variable in class org.molgenis.omx.xgap.Variant
 
ALLELE1 - Static variable in class org.molgenis.omx.patient.Patient
 
ALLELE2 - Static variable in class org.molgenis.omx.patient.Patient
 
AMINOSEQUENCE - Static variable in class org.molgenis.omx.xgap.Protein
 
AUTOID - Static variable in class org.molgenis.omx.xgap.Marker_ReportsFor
 
AUTOID - Static variable in class org.molgenis.omx.xgap.SNP_Polymorphism
 

B

BASE - Static variable in class org.molgenis.omx.xgap.Polymorphism
 
BPEND - Static variable in class org.molgenis.omx.xgap.Clone
 
BPEND - Static variable in class org.molgenis.omx.xgap.Gene
 
BPEND - Static variable in class org.molgenis.omx.xgap.Marker
 
BPEND - Static variable in class org.molgenis.omx.xgap.Probe
 
BPEND - Static variable in class org.molgenis.omx.xgap.ProbeSet
 
BPEND - Static variable in class org.molgenis.omx.xgap.Variant
 
BPLENGTH - Static variable in class org.molgenis.omx.xgap.Chromosome
 
BPSTART - Static variable in class org.molgenis.omx.xgap.Clone
 
BPSTART - Static variable in class org.molgenis.omx.xgap.Gene
 
BPSTART - Static variable in class org.molgenis.omx.xgap.Marker
 
BPSTART - Static variable in class org.molgenis.omx.xgap.Probe
 
BPSTART - Static variable in class org.molgenis.omx.xgap.ProbeSet
 
BPSTART - Static variable in class org.molgenis.omx.xgap.Variant
 

C

CDNANOTATION - Static variable in class org.molgenis.omx.xgap.Variant
 
CDNAPOSITION - Static variable in class org.molgenis.omx.xgap.Variant
 
Chromosome - Class in org.molgenis.omx.xgap
Chromosome: .
Chromosome() - Constructor for class org.molgenis.omx.xgap.Chromosome
 
CHROMOSOME - Static variable in class org.molgenis.omx.xgap.Clone
 
CHROMOSOME - Static variable in class org.molgenis.omx.xgap.Gene
 
CHROMOSOME - Static variable in class org.molgenis.omx.xgap.Marker
 
CHROMOSOME - Static variable in class org.molgenis.omx.xgap.Probe
 
CHROMOSOME - Static variable in class org.molgenis.omx.xgap.ProbeSet
 
CHROMOSOME - Static variable in class org.molgenis.omx.xgap.Variant
 
ChromosomeMetaData - Class in org.molgenis.omx.xgap
 
ChromosomeMetaData() - Constructor for class org.molgenis.omx.xgap.ChromosomeMetaData
 
ChromosomeRepository - Class in org.molgenis.omx.xgap
 
ChromosomeRepository(EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.ChromosomeRepository
 
ChromosomeRepository(EntityManager, EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.ChromosomeRepository
For testing purposes
Clone - Class in org.molgenis.omx.xgap
Clone: BAC clone fragment..
Clone() - Constructor for class org.molgenis.omx.xgap.Clone
 
CloneMetaData - Class in org.molgenis.omx.xgap
 
CloneMetaData() - Constructor for class org.molgenis.omx.xgap.CloneMetaData
 
CloneRepository - Class in org.molgenis.omx.xgap
 
CloneRepository(EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.CloneRepository
 
CloneRepository(EntityManager, EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.CloneRepository
For testing purposes
CM - Static variable in class org.molgenis.omx.xgap.Clone
 
CM - Static variable in class org.molgenis.omx.xgap.Gene
 
CM - Static variable in class org.molgenis.omx.xgap.Marker
 
CM - Static variable in class org.molgenis.omx.xgap.Probe
 
CM - Static variable in class org.molgenis.omx.xgap.ProbeSet
 
CM - Static variable in class org.molgenis.omx.xgap.Variant
 
CODONCHANGE - Static variable in class org.molgenis.omx.xgap.Variant
 
CONSEQUENCE - Static variable in class org.molgenis.omx.xgap.Variant
 
CONTROL - Static variable in class org.molgenis.omx.xgap.Gene
 
createDasFeature(Integer, Integer, String, String, String, String, DasType, String, Double) - Method in class org.molgenis.omx.das.impl.RepositoryRangeHandlingDataSource
 
createDasFeature(Integer, Integer, String, String, String, String, DasType, DasMethod, String, String) - Method in class org.molgenis.omx.das.RangeHandlingDataSource
 

D

DasURLFilter - Class in org.molgenis.omx.das.impl
 
DasURLFilter() - Constructor for class org.molgenis.omx.das.impl.DasURLFilter
 
DATASET_PREFIX - Static variable in class org.molgenis.omx.das.impl.DasURLFilter
 
DerivedTrait - Class in org.molgenis.omx.xgap
DerivedTrait: Any meta trait, eg.
DerivedTrait() - Constructor for class org.molgenis.omx.xgap.DerivedTrait
 
DerivedTraitMetaData - Class in org.molgenis.omx.xgap
 
DerivedTraitMetaData() - Constructor for class org.molgenis.omx.xgap.DerivedTraitMetaData
 
DerivedTraitRepository - Class in org.molgenis.omx.xgap
 
DerivedTraitRepository(EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.DerivedTraitRepository
 
DerivedTraitRepository(EntityManager, EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.DerivedTraitRepository
For testing purposes
destroy() - Method in class org.molgenis.omx.das.impl.DasURLFilter
 
destroy() - Method in class org.molgenis.omx.das.RangeHandlingDataSource
 
DETAILSFORMUTATION - Static variable in class org.molgenis.omx.xgap.Variant
 
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class org.molgenis.omx.das.impl.DasURLFilter
 

E

EFFECTONSPLICING - Static variable in class org.molgenis.omx.xgap.Variant
 
ENTITY_NAME - Static variable in class org.molgenis.omx.patient.Patient
 
ENTITY_NAME - Static variable in class org.molgenis.omx.xgap.Chromosome
 
ENTITY_NAME - Static variable in class org.molgenis.omx.xgap.Clone
 
ENTITY_NAME - Static variable in class org.molgenis.omx.xgap.DerivedTrait
 
ENTITY_NAME - Static variable in class org.molgenis.omx.xgap.EnvironmentalFactor
 
ENTITY_NAME - Static variable in class org.molgenis.omx.xgap.Gene
 
ENTITY_NAME - Static variable in class org.molgenis.omx.xgap.Marker
 
ENTITY_NAME - Static variable in class org.molgenis.omx.xgap.Marker_ReportsFor
 
ENTITY_NAME - Static variable in class org.molgenis.omx.xgap.MassPeak
 
ENTITY_NAME - Static variable in class org.molgenis.omx.xgap.Metabolite
 
ENTITY_NAME - Static variable in class org.molgenis.omx.xgap.NMRBin
 
ENTITY_NAME - Static variable in class org.molgenis.omx.xgap.PairedSample
 
ENTITY_NAME - Static variable in class org.molgenis.omx.xgap.Polymorphism
 
ENTITY_NAME - Static variable in class org.molgenis.omx.xgap.Probe
 
ENTITY_NAME - Static variable in class org.molgenis.omx.xgap.ProbeSet
 
ENTITY_NAME - Static variable in class org.molgenis.omx.xgap.Protein
 
ENTITY_NAME - Static variable in class org.molgenis.omx.xgap.Sample
 
ENTITY_NAME - Static variable in class org.molgenis.omx.xgap.SNP
 
ENTITY_NAME - Static variable in class org.molgenis.omx.xgap.SNP_Polymorphism
 
ENTITY_NAME - Static variable in class org.molgenis.omx.xgap.Spot
 
ENTITY_NAME - Static variable in class org.molgenis.omx.xgap.Track
 
ENTITY_NAME - Static variable in class org.molgenis.omx.xgap.Transcript
 
ENTITY_NAME - Static variable in class org.molgenis.omx.xgap.Variant
 
EnvironmentalFactor - Class in org.molgenis.omx.xgap
EnvironmentalFactor: Experimental conditions, such as temperature differences, batch effects etc..
EnvironmentalFactor() - Constructor for class org.molgenis.omx.xgap.EnvironmentalFactor
 
EnvironmentalFactorMetaData - Class in org.molgenis.omx.xgap
 
EnvironmentalFactorMetaData() - Constructor for class org.molgenis.omx.xgap.EnvironmentalFactorMetaData
 
EnvironmentalFactorRepository - Class in org.molgenis.omx.xgap
 
EnvironmentalFactorRepository(EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.EnvironmentalFactorRepository
 
