A B C D E F G H I L M N O P Q R S T U 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

AccessionSecurityDecorator<E extends Accession> - Class in org.molgenis.omx.observ.target.db

TODO add column level security filters

AccessionSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.target.db.AccessionSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.auth.db.InstituteSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.auth.db.PersonRoleSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.auth.db.PersonSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.core.db.MolgenisEntitySecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.core.db.MolgenisFileSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.core.db.RuntimePropertySecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.db.CategorySecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.db.CharacteristicSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.db.DataSetSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.db.ObservableFeatureSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.db.ObservationSetSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.db.ObservationTargetSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.db.ObservedValueSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.db.ProtocolSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.target.db.AccessionSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.target.db.IndividualSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.target.db.OntologySecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.target.db.OntologyTermSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.target.db.PanelSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.target.db.PanelSourceSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.target.db.SpeciesSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.value.db.BoolValueSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.value.db.DateValueSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.value.db.DecimalValueSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.value.db.EmailValueSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.value.db.HtmlValueSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.value.db.IntValueSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.value.db.LongValueSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.value.db.MrefValueSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.value.db.StringValueSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.value.db.TextValueSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.value.db.ValueSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.observ.value.db.XrefValueSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.patient.db.PatientSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.xgap.db.ChromosomeSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.xgap.db.CloneSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.xgap.db.DerivedTraitSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.xgap.db.GeneSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.xgap.db.Marker_ReportsForSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.xgap.db.MarkerSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.xgap.db.MassPeakSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.xgap.db.MetaboliteSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.xgap.db.NMRBinSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.xgap.db.PairedSampleSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.xgap.db.PolymorphismSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.xgap.db.ProbeSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.xgap.db.ProbeSetSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.xgap.db.ProteinSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.xgap.db.SampleSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.xgap.db.SNP_PolymorphismSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.xgap.db.SNPSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.xgap.db.SpotSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.xgap.db.TrackSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.xgap.db.TranscriptSecurityDecorator

add(List<E>) - Method in class org.molgenis.omx.xgap.db.VariantSecurityDecorator

ALLELE1 - Static variable in class org.molgenis.omx.patient.Patient

ALLELE1_IDENTIFIER - Static variable in class org.molgenis.omx.patient.Patient

ALLELE2 - Static variable in class org.molgenis.omx.patient.Patient

ALLELE2_IDENTIFIER - 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

BoolValueSecurityDecorator<E extends BoolValue> - Class in org.molgenis.omx.observ.value.db

TODO add column level security filters

BoolValueSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.value.db.BoolValueSecurityDecorator

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

CategoricalValueSecurityDecorator<E extends CategoricalValue> - Class in org.molgenis.omx.observ.value.db

TODO add column level security filters

CategoricalValueSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.value.db.CategoricalValueSecurityDecorator

CategorySecurityDecorator<E extends Category> - Class in org.molgenis.omx.observ.db

TODO add column level security filters

CategorySecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.db.CategorySecurityDecorator

CDNANOTATION - Static variable in class org.molgenis.omx.xgap.Variant

CDNAPOSITION - Static variable in class org.molgenis.omx.xgap.Variant

CharacteristicSecurityDecorator<E extends Characteristic> - Class in org.molgenis.omx.observ.db

TODO add column level security filters

CharacteristicSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.db.CharacteristicSecurityDecorator

Chromosome - Class in org.molgenis.omx.xgap

Chromosome: .

Chromosome() - Constructor for class org.molgenis.omx.xgap.Chromosome

Chromosome(Chromosome) - Constructor for class org.molgenis.omx.xgap.Chromosome

copy constructor

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

CHROMOSOME_IDENTIFIER - Static variable in class org.molgenis.omx.xgap.Clone

CHROMOSOME_IDENTIFIER - Static variable in class org.molgenis.omx.xgap.Gene

CHROMOSOME_IDENTIFIER - Static variable in class org.molgenis.omx.xgap.Marker

CHROMOSOME_IDENTIFIER - Static variable in class org.molgenis.omx.xgap.Probe

CHROMOSOME_IDENTIFIER - Static variable in class org.molgenis.omx.xgap.ProbeSet

CHROMOSOME_IDENTIFIER - Static variable in class org.molgenis.omx.xgap.Variant

ChromosomeEntityImporter - Class in org.molgenis.omx.xgap.db

Reads Chromosome from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

ChromosomeEntityImporter() - Constructor for class org.molgenis.omx.xgap.db.ChromosomeEntityImporter

ChromosomeJpaMapper - Class in org.molgenis.omx.xgap.db

ChromosomeJpaMapper(Database) - Constructor for class org.molgenis.omx.xgap.db.ChromosomeJpaMapper

ChromosomeSecurityDecorator<E extends Chromosome> - Class in org.molgenis.omx.xgap.db

TODO add column level security filters

ChromosomeSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.ChromosomeSecurityDecorator

ChromosomeService - Class in org.molgenis.service

ChromosomeService() - Constructor for class org.molgenis.service.ChromosomeService

Clone - Class in org.molgenis.omx.xgap

Clone: BAC clone fragment..

Clone() - Constructor for class org.molgenis.omx.xgap.Clone

Clone(Clone) - Constructor for class org.molgenis.omx.xgap.Clone

copy constructor

CloneEntityImporter - Class in org.molgenis.omx.xgap.db

Reads Clone from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

CloneEntityImporter() - Constructor for class org.molgenis.omx.xgap.db.CloneEntityImporter

CloneJpaMapper - Class in org.molgenis.omx.xgap.db

CloneJpaMapper(Database) - Constructor for class org.molgenis.omx.xgap.db.CloneJpaMapper

CloneSecurityDecorator<E extends Clone> - Class in org.molgenis.omx.xgap.db

TODO add column level security filters

CloneSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.CloneSecurityDecorator

CloneService - Class in org.molgenis.service

CloneService() - Constructor for class org.molgenis.service.CloneService

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

count(QueryRule...) - Method in class org.molgenis.omx.auth.db.InstituteSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.auth.db.PersonRoleSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.auth.db.PersonSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.core.db.MolgenisEntitySecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.core.db.MolgenisFileSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.core.db.RuntimePropertySecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.db.CategorySecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.db.CharacteristicSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.db.DataSetSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.db.ObservableFeatureSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.db.ObservationSetSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.db.ObservationTargetSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.db.ObservedValueSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.db.ProtocolSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.target.db.AccessionSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.target.db.IndividualSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.target.db.OntologySecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.target.db.OntologyTermSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.target.db.PanelSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.target.db.PanelSourceSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.target.db.SpeciesSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.BoolValueSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.DateValueSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.DecimalValueSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.EmailValueSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.HtmlValueSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.IntValueSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.LongValueSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.MrefValueSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.StringValueSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.TextValueSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.ValueSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.XrefValueSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.patient.db.PatientSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.xgap.db.ChromosomeSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.xgap.db.CloneSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.xgap.db.DerivedTraitSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.xgap.db.GeneSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.xgap.db.Marker_ReportsForSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.xgap.db.MarkerSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.xgap.db.MassPeakSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.xgap.db.MetaboliteSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.xgap.db.NMRBinSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.xgap.db.PairedSampleSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.xgap.db.PolymorphismSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.xgap.db.ProbeSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.xgap.db.ProbeSetSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.xgap.db.ProteinSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.xgap.db.SampleSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.xgap.db.SNP_PolymorphismSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.xgap.db.SNPSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.xgap.db.SpotSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.xgap.db.TrackSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.xgap.db.TranscriptSecurityDecorator

count(QueryRule...) - Method in class org.molgenis.omx.xgap.db.VariantSecurityDecorator

create(Patient) - Method in class org.molgenis.omx.patient.db.PatientJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.patient.db.PatientJpaMapper

create(Entity) - Method in class org.molgenis.omx.patient.Patient

create(Entity) - Method in class org.molgenis.omx.xgap.Chromosome

create(Entity) - Method in class org.molgenis.omx.xgap.Clone

create(Chromosome) - Method in class org.molgenis.omx.xgap.db.ChromosomeJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.xgap.db.ChromosomeJpaMapper

create(Clone) - Method in class org.molgenis.omx.xgap.db.CloneJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.xgap.db.CloneJpaMapper

create(DerivedTrait) - Method in class org.molgenis.omx.xgap.db.DerivedTraitJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.xgap.db.DerivedTraitJpaMapper

create(EnvironmentalFactor) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorJpaMapper

create(Gene) - Method in class org.molgenis.omx.xgap.db.GeneJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.xgap.db.GeneJpaMapper

create(Marker_ReportsFor) - Method in class org.molgenis.omx.xgap.db.Marker_ReportsForJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.xgap.db.Marker_ReportsForJpaMapper

create(Marker) - Method in class org.molgenis.omx.xgap.db.MarkerJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.xgap.db.MarkerJpaMapper

create(MassPeak) - Method in class org.molgenis.omx.xgap.db.MassPeakJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.xgap.db.MassPeakJpaMapper

create(Metabolite) - Method in class org.molgenis.omx.xgap.db.MetaboliteJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.xgap.db.MetaboliteJpaMapper

create(NMRBin) - Method in class org.molgenis.omx.xgap.db.NMRBinJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.xgap.db.NMRBinJpaMapper

create(PairedSample) - Method in class org.molgenis.omx.xgap.db.PairedSampleJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.xgap.db.PairedSampleJpaMapper

create(Polymorphism) - Method in class org.molgenis.omx.xgap.db.PolymorphismJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.xgap.db.PolymorphismJpaMapper

create(Probe) - Method in class org.molgenis.omx.xgap.db.ProbeJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.xgap.db.ProbeJpaMapper

create(ProbeSet) - Method in class org.molgenis.omx.xgap.db.ProbeSetJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.xgap.db.ProbeSetJpaMapper

create(Protein) - Method in class org.molgenis.omx.xgap.db.ProteinJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.xgap.db.ProteinJpaMapper

create(Sample) - Method in class org.molgenis.omx.xgap.db.SampleJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.xgap.db.SampleJpaMapper

create(SNP_Polymorphism) - Method in class org.molgenis.omx.xgap.db.SNP_PolymorphismJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.xgap.db.SNP_PolymorphismJpaMapper

create(SNP) - Method in class org.molgenis.omx.xgap.db.SNPJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.xgap.db.SNPJpaMapper

create(Spot) - Method in class org.molgenis.omx.xgap.db.SpotJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.xgap.db.SpotJpaMapper

create(Track) - Method in class org.molgenis.omx.xgap.db.TrackJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.xgap.db.TrackJpaMapper

create(Transcript) - Method in class org.molgenis.omx.xgap.db.TranscriptJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.xgap.db.TranscriptJpaMapper

create(Variant) - Method in class org.molgenis.omx.xgap.db.VariantJpaMapper

This method first saves the objects that are being refered to by entity, then the entity itself and finally the objects that refer to this object

create() - Method in class org.molgenis.omx.xgap.db.VariantJpaMapper

create(Entity) - Method in class org.molgenis.omx.xgap.DerivedTrait

create(Entity) - Method in class org.molgenis.omx.xgap.EnvironmentalFactor

create(Entity) - Method in class org.molgenis.omx.xgap.Gene

create(Entity) - Method in class org.molgenis.omx.xgap.Marker

create(Entity) - Method in class org.molgenis.omx.xgap.Marker_ReportsFor

create(Entity) - Method in class org.molgenis.omx.xgap.MassPeak

create(Entity) - Method in class org.molgenis.omx.xgap.Metabolite

create(Entity) - Method in class org.molgenis.omx.xgap.NMRBin

create(Entity) - Method in class org.molgenis.omx.xgap.PairedSample

create(Entity) - Method in class org.molgenis.omx.xgap.Polymorphism

create(Entity) - Method in class org.molgenis.omx.xgap.Probe

create(Entity) - Method in class org.molgenis.omx.xgap.ProbeSet

create(Entity) - Method in class org.molgenis.omx.xgap.Protein

create(Entity) - Method in class org.molgenis.omx.xgap.Sample

create(Entity) - Method in class org.molgenis.omx.xgap.SNP

create(Entity) - Method in class org.molgenis.omx.xgap.SNP_Polymorphism

create(Entity) - Method in class org.molgenis.omx.xgap.Spot

create(Entity) - Method in class org.molgenis.omx.xgap.Track

create(Entity) - Method in class org.molgenis.omx.xgap.Transcript

create(Entity) - Method in class org.molgenis.omx.xgap.Variant

create(Chromosome) - Method in class org.molgenis.service.ChromosomeService

create(Clone) - Method in class org.molgenis.service.CloneService

create(DerivedTrait) - Method in class org.molgenis.service.DerivedTraitService

create(EnvironmentalFactor) - Method in class org.molgenis.service.EnvironmentalFactorService

create(Gene) - Method in class org.molgenis.service.GeneService

create(Marker) - Method in class org.molgenis.service.MarkerService

create(MassPeak) - Method in class org.molgenis.service.MassPeakService

create(Metabolite) - Method in class org.molgenis.service.MetaboliteService

create(NMRBin) - Method in class org.molgenis.service.NMRBinService

create(PairedSample) - Method in class org.molgenis.service.PairedSampleService

create(Patient) - Method in class org.molgenis.service.PatientService

create(Polymorphism) - Method in class org.molgenis.service.PolymorphismService

create(Probe) - Method in class org.molgenis.service.ProbeService

create(ProbeSet) - Method in class org.molgenis.service.ProbeSetService

create(Protein) - Method in class org.molgenis.service.ProteinService

create(Sample) - Method in class org.molgenis.service.SampleService

create(SNP) - Method in class org.molgenis.service.SNPService

create(Spot) - Method in class org.molgenis.service.SpotService

create(Track) - Method in class org.molgenis.service.TrackService

create(Transcript) - Method in class org.molgenis.service.TranscriptService

create(Variant) - Method in class org.molgenis.service.VariantService

createDasFeature(Variant) - Method in class org.molgenis.omx.das.DasOmxDataSource

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.auth.db.InstituteSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.auth.db.PersonRoleSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.auth.db.PersonSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.core.db.MolgenisEntitySecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.core.db.MolgenisFileSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.core.db.RuntimePropertySecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.db.CategorySecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.db.CharacteristicSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.db.DataSetSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.db.ObservableFeatureSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.db.ObservationSetSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.db.ObservationTargetSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.db.ObservedValueSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.db.ProtocolSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.target.db.AccessionSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.target.db.IndividualSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.target.db.OntologySecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.target.db.OntologyTermSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.target.db.PanelSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.target.db.PanelSourceSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.target.db.SpeciesSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.BoolValueSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.DateValueSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.DecimalValueSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.EmailValueSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.HtmlValueSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.IntValueSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.LongValueSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.MrefValueSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.StringValueSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.TextValueSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.ValueSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.observ.value.db.XrefValueSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.patient.db.PatientJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.patient.db.PatientSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.ChromosomeJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.ChromosomeSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.CloneJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.CloneSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.DerivedTraitJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.DerivedTraitSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.GeneJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.GeneSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.Marker_ReportsForJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.Marker_ReportsForSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.MarkerJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.MarkerSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.MassPeakJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.MassPeakSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.MetaboliteJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.MetaboliteSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.NMRBinJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.NMRBinSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.PairedSampleJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.PairedSampleSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.PolymorphismJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.PolymorphismSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.ProbeJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.ProbeSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.ProbeSetJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.ProbeSetSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.ProteinJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.ProteinSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.SampleJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.SampleSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.SNP_PolymorphismJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.SNP_PolymorphismSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.SNPJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.SNPSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.SpotJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.SpotSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.TrackJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.TrackSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.TranscriptJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.TranscriptSecurityDecorator

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.VariantJpaMapper

createFindSqlInclRules(QueryRule[]) - Method in class org.molgenis.omx.xgap.db.VariantSecurityDecorator

createList(int) - Method in class org.molgenis.omx.patient.db.PatientJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.xgap.db.ChromosomeJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.xgap.db.CloneJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.xgap.db.DerivedTraitJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.xgap.db.GeneJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.xgap.db.Marker_ReportsForJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.xgap.db.MarkerJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.xgap.db.MassPeakJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.xgap.db.MetaboliteJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.xgap.db.NMRBinJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.xgap.db.PairedSampleJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.xgap.db.PolymorphismJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.xgap.db.ProbeJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.xgap.db.ProbeSetJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.xgap.db.ProteinJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.xgap.db.SampleJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.xgap.db.SNP_PolymorphismJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.xgap.db.SNPJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.xgap.db.SpotJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.xgap.db.TrackJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.xgap.db.TranscriptJpaMapper

Return EMPTY list of given allocated size

createList(int) - Method in class org.molgenis.omx.xgap.db.VariantJpaMapper

Return EMPTY list of given allocated size

D

DasOmxDataSource - Class in org.molgenis.omx.das

DasOmxDataSource(Database) - Constructor for class org.molgenis.omx.das.DasOmxDataSource

DasOmxDataSource() - Constructor for class org.molgenis.omx.das.DasOmxDataSource

DasPatientFilter - Class in org.molgenis.omx.das

DasPatientFilter() - Constructor for class org.molgenis.omx.das.DasPatientFilter

DataSetSecurityDecorator<E extends DataSet> - Class in org.molgenis.omx.observ.db

TODO add column level security filters

DataSetSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.db.DataSetSecurityDecorator

DateTimeValueSecurityDecorator<E extends DateTimeValue> - Class in org.molgenis.omx.observ.value.db

TODO add column level security filters

DateTimeValueSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.value.db.DateTimeValueSecurityDecorator

DateValueSecurityDecorator<E extends DateValue> - Class in org.molgenis.omx.observ.value.db

TODO add column level security filters

DateValueSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.value.db.DateValueSecurityDecorator

DecimalValueSecurityDecorator<E extends DecimalValue> - Class in org.molgenis.omx.observ.value.db

TODO add column level security filters

DecimalValueSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.value.db.DecimalValueSecurityDecorator

deleteById(Integer) - Method in class org.molgenis.service.ChromosomeService

deleteById(Integer) - Method in class org.molgenis.service.CloneService

deleteById(Integer) - Method in class org.molgenis.service.DerivedTraitService

deleteById(Integer) - Method in class org.molgenis.service.EnvironmentalFactorService

deleteById(Integer) - Method in class org.molgenis.service.GeneService

deleteById(Integer) - Method in class org.molgenis.service.MarkerService

deleteById(Integer) - Method in class org.molgenis.service.MassPeakService

deleteById(Integer) - Method in class org.molgenis.service.MetaboliteService

deleteById(Integer) - Method in class org.molgenis.service.NMRBinService

deleteById(Integer) - Method in class org.molgenis.service.PairedSampleService

deleteById(Integer) - Method in class org.molgenis.service.PatientService

deleteById(Integer) - Method in class org.molgenis.service.PolymorphismService

deleteById(Integer) - Method in class org.molgenis.service.ProbeService

deleteById(Integer) - Method in class org.molgenis.service.ProbeSetService

deleteById(Integer) - Method in class org.molgenis.service.ProteinService

deleteById(Integer) - Method in class org.molgenis.service.SampleService

deleteById(Integer) - Method in class org.molgenis.service.SNPService

deleteById(Integer) - Method in class org.molgenis.service.SpotService

deleteById(Integer) - Method in class org.molgenis.service.TrackService

deleteById(Integer) - Method in class org.molgenis.service.TranscriptService

deleteById(Integer) - Method in class org.molgenis.service.VariantService

DerivedTrait - Class in org.molgenis.omx.xgap

DerivedTrait: Any meta trait, eg.

DerivedTrait() - Constructor for class org.molgenis.omx.xgap.DerivedTrait

DerivedTrait(DerivedTrait) - Constructor for class org.molgenis.omx.xgap.DerivedTrait

copy constructor

DerivedTraitEntityImporter - Class in org.molgenis.omx.xgap.db

Reads DerivedTrait from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

DerivedTraitEntityImporter() - Constructor for class org.molgenis.omx.xgap.db.DerivedTraitEntityImporter

DerivedTraitJpaMapper - Class in org.molgenis.omx.xgap.db

DerivedTraitJpaMapper(Database) - Constructor for class org.molgenis.omx.xgap.db.DerivedTraitJpaMapper

DerivedTraitSecurityDecorator<E extends DerivedTrait> - Class in org.molgenis.omx.xgap.db

TODO add column level security filters

DerivedTraitSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.DerivedTraitSecurityDecorator

DerivedTraitService - Class in org.molgenis.service

DerivedTraitService() - Constructor for class org.molgenis.service.DerivedTraitService

DESCRIPTION - Static variable in class org.molgenis.omx.xgap.Variant

destroy() - Method in class org.molgenis.omx.das.DasOmxDataSource

destroy() - Method in class org.molgenis.omx.das.DasPatientFilter

destroy(Patient) - Method in class org.molgenis.omx.patient.db.PatientJpaMapper

destroy(Chromosome) - Method in class org.molgenis.omx.xgap.db.ChromosomeJpaMapper

destroy(Clone) - Method in class org.molgenis.omx.xgap.db.CloneJpaMapper

destroy(DerivedTrait) - Method in class org.molgenis.omx.xgap.db.DerivedTraitJpaMapper

destroy(EnvironmentalFactor) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorJpaMapper

destroy(Gene) - Method in class org.molgenis.omx.xgap.db.GeneJpaMapper

destroy(Marker_ReportsFor) - Method in class org.molgenis.omx.xgap.db.Marker_ReportsForJpaMapper

destroy(Marker) - Method in class org.molgenis.omx.xgap.db.MarkerJpaMapper

destroy(MassPeak) - Method in class org.molgenis.omx.xgap.db.MassPeakJpaMapper

destroy(Metabolite) - Method in class org.molgenis.omx.xgap.db.MetaboliteJpaMapper

destroy(NMRBin) - Method in class org.molgenis.omx.xgap.db.NMRBinJpaMapper

destroy(PairedSample) - Method in class org.molgenis.omx.xgap.db.PairedSampleJpaMapper

destroy(Polymorphism) - Method in class org.molgenis.omx.xgap.db.PolymorphismJpaMapper

destroy(Probe) - Method in class org.molgenis.omx.xgap.db.ProbeJpaMapper

destroy(ProbeSet) - Method in class org.molgenis.omx.xgap.db.ProbeSetJpaMapper

destroy(Protein) - Method in class org.molgenis.omx.xgap.db.ProteinJpaMapper

destroy(Sample) - Method in class org.molgenis.omx.xgap.db.SampleJpaMapper

destroy(SNP_Polymorphism) - Method in class org.molgenis.omx.xgap.db.SNP_PolymorphismJpaMapper

destroy(SNP) - Method in class org.molgenis.omx.xgap.db.SNPJpaMapper

destroy(Spot) - Method in class org.molgenis.omx.xgap.db.SpotJpaMapper

destroy(Track) - Method in class org.molgenis.omx.xgap.db.TrackJpaMapper

destroy(Transcript) - Method in class org.molgenis.omx.xgap.db.TranscriptJpaMapper

destroy(Variant) - Method in class org.molgenis.omx.xgap.db.VariantJpaMapper

DETAILSFORMUTATION - Static variable in class org.molgenis.omx.xgap.Variant

doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class org.molgenis.omx.das.DasPatientFilter

E

edit(Patient) - Method in class org.molgenis.omx.patient.db.PatientJpaMapper

edit(Chromosome) - Method in class org.molgenis.omx.xgap.db.ChromosomeJpaMapper

edit(Clone) - Method in class org.molgenis.omx.xgap.db.CloneJpaMapper

edit(DerivedTrait) - Method in class org.molgenis.omx.xgap.db.DerivedTraitJpaMapper

edit(EnvironmentalFactor) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorJpaMapper

edit(Gene) - Method in class org.molgenis.omx.xgap.db.GeneJpaMapper

edit(Marker_ReportsFor) - Method in class org.molgenis.omx.xgap.db.Marker_ReportsForJpaMapper

edit(Marker) - Method in class org.molgenis.omx.xgap.db.MarkerJpaMapper

edit(MassPeak) - Method in class org.molgenis.omx.xgap.db.MassPeakJpaMapper

edit(Metabolite) - Method in class org.molgenis.omx.xgap.db.MetaboliteJpaMapper

edit(NMRBin) - Method in class org.molgenis.omx.xgap.db.NMRBinJpaMapper

edit(PairedSample) - Method in class org.molgenis.omx.xgap.db.PairedSampleJpaMapper

edit(Polymorphism) - Method in class org.molgenis.omx.xgap.db.PolymorphismJpaMapper

edit(Probe) - Method in class org.molgenis.omx.xgap.db.ProbeJpaMapper

edit(ProbeSet) - Method in class org.molgenis.omx.xgap.db.ProbeSetJpaMapper

edit(Protein) - Method in class org.molgenis.omx.xgap.db.ProteinJpaMapper

edit(Sample) - Method in class org.molgenis.omx.xgap.db.SampleJpaMapper

edit(SNP_Polymorphism) - Method in class org.molgenis.omx.xgap.db.SNP_PolymorphismJpaMapper

edit(SNP) - Method in class org.molgenis.omx.xgap.db.SNPJpaMapper

edit(Spot) - Method in class org.molgenis.omx.xgap.db.SpotJpaMapper

edit(Track) - Method in class org.molgenis.omx.xgap.db.TrackJpaMapper

edit(Transcript) - Method in class org.molgenis.omx.xgap.db.TranscriptJpaMapper

edit(Variant) - Method in class org.molgenis.omx.xgap.db.VariantJpaMapper

EFFECTONSPLICING - Static variable in class org.molgenis.omx.xgap.Variant

EmailValueSecurityDecorator<E extends EmailValue> - Class in org.molgenis.omx.observ.value.db

TODO add column level security filters

EmailValueSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.value.db.EmailValueSecurityDecorator

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

EnvironmentalFactor(EnvironmentalFactor) - Constructor for class org.molgenis.omx.xgap.EnvironmentalFactor

copy constructor

EnvironmentalFactorEntityImporter - Class in org.molgenis.omx.xgap.db

Reads EnvironmentalFactor from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

EnvironmentalFactorEntityImporter() - Constructor for class org.molgenis.omx.xgap.db.EnvironmentalFactorEntityImporter

EnvironmentalFactorJpaMapper - Class in org.molgenis.omx.xgap.db

EnvironmentalFactorJpaMapper(Database) - Constructor for class org.molgenis.omx.xgap.db.EnvironmentalFactorJpaMapper

EnvironmentalFactorSecurityDecorator<E extends EnvironmentalFactor> - Class in org.molgenis.omx.xgap.db

TODO add column level security filters

EnvironmentalFactorSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.EnvironmentalFactorSecurityDecorator

EnvironmentalFactorService - Class in org.molgenis.service

EnvironmentalFactorService() - Constructor for class org.molgenis.service.EnvironmentalFactorService

equals(Object) - Method in class org.molgenis.omx.das.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

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.auth.db.InstituteSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.auth.db.PersonRoleSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.auth.db.PersonSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.core.db.MolgenisEntitySecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.core.db.MolgenisFileSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.core.db.RuntimePropertySecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.db.CategorySecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.db.CharacteristicSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.db.DataSetSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.db.ObservableFeatureSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.db.ObservationSetSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.db.ObservationTargetSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.db.ObservedValueSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.db.ProtocolSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.target.db.AccessionSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.target.db.IndividualSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.target.db.OntologySecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.target.db.OntologyTermSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.target.db.PanelSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.target.db.PanelSourceSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.target.db.SpeciesSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.BoolValueSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.DateValueSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.DecimalValueSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.EmailValueSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.HtmlValueSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.IntValueSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.LongValueSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.MrefValueSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.StringValueSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.TextValueSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.ValueSecurityDecorator

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.XrefValueSecurityDecorator

executeAdd(List<? extends Patient>) - Method in class org.molgenis.omx.patient.db.PatientJpaMapper

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.patient.db.PatientSecurityDecorator

executeAdd(List<? extends Chromosome>) - Method in class org.molgenis.omx.xgap.db.ChromosomeJpaMapper

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.ChromosomeSecurityDecorator

executeAdd(List<? extends Clone>) - Method in class org.molgenis.omx.xgap.db.CloneJpaMapper

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.CloneSecurityDecorator

executeAdd(List<? extends DerivedTrait>) - Method in class org.molgenis.omx.xgap.db.DerivedTraitJpaMapper

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.DerivedTraitSecurityDecorator

executeAdd(List<? extends EnvironmentalFactor>) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorJpaMapper

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorSecurityDecorator

executeAdd(List<? extends Gene>) - Method in class org.molgenis.omx.xgap.db.GeneJpaMapper

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.GeneSecurityDecorator

executeAdd(List<? extends Marker_ReportsFor>) - Method in class org.molgenis.omx.xgap.db.Marker_ReportsForJpaMapper

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.Marker_ReportsForSecurityDecorator

executeAdd(List<? extends Marker>) - Method in class org.molgenis.omx.xgap.db.MarkerJpaMapper

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.MarkerSecurityDecorator

executeAdd(List<? extends MassPeak>) - Method in class org.molgenis.omx.xgap.db.MassPeakJpaMapper

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.MassPeakSecurityDecorator

executeAdd(List<? extends Metabolite>) - Method in class org.molgenis.omx.xgap.db.MetaboliteJpaMapper

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.MetaboliteSecurityDecorator

executeAdd(List<? extends NMRBin>) - Method in class org.molgenis.omx.xgap.db.NMRBinJpaMapper

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.NMRBinSecurityDecorator

executeAdd(List<? extends PairedSample>) - Method in class org.molgenis.omx.xgap.db.PairedSampleJpaMapper

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.PairedSampleSecurityDecorator

executeAdd(List<? extends Polymorphism>) - Method in class org.molgenis.omx.xgap.db.PolymorphismJpaMapper

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.PolymorphismSecurityDecorator

executeAdd(List<? extends Probe>) - Method in class org.molgenis.omx.xgap.db.ProbeJpaMapper

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.ProbeSecurityDecorator

executeAdd(List<? extends ProbeSet>) - Method in class org.molgenis.omx.xgap.db.ProbeSetJpaMapper

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.ProbeSetSecurityDecorator

executeAdd(List<? extends Protein>) - Method in class org.molgenis.omx.xgap.db.ProteinJpaMapper

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.ProteinSecurityDecorator

executeAdd(List<? extends Sample>) - Method in class org.molgenis.omx.xgap.db.SampleJpaMapper

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.SampleSecurityDecorator

executeAdd(List<? extends SNP_Polymorphism>) - Method in class org.molgenis.omx.xgap.db.SNP_PolymorphismJpaMapper

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.SNP_PolymorphismSecurityDecorator

executeAdd(List<? extends SNP>) - Method in class org.molgenis.omx.xgap.db.SNPJpaMapper

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.SNPSecurityDecorator

executeAdd(List<? extends Spot>) - Method in class org.molgenis.omx.xgap.db.SpotJpaMapper

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.SpotSecurityDecorator

executeAdd(List<? extends Track>) - Method in class org.molgenis.omx.xgap.db.TrackJpaMapper

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.TrackSecurityDecorator

executeAdd(List<? extends Transcript>) - Method in class org.molgenis.omx.xgap.db.TranscriptJpaMapper

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.TranscriptSecurityDecorator

executeAdd(List<? extends Variant>) - Method in class org.molgenis.omx.xgap.db.VariantJpaMapper

executeAdd(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.VariantSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.auth.db.InstituteSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.auth.db.PersonRoleSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.auth.db.PersonSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.core.db.MolgenisEntitySecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.core.db.MolgenisFileSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.core.db.RuntimePropertySecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.db.CategorySecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.db.CharacteristicSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.db.DataSetSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.db.ObservableFeatureSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.db.ObservationSetSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.db.ObservationTargetSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.db.ObservedValueSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.db.ProtocolSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.target.db.AccessionSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.target.db.IndividualSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.target.db.OntologySecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.target.db.OntologyTermSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.target.db.PanelSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.target.db.PanelSourceSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.target.db.SpeciesSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.BoolValueSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.DateValueSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.DecimalValueSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.EmailValueSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.HtmlValueSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.IntValueSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.LongValueSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.MrefValueSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.StringValueSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.TextValueSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.ValueSecurityDecorator

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.XrefValueSecurityDecorator

executeRemove(List<? extends Patient>) - Method in class org.molgenis.omx.patient.db.PatientJpaMapper

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.patient.db.PatientSecurityDecorator

executeRemove(List<? extends Chromosome>) - Method in class org.molgenis.omx.xgap.db.ChromosomeJpaMapper

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.ChromosomeSecurityDecorator

executeRemove(List<? extends Clone>) - Method in class org.molgenis.omx.xgap.db.CloneJpaMapper

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.CloneSecurityDecorator

executeRemove(List<? extends DerivedTrait>) - Method in class org.molgenis.omx.xgap.db.DerivedTraitJpaMapper

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.DerivedTraitSecurityDecorator

executeRemove(List<? extends EnvironmentalFactor>) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorJpaMapper

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorSecurityDecorator

executeRemove(List<? extends Gene>) - Method in class org.molgenis.omx.xgap.db.GeneJpaMapper

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.GeneSecurityDecorator

executeRemove(List<? extends Marker_ReportsFor>) - Method in class org.molgenis.omx.xgap.db.Marker_ReportsForJpaMapper

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.Marker_ReportsForSecurityDecorator

executeRemove(List<? extends Marker>) - Method in class org.molgenis.omx.xgap.db.MarkerJpaMapper

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.MarkerSecurityDecorator

executeRemove(List<? extends MassPeak>) - Method in class org.molgenis.omx.xgap.db.MassPeakJpaMapper

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.MassPeakSecurityDecorator

executeRemove(List<? extends Metabolite>) - Method in class org.molgenis.omx.xgap.db.MetaboliteJpaMapper

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.MetaboliteSecurityDecorator

executeRemove(List<? extends NMRBin>) - Method in class org.molgenis.omx.xgap.db.NMRBinJpaMapper

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.NMRBinSecurityDecorator

executeRemove(List<? extends PairedSample>) - Method in class org.molgenis.omx.xgap.db.PairedSampleJpaMapper