EnvironmentalFactorRepository(EntityManager, EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.EnvironmentalFactorRepository
For testing purposes
equals(Object) - Method in class org.molgenis.omx.das.impl.MolgenisDasTarget
 
equals(Object) - Method in class org.molgenis.omx.patient.Patient
 
equals(Object) - Method in class org.molgenis.omx.xgap.Chromosome
 
equals(Object) - Method in class org.molgenis.omx.xgap.Clone
 
equals(Object) - Method in class org.molgenis.omx.xgap.DerivedTrait
 
equals(Object) - Method in class org.molgenis.omx.xgap.EnvironmentalFactor
 
equals(Object) - Method in class org.molgenis.omx.xgap.Gene
 
equals(Object) - Method in class org.molgenis.omx.xgap.Marker
 
equals(Object) - Method in class org.molgenis.omx.xgap.Marker_ReportsFor
 
equals(Object) - Method in class org.molgenis.omx.xgap.MassPeak
 
equals(Object) - Method in class org.molgenis.omx.xgap.Metabolite
 
equals(Object) - Method in class org.molgenis.omx.xgap.NMRBin
 
equals(Object) - Method in class org.molgenis.omx.xgap.PairedSample
 
equals(Object) - Method in class org.molgenis.omx.xgap.Polymorphism
 
equals(Object) - Method in class org.molgenis.omx.xgap.Probe
 
equals(Object) - Method in class org.molgenis.omx.xgap.ProbeSet
 
equals(Object) - Method in class org.molgenis.omx.xgap.Protein
 
equals(Object) - Method in class org.molgenis.omx.xgap.Sample
 
equals(Object) - Method in class org.molgenis.omx.xgap.SNP
 
equals(Object) - Method in class org.molgenis.omx.xgap.SNP_Polymorphism
 
equals(Object) - Method in class org.molgenis.omx.xgap.Spot
 
equals(Object) - Method in class org.molgenis.omx.xgap.Track
 
equals(Object) - Method in class org.molgenis.omx.xgap.Transcript
 
equals(Object) - Method in class org.molgenis.omx.xgap.Variant
 
EVENT - Static variable in class org.molgenis.omx.xgap.Variant
 
EXON - Static variable in class org.molgenis.omx.xgap.Variant
 

F

FORMULA - Static variable in class org.molgenis.omx.xgap.Metabolite
 

G

GDNANOTATION - Static variable in class org.molgenis.omx.xgap.Variant
 
Gene - Class in org.molgenis.omx.xgap
Gene: Trait annotations specific for genes..
Gene() - Constructor for class org.molgenis.omx.xgap.Gene
 
GENE - Static variable in class org.molgenis.omx.xgap.Protein
 
GENE - Static variable in class org.molgenis.omx.xgap.Transcript
 
GENE - Static variable in class org.molgenis.omx.xgap.Variant
 
GeneMetaData - Class in org.molgenis.omx.xgap
 
GeneMetaData() - Constructor for class org.molgenis.omx.xgap.GeneMetaData
 
GeneRepository - Class in org.molgenis.omx.xgap
 
GeneRepository(EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.GeneRepository
 
GeneRepository(EntityManager, EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.GeneRepository
For testing purposes
get(String) - Method in class org.molgenis.omx.patient.Patient
Generic getter.
get(String) - Method in class org.molgenis.omx.xgap.Chromosome
Generic getter.
get(String) - Method in class org.molgenis.omx.xgap.Clone
Generic getter.
get(String) - Method in class org.molgenis.omx.xgap.DerivedTrait
Generic getter.
get(String) - Method in class org.molgenis.omx.xgap.EnvironmentalFactor
Generic getter.
get(String) - Method in class org.molgenis.omx.xgap.Gene
Generic getter.
get(String) - Method in class org.molgenis.omx.xgap.Marker
Generic getter.
get(String) - Method in class org.molgenis.omx.xgap.Marker_ReportsFor
Generic getter.
get(String) - Method in class org.molgenis.omx.xgap.MassPeak
Generic getter.
get(String) - Method in class org.molgenis.omx.xgap.Metabolite
Generic getter.
get(String) - Method in class org.molgenis.omx.xgap.NMRBin
Generic getter.
get(String) - Method in class org.molgenis.omx.xgap.PairedSample
Generic getter.
get(String) - Method in class org.molgenis.omx.xgap.Polymorphism
Generic getter.
get(String) - Method in class org.molgenis.omx.xgap.Probe
Generic getter.
get(String) - Method in class org.molgenis.omx.xgap.ProbeSet
Generic getter.
get(String) - Method in class org.molgenis.omx.xgap.Protein
Generic getter.
get(String) - Method in class org.molgenis.omx.xgap.Sample
Generic getter.
get(String) - Method in class org.molgenis.omx.xgap.SNP
Generic getter.
get(String) - Method in class org.molgenis.omx.xgap.SNP_Polymorphism
Generic getter.
get(String) - Method in class org.molgenis.omx.xgap.Spot
Generic getter.
get(String) - Method in class org.molgenis.omx.xgap.Track
Generic getter.
get(String) - Method in class org.molgenis.omx.xgap.Transcript
Generic getter.
get(String) - Method in class org.molgenis.omx.xgap.Variant
Generic getter.
getAaNotation() - Method in class org.molgenis.omx.xgap.Variant
Get the .
getAaPosition() - Method in class org.molgenis.omx.xgap.Variant
Get the .
getAllele1() - Method in class org.molgenis.omx.patient.Patient
Get the .
getAllele2() - Method in class org.molgenis.omx.patient.Patient
Get the .
getAminoSequence() - Method in class org.molgenis.omx.xgap.Protein
Get the The aminoacid sequence..
getAttributeNames() - Method in class org.molgenis.omx.patient.Patient
 
getAttributeNames() - Method in class org.molgenis.omx.xgap.Chromosome
 
getAttributeNames() - Method in class org.molgenis.omx.xgap.Clone
 
getAttributeNames() - Method in class org.molgenis.omx.xgap.DerivedTrait
 
getAttributeNames() - Method in class org.molgenis.omx.xgap.EnvironmentalFactor
 
getAttributeNames() - Method in class org.molgenis.omx.xgap.Gene
 
getAttributeNames() - Method in class org.molgenis.omx.xgap.Marker
 
getAttributeNames() - Method in class org.molgenis.omx.xgap.Marker_ReportsFor
 
getAttributeNames() - Method in class org.molgenis.omx.xgap.MassPeak
 
getAttributeNames() - Method in class org.molgenis.omx.xgap.Metabolite
 
getAttributeNames() - Method in class org.molgenis.omx.xgap.NMRBin
 
getAttributeNames() - Method in class org.molgenis.omx.xgap.PairedSample
 
getAttributeNames() - Method in class org.molgenis.omx.xgap.Polymorphism
 
getAttributeNames() - Method in class org.molgenis.omx.xgap.Probe
 
getAttributeNames() - Method in class org.molgenis.omx.xgap.ProbeSet
 
getAttributeNames() - Method in class org.molgenis.omx.xgap.Protein
 
getAttributeNames() - Method in class org.molgenis.omx.xgap.Sample
 
getAttributeNames() - Method in class org.molgenis.omx.xgap.SNP
 
getAttributeNames() - Method in class org.molgenis.omx.xgap.SNP_Polymorphism
 
getAttributeNames() - Method in class org.molgenis.omx.xgap.Spot
 
getAttributeNames() - Method in class org.molgenis.omx.xgap.Track
 
getAttributeNames() - Method in class org.molgenis.omx.xgap.Transcript
 
getAttributeNames() - Method in class org.molgenis.omx.xgap.Variant
 
getAutoid() - Method in class org.molgenis.omx.xgap.Marker_ReportsFor
Get the automatic id field to ensure ordering of mrefs.
getAutoid() - Method in class org.molgenis.omx.xgap.SNP_Polymorphism
Get the automatic id field to ensure ordering of mrefs.
getBase() - Method in class org.molgenis.omx.xgap.Polymorphism
Get the The affected DNA base.
getBaseLabel() - Method in class org.molgenis.omx.xgap.Polymorphism
Get tha label for enum Base.
getBaseOptions() - Method in class org.molgenis.omx.xgap.Polymorphism
Base is enum.
getBpEnd() - Method in class org.molgenis.omx.xgap.Clone
Get the numeric basepair postion (3') on the chromosome.
getBpEnd() - Method in class org.molgenis.omx.xgap.Gene
Get the numeric basepair postion (3') on the chromosome.
getBpEnd() - Method in interface org.molgenis.omx.xgap.Locus
 
getBpEnd() - Method in class org.molgenis.omx.xgap.Marker
Get the numeric basepair postion (3') on the chromosome.
getBpEnd() - Method in class org.molgenis.omx.xgap.Probe
Get the numeric basepair postion (3') on the chromosome.
getBpEnd() - Method in class org.molgenis.omx.xgap.ProbeSet
Get the numeric basepair postion (3') on the chromosome.
getBpEnd() - Method in class org.molgenis.omx.xgap.Variant
Get the numeric basepair postion (3') on the chromosome.
getBpLength() - Method in class org.molgenis.omx.xgap.Chromosome
Get the Lenght of the chromsome in base pairs..
getBpStart() - Method in class org.molgenis.omx.xgap.Clone
Get the numeric basepair postion (5') on the chromosome.
getBpStart() - Method in class org.molgenis.omx.xgap.Gene
Get the numeric basepair postion (5') on the chromosome.
getBpStart() - Method in interface org.molgenis.omx.xgap.Locus
 
getBpStart() - Method in class org.molgenis.omx.xgap.Marker
Get the numeric basepair postion (5') on the chromosome.
getBpStart() - Method in class org.molgenis.omx.xgap.Probe
Get the numeric basepair postion (5') on the chromosome.
getBpStart() - Method in class org.molgenis.omx.xgap.ProbeSet
Get the numeric basepair postion (5') on the chromosome.
getBpStart() - Method in class org.molgenis.omx.xgap.Variant
Get the numeric basepair postion (5') on the chromosome.
getCdnaNotation() - Method in class org.molgenis.omx.xgap.Variant
Get the .
getCdnaPosition() - Method in class org.molgenis.omx.xgap.Variant
Get the .
getChromosome() - Method in class org.molgenis.omx.xgap.Clone
Get the Reference to the chromosome this position belongs to..
getChromosome() - Method in class org.molgenis.omx.xgap.Gene
Get the Reference to the chromosome this position belongs to..
getChromosome() - Method in interface org.molgenis.omx.xgap.Locus
 
getChromosome() - Method in class org.molgenis.omx.xgap.Marker
Get the Reference to the chromosome this position belongs to..
getChromosome() - Method in class org.molgenis.omx.xgap.Probe
Get the Reference to the chromosome this position belongs to..
getChromosome() - Method in class org.molgenis.omx.xgap.ProbeSet
Get the Reference to the chromosome this position belongs to..
getChromosome() - Method in class org.molgenis.omx.xgap.Variant
Get the Reference to the chromosome this position belongs to..
getCM() - Method in class org.molgenis.omx.xgap.Clone
Get the genetic map position in centi morgan (cM)..
getCM() - Method in class org.molgenis.omx.xgap.Gene
Get the genetic map position in centi morgan (cM)..
getCM() - Method in interface org.molgenis.omx.xgap.Locus
 