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.PairedSampleSecurityDecorator

executeRemove(List<? extends Polymorphism>) - Method in class org.molgenis.omx.xgap.db.PolymorphismJpaMapper

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.PolymorphismSecurityDecorator

executeRemove(List<? extends Probe>) - Method in class org.molgenis.omx.xgap.db.ProbeJpaMapper

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.ProbeSecurityDecorator

executeRemove(List<? extends ProbeSet>) - Method in class org.molgenis.omx.xgap.db.ProbeSetJpaMapper

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.ProbeSetSecurityDecorator

executeRemove(List<? extends Protein>) - Method in class org.molgenis.omx.xgap.db.ProteinJpaMapper

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.ProteinSecurityDecorator

executeRemove(List<? extends Sample>) - Method in class org.molgenis.omx.xgap.db.SampleJpaMapper

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.SampleSecurityDecorator

executeRemove(List<? extends SNP_Polymorphism>) - Method in class org.molgenis.omx.xgap.db.SNP_PolymorphismJpaMapper

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.SNP_PolymorphismSecurityDecorator

executeRemove(List<? extends SNP>) - Method in class org.molgenis.omx.xgap.db.SNPJpaMapper

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.SNPSecurityDecorator

executeRemove(List<? extends Spot>) - Method in class org.molgenis.omx.xgap.db.SpotJpaMapper

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.SpotSecurityDecorator

executeRemove(List<? extends Track>) - Method in class org.molgenis.omx.xgap.db.TrackJpaMapper

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.TrackSecurityDecorator

executeRemove(List<? extends Transcript>) - Method in class org.molgenis.omx.xgap.db.TranscriptJpaMapper

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.TranscriptSecurityDecorator

executeRemove(List<? extends Variant>) - Method in class org.molgenis.omx.xgap.db.VariantJpaMapper

executeRemove(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.VariantSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.auth.db.InstituteSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.auth.db.PersonRoleSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.auth.db.PersonSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.core.db.MolgenisEntitySecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.core.db.MolgenisFileSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.core.db.RuntimePropertySecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.db.CategorySecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.db.CharacteristicSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.db.DataSetSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.db.ObservableFeatureSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.db.ObservationSetSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.db.ObservationTargetSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.db.ObservedValueSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.db.ProtocolSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.target.db.AccessionSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.target.db.IndividualSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.target.db.OntologySecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.target.db.OntologyTermSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.target.db.PanelSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.target.db.PanelSourceSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.target.db.SpeciesSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.BoolValueSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.DateValueSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.DecimalValueSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.EmailValueSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.HtmlValueSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.IntValueSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.LongValueSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.MrefValueSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.StringValueSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.TextValueSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.ValueSecurityDecorator

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.observ.value.db.XrefValueSecurityDecorator

executeUpdate(List<? extends Patient>) - Method in class org.molgenis.omx.patient.db.PatientJpaMapper

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.patient.db.PatientSecurityDecorator

executeUpdate(List<? extends Chromosome>) - Method in class org.molgenis.omx.xgap.db.ChromosomeJpaMapper

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.ChromosomeSecurityDecorator

executeUpdate(List<? extends Clone>) - Method in class org.molgenis.omx.xgap.db.CloneJpaMapper

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.CloneSecurityDecorator

executeUpdate(List<? extends DerivedTrait>) - Method in class org.molgenis.omx.xgap.db.DerivedTraitJpaMapper

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.DerivedTraitSecurityDecorator

executeUpdate(List<? extends EnvironmentalFactor>) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorJpaMapper

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorSecurityDecorator

executeUpdate(List<? extends Gene>) - Method in class org.molgenis.omx.xgap.db.GeneJpaMapper

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.GeneSecurityDecorator

executeUpdate(List<? extends Marker_ReportsFor>) - Method in class org.molgenis.omx.xgap.db.Marker_ReportsForJpaMapper

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.Marker_ReportsForSecurityDecorator

executeUpdate(List<? extends Marker>) - Method in class org.molgenis.omx.xgap.db.MarkerJpaMapper

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.MarkerSecurityDecorator

executeUpdate(List<? extends MassPeak>) - Method in class org.molgenis.omx.xgap.db.MassPeakJpaMapper

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.MassPeakSecurityDecorator

executeUpdate(List<? extends Metabolite>) - Method in class org.molgenis.omx.xgap.db.MetaboliteJpaMapper

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.MetaboliteSecurityDecorator

executeUpdate(List<? extends NMRBin>) - Method in class org.molgenis.omx.xgap.db.NMRBinJpaMapper

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.NMRBinSecurityDecorator

executeUpdate(List<? extends PairedSample>) - Method in class org.molgenis.omx.xgap.db.PairedSampleJpaMapper

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.PairedSampleSecurityDecorator

executeUpdate(List<? extends Polymorphism>) - Method in class org.molgenis.omx.xgap.db.PolymorphismJpaMapper

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.PolymorphismSecurityDecorator

executeUpdate(List<? extends Probe>) - Method in class org.molgenis.omx.xgap.db.ProbeJpaMapper

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.ProbeSecurityDecorator

executeUpdate(List<? extends ProbeSet>) - Method in class org.molgenis.omx.xgap.db.ProbeSetJpaMapper

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.ProbeSetSecurityDecorator

executeUpdate(List<? extends Protein>) - Method in class org.molgenis.omx.xgap.db.ProteinJpaMapper

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.ProteinSecurityDecorator

executeUpdate(List<? extends Sample>) - Method in class org.molgenis.omx.xgap.db.SampleJpaMapper

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.SampleSecurityDecorator

executeUpdate(List<? extends SNP_Polymorphism>) - Method in class org.molgenis.omx.xgap.db.SNP_PolymorphismJpaMapper

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.SNP_PolymorphismSecurityDecorator

executeUpdate(List<? extends SNP>) - Method in class org.molgenis.omx.xgap.db.SNPJpaMapper

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.SNPSecurityDecorator

executeUpdate(List<? extends Spot>) - Method in class org.molgenis.omx.xgap.db.SpotJpaMapper

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.SpotSecurityDecorator

executeUpdate(List<? extends Track>) - Method in class org.molgenis.omx.xgap.db.TrackJpaMapper

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.TrackSecurityDecorator

executeUpdate(List<? extends Transcript>) - Method in class org.molgenis.omx.xgap.db.TranscriptJpaMapper

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.TranscriptSecurityDecorator

executeUpdate(List<? extends Variant>) - Method in class org.molgenis.omx.xgap.db.VariantJpaMapper

executeUpdate(List<? extends E>) - Method in class org.molgenis.omx.xgap.db.VariantSecurityDecorator

EXON - Static variable in class org.molgenis.omx.xgap.Variant

F

find(QueryRule...) - Method in class org.molgenis.omx.auth.db.InstituteSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.auth.db.PersonRoleSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.auth.db.PersonSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.core.db.MolgenisEntitySecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.core.db.MolgenisFileSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.core.db.RuntimePropertySecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.db.CategorySecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.db.CharacteristicSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.db.DataSetSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.db.ObservableFeatureSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.db.ObservationSetSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.db.ObservationTargetSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.db.ObservedValueSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.db.ProtocolSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.target.db.AccessionSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.target.db.IndividualSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.target.db.OntologySecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.target.db.OntologyTermSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.target.db.PanelSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.target.db.PanelSourceSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.target.db.SpeciesSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.BoolValueSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.DateValueSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.DecimalValueSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.EmailValueSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.HtmlValueSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.IntValueSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.LongValueSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.MrefValueSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.StringValueSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.TextValueSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.ValueSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.observ.value.db.XrefValueSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.patient.db.PatientSecurityDecorator

find(Database, QueryRule...) - Static method in class org.molgenis.omx.patient.Patient

Shorthand for db.find(Patient.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.xgap.Chromosome

Shorthand for db.find(Chromosome.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.xgap.Clone

Shorthand for db.find(Clone.class, org.molgenis.framework.db.QueryRule ...

find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.ChromosomeSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.CloneSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.DerivedTraitSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.GeneSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.Marker_ReportsForSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.MarkerSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.MassPeakSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.MetaboliteSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.NMRBinSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.PairedSampleSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.PolymorphismSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.ProbeSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.ProbeSetSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.ProteinSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.SampleSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.SNP_PolymorphismSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.SNPSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.SpotSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.TrackSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.TranscriptSecurityDecorator

find(QueryRule...) - Method in class org.molgenis.omx.xgap.db.VariantSecurityDecorator

find(Database, QueryRule...) - Static method in class org.molgenis.omx.xgap.DerivedTrait

Shorthand for db.find(DerivedTrait.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.xgap.EnvironmentalFactor

Shorthand for db.find(EnvironmentalFactor.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.xgap.Gene

Shorthand for db.find(Gene.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.xgap.Marker

Shorthand for db.find(Marker.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.xgap.Marker_ReportsFor

Shorthand for db.find(Marker_ReportsFor.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.xgap.MassPeak

Shorthand for db.find(MassPeak.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.xgap.Metabolite

Shorthand for db.find(Metabolite.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.xgap.NMRBin

Shorthand for db.find(NMRBin.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.xgap.PairedSample

Shorthand for db.find(PairedSample.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.xgap.Polymorphism

Shorthand for db.find(Polymorphism.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.xgap.Probe

Shorthand for db.find(Probe.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.xgap.ProbeSet

Shorthand for db.find(ProbeSet.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.xgap.Protein

Shorthand for db.find(Protein.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.xgap.Sample

Shorthand for db.find(Sample.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.xgap.SNP

Shorthand for db.find(SNP.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.xgap.SNP_Polymorphism

Shorthand for db.find(SNP_Polymorphism.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.xgap.Spot

Shorthand for db.find(Spot.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.xgap.Track

Shorthand for db.find(Track.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.xgap.Transcript

Shorthand for db.find(Transcript.class, org.molgenis.framework.db.QueryRule ...

find(Database, QueryRule...) - Static method in class org.molgenis.omx.xgap.Variant

Shorthand for db.find(Variant.class, org.molgenis.framework.db.QueryRule ...

findByAutoid(Database, Integer) - Static method in class org.molgenis.omx.xgap.Marker_ReportsFor

findByAutoid(Database, Integer) - Static method in class org.molgenis.omx.xgap.SNP_Polymorphism

findById(Object) - Method in class org.molgenis.omx.auth.db.InstituteSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.auth.db.PersonRoleSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.auth.db.PersonSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.core.db.MolgenisEntitySecurityDecorator

findById(Object) - Method in class org.molgenis.omx.core.db.MolgenisFileSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.core.db.RuntimePropertySecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.db.CategorySecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.db.CharacteristicSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.db.DataSetSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.db.ObservableFeatureSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.db.ObservationSetSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.db.ObservationTargetSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.db.ObservedValueSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.db.ProtocolSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.target.db.AccessionSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.target.db.IndividualSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.target.db.OntologySecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.target.db.OntologyTermSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.target.db.PanelSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.target.db.PanelSourceSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.target.db.SpeciesSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.value.db.BoolValueSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.value.db.DateValueSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.value.db.DecimalValueSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.value.db.EmailValueSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.value.db.HtmlValueSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.value.db.IntValueSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.value.db.LongValueSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.value.db.MrefValueSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.value.db.StringValueSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.value.db.TextValueSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.value.db.ValueSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.observ.value.db.XrefValueSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.patient.db.PatientSecurityDecorator

findById(Database, Integer) - Static method in class org.molgenis.omx.patient.Patient

findById(Database, Integer) - Static method in class org.molgenis.omx.xgap.Chromosome

findById(Database, Integer) - Static method in class org.molgenis.omx.xgap.Clone

findById(Object) - Method in class org.molgenis.omx.xgap.db.ChromosomeSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.xgap.db.CloneSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.xgap.db.DerivedTraitSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.xgap.db.GeneSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.xgap.db.Marker_ReportsForSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.xgap.db.MarkerSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.xgap.db.MassPeakSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.xgap.db.MetaboliteSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.xgap.db.NMRBinSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.xgap.db.PairedSampleSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.xgap.db.PolymorphismSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.xgap.db.ProbeSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.xgap.db.ProbeSetSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.xgap.db.ProteinSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.xgap.db.SampleSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.xgap.db.SNP_PolymorphismSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.xgap.db.SNPSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.xgap.db.SpotSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.xgap.db.TrackSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.xgap.db.TranscriptSecurityDecorator

findById(Object) - Method in class org.molgenis.omx.xgap.db.VariantSecurityDecorator

findById(Database, Integer) - Static method in class org.molgenis.omx.xgap.DerivedTrait

findById(Database, Integer) - Static method in class org.molgenis.omx.xgap.EnvironmentalFactor

findById(Database, Integer) - Static method in class org.molgenis.omx.xgap.Gene

findById(Database, Integer) - Static method in class org.molgenis.omx.xgap.Marker

findById(Database, Integer) - Static method in class org.molgenis.omx.xgap.MassPeak

findById(Database, Integer) - Static method in class org.molgenis.omx.xgap.Metabolite

findById(Database, Integer) - Static method in class org.molgenis.omx.xgap.NMRBin

findById(Database, Integer) - Static method in class org.molgenis.omx.xgap.PairedSample

findById(Database, Integer) - Static method in class org.molgenis.omx.xgap.Polymorphism

findById(Database, Integer) - Static method in class org.molgenis.omx.xgap.Probe

findById(Database, Integer) - Static method in class org.molgenis.omx.xgap.ProbeSet

findById(Database, Integer) - Static method in class org.molgenis.omx.xgap.Protein

findById(Database, Integer) - Static method in class org.molgenis.omx.xgap.Sample

findById(Database, Integer) - Static method in class org.molgenis.omx.xgap.SNP

findById(Database, Integer) - Static method in class org.molgenis.omx.xgap.Spot

findById(Database, Integer) - Static method in class org.molgenis.omx.xgap.Track

findById(Database, Integer) - Static method in class org.molgenis.omx.xgap.Transcript

findById(Database, Integer) - Static method in class org.molgenis.omx.xgap.Variant

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.patient.Patient

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.xgap.Chromosome

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.xgap.Clone

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.xgap.DerivedTrait

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.xgap.EnvironmentalFactor

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.xgap.Gene

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.xgap.Marker

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.xgap.MassPeak

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.xgap.Metabolite

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.xgap.NMRBin

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.xgap.PairedSample

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.xgap.Polymorphism

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.xgap.Probe

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.xgap.ProbeSet

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.xgap.Protein

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.xgap.Sample

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.xgap.SNP

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.xgap.Spot

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.xgap.Track

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.xgap.Transcript

findByIdentifier(Database, String) - Static method in class org.molgenis.omx.xgap.Variant

findByPolymorphismSNP(Database, Integer, Integer) - Static method in class org.molgenis.omx.xgap.SNP_Polymorphism

findByReportsForMarker(Database, Integer, Integer) - Static method in class org.molgenis.omx.xgap.Marker_ReportsFor

findByXYGridXGridY(Database, Integer, Integer, Integer, Integer) - Static method in class org.molgenis.omx.xgap.Spot

findPatient(String) - Method in class org.molgenis.omx.das.DasOmxDataSource

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(Gene) - Constructor for class org.molgenis.omx.xgap.Gene

copy constructor

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

GENE_IDENTIFIER - Static variable in class org.molgenis.omx.xgap.Protein

GENE_IDENTIFIER - Static variable in class org.molgenis.omx.xgap.Transcript

GeneEntityImporter - Class in org.molgenis.omx.xgap.db

Reads Gene from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

GeneEntityImporter() - Constructor for class org.molgenis.omx.xgap.db.GeneEntityImporter

GeneJpaMapper - Class in org.molgenis.omx.xgap.db

GeneJpaMapper(Database) - Constructor for class org.molgenis.omx.xgap.db.GeneJpaMapper

GeneSecurityDecorator<E extends Gene> - Class in org.molgenis.omx.xgap.db

TODO add column level security filters

GeneSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.GeneSecurityDecorator

GeneService - Class in org.molgenis.service

GeneService() - Constructor for class org.molgenis.service.GeneService

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 AaNotation.

getAaNotation(Database) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

getAaPosition() - Method in class org.molgenis.omx.xgap.Variant

Get the AaPosition.

getAaPosition(Database) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

getAllele1() - Method in class org.molgenis.omx.patient.Patient

Get the Allele1.

getAllele1(Database) - Method in class org.molgenis.omx.patient.Patient

Deprecated.

getAllele1_Id() - Method in class org.molgenis.omx.patient.Patient

getAllele1_Identifier() - Method in class org.molgenis.omx.patient.Patient

Get a pretty label Identifier for cross reference Allele1 to Variant.Id.

getAllele2() - Method in class org.molgenis.omx.patient.Patient

Get the Allele2.

getAllele2(Database) - Method in class org.molgenis.omx.patient.Patient

Deprecated.

getAllele2_Id() - Method in class org.molgenis.omx.patient.Patient

getAllele2_Identifier() - Method in class org.molgenis.omx.patient.Patient

Get a pretty label Identifier for cross reference Allele2 to Variant.Id.

getAminoSequence() - Method in class org.molgenis.omx.xgap.Protein

Get the The aminoacid sequence..

getAminoSequence(Database) - Method in class org.molgenis.omx.xgap.Protein

Deprecated.