getCM() - Method in class org.molgenis.omx.xgap.Marker
Get the genetic map position in centi morgan (cM)..
getCM() - Method in class org.molgenis.omx.xgap.Probe
Get the genetic map position in centi morgan (cM)..
getCM() - Method in class org.molgenis.omx.xgap.ProbeSet
Get the genetic map position in centi morgan (cM)..
getCM() - Method in class org.molgenis.omx.xgap.Variant
Get the genetic map position in centi morgan (cM)..
getCodonchange() - Method in class org.molgenis.omx.xgap.Variant
Get the .
getConsequence() - Method in class org.molgenis.omx.xgap.Variant
Get the .
getControl() - Method in class org.molgenis.omx.xgap.Gene
Get the Indicating whether this is a 'housekeeping' gene that can be used as control..
getDetailsForMutation() - Method in class org.molgenis.omx.xgap.Variant
Get the .
getEffectOnSplicing() - Method in class org.molgenis.omx.xgap.Variant
Get the .
getEntityMetaData() - Method in class org.molgenis.omx.patient.Patient
 
getEntityMetaData() - Method in class org.molgenis.omx.xgap.Chromosome
 
getEntityMetaData() - Method in class org.molgenis.omx.xgap.Clone
 
getEntityMetaData() - Method in class org.molgenis.omx.xgap.DerivedTrait
 
getEntityMetaData() - Method in class org.molgenis.omx.xgap.EnvironmentalFactor
 
getEntityMetaData() - Method in class org.molgenis.omx.xgap.Gene
 
getEntityMetaData() - Method in class org.molgenis.omx.xgap.Marker
 
getEntityMetaData() - Method in class org.molgenis.omx.xgap.Marker_ReportsFor
 
getEntityMetaData() - Method in class org.molgenis.omx.xgap.MassPeak
 
getEntityMetaData() - Method in class org.molgenis.omx.xgap.Metabolite
 
getEntityMetaData() - Method in class org.molgenis.omx.xgap.NMRBin
 
getEntityMetaData() - Method in class org.molgenis.omx.xgap.PairedSample
 
getEntityMetaData() - Method in class org.molgenis.omx.xgap.Polymorphism
 
getEntityMetaData() - Method in class org.molgenis.omx.xgap.Probe
 
getEntityMetaData() - Method in class org.molgenis.omx.xgap.ProbeSet
 
getEntityMetaData() - Method in class org.molgenis.omx.xgap.Protein
 
getEntityMetaData() - Method in class org.molgenis.omx.xgap.Sample
 
getEntityMetaData() - Method in class org.molgenis.omx.xgap.SNP
 
getEntityMetaData() - Method in class org.molgenis.omx.xgap.SNP_Polymorphism
 
getEntityMetaData() - Method in class org.molgenis.omx.xgap.Spot
 
getEntityMetaData() - Method in class org.molgenis.omx.xgap.Track
 
getEntityMetaData() - Method in class org.molgenis.omx.xgap.Transcript
 
getEntityMetaData() - Method in class org.molgenis.omx.xgap.Variant
 
getEntityName() - Method in class org.molgenis.omx.patient.Patient
 
getEntityName() - Method in class org.molgenis.omx.xgap.Chromosome
 
getEntityName() - Method in class org.molgenis.omx.xgap.Clone
 
getEntityName() - Method in class org.molgenis.omx.xgap.DerivedTrait
 
getEntityName() - Method in class org.molgenis.omx.xgap.EnvironmentalFactor
 
getEntityName() - Method in class org.molgenis.omx.xgap.Gene
 
getEntityName() - Method in class org.molgenis.omx.xgap.Marker
 
getEntityName() - Method in class org.molgenis.omx.xgap.Marker_ReportsFor
 
getEntityName() - Method in class org.molgenis.omx.xgap.MassPeak
 
getEntityName() - Method in class org.molgenis.omx.xgap.Metabolite
 
getEntityName() - Method in class org.molgenis.omx.xgap.NMRBin
 
getEntityName() - Method in class org.molgenis.omx.xgap.PairedSample
 
getEntityName() - Method in class org.molgenis.omx.xgap.Polymorphism
 
getEntityName() - Method in class org.molgenis.omx.xgap.Probe
 
getEntityName() - Method in class org.molgenis.omx.xgap.ProbeSet
 
getEntityName() - Method in class org.molgenis.omx.xgap.Protein
 
getEntityName() - Method in class org.molgenis.omx.xgap.Sample
 
getEntityName() - Method in class org.molgenis.omx.xgap.SNP
 
getEntityName() - Method in class org.molgenis.omx.xgap.SNP_Polymorphism
 
getEntityName() - Method in class org.molgenis.omx.xgap.Spot
 
getEntityName() - Method in class org.molgenis.omx.xgap.Track
 
getEntityName() - Method in class org.molgenis.omx.xgap.Transcript
 
getEntityName() - Method in class org.molgenis.omx.xgap.Variant
 
getEntryPoints(Integer, Integer) - Method in class org.molgenis.omx.das.RangeHandlingDataSource
 
getEntryPointVersion() - Method in class org.molgenis.omx.das.RangeHandlingDataSource
 
getEvent() - Method in class org.molgenis.omx.xgap.Variant
Get the .
getExon() - Method in class org.molgenis.omx.xgap.Variant
Get the .
getFeatures(String, int, int, Integer) - Method in class org.molgenis.omx.das.impl.RepositoryRangeHandlingDataSource
 
getFeatures(String, Integer) - Method in class org.molgenis.omx.das.RangeHandlingDataSource
 
getFeatures(Collection<String>, Integer, Range) - Method in class org.molgenis.omx.das.RangeHandlingDataSource
 
getFeatures(String, int, int, Integer, Range) - Method in class org.molgenis.omx.das.RangeHandlingDataSource
 
getFeatures(String, Integer, Range) - Method in class org.molgenis.omx.das.RangeHandlingDataSource
 
getFeatures(Collection<String>, Integer) - Method in class org.molgenis.omx.das.RangeHandlingDataSource
 
getFormula() - Method in class org.molgenis.omx.xgap.Metabolite
Get the The chemical formula of a metabolite..
getGdnaNotation() - Method in class org.molgenis.omx.xgap.Variant
Get the .
getGene() - Method in class org.molgenis.omx.xgap.Protein
Get the The gene that produces this protein.
getGene() - Method in class org.molgenis.omx.xgap.Transcript
Get the The gene that produces this protein.
getGene() - Method in class org.molgenis.omx.xgap.Variant
Get the .
getGridX() - Method in class org.molgenis.omx.xgap.Spot
Get the Meta Row.
getGridY() - Method in class org.molgenis.omx.xgap.Spot
Get the Meta Column.
getIdMutation() - Method in class org.molgenis.omx.xgap.Variant
Get the .
getIdValue() - Method in class org.molgenis.omx.patient.Patient
 
getIdValue() - Method in class org.molgenis.omx.xgap.Chromosome
 
getIdValue() - Method in class org.molgenis.omx.xgap.Clone
 
getIdValue() - Method in class org.molgenis.omx.xgap.DerivedTrait
 
getIdValue() - Method in class org.molgenis.omx.xgap.EnvironmentalFactor
 
getIdValue() - Method in class org.molgenis.omx.xgap.Gene
 
getIdValue() - Method in class org.molgenis.omx.xgap.Marker
 
getIdValue() - Method in class org.molgenis.omx.xgap.Marker_ReportsFor
 
getIdValue() - Method in class org.molgenis.omx.xgap.MassPeak
 
getIdValue() - Method in class org.molgenis.omx.xgap.Metabolite
 
getIdValue() - Method in class org.molgenis.omx.xgap.NMRBin
 
getIdValue() - Method in class org.molgenis.omx.xgap.PairedSample
 
getIdValue() - Method in class org.molgenis.omx.xgap.Polymorphism
 
getIdValue() - Method in class org.molgenis.omx.xgap.Probe
 
getIdValue() - Method in class org.molgenis.omx.xgap.ProbeSet
 
getIdValue() - Method in class org.molgenis.omx.xgap.Protein
 
getIdValue() - Method in class org.molgenis.omx.xgap.Sample
 
getIdValue() - Method in class org.molgenis.omx.xgap.SNP
 
getIdValue() - Method in class org.molgenis.omx.xgap.SNP_Polymorphism
 
getIdValue() - Method in class org.molgenis.omx.xgap.Spot
 
getIdValue() - Method in class org.molgenis.omx.xgap.Track
 
getIdValue() - Method in class org.molgenis.omx.xgap.Transcript
 
getIdValue() - Method in class org.molgenis.omx.xgap.Variant
 
getIndividual() - Method in class org.molgenis.omx.xgap.Sample
Get the The individual from which this sample was taken..
getInheritance() - Method in class org.molgenis.omx.xgap.Variant
Get the .
getIsAutosomal() - Method in class org.molgenis.omx.xgap.Chromosome
Get the Is 'yes' when number of chromosomes is equal in male and female individuals, i.e., if not a sex chromosome..
getLabel1() - Method in class org.molgenis.omx.xgap.PairedSample
Get the Which channel or Fluorescent labeling is associated with the first subject.
getLabel2() - Method in class org.molgenis.omx.xgap.PairedSample
Get the Which channel or Fluorescent labeling is associated with the second subject.
getLabelAttributeNames() - Method in class org.molgenis.omx.patient.Patient
 
getLabelAttributeNames() - Method in class org.molgenis.omx.xgap.Chromosome
 
getLabelAttributeNames() - Method in class org.molgenis.omx.xgap.Clone
 
getLabelAttributeNames() - Method in class org.molgenis.omx.xgap.DerivedTrait
 
getLabelAttributeNames() - Method in class org.molgenis.omx.xgap.EnvironmentalFactor
 
getLabelAttributeNames() - Method in class org.molgenis.omx.xgap.Gene
 
getLabelAttributeNames() - Method in class org.molgenis.omx.xgap.Marker
 
getLabelAttributeNames() - Method in class org.molgenis.omx.xgap.Marker_ReportsFor
 
getLabelAttributeNames() - Method in class org.molgenis.omx.xgap.MassPeak
 
getLabelAttributeNames() - Method in class org.molgenis.omx.xgap.Metabolite
 
getLabelAttributeNames() - Method in class org.molgenis.omx.xgap.NMRBin
 
getLabelAttributeNames() - Method in class org.molgenis.omx.xgap.PairedSample
 
getLabelAttributeNames() - Method in class org.molgenis.omx.xgap.Polymorphism
 
getLabelAttributeNames() - Method in class org.molgenis.omx.xgap.Probe
 
getLabelAttributeNames() - Method in class org.molgenis.omx.xgap.ProbeSet
 
getLabelAttributeNames() - Method in class org.molgenis.omx.xgap.Protein
 
getLabelAttributeNames() - Method in class org.molgenis.omx.xgap.Sample
 
getLabelAttributeNames() - Method in class org.molgenis.omx.xgap.SNP
 
getLabelAttributeNames() - Method in class org.molgenis.omx.xgap.SNP_Polymorphism
 
getLabelAttributeNames() - Method in class org.molgenis.omx.xgap.Spot
 
getLabelAttributeNames() - Method in class org.molgenis.omx.xgap.Track
 
getLabelAttributeNames() - Method in class org.molgenis.omx.xgap.Transcript
 
getLabelAttributeNames() - Method in class org.molgenis.omx.xgap.Variant
 
getLinkURL(String, String) - Method in class org.molgenis.omx.das.RangeHandlingDataSource
 
getMarker() - Method in class org.molgenis.omx.xgap.Marker_ReportsFor
Get the .
getMass() - Method in class org.molgenis.omx.xgap.Metabolite
Get the The mass of this metabolite.
getMass() - Method in class org.molgenis.omx.xgap.Protein
Get the The mass of this metabolite.
getMismatch() - Method in class org.molgenis.omx.xgap.Probe
Get the Indicating whether the probe is a match.
getMutationPosition() - Method in class org.molgenis.omx.xgap.Variant
Get the .
getMZ() - Method in class org.molgenis.omx.xgap.MassPeak
Get the Mass over charge ratio of this peak..
getNtChange() - Method in class org.molgenis.omx.xgap.Variant
Get the .
getOrderNr() - Method in class org.molgenis.omx.xgap.Chromosome
Get the .
getOrientation() - Method in class org.molgenis.omx.xgap.Gene
Get the Orientation of the gene on the genome (F=forward, R=reverse).
getOrientationLabel() - Method in class org.molgenis.omx.xgap.Gene
Get tha label for enum Orientation.
getOrientationOptions() - Method in class org.molgenis.omx.xgap.Gene
Orientation is enum.
getPathogenicity() - Method in class org.molgenis.omx.xgap.Variant
Get the .
getPheno() - Method in class org.molgenis.omx.patient.Patient
Get the .
getPolymorphism() - Method in class org.molgenis.omx.xgap.SNP
Get the The polymorphism that belongs to this SNP..
getPolymorphism() - Method in class org.molgenis.omx.xgap.SNP_Polymorphism
Get the .
getPolymorphismSNPCollection() - Method in class org.molgenis.omx.xgap.Polymorphism
 
getProbeSet() - Method in class org.molgenis.omx.xgap.Probe
Get the Optional: probeset this probe belongs to (e.g., in Affymetrix assays)..
getPubMedID() - Method in class org.molgenis.omx.patient.Patient
Get the .
getReference() - Method in class org.molgenis.omx.patient.Patient
Get the .
getReportedSNP() - Method in class org.molgenis.omx.xgap.Variant
Get the .
getReportsFor() - Method in class org.molgenis.omx.xgap.Marker
Get the The marker (or a subclass like 'SNP') this marker (or a subclass like 'SNP') reports for..
getReportsFor() - Method in class org.molgenis.omx.xgap.Marker_ReportsFor
Get the .
getReportsFor() - Method in class org.molgenis.omx.xgap.Probe
Get the The gene this probe reports for..
getReportsForMarkerCollection() - Method in class org.molgenis.omx.xgap.Marker
 
getRetentionTime() - Method in class org.molgenis.omx.xgap.MassPeak
Get the The retention-time of this peak in minutes..
getSeq() - Method in class org.molgenis.omx.xgap.Clone
Get the The FASTA text representation of the sequence..
getSeq() - Method in class org.molgenis.omx.xgap.Gene
Get the The FASTA text representation of the sequence..
getSeq() - Method in interface org.molgenis.omx.xgap.Locus
 
getSeq() - Method in class org.molgenis.omx.xgap.Marker
Get the The FASTA text representation of the sequence..
getSeq() - Method in class org.molgenis.omx.xgap.Probe
Get the The FASTA text representation of the sequence..
getSeq() - Method in class org.molgenis.omx.xgap.ProbeSet
Get the The FASTA text representation of the sequence..
getSeq() - Method in class org.molgenis.omx.xgap.Variant
Get the The FASTA text representation of the sequence..
getSNP() - Method in class org.molgenis.omx.xgap.SNP_Polymorphism
Get the .
getSpecies() - Method in class org.molgenis.omx.xgap.Chromosome
Get the Reference to the species this chromosome belongs to..
getStartCoordinate() - Method in class org.molgenis.omx.das.impl.MolgenisDasTarget
 
getStatus() - Method in class org.molgenis.omx.xgap.SNP
Get the The status of this SNP, eg 'confirmed'..
getStopCoordinate() - Method in class org.molgenis.omx.das.impl.MolgenisDasTarget
 
getStructure() - Method in class org.molgenis.omx.xgap.Metabolite
Get the The chemical structure of a metabolite (in SMILES representation)..
getSubject1() - Method in class org.molgenis.omx.xgap.PairedSample
Get the The first subject.
getSubject2() - Method in class org.molgenis.omx.xgap.PairedSample
Get the The second sample.
getSymbol() - Method in class org.molgenis.omx.xgap.Clone
Get the todo.
getSymbol() - Method in class org.molgenis.omx.xgap.Gene
Get the Main symbol this gene is known by (not necessarily unique, in constrast to 'name').
getSymbol() - Method in interface org.molgenis.omx.xgap.Locus
 
getSymbol() - Method in class org.molgenis.omx.xgap.Marker
Get the todo.
getSymbol() - Method in class org.molgenis.omx.xgap.Probe
Get the todo.
getSymbol() - Method in class org.molgenis.omx.xgap.ProbeSet
Get the todo.
getSymbol() - Method in class org.molgenis.omx.xgap.Variant
Get the todo.
getTargetId() - Method in class org.molgenis.omx.das.impl.MolgenisDasTarget
 
getTargetName() - Method in class org.molgenis.omx.das.impl.MolgenisDasTarget
 
getTissue() - Method in class org.molgenis.omx.xgap.Sample
Get the The tissue from which this sample was taken..
getTotalCountForType(DasType) - Method in class org.molgenis.omx.das.impl.RepositoryRangeHandlingDataSource
 
getTotalEntryPoints() - Method in class org.molgenis.omx.das.RangeHandlingDataSource
 
getTrack() - Method in class org.molgenis.omx.xgap.Variant
Get the .
getTranscript() - Method in class org.molgenis.omx.xgap.Protein
Get the The transcript variant that produces this protein.
getTypes() - Method in class org.molgenis.omx.das.impl.RepositoryRangeHandlingDataSource
 
getValue() - Method in class org.molgenis.omx.xgap.Polymorphism
Get the The strain/genotype for which this polymorphism was discovered.
getVariantLength() - Method in class org.molgenis.omx.xgap.Variant
Get the .
getX() - Method in class org.molgenis.omx.xgap.Spot
Get the Row.
getY() - Method in class org.molgenis.omx.xgap.Spot
Get the Column.
GRIDX - Static variable in class org.molgenis.omx.xgap.Spot
 