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.

getBase(Database) - Method in class org.molgenis.omx.xgap.Polymorphism

Deprecated.

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(Database) - Method in class org.molgenis.omx.xgap.Clone

Deprecated.

getBpEnd() - Method in class org.molgenis.omx.xgap.Gene

Get the numeric basepair postion (3') on the chromosome.

getBpEnd(Database) - Method in class org.molgenis.omx.xgap.Gene

Deprecated.

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(Database) - Method in class org.molgenis.omx.xgap.Marker

Deprecated.

getBpEnd() - Method in class org.molgenis.omx.xgap.Probe

Get the numeric basepair postion (3') on the chromosome.

getBpEnd(Database) - Method in class org.molgenis.omx.xgap.Probe

Deprecated.

getBpEnd() - Method in class org.molgenis.omx.xgap.ProbeSet

Get the numeric basepair postion (3') on the chromosome.

getBpEnd(Database) - Method in class org.molgenis.omx.xgap.ProbeSet

Deprecated.

getBpEnd() - Method in class org.molgenis.omx.xgap.Variant

Get the numeric basepair postion (3') on the chromosome.

getBpEnd(Database) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

getBpLength() - Method in class org.molgenis.omx.xgap.Chromosome

Get the Lenght of the chromsome in base pairs..

getBpLength(Database) - Method in class org.molgenis.omx.xgap.Chromosome

Deprecated.

getBpStart() - Method in class org.molgenis.omx.xgap.Clone

Get the numeric basepair postion (5') on the chromosome.

getBpStart(Database) - Method in class org.molgenis.omx.xgap.Clone

Deprecated.

getBpStart() - Method in class org.molgenis.omx.xgap.Gene

Get the numeric basepair postion (5') on the chromosome.

getBpStart(Database) - Method in class org.molgenis.omx.xgap.Gene

Deprecated.

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(Database) - Method in class org.molgenis.omx.xgap.Marker

Deprecated.

getBpStart() - Method in class org.molgenis.omx.xgap.Probe

Get the numeric basepair postion (5') on the chromosome.

getBpStart(Database) - Method in class org.molgenis.omx.xgap.Probe

Deprecated.

getBpStart() - Method in class org.molgenis.omx.xgap.ProbeSet

Get the numeric basepair postion (5') on the chromosome.

getBpStart(Database) - Method in class org.molgenis.omx.xgap.ProbeSet

Deprecated.

getBpStart() - Method in class org.molgenis.omx.xgap.Variant

Get the numeric basepair postion (5') on the chromosome.

getBpStart(Database) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

getCdnaNotation() - Method in class org.molgenis.omx.xgap.Variant

Get the CdnaNotation.

getCdnaNotation(Database) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

getCdnaPosition() - Method in class org.molgenis.omx.xgap.Variant

Get the CdnaPosition.

getCdnaPosition(Database) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

getChromosome(String) - Method in class org.molgenis.omx.das.DasOmxDataSource

getChromosome() - Method in class org.molgenis.omx.xgap.Clone

Get the Reference to the chromosome this position belongs to..

getChromosome(Database) - Method in class org.molgenis.omx.xgap.Clone

Deprecated.

getChromosome() - Method in class org.molgenis.omx.xgap.Gene

Get the Reference to the chromosome this position belongs to..

getChromosome(Database) - Method in class org.molgenis.omx.xgap.Gene

Deprecated.

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(Database) - Method in class org.molgenis.omx.xgap.Marker

Deprecated.

getChromosome() - Method in class org.molgenis.omx.xgap.Probe

Get the Reference to the chromosome this position belongs to..

getChromosome(Database) - Method in class org.molgenis.omx.xgap.Probe

Deprecated.

getChromosome() - Method in class org.molgenis.omx.xgap.ProbeSet

Get the Reference to the chromosome this position belongs to..

getChromosome(Database) - Method in class org.molgenis.omx.xgap.ProbeSet

Deprecated.

getChromosome() - Method in class org.molgenis.omx.xgap.Variant

Get the Reference to the chromosome this position belongs to..

getChromosome(Database) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

getChromosome_Id() - Method in class org.molgenis.omx.xgap.Clone

getChromosome_Id() - Method in class org.molgenis.omx.xgap.Gene

getChromosome_Id() - Method in interface org.molgenis.omx.xgap.Locus

getChromosome_Id() - Method in class org.molgenis.omx.xgap.Marker

getChromosome_Id() - Method in class org.molgenis.omx.xgap.Probe

getChromosome_Id() - Method in class org.molgenis.omx.xgap.ProbeSet

getChromosome_Id() - Method in class org.molgenis.omx.xgap.Variant

getChromosome_Identifier() - Method in class org.molgenis.omx.xgap.Clone

Get a pretty label Identifier for cross reference Chromosome to Chromosome.Id.

getChromosome_Identifier() - Method in class org.molgenis.omx.xgap.Gene

Get a pretty label Identifier for cross reference Chromosome to Chromosome.Id.

getChromosome_Identifier() - Method in interface org.molgenis.omx.xgap.Locus

getChromosome_Identifier() - Method in class org.molgenis.omx.xgap.Marker

Get a pretty label Identifier for cross reference Chromosome to Chromosome.Id.

getChromosome_Identifier() - Method in class org.molgenis.omx.xgap.Probe

Get a pretty label Identifier for cross reference Chromosome to Chromosome.Id.

getChromosome_Identifier() - Method in class org.molgenis.omx.xgap.ProbeSet

Get a pretty label Identifier for cross reference Chromosome to Chromosome.Id.

getChromosome_Identifier() - Method in class org.molgenis.omx.xgap.Variant

Get a pretty label Identifier for cross reference Chromosome to Chromosome.Id.

getCM() - Method in class org.molgenis.omx.xgap.Clone

Get the genetic map position in centi morgan (cM)..

getCM(Database) - Method in class org.molgenis.omx.xgap.Clone

Deprecated.

getCM() - Method in class org.molgenis.omx.xgap.Gene

Get the genetic map position in centi morgan (cM)..

getCM(Database) - Method in class org.molgenis.omx.xgap.Gene

Deprecated.

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(Database) - Method in class org.molgenis.omx.xgap.Marker

Deprecated.

getCM() - Method in class org.molgenis.omx.xgap.Probe

Get the genetic map position in centi morgan (cM)..

getCM(Database) - Method in class org.molgenis.omx.xgap.Probe

Deprecated.

getCM() - Method in class org.molgenis.omx.xgap.ProbeSet

Get the genetic map position in centi morgan (cM)..

getCM(Database) - Method in class org.molgenis.omx.xgap.ProbeSet

Deprecated.

getCM() - Method in class org.molgenis.omx.xgap.Variant

Get the genetic map position in centi morgan (cM)..

getCM(Database) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

getCodonchange() - Method in class org.molgenis.omx.xgap.Variant

Get the Codonchange.

getCodonchange(Database) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

getConsequence() - Method in class org.molgenis.omx.xgap.Variant

Get the Consequence.

getConsequence(Database) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

getControl() - Method in class org.molgenis.omx.xgap.Gene

Get the Indicating whether this is a 'housekeeping' gene that can be used as control..

getControl(Database) - Method in class org.molgenis.omx.xgap.Gene

Deprecated.

getDescription() - Method in class org.molgenis.omx.xgap.Variant

Get the Description.

getDescription(Database) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

getDetailsForMutation() - Method in class org.molgenis.omx.xgap.Variant

Get the DetailsForMutation.

getDetailsForMutation(Database) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

getEffectOnSplicing() - Method in class org.molgenis.omx.xgap.Variant

Get the EffectOnSplicing.

getEffectOnSplicing(Database) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

getEntity() - Method in class org.molgenis.service.ChromosomeService

getEntity() - Method in class org.molgenis.service.CloneService

getEntity() - Method in class org.molgenis.service.DerivedTraitService

getEntity() - Method in class org.molgenis.service.EnvironmentalFactorService

getEntity() - Method in class org.molgenis.service.GeneService

getEntity() - Method in class org.molgenis.service.MarkerService

getEntity() - Method in class org.molgenis.service.MassPeakService

getEntity() - Method in class org.molgenis.service.MetaboliteService

getEntity() - Method in class org.molgenis.service.NMRBinService

getEntity() - Method in class org.molgenis.service.PairedSampleService

getEntity() - Method in class org.molgenis.service.PatientService

getEntity() - Method in class org.molgenis.service.PolymorphismService

getEntity() - Method in class org.molgenis.service.ProbeService

getEntity() - Method in class org.molgenis.service.ProbeSetService

getEntity() - Method in class org.molgenis.service.ProteinService

getEntity() - Method in class org.molgenis.service.SampleService

getEntity() - Method in class org.molgenis.service.SNPService

getEntity() - Method in class org.molgenis.service.SpotService

getEntity() - Method in class org.molgenis.service.TrackService

getEntity() - Method in class org.molgenis.service.TranscriptService

getEntity() - Method in class org.molgenis.service.VariantService

getEntryPoints(Integer, Integer) - Method in class org.molgenis.omx.das.DasOmxDataSource

getEntryPointVersion() - Method in class org.molgenis.omx.das.DasOmxDataSource

getEvent() - Method in class org.molgenis.omx.xgap.Variant

Get the Event.

getEvent(Database) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

getExon() - Method in class org.molgenis.omx.xgap.Variant

Get the Exon.

getExon(Database) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

getFeatures(String, int, int, Integer) - Method in class org.molgenis.omx.das.DasOmxDataSource

getFeatures(String, Integer) - Method in class org.molgenis.omx.das.DasOmxDataSource

getFeatures(Collection<String>, Integer, Range) - Method in class org.molgenis.omx.das.DasOmxDataSource

getFeatures(String, int, int, Integer, Range) - Method in class org.molgenis.omx.das.DasOmxDataSource

getFeatures(String, Integer, Range) - Method in class org.molgenis.omx.das.DasOmxDataSource

getFeatures(Collection<String>, Integer) - Method in class org.molgenis.omx.das.DasOmxDataSource

getFields(boolean) - Method in class org.molgenis.omx.patient.Patient

Get the names of all public properties of Patient.

getFields() - Method in class org.molgenis.omx.patient.Patient

getFields(String) - Method in class org.molgenis.omx.patient.Patient

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.xgap.Chromosome

Get the names of all public properties of Chromosome.

getFields() - Method in class org.molgenis.omx.xgap.Chromosome

getFields(String) - Method in class org.molgenis.omx.xgap.Chromosome

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.xgap.Clone

Get the names of all public properties of Clone.

getFields() - Method in class org.molgenis.omx.xgap.Clone

getFields(String) - Method in class org.molgenis.omx.xgap.Clone

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.xgap.DerivedTrait

Get the names of all public properties of DerivedTrait.

getFields() - Method in class org.molgenis.omx.xgap.DerivedTrait

getFields(String) - Method in class org.molgenis.omx.xgap.DerivedTrait

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.xgap.EnvironmentalFactor

Get the names of all public properties of EnvironmentalFactor.

getFields() - Method in class org.molgenis.omx.xgap.EnvironmentalFactor

getFields(String) - Method in class org.molgenis.omx.xgap.EnvironmentalFactor

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.xgap.Gene

Get the names of all public properties of Gene.

getFields() - Method in class org.molgenis.omx.xgap.Gene

getFields(String) - Method in class org.molgenis.omx.xgap.Gene

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.xgap.Marker

Get the names of all public properties of Marker.

getFields() - Method in class org.molgenis.omx.xgap.Marker

getFields(String) - Method in class org.molgenis.omx.xgap.Marker

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.xgap.Marker_ReportsFor

Get the names of all public properties of Marker_ReportsFor.

getFields() - Method in class org.molgenis.omx.xgap.Marker_ReportsFor

getFields(String) - Method in class org.molgenis.omx.xgap.Marker_ReportsFor

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.xgap.MassPeak

Get the names of all public properties of MassPeak.

getFields() - Method in class org.molgenis.omx.xgap.MassPeak

getFields(String) - Method in class org.molgenis.omx.xgap.MassPeak

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.xgap.Metabolite

Get the names of all public properties of Metabolite.

getFields() - Method in class org.molgenis.omx.xgap.Metabolite

getFields(String) - Method in class org.molgenis.omx.xgap.Metabolite

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.xgap.NMRBin

Get the names of all public properties of NMRBin.

getFields() - Method in class org.molgenis.omx.xgap.NMRBin

getFields(String) - Method in class org.molgenis.omx.xgap.NMRBin

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.xgap.PairedSample

Get the names of all public properties of PairedSample.

getFields() - Method in class org.molgenis.omx.xgap.PairedSample

getFields(String) - Method in class org.molgenis.omx.xgap.PairedSample

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.xgap.Polymorphism

Get the names of all public properties of Polymorphism.

getFields() - Method in class org.molgenis.omx.xgap.Polymorphism

getFields(String) - Method in class org.molgenis.omx.xgap.Polymorphism

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.xgap.Probe

Get the names of all public properties of Probe.

getFields() - Method in class org.molgenis.omx.xgap.Probe

getFields(String) - Method in class org.molgenis.omx.xgap.Probe

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.xgap.ProbeSet

Get the names of all public properties of ProbeSet.

getFields() - Method in class org.molgenis.omx.xgap.ProbeSet

getFields(String) - Method in class org.molgenis.omx.xgap.ProbeSet

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.xgap.Protein

Get the names of all public properties of Protein.

getFields() - Method in class org.molgenis.omx.xgap.Protein

getFields(String) - Method in class org.molgenis.omx.xgap.Protein

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.xgap.Sample

Get the names of all public properties of Sample.

getFields() - Method in class org.molgenis.omx.xgap.Sample

getFields(String) - Method in class org.molgenis.omx.xgap.Sample

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.xgap.SNP

Get the names of all public properties of SNP.

getFields() - Method in class org.molgenis.omx.xgap.SNP

getFields(String) - Method in class org.molgenis.omx.xgap.SNP

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.xgap.SNP_Polymorphism

Get the names of all public properties of SNP_Polymorphism.

getFields() - Method in class org.molgenis.omx.xgap.SNP_Polymorphism

getFields(String) - Method in class org.molgenis.omx.xgap.SNP_Polymorphism

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.xgap.Spot

Get the names of all public properties of Spot.

getFields() - Method in class org.molgenis.omx.xgap.Spot

getFields(String) - Method in class org.molgenis.omx.xgap.Spot

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.xgap.Track

Get the names of all public properties of Track.

getFields() - Method in class org.molgenis.omx.xgap.Track

getFields(String) - Method in class org.molgenis.omx.xgap.Track

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.xgap.Transcript

Get the names of all public properties of Transcript.

getFields() - Method in class org.molgenis.omx.xgap.Transcript

getFields(String) - Method in class org.molgenis.omx.xgap.Transcript

Deprecated.

getFields(boolean) - Method in class org.molgenis.omx.xgap.Variant

Get the names of all public properties of Variant.

getFields() - Method in class org.molgenis.omx.xgap.Variant

getFields(String) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

getFieldType(String) - Method in class org.molgenis.omx.patient.db.PatientJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.xgap.db.ChromosomeJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.xgap.db.CloneJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.xgap.db.DerivedTraitJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.xgap.db.GeneJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.xgap.db.Marker_ReportsForJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.xgap.db.MarkerJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.xgap.db.MassPeakJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.xgap.db.MetaboliteJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.xgap.db.NMRBinJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.xgap.db.PairedSampleJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.xgap.db.PolymorphismJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.xgap.db.ProbeJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.xgap.db.ProbeSetJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.xgap.db.ProteinJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.xgap.db.SampleJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.xgap.db.SNP_PolymorphismJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.xgap.db.SNPJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.xgap.db.SpotJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.xgap.db.TrackJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.xgap.db.TranscriptJpaMapper

getFieldType(String) - Method in class org.molgenis.omx.xgap.db.VariantJpaMapper

getFormula() - Method in class org.molgenis.omx.xgap.Metabolite

Get the The chemical formula of a metabolite..

getFormula(Database) - Method in class org.molgenis.omx.xgap.Metabolite

Deprecated.

getGdnaNotation() - Method in class org.molgenis.omx.xgap.Variant

Get the GdnaNotation.

getGdnaNotation(Database) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

getGene() - Method in class org.molgenis.omx.xgap.Protein

Get the The gene that produces this protein.

getGene(Database) - Method in class org.molgenis.omx.xgap.Protein

Deprecated.

getGene() - Method in class org.molgenis.omx.xgap.Transcript

Get the The gene that produces this protein.

getGene(Database) - Method in class org.molgenis.omx.xgap.Transcript

Deprecated.

getGene() - Method in class org.molgenis.omx.xgap.Variant

Get the Gene.

getGene(Database) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

getGene_Id() - Method in class org.molgenis.omx.xgap.Protein

getGene_Id() - Method in class org.molgenis.omx.xgap.Transcript

getGene_Identifier() - Method in class org.molgenis.omx.xgap.Protein

Get a pretty label Identifier for cross reference Gene to Gene.Id.

getGene_Identifier() - Method in class org.molgenis.omx.xgap.Transcript

Get a pretty label Identifier for cross reference Gene to Gene.Id.

getGridX() - Method in class org.molgenis.omx.xgap.Spot

Get the Meta Row.

getGridX(Database) - Method in class org.molgenis.omx.xgap.Spot

Deprecated.

getGridY() - Method in class org.molgenis.omx.xgap.Spot

Get the Meta Column.

getGridY(Database) - Method in class org.molgenis.omx.xgap.Spot

Deprecated.

getIdField() - Method in class org.molgenis.omx.patient.Patient

getIdField() - Method in class org.molgenis.omx.xgap.Chromosome

getIdField() - Method in class org.molgenis.omx.xgap.Clone

getIdField() - Method in class org.molgenis.omx.xgap.DerivedTrait

getIdField() - Method in class org.molgenis.omx.xgap.EnvironmentalFactor

getIdField() - Method in class org.molgenis.omx.xgap.Gene

getIdField() - Method in class org.molgenis.omx.xgap.Marker

getIdField() - Method in class org.molgenis.omx.xgap.Marker_ReportsFor

getIdField() - Method in class org.molgenis.omx.xgap.MassPeak

getIdField() - Method in class org.molgenis.omx.xgap.Metabolite

getIdField() - Method in class org.molgenis.omx.xgap.NMRBin

getIdField() - Method in class org.molgenis.omx.xgap.PairedSample

getIdField() - Method in class org.molgenis.omx.xgap.Polymorphism

getIdField() - Method in class org.molgenis.omx.xgap.Probe

getIdField() - Method in class org.molgenis.omx.xgap.ProbeSet

getIdField() - Method in class org.molgenis.omx.xgap.Protein

getIdField() - Method in class org.molgenis.omx.xgap.Sample

getIdField() - Method in class org.molgenis.omx.xgap.SNP

getIdField() - Method in class org.molgenis.omx.xgap.SNP_Polymorphism

getIdField() - Method in class org.molgenis.omx.xgap.Spot

getIdField() - Method in class org.molgenis.omx.xgap.Track

getIdField() - Method in class org.molgenis.omx.xgap.Transcript

getIdField() - Method in class org.molgenis.omx.xgap.Variant

getIdMutation() - Method in class org.molgenis.omx.xgap.Variant

Get the IdMutation.

getIdMutation(Database) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

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..

getIndividual(Database) - Method in class org.molgenis.omx.xgap.Sample

Deprecated.

getIndividual_Id() - Method in class org.molgenis.omx.xgap.Sample

getIndividual_Identifier() - Method in class org.molgenis.omx.xgap.Sample

Get a pretty label Identifier for cross reference Individual to Individual.Id.

getInheritance() - Method in class org.molgenis.omx.xgap.Variant

Get the Inheritance.

getInheritance(Database) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

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..

getIsAutosomal(Database) - Method in class org.molgenis.omx.xgap.Chromosome

Deprecated.

getLabel1() - Method in class org.molgenis.omx.xgap.PairedSample

Get the Which channel or Fluorescent labeling is associated with the first subject.

getLabel1(Database) - Method in class org.molgenis.omx.xgap.PairedSample

Deprecated.

getLabel1_Id() - Method in class org.molgenis.omx.xgap.PairedSample

getLabel1_Identifier() - Method in class org.molgenis.omx.xgap.PairedSample

Get a pretty label Identifier for cross reference Label1 to OntologyTerm.Id.

getLabel2() - Method in class org.molgenis.omx.xgap.PairedSample

Get the Which channel or Fluorescent labeling is associated with the second subject.

getLabel2(Database) - Method in class org.molgenis.omx.xgap.PairedSample

Deprecated.

getLabel2_Id() - Method in class org.molgenis.omx.xgap.PairedSample

getLabel2_Identifier() - Method in class org.molgenis.omx.xgap.PairedSample

Get a pretty label Identifier for cross reference Label2 to OntologyTerm.Id.

getLabelFields() - Method in class org.molgenis.omx.patient.Patient

getLabelFields() - Method in class org.molgenis.omx.xgap.Chromosome

getLabelFields() - Method in class org.molgenis.omx.xgap.Clone

getLabelFields() - Method in class org.molgenis.omx.xgap.DerivedTrait

getLabelFields() - Method in class org.molgenis.omx.xgap.EnvironmentalFactor

getLabelFields() - Method in class org.molgenis.omx.xgap.Gene

getLabelFields() - Method in class org.molgenis.omx.xgap.Marker

getLabelFields() - Method in class org.molgenis.omx.xgap.Marker_ReportsFor

getLabelFields() - Method in class org.molgenis.omx.xgap.MassPeak

getLabelFields() - Method in class org.molgenis.omx.xgap.Metabolite

getLabelFields() - Method in class org.molgenis.omx.xgap.NMRBin

getLabelFields() - Method in class org.molgenis.omx.xgap.PairedSample

getLabelFields() - Method in class org.molgenis.omx.xgap.Polymorphism

getLabelFields() - Method in class org.molgenis.omx.xgap.Probe

getLabelFields() - Method in class org.molgenis.omx.xgap.ProbeSet

getLabelFields() - Method in class org.molgenis.omx.xgap.Protein

getLabelFields() - Method in class org.molgenis.omx.xgap.Sample

getLabelFields() - Method in class org.molgenis.omx.xgap.SNP

getLabelFields() - Method in class org.molgenis.omx.xgap.SNP_Polymorphism

getLabelFields() - Method in class org.molgenis.omx.xgap.Spot

getLabelFields() - Method in class org.molgenis.omx.xgap.Track

getLabelFields() - Method in class org.molgenis.omx.xgap.Transcript

getLabelFields() - Method in class org.molgenis.omx.xgap.Variant

getLinkURL(String, String) - Method in class org.molgenis.omx.das.DasOmxDataSource

getMarker() - Method in class org.molgenis.omx.xgap.Marker_ReportsFor

Get the .

getMarker(Database) - Method in class org.molgenis.omx.xgap.Marker_ReportsFor

Deprecated.

getMarker_Id() - Method in class org.molgenis.omx.xgap.Marker_ReportsFor

getMarker_Identifier() - Method in class org.molgenis.omx.xgap.Marker_ReportsFor

Get a pretty label Identifier for cross reference Marker to Marker.Id.

getMass() - Method in class org.molgenis.omx.xgap.Metabolite

Get the The mass of this metabolite.

getMass(Database) - Method in class org.molgenis.omx.xgap.Metabolite

Deprecated.

getMass() - Method in class org.molgenis.omx.xgap.Protein

Get the The mass of this metabolite.

getMass(Database) - Method in class org.molgenis.omx.xgap.Protein

Deprecated.

getMismatch() - Method in class org.molgenis.omx.xgap.Probe

Get the Indicating whether the probe is a match.

getMismatch(Database) - Method in class org.molgenis.omx.xgap.Probe

Deprecated.

getMutationPosition() - Method in class org.molgenis.omx.xgap.Variant

Get the MutationPosition.

getMutationPosition(Database) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

getMZ() - Method in class org.molgenis.omx.xgap.MassPeak

Get the Mass over charge ratio of this peak..

getMZ(Database) - Method in class org.molgenis.omx.xgap.MassPeak

Deprecated.

getNtChange() - Method in class org.molgenis.omx.xgap.Variant

Get the NtChange.

getNtChange(Database) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

getOrderNr() - Method in class org.molgenis.omx.xgap.Chromosome

Get the orderNr.

getOrderNr(Database) - Method in class org.molgenis.omx.xgap.Chromosome

Deprecated.

getOrientation() - Method in class org.molgenis.omx.xgap.Gene

Get the Orientation of the gene on the genome (F=forward, R=reverse).

getOrientation(Database) - Method in class org.molgenis.omx.xgap.Gene

Deprecated.

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 Pathogenicity.

getPathogenicity(Database) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

getPheno() - Method in class org.molgenis.omx.patient.Patient

Get the Pheno.

getPheno(Database) - Method in class org.molgenis.omx.patient.Patient

Deprecated.

getPolymorphism() - Method in class org.molgenis.omx.xgap.SNP

Get the The polymorphism that belongs to this SNP..

getPolymorphism(Database) - Method in class org.molgenis.omx.xgap.SNP

Deprecated.

getPolymorphism() - Method in class org.molgenis.omx.xgap.SNP_Polymorphism

Get the .

getPolymorphism(Database) - Method in class org.molgenis.omx.xgap.SNP_Polymorphism

Deprecated.

getPolymorphism_Id() - Method in class org.molgenis.omx.xgap.SNP

getPolymorphism_Id() - Method in class org.molgenis.omx.xgap.SNP_Polymorphism

getPolymorphism_Identifier() - Method in class org.molgenis.omx.xgap.SNP

Get a pretty label for cross reference Polymorphism to Polymorphism.Id.

getPolymorphism_Identifier() - Method in class org.molgenis.omx.xgap.SNP_Polymorphism

Get a pretty label Identifier for cross reference Polymorphism to Polymorphism.Id.

getPolymorphismSNPCollection() - Method in class org.molgenis.omx.xgap.Polymorphism

getPolymorphismSNPCollection(Database) - 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)..

getProbeSet(Database) - Method in class org.molgenis.omx.xgap.Probe

Deprecated.

getProbeSet_Id() - Method in class org.molgenis.omx.xgap.Probe

getProbeSet_Identifier() - Method in class org.molgenis.omx.xgap.Probe

Get a pretty label Identifier for cross reference ProbeSet to ProbeSet.Id.

getPubMedID() - Method in class org.molgenis.omx.patient.Patient

Get the PubMedID.

getPubMedID(Database) - Method in class org.molgenis.omx.patient.Patient

Deprecated.

getReference() - Method in class org.molgenis.omx.patient.Patient

Get the Reference.

getReference(Database) - Method in class org.molgenis.omx.patient.Patient

Deprecated.

getReportedSNP() - Method in class org.molgenis.omx.xgap.Variant

Get the ReportedSNP.

getReportedSNP(Database) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

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(Database) - Method in class org.molgenis.omx.xgap.Marker

Deprecated.

getReportsFor() - Method in class org.molgenis.omx.xgap.Marker_ReportsFor

Get the .

getReportsFor(Database) - Method in class org.molgenis.omx.xgap.Marker_ReportsFor

Deprecated.

getReportsFor() - Method in class org.molgenis.omx.xgap.Probe

Get the The gene this probe reports for..

getReportsFor(Database) - Method in class org.molgenis.omx.xgap.Probe

Deprecated.

getReportsFor_Id() - Method in class org.molgenis.omx.xgap.Marker

getReportsFor_Id() - Method in class org.molgenis.omx.xgap.Marker_ReportsFor

getReportsFor_Id() - Method in class org.molgenis.omx.xgap.Probe

getReportsFor_Identifier() - Method in class org.molgenis.omx.xgap.Marker

Get a pretty label for cross reference ReportsFor to Marker.Id.

getReportsFor_Identifier() - Method in class org.molgenis.omx.xgap.Marker_ReportsFor

Get a pretty label Identifier for cross reference ReportsFor to Marker.Id.

getReportsFor_Identifier() - Method in class org.molgenis.omx.xgap.Probe

Get a pretty label Identifier for cross reference ReportsFor to Gene.Id.

getReportsForMarkerCollection() - Method in class org.molgenis.omx.xgap.Marker

getReportsForMarkerCollection(Database) - 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..

getRetentionTime(Database) - Method in class org.molgenis.omx.xgap.MassPeak

Deprecated.

getSeq() - Method in class org.molgenis.omx.xgap.Clone

Get the The FASTA text representation of the sequence..

getSeq(Database) - Method in class org.molgenis.omx.xgap.Clone

Deprecated.

getSeq() - Method in class org.molgenis.omx.xgap.Gene

Get the The FASTA text representation of the sequence..

getSeq(Database) - Method in class org.molgenis.omx.xgap.Gene

Deprecated.

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(Database) - Method in class org.molgenis.omx.xgap.Marker

Deprecated.

getSeq() - Method in class org.molgenis.omx.xgap.Probe

Get the The FASTA text representation of the sequence..

getSeq(Database) - Method in class org.molgenis.omx.xgap.Probe

Deprecated.

getSeq() - Method in class org.molgenis.omx.xgap.ProbeSet

Get the The FASTA text representation of the sequence..

getSeq(Database) - Method in class org.molgenis.omx.xgap.ProbeSet

Deprecated.

getSeq() - Method in class org.molgenis.omx.xgap.Variant

Get the The FASTA text representation of the sequence..

getSeq(Database) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

getSNP() - Method in class org.molgenis.omx.xgap.SNP_Polymorphism

Get the .

getSNP(Database) - Method in class org.molgenis.omx.xgap.SNP_Polymorphism

Deprecated.

getSNP_Id() - Method in class org.molgenis.omx.xgap.SNP_Polymorphism

getSNP_Identifier() - Method in class org.molgenis.omx.xgap.SNP_Polymorphism

Get a pretty label Identifier for cross reference SNP to SNP.Id.

getSpecies() - Method in class org.molgenis.omx.xgap.Chromosome

Get the Reference to the species this chromosome belongs to..

getSpecies(Database) - Method in class org.molgenis.omx.xgap.Chromosome

Deprecated.

getSpecies_Id() - Method in class org.molgenis.omx.xgap.Chromosome

getSpecies_Identifier() - Method in class org.molgenis.omx.xgap.Chromosome

Get a pretty label Identifier for cross reference Species to OntologyTerm.Id.

getStartCoordinate() - Method in class org.molgenis.omx.das.MolgenisDasTarget

getStatus() - Method in class org.molgenis.omx.xgap.SNP

Get the The status of this SNP, eg 'confirmed'..

getStatus(Database) - Method in class org.molgenis.omx.xgap.SNP

Deprecated.

getStopCoordinate() - Method in class org.molgenis.omx.das.MolgenisDasTarget

getStructure() - Method in class org.molgenis.omx.xgap.Metabolite

Get the The chemical structure of a metabolite (in SMILES representation)..

getStructure(Database) - Method in class org.molgenis.omx.xgap.Metabolite

Deprecated.

getSubject1() - Method in class org.molgenis.omx.xgap.PairedSample

Get the The first subject.

getSubject1(Database) - Method in class org.molgenis.omx.xgap.PairedSample

Deprecated.

getSubject1_Id() - Method in class org.molgenis.omx.xgap.PairedSample

getSubject1_Identifier() - Method in class org.molgenis.omx.xgap.PairedSample

Get a pretty label Identifier for cross reference Subject1 to Individual.Id.

getSubject2() - Method in class org.molgenis.omx.xgap.PairedSample

Get the The second sample.

getSubject2(Database) - Method in class org.molgenis.omx.xgap.PairedSample

Deprecated.

getSubject2_Id() - Method in class org.molgenis.omx.xgap.PairedSample

getSubject2_Identifier() - Method in class org.molgenis.omx.xgap.PairedSample

Get a pretty label Identifier for cross reference Subject2 to Individual.Id.

getSymbol() - Method in class org.molgenis.omx.xgap.Clone

Get the todo.

getSymbol(Database) - Method in class org.molgenis.omx.xgap.Clone

Deprecated.