GRIDY - Static variable in class org.molgenis.omx.xgap.Spot
 

H

hashCode() - Method in class org.molgenis.omx.patient.Patient
 
hashCode() - Method in class org.molgenis.omx.xgap.Chromosome
 
hashCode() - Method in class org.molgenis.omx.xgap.Clone
 
hashCode() - Method in class org.molgenis.omx.xgap.DerivedTrait
 
hashCode() - Method in class org.molgenis.omx.xgap.EnvironmentalFactor
 
hashCode() - Method in class org.molgenis.omx.xgap.Gene
 
hashCode() - Method in class org.molgenis.omx.xgap.Marker
 
hashCode() - Method in class org.molgenis.omx.xgap.Marker_ReportsFor
 
hashCode() - Method in class org.molgenis.omx.xgap.MassPeak
 
hashCode() - Method in class org.molgenis.omx.xgap.Metabolite
 
hashCode() - Method in class org.molgenis.omx.xgap.NMRBin
 
hashCode() - Method in class org.molgenis.omx.xgap.PairedSample
 
hashCode() - Method in class org.molgenis.omx.xgap.Polymorphism
 
hashCode() - Method in class org.molgenis.omx.xgap.Probe
 
hashCode() - Method in class org.molgenis.omx.xgap.ProbeSet
 
hashCode() - Method in class org.molgenis.omx.xgap.Protein
 
hashCode() - Method in class org.molgenis.omx.xgap.Sample
 
hashCode() - Method in class org.molgenis.omx.xgap.SNP
 
hashCode() - Method in class org.molgenis.omx.xgap.SNP_Polymorphism
 
hashCode() - Method in class org.molgenis.omx.xgap.Spot
 
hashCode() - Method in class org.molgenis.omx.xgap.Track
 
hashCode() - Method in class org.molgenis.omx.xgap.Transcript
 
hashCode() - Method in class org.molgenis.omx.xgap.Variant
 

I

ID - Static variable in class org.molgenis.omx.patient.Patient
 
ID - Static variable in class org.molgenis.omx.xgap.Chromosome
 
ID - Static variable in class org.molgenis.omx.xgap.Clone
 
ID - Static variable in class org.molgenis.omx.xgap.DerivedTrait
 
ID - Static variable in class org.molgenis.omx.xgap.EnvironmentalFactor
 
ID - Static variable in class org.molgenis.omx.xgap.Gene
 
ID - Static variable in class org.molgenis.omx.xgap.Marker
 
ID - Static variable in class org.molgenis.omx.xgap.MassPeak
 
ID - Static variable in class org.molgenis.omx.xgap.Metabolite
 
ID - Static variable in class org.molgenis.omx.xgap.NMRBin
 
ID - Static variable in class org.molgenis.omx.xgap.PairedSample
 
ID - Static variable in class org.molgenis.omx.xgap.Polymorphism
 
ID - Static variable in class org.molgenis.omx.xgap.Probe
 
ID - Static variable in class org.molgenis.omx.xgap.ProbeSet
 
ID - Static variable in class org.molgenis.omx.xgap.Protein
 
ID - Static variable in class org.molgenis.omx.xgap.Sample
 
ID - Static variable in class org.molgenis.omx.xgap.SNP
 
ID - Static variable in class org.molgenis.omx.xgap.Spot
 
ID - Static variable in class org.molgenis.omx.xgap.Track
 
ID - Static variable in class org.molgenis.omx.xgap.Transcript
 
ID - Static variable in class org.molgenis.omx.xgap.Variant
 
IDMUTATION - Static variable in class org.molgenis.omx.xgap.Variant
 
INDIVIDUAL - Static variable in class org.molgenis.omx.xgap.Sample
 
INHERITANCE - Static variable in class org.molgenis.omx.xgap.Variant
 
init(FilterConfig) - Method in class org.molgenis.omx.das.impl.DasURLFilter
 
init(ServletContext, Map<String, PropertyType>, DataSourceConfiguration) - Method in class org.molgenis.omx.das.impl.RepositoryRangeHandlingDataSource
 
ISAUTOSOMAL - Static variable in class org.molgenis.omx.xgap.Chromosome
 

J

JDBCMetaDatabase - Class in org.molgenis
This class is an in memory representation of the contents of your *_db.xml file Utility of this class is to allow for dynamic querying and/or user interfacing for example within a query tool or a security module.
JDBCMetaDatabase() - Constructor for class org.molgenis.JDBCMetaDatabase
 

L

LABEL1 - Static variable in class org.molgenis.omx.xgap.PairedSample
 
LABEL2 - Static variable in class org.molgenis.omx.xgap.PairedSample
 
Locus - Interface in org.molgenis.omx.xgap
Locus: position.

M

Marker - Class in org.molgenis.omx.xgap
Marker: Trait annotations specific for markers..
Marker() - Constructor for class org.molgenis.omx.xgap.Marker
 
MARKER - Static variable in class org.molgenis.omx.xgap.Marker_ReportsFor
 
Marker_ReportsFor - Class in org.molgenis.omx.xgap
Marker_ReportsFor: Link table for many-to-many relationship 'Marker.ReportsFor'..
Marker_ReportsFor() - Constructor for class org.molgenis.omx.xgap.Marker_ReportsFor
 
Marker_ReportsForMetaData - Class in org.molgenis.omx.xgap
 
Marker_ReportsForMetaData() - Constructor for class org.molgenis.omx.xgap.Marker_ReportsForMetaData
 
Marker_ReportsForRepository - Class in org.molgenis.omx.xgap
 
Marker_ReportsForRepository(EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.Marker_ReportsForRepository
 
Marker_ReportsForRepository(EntityManager, EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.Marker_ReportsForRepository
For testing purposes
MarkerMetaData - Class in org.molgenis.omx.xgap
 
MarkerMetaData() - Constructor for class org.molgenis.omx.xgap.MarkerMetaData
 
MarkerRepository - Class in org.molgenis.omx.xgap
 
MarkerRepository(EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.MarkerRepository
 
MarkerRepository(EntityManager, EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.MarkerRepository
For testing purposes
MASS - Static variable in class org.molgenis.omx.xgap.Metabolite
 
MASS - Static variable in class org.molgenis.omx.xgap.Protein
 
MassPeak - Class in org.molgenis.omx.xgap
MassPeak: A peak that has been selected within a mass spectrometry experiment..
MassPeak() - Constructor for class org.molgenis.omx.xgap.MassPeak
 
MassPeakMetaData - Class in org.molgenis.omx.xgap
 
MassPeakMetaData() - Constructor for class org.molgenis.omx.xgap.MassPeakMetaData
 
MassPeakRepository - Class in org.molgenis.omx.xgap
 
MassPeakRepository(EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.MassPeakRepository
 
MassPeakRepository(EntityManager, EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.MassPeakRepository
For testing purposes
Metabolite - Class in org.molgenis.omx.xgap
Metabolite: Trait annotations specific for metabolites.
Metabolite() - Constructor for class org.molgenis.omx.xgap.Metabolite
 
MetaboliteMetaData - Class in org.molgenis.omx.xgap
 
MetaboliteMetaData() - Constructor for class org.molgenis.omx.xgap.MetaboliteMetaData
 
MetaboliteRepository - Class in org.molgenis.omx.xgap
 
MetaboliteRepository(EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.MetaboliteRepository
 
MetaboliteRepository(EntityManager, EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.MetaboliteRepository
For testing purposes
MISMATCH - Static variable in class org.molgenis.omx.xgap.Probe
 
MolgenisDasTarget - Class in org.molgenis.omx.das.impl
 
MolgenisDasTarget(String, int, int, String) - Constructor for class org.molgenis.omx.das.impl.MolgenisDasTarget
 
MUTATIONPOSITION - Static variable in class org.molgenis.omx.xgap.Variant
 
MZ - Static variable in class org.molgenis.omx.xgap.MassPeak
 

N

NMRBin - Class in org.molgenis.omx.xgap
NMRBin: Shift of the NMR frequency due to the chemical environment..
NMRBin() - Constructor for class org.molgenis.omx.xgap.NMRBin
 
NMRBinMetaData - Class in org.molgenis.omx.xgap
 
NMRBinMetaData() - Constructor for class org.molgenis.omx.xgap.NMRBinMetaData
 
NMRBinRepository - Class in org.molgenis.omx.xgap
 
NMRBinRepository(EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.NMRBinRepository
 
NMRBinRepository(EntityManager, EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.NMRBinRepository
For testing purposes
NTCHANGE - Static variable in class org.molgenis.omx.xgap.Variant
 

O

onStartup(ServletContext) - Method in class org.molgenis.omx.das.impl.WebAppInitializer
 
ORDERNR - Static variable in class org.molgenis.omx.xgap.Chromosome
 
org.molgenis - package org.molgenis
 
org.molgenis.omx.das - package org.molgenis.omx.das
 
org.molgenis.omx.das.impl - package org.molgenis.omx.das.impl
 
org.molgenis.omx.patient - package org.molgenis.omx.patient
 
org.molgenis.omx.xgap - package org.molgenis.omx.xgap
 
ORIENTATION - Static variable in class org.molgenis.omx.xgap.Gene
 

P

PairedSample - Class in org.molgenis.omx.xgap
PairedSample: A pair of samples labeled for a two-color microarray experiment..
PairedSample() - Constructor for class org.molgenis.omx.xgap.PairedSample
 
PairedSampleMetaData - Class in org.molgenis.omx.xgap
 
PairedSampleMetaData() - Constructor for class org.molgenis.omx.xgap.PairedSampleMetaData
 
PairedSampleRepository - Class in org.molgenis.omx.xgap
 
PairedSampleRepository(EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.PairedSampleRepository
 
PairedSampleRepository(EntityManager, EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.PairedSampleRepository
For testing purposes
PATHOGENICITY - Static variable in class org.molgenis.omx.xgap.Variant
 
Patient - Class in org.molgenis.omx.patient
Patient: .
Patient() - Constructor for class org.molgenis.omx.patient.Patient
 
PatientMetaData - Class in org.molgenis.omx.patient
 
PatientMetaData() - Constructor for class org.molgenis.omx.patient.PatientMetaData
 
PatientRepository - Class in org.molgenis.omx.patient
 
PatientRepository(EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.patient.PatientRepository
 
PatientRepository(EntityManager, EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.patient.PatientRepository
For testing purposes
PHENO - Static variable in class org.molgenis.omx.patient.Patient
 
Polymorphism - Class in org.molgenis.omx.xgap
Polymorphism: The difference of a single base discovered between two sequenced individuals..
Polymorphism() - Constructor for class org.molgenis.omx.xgap.Polymorphism
 
POLYMORPHISM - Static variable in class org.molgenis.omx.xgap.SNP
 
POLYMORPHISM - Static variable in class org.molgenis.omx.xgap.SNP_Polymorphism
 
PolymorphismMetaData - Class in org.molgenis.omx.xgap
 
PolymorphismMetaData() - Constructor for class org.molgenis.omx.xgap.PolymorphismMetaData
 
PolymorphismRepository - Class in org.molgenis.omx.xgap
 
PolymorphismRepository(EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.PolymorphismRepository
 
PolymorphismRepository(EntityManager, EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.PolymorphismRepository
For testing purposes
Probe - Class in org.molgenis.omx.xgap
Probe: A piece of sequence that reports for the expression of a gene, typically spotted onto a microarray..
Probe() - Constructor for class org.molgenis.omx.xgap.Probe
 
ProbeMetaData - Class in org.molgenis.omx.xgap
 
ProbeMetaData() - Constructor for class org.molgenis.omx.xgap.ProbeMetaData
 
ProbeRepository - Class in org.molgenis.omx.xgap
 
ProbeRepository(EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.ProbeRepository
 
ProbeRepository(EntityManager, EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.ProbeRepository
For testing purposes
PROBESET - Static variable in class org.molgenis.omx.xgap.Probe
 
ProbeSet - Class in org.molgenis.omx.xgap
ProbeSet: A set of Probes.
ProbeSet() - Constructor for class org.molgenis.omx.xgap.ProbeSet
 
ProbeSetMetaData - Class in org.molgenis.omx.xgap
 
ProbeSetMetaData() - Constructor for class org.molgenis.omx.xgap.ProbeSetMetaData
 
ProbeSetRepository - Class in org.molgenis.omx.xgap
 
ProbeSetRepository(EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.ProbeSetRepository
 
ProbeSetRepository(EntityManager, EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.ProbeSetRepository
For testing purposes
Protein - Class in org.molgenis.omx.xgap
Protein: Trait annotations specific for proteins..
Protein() - Constructor for class org.molgenis.omx.xgap.Protein
 
ProteinMetaData - Class in org.molgenis.omx.xgap
 
ProteinMetaData() - Constructor for class org.molgenis.omx.xgap.ProteinMetaData
 
ProteinRepository - Class in org.molgenis.omx.xgap
 
ProteinRepository(EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.ProteinRepository
 
ProteinRepository(EntityManager, EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.ProteinRepository
For testing purposes
PUBMEDID - Static variable in class org.molgenis.omx.patient.Patient
 

Q

queryDataSet(String, String, int) - Method in class org.molgenis.omx.das.impl.RepositoryRangeHandlingDataSource
 

R

RangeHandlingDataSource - Class in org.molgenis.omx.das
 
RangeHandlingDataSource() - Constructor for class org.molgenis.omx.das.RangeHandlingDataSource
 
REFERENCE - Static variable in class org.molgenis.omx.patient.Patient
 
REPORTEDSNP - Static variable in class org.molgenis.omx.xgap.Variant
 
REPORTSFOR - Static variable in class org.molgenis.omx.xgap.Marker
 
REPORTSFOR - Static variable in class org.molgenis.omx.xgap.Marker_ReportsFor
 
REPORTSFOR - Static variable in class org.molgenis.omx.xgap.Probe
 
RepositoryRangeHandlingDataSource - Class in org.molgenis.omx.das.impl
 
RepositoryRangeHandlingDataSource() - Constructor for class org.molgenis.omx.das.impl.RepositoryRangeHandlingDataSource
 
RETENTIONTIME - Static variable in class org.molgenis.omx.xgap.MassPeak
 

S

Sample - Class in org.molgenis.omx.xgap
Sample: .
Sample() - Constructor for class org.molgenis.omx.xgap.Sample
 
SampleMetaData - Class in org.molgenis.omx.xgap
 
SampleMetaData() - Constructor for class org.molgenis.omx.xgap.SampleMetaData
 
SampleRepository - Class in org.molgenis.omx.xgap
 
SampleRepository(EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.SampleRepository
 
SampleRepository(EntityManager, EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.SampleRepository
For testing purposes
SEQ - Static variable in class org.molgenis.omx.xgap.Clone
 
SEQ - Static variable in class org.molgenis.omx.xgap.Gene
 
SEQ - Static variable in class org.molgenis.omx.xgap.Marker
 
SEQ - Static variable in class org.molgenis.omx.xgap.Probe
 
SEQ - Static variable in class org.molgenis.omx.xgap.ProbeSet
 
SEQ - Static variable in class org.molgenis.omx.xgap.Variant
 
set(Entity, boolean) - Method in class org.molgenis.omx.patient.Patient
 
set(String, Object) - Method in class org.molgenis.omx.patient.Patient
 
set(Entity, boolean) - Method in class org.molgenis.omx.xgap.Chromosome
 
set(String, Object) - Method in class org.molgenis.omx.xgap.Chromosome
 
set(Entity, boolean) - Method in class org.molgenis.omx.xgap.Clone
 
set(String, Object) - Method in class org.molgenis.omx.xgap.Clone
 
set(Entity, boolean) - Method in class org.molgenis.omx.xgap.DerivedTrait
 
set(String, Object) - Method in class org.molgenis.omx.xgap.DerivedTrait
 
set(Entity, boolean) - Method in class org.molgenis.omx.xgap.EnvironmentalFactor
 
set(String, Object) - Method in class org.molgenis.omx.xgap.EnvironmentalFactor
 
set(Entity, boolean) - Method in class org.molgenis.omx.xgap.Gene
 
set(String, Object) - Method in class org.molgenis.omx.xgap.Gene
 
set(Entity, boolean) - Method in class org.molgenis.omx.xgap.Marker
 
set(String, Object) - Method in class org.molgenis.omx.xgap.Marker
 
set(Entity, boolean) - Method in class org.molgenis.omx.xgap.Marker_ReportsFor
 
set(String, Object) - Method in class org.molgenis.omx.xgap.Marker_ReportsFor
 
set(Entity, boolean) - Method in class org.molgenis.omx.xgap.MassPeak
 
set(String, Object) - Method in class org.molgenis.omx.xgap.MassPeak
 
set(Entity, boolean) - Method in class org.molgenis.omx.xgap.Metabolite
 
set(String, Object) - Method in class org.molgenis.omx.xgap.Metabolite
 
set(Entity, boolean) - Method in class org.molgenis.omx.xgap.NMRBin
 
set(String, Object) - Method in class org.molgenis.omx.xgap.NMRBin
 
set(Entity, boolean) - Method in class org.molgenis.omx.xgap.PairedSample
 
set(String, Object) - Method in class org.molgenis.omx.xgap.PairedSample
 
set(Entity, boolean) - Method in class org.molgenis.omx.xgap.Polymorphism
 
set(String, Object) - Method in class org.molgenis.omx.xgap.Polymorphism
 
set(Entity, boolean) - Method in class org.molgenis.omx.xgap.Probe
 
set(String, Object) - Method in class org.molgenis.omx.xgap.Probe
 
set(Entity, boolean) - Method in class org.molgenis.omx.xgap.ProbeSet
 
set(String, Object) - Method in class org.molgenis.omx.xgap.ProbeSet
 
set(Entity, boolean) - Method in class org.molgenis.omx.xgap.Protein
 
set(String, Object) - Method in class org.molgenis.omx.xgap.Protein
 
set(Entity, boolean) - Method in class org.molgenis.omx.xgap.Sample
 
set(String, Object) - Method in class org.molgenis.omx.xgap.Sample
 
set(Entity, boolean) - Method in class org.molgenis.omx.xgap.SNP
 
set(String, Object) - Method in class org.molgenis.omx.xgap.SNP
 
set(Entity, boolean) - Method in class org.molgenis.omx.xgap.SNP_Polymorphism
 
set(String, Object) - Method in class org.molgenis.omx.xgap.SNP_Polymorphism
 
set(Entity, boolean) - Method in class org.molgenis.omx.xgap.Spot
 
set(String, Object) - Method in class org.molgenis.omx.xgap.Spot
 
set(Entity, boolean) - Method in class org.molgenis.omx.xgap.Track
 
set(String, Object) - Method in class org.molgenis.omx.xgap.Track
 
set(Entity, boolean) - Method in class org.molgenis.omx.xgap.Transcript
 
set(String, Object) - Method in class org.molgenis.omx.xgap.Transcript
 
set(Entity, boolean) - Method in class org.molgenis.omx.xgap.Variant
 
set(String, Object) - Method in class org.molgenis.omx.xgap.Variant
 
setAaNotation(String) - Method in class org.molgenis.omx.xgap.Variant
Set the .
setAaPosition(Integer) - Method in class org.molgenis.omx.xgap.Variant
Set the .
setAllele1(Variant) - Method in class org.molgenis.omx.patient.Patient
Set the .
setAllele2(Variant) - Method in class org.molgenis.omx.patient.Patient
Set the .
setAminoSequence(String) - Method in class org.molgenis.omx.xgap.Protein
Set the The aminoacid sequence..
setAutoid(Integer) - Method in class org.molgenis.omx.xgap.Marker_ReportsFor
Set the automatic id field to ensure ordering of mrefs.
setAutoid(Integer) - Method in class org.molgenis.omx.xgap.SNP_Polymorphism
Set the automatic id field to ensure ordering of mrefs.
setBase(String) - Method in class org.molgenis.omx.xgap.Polymorphism
Set the The affected DNA base.
setBpEnd(Long) - Method in class org.molgenis.omx.xgap.Clone
Set the numeric basepair postion (3') on the chromosome.
setBpEnd(Long) - Method in class org.molgenis.omx.xgap.Gene
Set the numeric basepair postion (3') on the chromosome.
setBpEnd(Long) - Method in interface org.molgenis.omx.xgap.Locus
 
setBpEnd(Long) - Method in class org.molgenis.omx.xgap.Marker
Set the numeric basepair postion (3') on the chromosome.
setBpEnd(Long) - Method in class org.molgenis.omx.xgap.Probe
Set the numeric basepair postion (3') on the chromosome.
setBpEnd(Long) - Method in class org.molgenis.omx.xgap.ProbeSet
Set the numeric basepair postion (3') on the chromosome.
setBpEnd(Long) - Method in class org.molgenis.omx.xgap.Variant
Set the numeric basepair postion (3') on the chromosome.
setBpLength(Integer) - Method in class org.molgenis.omx.xgap.Chromosome
Set the Lenght of the chromsome in base pairs..
setBpStart(Long) - Method in class org.molgenis.omx.xgap.Clone
Set the numeric basepair postion (5') on the chromosome.
setBpStart(Long) - Method in class org.molgenis.omx.xgap.Gene
Set the numeric basepair postion (5') on the chromosome.
setBpStart(Long) - Method in interface org.molgenis.omx.xgap.Locus
 