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(Database) - Method in class org.molgenis.omx.xgap.Gene

Deprecated.

getSymbol() - Method in interface org.molgenis.omx.xgap.Locus

getSymbol() - Method in class org.molgenis.omx.xgap.Marker

Get the todo.

getSymbol(Database) - Method in class org.molgenis.omx.xgap.Marker

Deprecated.

getSymbol() - Method in class org.molgenis.omx.xgap.Probe

Get the todo.

getSymbol(Database) - Method in class org.molgenis.omx.xgap.Probe

Deprecated.

getSymbol() - Method in class org.molgenis.omx.xgap.ProbeSet

Get the todo.

getSymbol(Database) - Method in class org.molgenis.omx.xgap.ProbeSet

Deprecated.

getSymbol() - Method in class org.molgenis.omx.xgap.Variant

Get the todo.

getSymbol(Database) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

getTableFieldName(String) - Method in class org.molgenis.omx.patient.db.PatientJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.xgap.db.ChromosomeJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.xgap.db.CloneJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.xgap.db.DerivedTraitJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.xgap.db.GeneJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.xgap.db.Marker_ReportsForJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.xgap.db.MarkerJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.xgap.db.MassPeakJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.xgap.db.MetaboliteJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.xgap.db.NMRBinJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.xgap.db.PairedSampleJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.xgap.db.PolymorphismJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.xgap.db.ProbeJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.xgap.db.ProbeSetJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.xgap.db.ProteinJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.xgap.db.SampleJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.xgap.db.SNP_PolymorphismJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.xgap.db.SNPJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.xgap.db.SpotJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.xgap.db.TrackJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.xgap.db.TranscriptJpaMapper

getTableFieldName(String) - Method in class org.molgenis.omx.xgap.db.VariantJpaMapper

getTargetId() - Method in class org.molgenis.omx.das.MolgenisDasTarget

getTargetName() - Method in class org.molgenis.omx.das.MolgenisDasTarget

getTissue() - Method in class org.molgenis.omx.xgap.Sample

Get the The tissue from which this sample was taken..

getTissue(Database) - Method in class org.molgenis.omx.xgap.Sample

Deprecated.

getTissue_Id() - Method in class org.molgenis.omx.xgap.Sample

getTissue_Identifier() - Method in class org.molgenis.omx.xgap.Sample

Get a pretty label Identifier for cross reference Tissue to OntologyTerm.Id.

getTotalCountForType(DasType) - Method in class org.molgenis.omx.das.DasOmxDataSource

getTotalEntryPoints() - Method in class org.molgenis.omx.das.DasOmxDataSource

getTrack() - Method in class org.molgenis.omx.xgap.Variant

Get the Track.

getTrack(Database) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

getTrack_Id() - Method in class org.molgenis.omx.xgap.Variant

getTrack_Identifier() - Method in class org.molgenis.omx.xgap.Variant

Get a pretty label Identifier for cross reference Track to Track.Id.

getTranscript() - Method in class org.molgenis.omx.xgap.Protein

Get the The transcript variant that produces this protein.

getTranscript(Database) - Method in class org.molgenis.omx.xgap.Protein

Deprecated.

getTranscript_Id() - Method in class org.molgenis.omx.xgap.Protein

getTranscript_Identifier() - Method in class org.molgenis.omx.xgap.Protein

Get a pretty label Identifier for cross reference Transcript to Transcript.Id.

getTypes() - Method in class org.molgenis.omx.das.DasOmxDataSource

getValue() - Method in class org.molgenis.omx.xgap.Polymorphism

Get the The strain/genotype for which this polymorphism was discovered.

getValue(Database) - Method in class org.molgenis.omx.xgap.Polymorphism

Deprecated.

getValues(String) - Method in class org.molgenis.omx.patient.Patient

Deprecated.

getValues(String) - Method in class org.molgenis.omx.xgap.Chromosome

Deprecated.

getValues(String) - Method in class org.molgenis.omx.xgap.Clone

Deprecated.

getValues(String) - Method in class org.molgenis.omx.xgap.DerivedTrait

Deprecated.

getValues(String) - Method in class org.molgenis.omx.xgap.EnvironmentalFactor

Deprecated.

getValues(String) - Method in class org.molgenis.omx.xgap.Gene

Deprecated.

getValues(String) - Method in class org.molgenis.omx.xgap.Marker

Deprecated.

getValues(String) - Method in class org.molgenis.omx.xgap.Marker_ReportsFor

Deprecated.

getValues(String) - Method in class org.molgenis.omx.xgap.MassPeak

Deprecated.

getValues(String) - Method in class org.molgenis.omx.xgap.Metabolite

Deprecated.

getValues(String) - Method in class org.molgenis.omx.xgap.NMRBin

Deprecated.

getValues(String) - Method in class org.molgenis.omx.xgap.PairedSample

Deprecated.

getValues(String) - Method in class org.molgenis.omx.xgap.Polymorphism

Deprecated.

getValues(String) - Method in class org.molgenis.omx.xgap.Probe

Deprecated.

getValues(String) - Method in class org.molgenis.omx.xgap.ProbeSet

Deprecated.

getValues(String) - Method in class org.molgenis.omx.xgap.Protein

Deprecated.

getValues(String) - Method in class org.molgenis.omx.xgap.Sample

Deprecated.

getValues(String) - Method in class org.molgenis.omx.xgap.SNP

Deprecated.

getValues(String) - Method in class org.molgenis.omx.xgap.SNP_Polymorphism

Deprecated.

getValues(String) - Method in class org.molgenis.omx.xgap.Spot

Deprecated.

getValues(String) - Method in class org.molgenis.omx.xgap.Track

Deprecated.

getValues(String) - Method in class org.molgenis.omx.xgap.Transcript

Deprecated.

getValues(String) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

getVariantLength() - Method in class org.molgenis.omx.xgap.Variant

Get the VariantLength.

getVariantLength(Database) - Method in class org.molgenis.omx.xgap.Variant

Deprecated.

getX() - Method in class org.molgenis.omx.xgap.Spot

Get the Row.

getX(Database) - Method in class org.molgenis.omx.xgap.Spot

Deprecated.

getXrefIdFieldName(String) - Method in class org.molgenis.omx.patient.Patient

getXrefIdFieldName(String) - Method in class org.molgenis.omx.xgap.Chromosome

getXrefIdFieldName(String) - Method in class org.molgenis.omx.xgap.Clone

getXrefIdFieldName(String) - Method in class org.molgenis.omx.xgap.DerivedTrait

getXrefIdFieldName(String) - Method in class org.molgenis.omx.xgap.EnvironmentalFactor

getXrefIdFieldName(String) - Method in class org.molgenis.omx.xgap.Gene

getXrefIdFieldName(String) - Method in class org.molgenis.omx.xgap.Marker

getXrefIdFieldName(String) - Method in class org.molgenis.omx.xgap.Marker_ReportsFor

getXrefIdFieldName(String) - Method in class org.molgenis.omx.xgap.MassPeak

getXrefIdFieldName(String) - Method in class org.molgenis.omx.xgap.Metabolite

getXrefIdFieldName(String) - Method in class org.molgenis.omx.xgap.NMRBin

getXrefIdFieldName(String) - Method in class org.molgenis.omx.xgap.PairedSample

getXrefIdFieldName(String) - Method in class org.molgenis.omx.xgap.Polymorphism

getXrefIdFieldName(String) - Method in class org.molgenis.omx.xgap.Probe

getXrefIdFieldName(String) - Method in class org.molgenis.omx.xgap.ProbeSet

getXrefIdFieldName(String) - Method in class org.molgenis.omx.xgap.Protein

getXrefIdFieldName(String) - Method in class org.molgenis.omx.xgap.Sample

getXrefIdFieldName(String) - Method in class org.molgenis.omx.xgap.SNP

getXrefIdFieldName(String) - Method in class org.molgenis.omx.xgap.SNP_Polymorphism

getXrefIdFieldName(String) - Method in class org.molgenis.omx.xgap.Spot

getXrefIdFieldName(String) - Method in class org.molgenis.omx.xgap.Track

getXrefIdFieldName(String) - Method in class org.molgenis.omx.xgap.Transcript

getXrefIdFieldName(String) - Method in class org.molgenis.omx.xgap.Variant

getY() - Method in class org.molgenis.omx.xgap.Spot

Get the Column.

getY(Database) - Method in class org.molgenis.omx.xgap.Spot

Deprecated.

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

HtmlValueSecurityDecorator<E extends HtmlValue> - Class in org.molgenis.omx.observ.value.db

TODO add column level security filters

HtmlValueSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.value.db.HtmlValueSecurityDecorator

HyperlinkValueSecurityDecorator<E extends HyperlinkValue> - Class in org.molgenis.omx.observ.value.db

TODO add column level security filters

HyperlinkValueSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.value.db.HyperlinkValueSecurityDecorator

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

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.patient.db.PatientEntityImporter

Imports Patient from tab/comma delimited File

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.xgap.db.ChromosomeEntityImporter

Imports Chromosome from tab/comma delimited File

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.xgap.db.CloneEntityImporter

Imports Clone from tab/comma delimited File

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.xgap.db.DerivedTraitEntityImporter

Imports DerivedTrait from tab/comma delimited File

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorEntityImporter

Imports EnvironmentalFactor from tab/comma delimited File

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.xgap.db.GeneEntityImporter

Imports Gene from tab/comma delimited File

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.xgap.db.Marker_ReportsForEntityImporter

Imports Marker_ReportsFor from tab/comma delimited File

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.xgap.db.MarkerEntityImporter

Imports Marker from tab/comma delimited File

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.xgap.db.MassPeakEntityImporter

Imports MassPeak from tab/comma delimited File

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.xgap.db.MetaboliteEntityImporter

Imports Metabolite from tab/comma delimited File

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.xgap.db.NMRBinEntityImporter

Imports NMRBin from tab/comma delimited File

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.xgap.db.PairedSampleEntityImporter

Imports PairedSample from tab/comma delimited File

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.xgap.db.PolymorphismEntityImporter

Imports Polymorphism from tab/comma delimited File

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.xgap.db.ProbeEntityImporter

Imports Probe from tab/comma delimited File

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.xgap.db.ProbeSetEntityImporter

Imports ProbeSet from tab/comma delimited File

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.xgap.db.ProteinEntityImporter

Imports Protein from tab/comma delimited File

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.xgap.db.SampleEntityImporter

Imports Sample from tab/comma delimited File

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.xgap.db.SNP_PolymorphismEntityImporter

Imports SNP_Polymorphism from tab/comma delimited File

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.xgap.db.SNPEntityImporter

Imports SNP from tab/comma delimited File

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.xgap.db.SpotEntityImporter

Imports Spot from tab/comma delimited File

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.xgap.db.TrackEntityImporter

Imports Track from tab/comma delimited File

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.xgap.db.TranscriptEntityImporter

Imports Transcript from tab/comma delimited File

importEntity(Repository<? extends Entity>, Database, Database.DatabaseAction) - Method in class org.molgenis.omx.xgap.db.VariantEntityImporter

Imports Variant from tab/comma delimited File

INDIVIDUAL - Static variable in class org.molgenis.omx.xgap.Sample

INDIVIDUAL_IDENTIFIER - Static variable in class org.molgenis.omx.xgap.Sample

IndividualSecurityDecorator<E extends Individual> - Class in org.molgenis.omx.observ.target.db

TODO add column level security filters

IndividualSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.target.db.IndividualSecurityDecorator

INHERITANCE - Static variable in class org.molgenis.omx.xgap.Variant

init(ServletContext, Map<String, PropertyType>, DataSourceConfiguration) - Method in class org.molgenis.omx.das.DasOmxDataSource

init(FilterConfig) - Method in class org.molgenis.omx.das.DasPatientFilter

InstituteSecurityDecorator<E extends Institute> - Class in org.molgenis.omx.auth.db

TODO add column level security filters

InstituteSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.auth.db.InstituteSecurityDecorator

IntValueSecurityDecorator<E extends IntValue> - Class in org.molgenis.omx.observ.value.db

TODO add column level security filters

IntValueSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.value.db.IntValueSecurityDecorator

ISAUTOSOMAL - Static variable in class org.molgenis.omx.xgap.Chromosome

L

LABEL1 - Static variable in class org.molgenis.omx.xgap.PairedSample

LABEL1_IDENTIFIER - Static variable in class org.molgenis.omx.xgap.PairedSample

LABEL2 - Static variable in class org.molgenis.omx.xgap.PairedSample

LABEL2_IDENTIFIER - Static variable in class org.molgenis.omx.xgap.PairedSample

Locus - Interface in org.molgenis.omx.xgap

Locus: position.

LongValueSecurityDecorator<E extends LongValue> - Class in org.molgenis.omx.observ.value.db

TODO add column level security filters

LongValueSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.value.db.LongValueSecurityDecorator

M

Marker - Class in org.molgenis.omx.xgap

Marker: Trait annotations specific for markers..

Marker() - Constructor for class org.molgenis.omx.xgap.Marker

Marker(Marker) - Constructor for class org.molgenis.omx.xgap.Marker

copy constructor

MARKER - Static variable in class org.molgenis.omx.xgap.Marker_ReportsFor

MARKER_IDENTIFIER - 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_ReportsFor(Marker_ReportsFor) - Constructor for class org.molgenis.omx.xgap.Marker_ReportsFor

copy constructor

Marker_ReportsForEntityImporter - Class in org.molgenis.omx.xgap.db

Reads Marker_ReportsFor from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

Marker_ReportsForEntityImporter() - Constructor for class org.molgenis.omx.xgap.db.Marker_ReportsForEntityImporter

Marker_ReportsForJpaMapper - Class in org.molgenis.omx.xgap.db

Marker_ReportsForJpaMapper(Database) - Constructor for class org.molgenis.omx.xgap.db.Marker_ReportsForJpaMapper

Marker_ReportsForSecurityDecorator<E extends Marker_ReportsFor> - Class in org.molgenis.omx.xgap.db

TODO add column level security filters

Marker_ReportsForSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.Marker_ReportsForSecurityDecorator

MarkerEntityImporter - Class in org.molgenis.omx.xgap.db

Reads Marker from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

MarkerEntityImporter() - Constructor for class org.molgenis.omx.xgap.db.MarkerEntityImporter

MarkerJpaMapper - Class in org.molgenis.omx.xgap.db

MarkerJpaMapper(Database) - Constructor for class org.molgenis.omx.xgap.db.MarkerJpaMapper

MarkerSecurityDecorator<E extends Marker> - Class in org.molgenis.omx.xgap.db

TODO add column level security filters

MarkerSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.MarkerSecurityDecorator

MarkerService - Class in org.molgenis.service

MarkerService() - Constructor for class org.molgenis.service.MarkerService

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

MassPeak(MassPeak) - Constructor for class org.molgenis.omx.xgap.MassPeak

copy constructor

MassPeakEntityImporter - Class in org.molgenis.omx.xgap.db

Reads MassPeak from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

MassPeakEntityImporter() - Constructor for class org.molgenis.omx.xgap.db.MassPeakEntityImporter

MassPeakJpaMapper - Class in org.molgenis.omx.xgap.db

MassPeakJpaMapper(Database) - Constructor for class org.molgenis.omx.xgap.db.MassPeakJpaMapper

MassPeakSecurityDecorator<E extends MassPeak> - Class in org.molgenis.omx.xgap.db

TODO add column level security filters

MassPeakSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.MassPeakSecurityDecorator

MassPeakService - Class in org.molgenis.service

MassPeakService() - Constructor for class org.molgenis.service.MassPeakService

Metabolite - Class in org.molgenis.omx.xgap

Metabolite: Trait annotations specific for metabolites.

Metabolite() - Constructor for class org.molgenis.omx.xgap.Metabolite

Metabolite(Metabolite) - Constructor for class org.molgenis.omx.xgap.Metabolite

copy constructor

MetaboliteEntityImporter - Class in org.molgenis.omx.xgap.db

Reads Metabolite from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

MetaboliteEntityImporter() - Constructor for class org.molgenis.omx.xgap.db.MetaboliteEntityImporter

MetaboliteJpaMapper - Class in org.molgenis.omx.xgap.db

MetaboliteJpaMapper(Database) - Constructor for class org.molgenis.omx.xgap.db.MetaboliteJpaMapper

MetaboliteSecurityDecorator<E extends Metabolite> - Class in org.molgenis.omx.xgap.db

TODO add column level security filters

MetaboliteSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.MetaboliteSecurityDecorator

MetaboliteService - Class in org.molgenis.service

MetaboliteService() - Constructor for class org.molgenis.service.MetaboliteService

MISMATCH - Static variable in class org.molgenis.omx.xgap.Probe

MolgenisDasTarget - Class in org.molgenis.omx.das

MolgenisDasTarget(String, int, int, String) - Constructor for class org.molgenis.omx.das.MolgenisDasTarget

MolgenisEntitySecurityDecorator<E extends MolgenisEntity> - Class in org.molgenis.omx.core.db

TODO add column level security filters

MolgenisEntitySecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.core.db.MolgenisEntitySecurityDecorator

MolgenisFileSecurityDecorator<E extends MolgenisFile> - Class in org.molgenis.omx.core.db

TODO add column level security filters

MolgenisFileSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.core.db.MolgenisFileSecurityDecorator

MrefValueSecurityDecorator<E extends MrefValue> - Class in org.molgenis.omx.observ.value.db

TODO add column level security filters

MrefValueSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.value.db.MrefValueSecurityDecorator

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

NMRBin(NMRBin) - Constructor for class org.molgenis.omx.xgap.NMRBin

copy constructor

NMRBinEntityImporter - Class in org.molgenis.omx.xgap.db

Reads NMRBin from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

NMRBinEntityImporter() - Constructor for class org.molgenis.omx.xgap.db.NMRBinEntityImporter

NMRBinJpaMapper - Class in org.molgenis.omx.xgap.db

NMRBinJpaMapper(Database) - Constructor for class org.molgenis.omx.xgap.db.NMRBinJpaMapper

NMRBinSecurityDecorator<E extends NMRBin> - Class in org.molgenis.omx.xgap.db

TODO add column level security filters

NMRBinSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.NMRBinSecurityDecorator

NMRBinService - Class in org.molgenis.service

NMRBinService() - Constructor for class org.molgenis.service.NMRBinService

NTCHANGE - Static variable in class org.molgenis.omx.xgap.Variant

O

ObservableFeatureSecurityDecorator<E extends ObservableFeature> - Class in org.molgenis.omx.observ.db

TODO add column level security filters

ObservableFeatureSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.db.ObservableFeatureSecurityDecorator

ObservationSetSecurityDecorator<E extends ObservationSet> - Class in org.molgenis.omx.observ.db

TODO add column level security filters

ObservationSetSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.db.ObservationSetSecurityDecorator

ObservationTargetSecurityDecorator<E extends ObservationTarget> - Class in org.molgenis.omx.observ.db

TODO add column level security filters

ObservationTargetSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.db.ObservationTargetSecurityDecorator

ObservedValueSecurityDecorator<E extends ObservedValue> - Class in org.molgenis.omx.observ.db

TODO add column level security filters

ObservedValueSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.db.ObservedValueSecurityDecorator

onStartup(ServletContext) - Method in class org.molgenis.omx.das.WebAppInitializer

OntologySecurityDecorator<E extends Ontology> - Class in org.molgenis.omx.observ.target.db

TODO add column level security filters

OntologySecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.target.db.OntologySecurityDecorator

OntologyTermSecurityDecorator<E extends OntologyTerm> - Class in org.molgenis.omx.observ.target.db

TODO add column level security filters

OntologyTermSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.target.db.OntologyTermSecurityDecorator

ORDERNR - Static variable in class org.molgenis.omx.xgap.Chromosome

org.molgenis.omx.auth.db - package org.molgenis.omx.auth.db

org.molgenis.omx.core.db - package org.molgenis.omx.core.db

org.molgenis.omx.das - package org.molgenis.omx.das

org.molgenis.omx.observ.db - package org.molgenis.omx.observ.db

org.molgenis.omx.observ.target.db - package org.molgenis.omx.observ.target.db

org.molgenis.omx.observ.value.db - package org.molgenis.omx.observ.value.db

org.molgenis.omx.patient - package org.molgenis.omx.patient

org.molgenis.omx.patient.db - package org.molgenis.omx.patient.db

org.molgenis.omx.xgap - package org.molgenis.omx.xgap

org.molgenis.omx.xgap.db - package org.molgenis.omx.xgap.db

org.molgenis.service - package org.molgenis.service

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

PairedSample(PairedSample) - Constructor for class org.molgenis.omx.xgap.PairedSample

copy constructor

PairedSampleEntityImporter - Class in org.molgenis.omx.xgap.db

Reads PairedSample from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

PairedSampleEntityImporter() - Constructor for class org.molgenis.omx.xgap.db.PairedSampleEntityImporter

PairedSampleJpaMapper - Class in org.molgenis.omx.xgap.db

PairedSampleJpaMapper(Database) - Constructor for class org.molgenis.omx.xgap.db.PairedSampleJpaMapper

PairedSampleSecurityDecorator<E extends PairedSample> - Class in org.molgenis.omx.xgap.db

TODO add column level security filters

PairedSampleSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.PairedSampleSecurityDecorator

PairedSampleService - Class in org.molgenis.service

PairedSampleService() - Constructor for class org.molgenis.service.PairedSampleService

PanelSecurityDecorator<E extends Panel> - Class in org.molgenis.omx.observ.target.db

TODO add column level security filters

PanelSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.target.db.PanelSecurityDecorator

PanelSourceSecurityDecorator<E extends PanelSource> - Class in org.molgenis.omx.observ.target.db

TODO add column level security filters

PanelSourceSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.target.db.PanelSourceSecurityDecorator

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

Patient(Patient) - Constructor for class org.molgenis.omx.patient.Patient

copy constructor

PatientEntityImporter - Class in org.molgenis.omx.patient.db

Reads Patient from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

PatientEntityImporter() - Constructor for class org.molgenis.omx.patient.db.PatientEntityImporter

PatientJpaMapper - Class in org.molgenis.omx.patient.db

PatientJpaMapper(Database) - Constructor for class org.molgenis.omx.patient.db.PatientJpaMapper

PatientSecurityDecorator<E extends Patient> - Class in org.molgenis.omx.patient.db

TODO add column level security filters

PatientSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.patient.db.PatientSecurityDecorator

PatientService - Class in org.molgenis.service

PatientService() - Constructor for class org.molgenis.service.PatientService

PersonRoleSecurityDecorator<E extends PersonRole> - Class in org.molgenis.omx.auth.db

TODO add column level security filters

PersonRoleSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.auth.db.PersonRoleSecurityDecorator

PersonSecurityDecorator<E extends Person> - Class in org.molgenis.omx.auth.db

TODO add column level security filters

PersonSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.auth.db.PersonSecurityDecorator

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(Polymorphism) - Constructor for class org.molgenis.omx.xgap.Polymorphism

copy constructor

POLYMORPHISM - Static variable in class org.molgenis.omx.xgap.SNP

POLYMORPHISM - Static variable in class org.molgenis.omx.xgap.SNP_Polymorphism

POLYMORPHISM_IDENTIFIER - Static variable in class org.molgenis.omx.xgap.SNP

POLYMORPHISM_IDENTIFIER - Static variable in class org.molgenis.omx.xgap.SNP_Polymorphism

PolymorphismEntityImporter - Class in org.molgenis.omx.xgap.db

Reads Polymorphism from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

PolymorphismEntityImporter() - Constructor for class org.molgenis.omx.xgap.db.PolymorphismEntityImporter

PolymorphismJpaMapper - Class in org.molgenis.omx.xgap.db

PolymorphismJpaMapper(Database) - Constructor for class org.molgenis.omx.xgap.db.PolymorphismJpaMapper

PolymorphismSecurityDecorator<E extends Polymorphism> - Class in org.molgenis.omx.xgap.db

TODO add column level security filters

PolymorphismSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.PolymorphismSecurityDecorator

PolymorphismService - Class in org.molgenis.service

PolymorphismService() - Constructor for class org.molgenis.service.PolymorphismService

prepareFileAttachements(List<Patient>, File) - Method in class org.molgenis.omx.patient.db.PatientJpaMapper

prepareFileAttachements(List<Chromosome>, File) - Method in class org.molgenis.omx.xgap.db.ChromosomeJpaMapper

prepareFileAttachements(List<Clone>, File) - Method in class org.molgenis.omx.xgap.db.CloneJpaMapper

prepareFileAttachements(List<DerivedTrait>, File) - Method in class org.molgenis.omx.xgap.db.DerivedTraitJpaMapper

prepareFileAttachements(List<EnvironmentalFactor>, File) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorJpaMapper

prepareFileAttachements(List<Gene>, File) - Method in class org.molgenis.omx.xgap.db.GeneJpaMapper

prepareFileAttachements(List<Marker_ReportsFor>, File) - Method in class org.molgenis.omx.xgap.db.Marker_ReportsForJpaMapper

prepareFileAttachements(List<Marker>, File) - Method in class org.molgenis.omx.xgap.db.MarkerJpaMapper

prepareFileAttachements(List<MassPeak>, File) - Method in class org.molgenis.omx.xgap.db.MassPeakJpaMapper

prepareFileAttachements(List<Metabolite>, File) - Method in class org.molgenis.omx.xgap.db.MetaboliteJpaMapper

prepareFileAttachements(List<NMRBin>, File) - Method in class org.molgenis.omx.xgap.db.NMRBinJpaMapper

prepareFileAttachements(List<PairedSample>, File) - Method in class org.molgenis.omx.xgap.db.PairedSampleJpaMapper

prepareFileAttachements(List<Polymorphism>, File) - Method in class org.molgenis.omx.xgap.db.PolymorphismJpaMapper

prepareFileAttachements(List<Probe>, File) - Method in class org.molgenis.omx.xgap.db.ProbeJpaMapper

prepareFileAttachements(List<ProbeSet>, File) - Method in class org.molgenis.omx.xgap.db.ProbeSetJpaMapper

prepareFileAttachements(List<Protein>, File) - Method in class org.molgenis.omx.xgap.db.ProteinJpaMapper

prepareFileAttachements(List<Sample>, File) - Method in class org.molgenis.omx.xgap.db.SampleJpaMapper

prepareFileAttachements(List<SNP_Polymorphism>, File) - Method in class org.molgenis.omx.xgap.db.SNP_PolymorphismJpaMapper

prepareFileAttachements(List<SNP>, File) - Method in class org.molgenis.omx.xgap.db.SNPJpaMapper

prepareFileAttachements(List<Spot>, File) - Method in class org.molgenis.omx.xgap.db.SpotJpaMapper

prepareFileAttachements(List<Track>, File) - Method in class org.molgenis.omx.xgap.db.TrackJpaMapper

prepareFileAttachements(List<Transcript>, File) - Method in class org.molgenis.omx.xgap.db.TranscriptJpaMapper

prepareFileAttachements(List<Variant>, File) - Method in class org.molgenis.omx.xgap.db.VariantJpaMapper

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

Probe(Probe) - Constructor for class org.molgenis.omx.xgap.Probe

copy constructor

ProbeEntityImporter - Class in org.molgenis.omx.xgap.db

Reads Probe from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

ProbeEntityImporter() - Constructor for class org.molgenis.omx.xgap.db.ProbeEntityImporter

ProbeJpaMapper - Class in org.molgenis.omx.xgap.db

ProbeJpaMapper(Database) - Constructor for class org.molgenis.omx.xgap.db.ProbeJpaMapper

ProbeSecurityDecorator<E extends Probe> - Class in org.molgenis.omx.xgap.db

TODO add column level security filters

ProbeSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.ProbeSecurityDecorator

ProbeService - Class in org.molgenis.service

ProbeService() - Constructor for class org.molgenis.service.ProbeService

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

ProbeSet(ProbeSet) - Constructor for class org.molgenis.omx.xgap.ProbeSet

copy constructor

PROBESET_IDENTIFIER - Static variable in class org.molgenis.omx.xgap.Probe

ProbeSetEntityImporter - Class in org.molgenis.omx.xgap.db

Reads ProbeSet from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

ProbeSetEntityImporter() - Constructor for class org.molgenis.omx.xgap.db.ProbeSetEntityImporter

ProbeSetJpaMapper - Class in org.molgenis.omx.xgap.db

ProbeSetJpaMapper(Database) - Constructor for class org.molgenis.omx.xgap.db.ProbeSetJpaMapper

ProbeSetSecurityDecorator<E extends ProbeSet> - Class in org.molgenis.omx.xgap.db

TODO add column level security filters

ProbeSetSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.ProbeSetSecurityDecorator

ProbeSetService - Class in org.molgenis.service

ProbeSetService() - Constructor for class org.molgenis.service.ProbeSetService

Protein - Class in org.molgenis.omx.xgap

Protein: Trait annotations specific for proteins..

Protein() - Constructor for class org.molgenis.omx.xgap.Protein

Protein(Protein) - Constructor for class org.molgenis.omx.xgap.Protein

copy constructor

ProteinEntityImporter - Class in org.molgenis.omx.xgap.db

Reads Protein from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

ProteinEntityImporter() - Constructor for class org.molgenis.omx.xgap.db.ProteinEntityImporter

ProteinJpaMapper - Class in org.molgenis.omx.xgap.db

ProteinJpaMapper(Database) - Constructor for class org.molgenis.omx.xgap.db.ProteinJpaMapper

ProteinSecurityDecorator<E extends Protein> - Class in org.molgenis.omx.xgap.db

TODO add column level security filters

ProteinSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.ProteinSecurityDecorator

ProteinService - Class in org.molgenis.service

ProteinService() - Constructor for class org.molgenis.service.ProteinService

ProtocolSecurityDecorator<E extends Protocol> - Class in org.molgenis.omx.observ.db

TODO add column level security filters

ProtocolSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.db.ProtocolSecurityDecorator

PUBMEDID - Static variable in class org.molgenis.omx.patient.Patient

Q

query(Database) - Static method in class org.molgenis.omx.patient.Patient

Shorthand for db.query(Patient.class).

query(Database) - Static method in class org.molgenis.omx.xgap.Chromosome

Shorthand for db.query(Chromosome.class).

query(Database) - Static method in class org.molgenis.omx.xgap.Clone

Shorthand for db.query(Clone.class).

query(Database) - Static method in class org.molgenis.omx.xgap.DerivedTrait

Shorthand for db.query(DerivedTrait.class).

query(Database) - Static method in class org.molgenis.omx.xgap.EnvironmentalFactor

Shorthand for db.query(EnvironmentalFactor.class).

query(Database) - Static method in class org.molgenis.omx.xgap.Gene

Shorthand for db.query(Gene.class).

query(Database) - Static method in class org.molgenis.omx.xgap.Marker

Shorthand for db.query(Marker.class).

query(Database) - Static method in class org.molgenis.omx.xgap.Marker_ReportsFor

Shorthand for db.query(Marker_ReportsFor.class).

query(Database) - Static method in class org.molgenis.omx.xgap.MassPeak

Shorthand for db.query(MassPeak.class).

query(Database) - Static method in class org.molgenis.omx.xgap.Metabolite

Shorthand for db.query(Metabolite.class).

query(Database) - Static method in class org.molgenis.omx.xgap.NMRBin

Shorthand for db.query(NMRBin.class).

query(Database) - Static method in class org.molgenis.omx.xgap.PairedSample

Shorthand for db.query(PairedSample.class).

query(Database) - Static method in class org.molgenis.omx.xgap.Polymorphism

Shorthand for db.query(Polymorphism.class).

query(Database) - Static method in class org.molgenis.omx.xgap.Probe

Shorthand for db.query(Probe.class).

query(Database) - Static method in class org.molgenis.omx.xgap.ProbeSet

Shorthand for db.query(ProbeSet.class).

query(Database) - Static method in class org.molgenis.omx.xgap.Protein

Shorthand for db.query(Protein.class).

query(Database) - Static method in class org.molgenis.omx.xgap.Sample

Shorthand for db.query(Sample.class).

query(Database) - Static method in class org.molgenis.omx.xgap.SNP

Shorthand for db.query(SNP.class).

query(Database) - Static method in class org.molgenis.omx.xgap.SNP_Polymorphism

Shorthand for db.query(SNP_Polymorphism.class).

query(Database) - Static method in class org.molgenis.omx.xgap.Spot

Shorthand for db.query(Spot.class).

query(Database) - Static method in class org.molgenis.omx.xgap.Track

Shorthand for db.query(Track.class).

query(Database) - Static method in class org.molgenis.omx.xgap.Transcript

Shorthand for db.query(Transcript.class).

query(Database) - Static method in class org.molgenis.omx.xgap.Variant

Shorthand for db.query(Variant.class).

queryVariants(String, int, int, Patient) - Method in class org.molgenis.omx.das.DasOmxDataSource

R

read(Integer) - Method in class org.molgenis.service.ChromosomeService

read(Integer) - Method in class org.molgenis.service.CloneService

read(Integer) - Method in class org.molgenis.service.DerivedTraitService

read(Integer) - Method in class org.molgenis.service.EnvironmentalFactorService

read(Integer) - Method in class org.molgenis.service.GeneService

read(Integer) - Method in class org.molgenis.service.MarkerService

read(Integer) - Method in class org.molgenis.service.MassPeakService

read(Integer) - Method in class org.molgenis.service.MetaboliteService

read(Integer) - Method in class org.molgenis.service.NMRBinService

read(Integer) - Method in class org.molgenis.service.PairedSampleService

read(Integer) - Method in class org.molgenis.service.PatientService

read(Integer) - Method in class org.molgenis.service.PolymorphismService

read(Integer) - Method in class org.molgenis.service.ProbeService

read(Integer) - Method in class org.molgenis.service.ProbeSetService

read(Integer) - Method in class org.molgenis.service.ProteinService

read(Integer) - Method in class org.molgenis.service.SampleService

read(Integer) - Method in class org.molgenis.service.SNPService

read(Integer) - Method in class org.molgenis.service.SpotService

read(Integer) - Method in class org.molgenis.service.TrackService

read(Integer) - Method in class org.molgenis.service.TranscriptService

read(Integer) - Method in class org.molgenis.service.VariantService

readAll() - Method in class org.molgenis.service.ChromosomeService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.ChromosomeService

readAll() - Method in class org.molgenis.service.CloneService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.CloneService

readAll() - Method in class org.molgenis.service.DerivedTraitService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.DerivedTraitService

readAll() - Method in class org.molgenis.service.EnvironmentalFactorService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.EnvironmentalFactorService

readAll() - Method in class org.molgenis.service.GeneService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.GeneService

readAll() - Method in class org.molgenis.service.MarkerService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.MarkerService

readAll() - Method in class org.molgenis.service.MassPeakService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.MassPeakService

readAll() - Method in class org.molgenis.service.MetaboliteService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.MetaboliteService

readAll() - Method in class org.molgenis.service.NMRBinService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.NMRBinService

readAll() - Method in class org.molgenis.service.PairedSampleService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.PairedSampleService

readAll() - Method in class org.molgenis.service.PatientService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.PatientService

readAll() - Method in class org.molgenis.service.PolymorphismService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.PolymorphismService

readAll() - Method in class org.molgenis.service.ProbeService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.ProbeService

readAll() - Method in class org.molgenis.service.ProbeSetService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.ProbeSetService

readAll() - Method in class org.molgenis.service.ProteinService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.ProteinService

readAll() - Method in class org.molgenis.service.SampleService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.SampleService

readAll() - Method in class org.molgenis.service.SNPService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.SNPService

readAll() - Method in class org.molgenis.service.SpotService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.SpotService

readAll() - Method in class org.molgenis.service.TrackService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.TrackService

readAll() - Method in class org.molgenis.service.TranscriptService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.TranscriptService

readAll() - Method in class org.molgenis.service.VariantService

readAll(int, int, List<QueryRule>) - Method in class org.molgenis.service.VariantService