setBpStart(Long) - Method in class org.molgenis.omx.xgap.Marker
Set the numeric basepair postion (5') on the chromosome.
setBpStart(Long) - Method in class org.molgenis.omx.xgap.Probe
Set the numeric basepair postion (5') on the chromosome.
setBpStart(Long) - Method in class org.molgenis.omx.xgap.ProbeSet
Set the numeric basepair postion (5') on the chromosome.
setBpStart(Long) - Method in class org.molgenis.omx.xgap.Variant
Set the numeric basepair postion (5') on the chromosome.
setCdnaNotation(String) - Method in class org.molgenis.omx.xgap.Variant
Set the .
setCdnaPosition(Integer) - Method in class org.molgenis.omx.xgap.Variant
Set the .
setChromosome(Chromosome) - Method in class org.molgenis.omx.xgap.Clone
Set the Reference to the chromosome this position belongs to..
setChromosome(Chromosome) - Method in class org.molgenis.omx.xgap.Gene
Set the Reference to the chromosome this position belongs to..
setChromosome(Chromosome) - Method in interface org.molgenis.omx.xgap.Locus
 
setChromosome(Chromosome) - Method in class org.molgenis.omx.xgap.Marker
Set the Reference to the chromosome this position belongs to..
setChromosome(Chromosome) - Method in class org.molgenis.omx.xgap.Probe
Set the Reference to the chromosome this position belongs to..
setChromosome(Chromosome) - Method in class org.molgenis.omx.xgap.ProbeSet
Set the Reference to the chromosome this position belongs to..
setChromosome(Chromosome) - Method in class org.molgenis.omx.xgap.Variant
Set the Reference to the chromosome this position belongs to..
setCM(Double) - Method in class org.molgenis.omx.xgap.Clone
Set the genetic map position in centi morgan (cM)..
setCM(Double) - Method in class org.molgenis.omx.xgap.Gene
Set the genetic map position in centi morgan (cM)..
setCM(Double) - Method in interface org.molgenis.omx.xgap.Locus
 
setCM(Double) - Method in class org.molgenis.omx.xgap.Marker
Set the genetic map position in centi morgan (cM)..
setCM(Double) - Method in class org.molgenis.omx.xgap.Probe
Set the genetic map position in centi morgan (cM)..
setCM(Double) - Method in class org.molgenis.omx.xgap.ProbeSet
Set the genetic map position in centi morgan (cM)..
setCM(Double) - Method in class org.molgenis.omx.xgap.Variant
Set the genetic map position in centi morgan (cM)..
setCodonchange(String) - Method in class org.molgenis.omx.xgap.Variant
Set the .
setConsequence(String) - Method in class org.molgenis.omx.xgap.Variant
Set the .
setControl(Boolean) - Method in class org.molgenis.omx.xgap.Gene
Set the Indicating whether this is a 'housekeeping' gene that can be used as control..
setDetailsForMutation(String) - Method in class org.molgenis.omx.xgap.Variant
Set the .
setEffectOnSplicing(Boolean) - Method in class org.molgenis.omx.xgap.Variant
Set the .
setEvent(String) - Method in class org.molgenis.omx.xgap.Variant
Set the .
setExon(String) - Method in class org.molgenis.omx.xgap.Variant
Set the .
setFormula(String) - Method in class org.molgenis.omx.xgap.Metabolite
Set the The chemical formula of a metabolite..
setGdnaNotation(String) - Method in class org.molgenis.omx.xgap.Variant
Set the .
setGene(Gene) - Method in class org.molgenis.omx.xgap.Protein
Set the The gene that produces this protein.
setGene(Gene) - Method in class org.molgenis.omx.xgap.Transcript
Set the The gene that produces this protein.
setGene(String) - Method in class org.molgenis.omx.xgap.Variant
Set the .
setGridX(Integer) - Method in class org.molgenis.omx.xgap.Spot
Set the Meta Row.
setGridY(Integer) - Method in class org.molgenis.omx.xgap.Spot
Set the Meta Column.
setIdMutation(Integer) - Method in class org.molgenis.omx.xgap.Variant
Set the .
setIndividual(Individual) - Method in class org.molgenis.omx.xgap.Sample
Set the The individual from which this sample was taken..
setInheritance(String) - Method in class org.molgenis.omx.xgap.Variant
Set the .
setIsAutosomal(Boolean) - Method in class org.molgenis.omx.xgap.Chromosome
Set the Is 'yes' when number of chromosomes is equal in male and female individuals, i.e., if not a sex chromosome..
setLabel1(OntologyTerm) - Method in class org.molgenis.omx.xgap.PairedSample
Set the Which channel or Fluorescent labeling is associated with the first subject.
setLabel2(OntologyTerm) - Method in class org.molgenis.omx.xgap.PairedSample
Set the Which channel or Fluorescent labeling is associated with the second subject.
setMarker(Marker) - Method in class org.molgenis.omx.xgap.Marker_ReportsFor
Set the .
setMass(Double) - Method in class org.molgenis.omx.xgap.Metabolite
Set the The mass of this metabolite.
setMass(Double) - Method in class org.molgenis.omx.xgap.Protein
Set the The mass of this metabolite.
setMismatch(Boolean) - Method in class org.molgenis.omx.xgap.Probe
Set the Indicating whether the probe is a match.
setMutationPosition(Integer) - Method in class org.molgenis.omx.xgap.Variant
Set the .
setMZ(Double) - Method in class org.molgenis.omx.xgap.MassPeak
Set the Mass over charge ratio of this peak..
setNtChange(String) - Method in class org.molgenis.omx.xgap.Variant
Set the .
setOrderNr(Integer) - Method in class org.molgenis.omx.xgap.Chromosome
Set the .
setOrientation(String) - Method in class org.molgenis.omx.xgap.Gene
Set the Orientation of the gene on the genome (F=forward, R=reverse).
setPathogenicity(String) - Method in class org.molgenis.omx.xgap.Variant
Set the .
setPheno(String) - Method in class org.molgenis.omx.patient.Patient
Set the .
setPolymorphism(List<Polymorphism>) - Method in class org.molgenis.omx.xgap.SNP
Set the The polymorphism that belongs to this SNP..
setPolymorphism(Polymorphism) - Method in class org.molgenis.omx.xgap.SNP_Polymorphism
Set the .
setPolymorphismSNPCollection(Collection<SNP>) - Method in class org.molgenis.omx.xgap.Polymorphism
 
setProbeSet(ProbeSet) - Method in class org.molgenis.omx.xgap.Probe
Set the Optional: probeset this probe belongs to (e.g., in Affymetrix assays)..
setPubMedID(String) - Method in class org.molgenis.omx.patient.Patient
Set the .
setReference(String) - Method in class org.molgenis.omx.patient.Patient
Set the .
setReportedSNP(Boolean) - Method in class org.molgenis.omx.xgap.Variant
Set the .
setReportsFor(List<Marker>) - Method in class org.molgenis.omx.xgap.Marker
Set the The marker (or a subclass like 'SNP') this marker (or a subclass like 'SNP') reports for..
setReportsFor(Marker) - Method in class org.molgenis.omx.xgap.Marker_ReportsFor
Set the .
setReportsFor(Gene) - Method in class org.molgenis.omx.xgap.Probe
Set the The gene this probe reports for..
setReportsForMarkerCollection(Collection<Marker>) - Method in class org.molgenis.omx.xgap.Marker
 
setRetentionTime(Double) - Method in class org.molgenis.omx.xgap.MassPeak
Set the The retention-time of this peak in minutes..
setSeq(String) - Method in class org.molgenis.omx.xgap.Clone
Set the The FASTA text representation of the sequence..
setSeq(String) - Method in class org.molgenis.omx.xgap.Gene
Set the The FASTA text representation of the sequence..
setSeq(String) - Method in interface org.molgenis.omx.xgap.Locus
 
setSeq(String) - Method in class org.molgenis.omx.xgap.Marker
Set the The FASTA text representation of the sequence..
setSeq(String) - Method in class org.molgenis.omx.xgap.Probe
Set the The FASTA text representation of the sequence..
setSeq(String) - Method in class org.molgenis.omx.xgap.ProbeSet
Set the The FASTA text representation of the sequence..
setSeq(String) - Method in class org.molgenis.omx.xgap.Variant
Set the The FASTA text representation of the sequence..
setSNP(SNP) - Method in class org.molgenis.omx.xgap.SNP_Polymorphism
Set the .
setSpecies(OntologyTerm) - Method in class org.molgenis.omx.xgap.Chromosome
Set the Reference to the species this chromosome belongs to..
setStatus(String) - Method in class org.molgenis.omx.xgap.SNP
Set the The status of this SNP, eg 'confirmed'..
setStructure(String) - Method in class org.molgenis.omx.xgap.Metabolite
Set the The chemical structure of a metabolite (in SMILES representation)..
setSubject1(Individual) - Method in class org.molgenis.omx.xgap.PairedSample
Set the The first subject.
setSubject2(Individual) - Method in class org.molgenis.omx.xgap.PairedSample
Set the The second sample.
setSymbol(String) - Method in class org.molgenis.omx.xgap.Clone
Set the todo.
setSymbol(String) - Method in class org.molgenis.omx.xgap.Gene
Set the Main symbol this gene is known by (not necessarily unique, in constrast to 'name').
setSymbol(String) - Method in interface org.molgenis.omx.xgap.Locus
 
setSymbol(String) - Method in class org.molgenis.omx.xgap.Marker
Set the todo.
setSymbol(String) - Method in class org.molgenis.omx.xgap.Probe
Set the todo.
setSymbol(String) - Method in class org.molgenis.omx.xgap.ProbeSet
Set the todo.
setSymbol(String) - Method in class org.molgenis.omx.xgap.Variant
Set the todo.
setTissue(OntologyTerm) - Method in class org.molgenis.omx.xgap.Sample
Set the The tissue from which this sample was taken..
setTrack(Track) - Method in class org.molgenis.omx.xgap.Variant
Set the .
setTranscript(Transcript) - Method in class org.molgenis.omx.xgap.Protein
Set the The transcript variant that produces this protein.
setValue(String) - Method in class org.molgenis.omx.xgap.Polymorphism
Set the The strain/genotype for which this polymorphism was discovered.
setVariantLength(Integer) - Method in class org.molgenis.omx.xgap.Variant
Set the .
setX(Integer) - Method in class org.molgenis.omx.xgap.Spot
Set the Row.
setY(Integer) - Method in class org.molgenis.omx.xgap.Spot
Set the Column.
SNP - Class in org.molgenis.omx.xgap
SNP: A SNP is a special kind of Marker, but can also be seen as a phenotype to map against in some cases.
SNP() - Constructor for class org.molgenis.omx.xgap.SNP
 
SNP - Static variable in class org.molgenis.omx.xgap.SNP_Polymorphism
 
SNP_Polymorphism - Class in org.molgenis.omx.xgap
SNP_Polymorphism: Link table for many-to-many relationship 'SNP.Polymorphism'..
SNP_Polymorphism() - Constructor for class org.molgenis.omx.xgap.SNP_Polymorphism
 
SNP_PolymorphismMetaData - Class in org.molgenis.omx.xgap
 
SNP_PolymorphismMetaData() - Constructor for class org.molgenis.omx.xgap.SNP_PolymorphismMetaData
 
SNP_PolymorphismRepository - Class in org.molgenis.omx.xgap
 
SNP_PolymorphismRepository(EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.SNP_PolymorphismRepository
 
SNP_PolymorphismRepository(EntityManager, EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.SNP_PolymorphismRepository
For testing purposes
SNPMetaData - Class in org.molgenis.omx.xgap
 
SNPMetaData() - Constructor for class org.molgenis.omx.xgap.SNPMetaData
 
SNPRepository - Class in org.molgenis.omx.xgap
 
SNPRepository(EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.SNPRepository
 
SNPRepository(EntityManager, EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.SNPRepository
For testing purposes
SPECIES - Static variable in class org.molgenis.omx.xgap.Chromosome
 
Spot - Class in org.molgenis.omx.xgap
Spot: This is the spot on a microarray.
Spot() - Constructor for class org.molgenis.omx.xgap.Spot
 
SpotMetaData - Class in org.molgenis.omx.xgap
 
SpotMetaData() - Constructor for class org.molgenis.omx.xgap.SpotMetaData
 
SpotRepository - Class in org.molgenis.omx.xgap
 
SpotRepository(EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.SpotRepository
 
SpotRepository(EntityManager, EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.SpotRepository
For testing purposes
STATUS - Static variable in class org.molgenis.omx.xgap.SNP
 
STRUCTURE - Static variable in class org.molgenis.omx.xgap.Metabolite
 
SUBJECT1 - Static variable in class org.molgenis.omx.xgap.PairedSample
 
SUBJECT2 - Static variable in class org.molgenis.omx.xgap.PairedSample
 
SYMBOL - Static variable in class org.molgenis.omx.xgap.Clone
 
SYMBOL - Static variable in class org.molgenis.omx.xgap.Gene
 
SYMBOL - Static variable in class org.molgenis.omx.xgap.Marker
 
SYMBOL - Static variable in class org.molgenis.omx.xgap.Probe
 
SYMBOL - Static variable in class org.molgenis.omx.xgap.ProbeSet
 
SYMBOL - Static variable in class org.molgenis.omx.xgap.Variant
 

T

TISSUE - Static variable in class org.molgenis.omx.xgap.Sample
 
toString() - Method in class org.molgenis.omx.patient.Patient
 
toString(boolean) - Method in class org.molgenis.omx.patient.Patient
 
toString() - Method in class org.molgenis.omx.xgap.Chromosome
 
toString(boolean) - Method in class org.molgenis.omx.xgap.Chromosome
 
toString() - Method in class org.molgenis.omx.xgap.Clone
 
toString(boolean) - Method in class org.molgenis.omx.xgap.Clone
 
toString() - Method in class org.molgenis.omx.xgap.DerivedTrait
 
toString(boolean) - Method in class org.molgenis.omx.xgap.DerivedTrait
 
toString() - Method in class org.molgenis.omx.xgap.EnvironmentalFactor
 
toString(boolean) - Method in class org.molgenis.omx.xgap.EnvironmentalFactor
 
toString() - Method in class org.molgenis.omx.xgap.Gene
 
toString(boolean) - Method in class org.molgenis.omx.xgap.Gene
 
toString() - Method in class org.molgenis.omx.xgap.Marker
 
toString(boolean) - Method in class org.molgenis.omx.xgap.Marker
 
toString() - Method in class org.molgenis.omx.xgap.Marker_ReportsFor
 
toString(boolean) - Method in class org.molgenis.omx.xgap.Marker_ReportsFor
 
toString() - Method in class org.molgenis.omx.xgap.MassPeak
 
toString(boolean) - Method in class org.molgenis.omx.xgap.MassPeak
 
toString() - Method in class org.molgenis.omx.xgap.Metabolite
 
toString(boolean) - Method in class org.molgenis.omx.xgap.Metabolite
 
toString() - Method in class org.molgenis.omx.xgap.NMRBin
 
toString(boolean) - Method in class org.molgenis.omx.xgap.NMRBin
 
toString() - Method in class org.molgenis.omx.xgap.PairedSample
 
toString(boolean) - Method in class org.molgenis.omx.xgap.PairedSample
 
toString() - Method in class org.molgenis.omx.xgap.Polymorphism
 
toString(boolean) - Method in class org.molgenis.omx.xgap.Polymorphism
 
toString() - Method in class org.molgenis.omx.xgap.Probe
 
toString(boolean) - Method in class org.molgenis.omx.xgap.Probe
 
toString() - Method in class org.molgenis.omx.xgap.ProbeSet
 
toString(boolean) - Method in class org.molgenis.omx.xgap.ProbeSet
 
toString() - Method in class org.molgenis.omx.xgap.Protein
 
toString(boolean) - Method in class org.molgenis.omx.xgap.Protein
 
toString() - Method in class org.molgenis.omx.xgap.Sample
 
toString(boolean) - Method in class org.molgenis.omx.xgap.Sample
 
toString() - Method in class org.molgenis.omx.xgap.SNP
 
toString(boolean) - Method in class org.molgenis.omx.xgap.SNP
 
toString() - Method in class org.molgenis.omx.xgap.SNP_Polymorphism
 
toString(boolean) - Method in class org.molgenis.omx.xgap.SNP_Polymorphism
 
toString() - Method in class org.molgenis.omx.xgap.Spot
 
toString(boolean) - Method in class org.molgenis.omx.xgap.Spot
 
toString() - Method in class org.molgenis.omx.xgap.Track
 
toString(boolean) - Method in class org.molgenis.omx.xgap.Track
 
toString() - Method in class org.molgenis.omx.xgap.Transcript
 
toString(boolean) - Method in class org.molgenis.omx.xgap.Transcript
 
toString() - Method in class org.molgenis.omx.xgap.Variant
 
toString(boolean) - Method in class org.molgenis.omx.xgap.Variant
 
Track - Class in org.molgenis.omx.xgap
Track: .
Track() - Constructor for class org.molgenis.omx.xgap.Track
 
TRACK - Static variable in class org.molgenis.omx.xgap.Variant
 
TrackMetaData - Class in org.molgenis.omx.xgap
 
TrackMetaData() - Constructor for class org.molgenis.omx.xgap.TrackMetaData
 
TrackRepository - Class in org.molgenis.omx.xgap
 
TrackRepository(EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.TrackRepository
 
TrackRepository(EntityManager, EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.TrackRepository
For testing purposes
TRANSCRIPT - Static variable in class org.molgenis.omx.xgap.Protein
 
Transcript - Class in org.molgenis.omx.xgap
Transcript: Trait annotations specific for transcripts.
Transcript() - Constructor for class org.molgenis.omx.xgap.Transcript
 
TranscriptMetaData - Class in org.molgenis.omx.xgap
 
TranscriptMetaData() - Constructor for class org.molgenis.omx.xgap.TranscriptMetaData
 
TranscriptRepository - Class in org.molgenis.omx.xgap
 
TranscriptRepository(EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.TranscriptRepository
 
TranscriptRepository(EntityManager, EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.TranscriptRepository
For testing purposes

V

VALUE - Static variable in class org.molgenis.omx.xgap.Polymorphism
 
Variant - Class in org.molgenis.omx.xgap
Variant: A SNP is a special kind of Marker, but can also be seen as a phenotype to map against in some cases.
Variant() - Constructor for class org.molgenis.omx.xgap.Variant
 
VARIANTLENGTH - Static variable in class org.molgenis.omx.xgap.Variant
 
VariantMetaData - Class in org.molgenis.omx.xgap
 
VariantMetaData() - Constructor for class org.molgenis.omx.xgap.VariantMetaData
 
VariantRepository - Class in org.molgenis.omx.xgap
 
VariantRepository(EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.VariantRepository
 
VariantRepository(EntityManager, EntityValidator, QueryResolver) - Constructor for class org.molgenis.omx.xgap.VariantRepository
For testing purposes

W

WebAppInitializer - Class in org.molgenis.omx.das.impl
 
WebAppInitializer() - Constructor for class org.molgenis.omx.das.impl.WebAppInitializer
 

X

X - Static variable in class org.molgenis.omx.xgap.Spot
 

Y

Y - Static variable in class org.molgenis.omx.xgap.Spot
 
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