REFERENCE - Static variable in class org.molgenis.omx.patient.Patient

remove(List<E>) - Method in class org.molgenis.omx.auth.db.InstituteSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.auth.db.PersonRoleSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.auth.db.PersonSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.core.db.MolgenisEntitySecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.core.db.MolgenisFileSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.core.db.RuntimePropertySecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.db.CategorySecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.db.CharacteristicSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.db.DataSetSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.db.ObservableFeatureSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.db.ObservationSetSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.db.ObservationTargetSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.db.ObservedValueSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.db.ProtocolSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.target.db.AccessionSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.target.db.IndividualSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.target.db.OntologySecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.target.db.OntologyTermSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.target.db.PanelSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.target.db.PanelSourceSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.target.db.SpeciesSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.value.db.BoolValueSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.value.db.DateValueSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.value.db.DecimalValueSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.value.db.EmailValueSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.value.db.HtmlValueSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.value.db.IntValueSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.value.db.LongValueSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.value.db.MrefValueSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.value.db.StringValueSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.value.db.TextValueSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.value.db.ValueSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.observ.value.db.XrefValueSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.patient.db.PatientSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.xgap.db.ChromosomeSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.xgap.db.CloneSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.xgap.db.DerivedTraitSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.xgap.db.GeneSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.xgap.db.Marker_ReportsForSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.xgap.db.MarkerSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.xgap.db.MassPeakSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.xgap.db.MetaboliteSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.xgap.db.NMRBinSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.xgap.db.PairedSampleSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.xgap.db.PolymorphismSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.xgap.db.ProbeSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.xgap.db.ProbeSetSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.xgap.db.ProteinSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.xgap.db.SampleSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.xgap.db.SNP_PolymorphismSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.xgap.db.SNPSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.xgap.db.SpotSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.xgap.db.TrackSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.xgap.db.TranscriptSecurityDecorator

remove(List<E>) - Method in class org.molgenis.omx.xgap.db.VariantSecurityDecorator

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

REPORTSFOR_IDENTIFIER - Static variable in class org.molgenis.omx.xgap.Marker

REPORTSFOR_IDENTIFIER - Static variable in class org.molgenis.omx.xgap.Marker_ReportsFor

REPORTSFOR_IDENTIFIER - Static variable in class org.molgenis.omx.xgap.Probe

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.auth.db.InstituteSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.auth.db.PersonRoleSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.auth.db.PersonSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.core.db.MolgenisEntitySecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.core.db.MolgenisFileSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.core.db.RuntimePropertySecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.db.CategorySecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.db.CharacteristicSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.db.DataSetSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.db.ObservableFeatureSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.db.ObservationSetSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.db.ObservationTargetSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.db.ObservedValueSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.db.ProtocolSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.target.db.AccessionSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.target.db.IndividualSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.target.db.OntologySecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.target.db.OntologyTermSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.target.db.PanelSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.target.db.PanelSourceSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.target.db.SpeciesSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.value.db.BoolValueSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.value.db.DateValueSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.value.db.DecimalValueSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.value.db.EmailValueSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.value.db.HtmlValueSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.value.db.IntValueSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.value.db.LongValueSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.value.db.MrefValueSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.value.db.StringValueSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.value.db.TextValueSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.value.db.ValueSecurityDecorator

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.observ.value.db.XrefValueSecurityDecorator

resolveForeignKeys(List<Patient>) - Method in class org.molgenis.omx.patient.db.PatientJpaMapper

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.patient.db.PatientSecurityDecorator

resolveForeignKeys(List<Chromosome>) - Method in class org.molgenis.omx.xgap.db.ChromosomeJpaMapper

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.xgap.db.ChromosomeSecurityDecorator

resolveForeignKeys(List<Clone>) - Method in class org.molgenis.omx.xgap.db.CloneJpaMapper

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.xgap.db.CloneSecurityDecorator

resolveForeignKeys(List<DerivedTrait>) - Method in class org.molgenis.omx.xgap.db.DerivedTraitJpaMapper

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.xgap.db.DerivedTraitSecurityDecorator

resolveForeignKeys(List<EnvironmentalFactor>) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorJpaMapper

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorSecurityDecorator

resolveForeignKeys(List<Gene>) - Method in class org.molgenis.omx.xgap.db.GeneJpaMapper

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.xgap.db.GeneSecurityDecorator

resolveForeignKeys(List<Marker_ReportsFor>) - Method in class org.molgenis.omx.xgap.db.Marker_ReportsForJpaMapper

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.xgap.db.Marker_ReportsForSecurityDecorator

resolveForeignKeys(List<Marker>) - Method in class org.molgenis.omx.xgap.db.MarkerJpaMapper

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.xgap.db.MarkerSecurityDecorator

resolveForeignKeys(List<MassPeak>) - Method in class org.molgenis.omx.xgap.db.MassPeakJpaMapper

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.xgap.db.MassPeakSecurityDecorator

resolveForeignKeys(List<Metabolite>) - Method in class org.molgenis.omx.xgap.db.MetaboliteJpaMapper

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.xgap.db.MetaboliteSecurityDecorator

resolveForeignKeys(List<NMRBin>) - Method in class org.molgenis.omx.xgap.db.NMRBinJpaMapper

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.xgap.db.NMRBinSecurityDecorator

resolveForeignKeys(List<PairedSample>) - Method in class org.molgenis.omx.xgap.db.PairedSampleJpaMapper

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.xgap.db.PairedSampleSecurityDecorator

resolveForeignKeys(List<Polymorphism>) - Method in class org.molgenis.omx.xgap.db.PolymorphismJpaMapper

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.xgap.db.PolymorphismSecurityDecorator

resolveForeignKeys(List<Probe>) - Method in class org.molgenis.omx.xgap.db.ProbeJpaMapper

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.xgap.db.ProbeSecurityDecorator

resolveForeignKeys(List<ProbeSet>) - Method in class org.molgenis.omx.xgap.db.ProbeSetJpaMapper

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.xgap.db.ProbeSetSecurityDecorator

resolveForeignKeys(List<Protein>) - Method in class org.molgenis.omx.xgap.db.ProteinJpaMapper

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.xgap.db.ProteinSecurityDecorator

resolveForeignKeys(List<Sample>) - Method in class org.molgenis.omx.xgap.db.SampleJpaMapper

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.xgap.db.SampleSecurityDecorator

resolveForeignKeys(List<SNP_Polymorphism>) - Method in class org.molgenis.omx.xgap.db.SNP_PolymorphismJpaMapper

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.xgap.db.SNP_PolymorphismSecurityDecorator

resolveForeignKeys(List<SNP>) - Method in class org.molgenis.omx.xgap.db.SNPJpaMapper

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.xgap.db.SNPSecurityDecorator

resolveForeignKeys(List<Spot>) - Method in class org.molgenis.omx.xgap.db.SpotJpaMapper

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.xgap.db.SpotSecurityDecorator

resolveForeignKeys(List<Track>) - Method in class org.molgenis.omx.xgap.db.TrackJpaMapper

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.xgap.db.TrackSecurityDecorator

resolveForeignKeys(List<Transcript>) - Method in class org.molgenis.omx.xgap.db.TranscriptJpaMapper

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.xgap.db.TranscriptSecurityDecorator

resolveForeignKeys(List<Variant>) - Method in class org.molgenis.omx.xgap.db.VariantJpaMapper

resolveForeignKeys(List<E>) - Method in class org.molgenis.omx.xgap.db.VariantSecurityDecorator

RETENTIONTIME - Static variable in class org.molgenis.omx.xgap.MassPeak

RuntimePropertySecurityDecorator<E extends RuntimeProperty> - Class in org.molgenis.omx.core.db

TODO add column level security filters

RuntimePropertySecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.core.db.RuntimePropertySecurityDecorator

S

Sample - Class in org.molgenis.omx.xgap

Sample: .

Sample() - Constructor for class org.molgenis.omx.xgap.Sample

Sample(Sample) - Constructor for class org.molgenis.omx.xgap.Sample

copy constructor

SampleEntityImporter - Class in org.molgenis.omx.xgap.db

Reads Sample from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

SampleEntityImporter() - Constructor for class org.molgenis.omx.xgap.db.SampleEntityImporter

SampleJpaMapper - Class in org.molgenis.omx.xgap.db

SampleJpaMapper(Database) - Constructor for class org.molgenis.omx.xgap.db.SampleJpaMapper

SampleSecurityDecorator<E extends Sample> - Class in org.molgenis.omx.xgap.db

TODO add column level security filters

SampleSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.SampleSecurityDecorator

SampleService - Class in org.molgenis.service

SampleService() - Constructor for class org.molgenis.service.SampleService

saveFileAttachements(List<Patient>, File) - Method in class org.molgenis.omx.patient.db.PatientJpaMapper

saveFileAttachements(List<Chromosome>, File) - Method in class org.molgenis.omx.xgap.db.ChromosomeJpaMapper

saveFileAttachements(List<Clone>, File) - Method in class org.molgenis.omx.xgap.db.CloneJpaMapper

saveFileAttachements(List<DerivedTrait>, File) - Method in class org.molgenis.omx.xgap.db.DerivedTraitJpaMapper

saveFileAttachements(List<EnvironmentalFactor>, File) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorJpaMapper

saveFileAttachements(List<Gene>, File) - Method in class org.molgenis.omx.xgap.db.GeneJpaMapper

saveFileAttachements(List<Marker_ReportsFor>, File) - Method in class org.molgenis.omx.xgap.db.Marker_ReportsForJpaMapper

saveFileAttachements(List<Marker>, File) - Method in class org.molgenis.omx.xgap.db.MarkerJpaMapper

saveFileAttachements(List<MassPeak>, File) - Method in class org.molgenis.omx.xgap.db.MassPeakJpaMapper

saveFileAttachements(List<Metabolite>, File) - Method in class org.molgenis.omx.xgap.db.MetaboliteJpaMapper

saveFileAttachements(List<NMRBin>, File) - Method in class org.molgenis.omx.xgap.db.NMRBinJpaMapper

saveFileAttachements(List<PairedSample>, File) - Method in class org.molgenis.omx.xgap.db.PairedSampleJpaMapper

saveFileAttachements(List<Polymorphism>, File) - Method in class org.molgenis.omx.xgap.db.PolymorphismJpaMapper

saveFileAttachements(List<Probe>, File) - Method in class org.molgenis.omx.xgap.db.ProbeJpaMapper

saveFileAttachements(List<ProbeSet>, File) - Method in class org.molgenis.omx.xgap.db.ProbeSetJpaMapper

saveFileAttachements(List<Protein>, File) - Method in class org.molgenis.omx.xgap.db.ProteinJpaMapper

saveFileAttachements(List<Sample>, File) - Method in class org.molgenis.omx.xgap.db.SampleJpaMapper

saveFileAttachements(List<SNP_Polymorphism>, File) - Method in class org.molgenis.omx.xgap.db.SNP_PolymorphismJpaMapper

saveFileAttachements(List<SNP>, File) - Method in class org.molgenis.omx.xgap.db.SNPJpaMapper

saveFileAttachements(List<Spot>, File) - Method in class org.molgenis.omx.xgap.db.SpotJpaMapper

saveFileAttachements(List<Track>, File) - Method in class org.molgenis.omx.xgap.db.TrackJpaMapper

saveFileAttachements(List<Transcript>, File) - Method in class org.molgenis.omx.xgap.db.TranscriptJpaMapper

saveFileAttachements(List<Variant>, File) - Method in class org.molgenis.omx.xgap.db.VariantJpaMapper

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(Entity, boolean) - Method in class org.molgenis.omx.xgap.Chromosome

set(Entity, boolean) - Method in class org.molgenis.omx.xgap.Clone

set(Entity, boolean) - Method in class org.molgenis.omx.xgap.DerivedTrait

set(Entity, boolean) - Method in class org.molgenis.omx.xgap.EnvironmentalFactor

set(Entity, boolean) - Method in class org.molgenis.omx.xgap.Gene

set(Entity, boolean) - Method in class org.molgenis.omx.xgap.Marker

set(Entity, boolean) - Method in class org.molgenis.omx.xgap.Marker_ReportsFor

set(Entity, boolean) - Method in class org.molgenis.omx.xgap.MassPeak

set(Entity, boolean) - Method in class org.molgenis.omx.xgap.Metabolite

set(Entity, boolean) - Method in class org.molgenis.omx.xgap.NMRBin

set(Entity, boolean) - Method in class org.molgenis.omx.xgap.PairedSample

set(Entity, boolean) - Method in class org.molgenis.omx.xgap.Polymorphism

set(Entity, boolean) - Method in class org.molgenis.omx.xgap.Probe

set(Entity, boolean) - Method in class org.molgenis.omx.xgap.ProbeSet

set(Entity, boolean) - Method in class org.molgenis.omx.xgap.Protein

set(Entity, boolean) - Method in class org.molgenis.omx.xgap.Sample

set(Entity, boolean) - Method in class org.molgenis.omx.xgap.SNP

set(Entity, boolean) - Method in class org.molgenis.omx.xgap.SNP_Polymorphism

set(Entity, boolean) - Method in class org.molgenis.omx.xgap.Spot

set(Entity, boolean) - Method in class org.molgenis.omx.xgap.Track

set(Entity, boolean) - Method in class org.molgenis.omx.xgap.Transcript

set(Entity, boolean) - Method in class org.molgenis.omx.xgap.Variant

setAaNotation(String) - Method in class org.molgenis.omx.xgap.Variant

Set the AaNotation.

setAaPosition(Integer) - Method in class org.molgenis.omx.xgap.Variant

Set the AaPosition.

setAllele1(Variant) - Method in class org.molgenis.omx.patient.Patient

Set the Allele1.

setAllele1(Integer) - Method in class org.molgenis.omx.patient.Patient

setAllele1_Id(Integer) - Method in class org.molgenis.omx.patient.Patient

Set foreign key for field allele1.

setAllele1_Identifier(String) - Method in class org.molgenis.omx.patient.Patient

Set a pretty label for cross reference Allele1 to Variant.Id.

setAllele2(Variant) - Method in class org.molgenis.omx.patient.Patient

Set the Allele2.

setAllele2(Integer) - Method in class org.molgenis.omx.patient.Patient

setAllele2_Id(Integer) - Method in class org.molgenis.omx.patient.Patient

Set foreign key for field allele2.

setAllele2_Identifier(String) - Method in class org.molgenis.omx.patient.Patient

Set a pretty label for cross reference Allele2 to Variant.Id.

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 CdnaNotation.

setCdnaPosition(Integer) - Method in class org.molgenis.omx.xgap.Variant

Set the CdnaPosition.

setChromosome(Chromosome) - Method in class org.molgenis.omx.xgap.Clone

Set the Reference to the chromosome this position belongs to..

setChromosome(Integer) - Method in class org.molgenis.omx.xgap.Clone

setChromosome(Chromosome) - Method in class org.molgenis.omx.xgap.Gene

Set the Reference to the chromosome this position belongs to..

setChromosome(Integer) - Method in class org.molgenis.omx.xgap.Gene

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(Integer) - Method in class org.molgenis.omx.xgap.Marker

setChromosome(Chromosome) - Method in class org.molgenis.omx.xgap.Probe

Set the Reference to the chromosome this position belongs to..

setChromosome(Integer) - Method in class org.molgenis.omx.xgap.Probe

setChromosome(Chromosome) - Method in class org.molgenis.omx.xgap.ProbeSet

Set the Reference to the chromosome this position belongs to..

setChromosome(Integer) - Method in class org.molgenis.omx.xgap.ProbeSet

setChromosome(Chromosome) - Method in class org.molgenis.omx.xgap.Variant

Set the Reference to the chromosome this position belongs to..

setChromosome(Integer) - Method in class org.molgenis.omx.xgap.Variant

setChromosome_Id(Integer) - Method in class org.molgenis.omx.xgap.Clone

Set foreign key for field chromosome.

setChromosome_Id(Integer) - Method in class org.molgenis.omx.xgap.Gene

Set foreign key for field chromosome.

setChromosome_Id(Integer) - Method in interface org.molgenis.omx.xgap.Locus

setChromosome_Id(Integer) - Method in class org.molgenis.omx.xgap.Marker

Set foreign key for field chromosome.

setChromosome_Id(Integer) - Method in class org.molgenis.omx.xgap.Probe

Set foreign key for field chromosome.

setChromosome_Id(Integer) - Method in class org.molgenis.omx.xgap.ProbeSet

Set foreign key for field chromosome.

setChromosome_Id(Integer) - Method in class org.molgenis.omx.xgap.Variant

Set foreign key for field chromosome.

setChromosome_Identifier(String) - Method in class org.molgenis.omx.xgap.Clone

Set a pretty label for cross reference Chromosome to Chromosome.Id.

setChromosome_Identifier(String) - Method in class org.molgenis.omx.xgap.Gene

Set a pretty label for cross reference Chromosome to Chromosome.Id.

setChromosome_Identifier(String) - Method in interface org.molgenis.omx.xgap.Locus

setChromosome_Identifier(String) - Method in class org.molgenis.omx.xgap.Marker

Set a pretty label for cross reference Chromosome to Chromosome.Id.

setChromosome_Identifier(String) - Method in class org.molgenis.omx.xgap.Probe

Set a pretty label for cross reference Chromosome to Chromosome.Id.

setChromosome_Identifier(String) - Method in class org.molgenis.omx.xgap.ProbeSet

Set a pretty label for cross reference Chromosome to Chromosome.Id.

setChromosome_Identifier(String) - Method in class org.molgenis.omx.xgap.Variant

Set a pretty label for cross reference Chromosome to Chromosome.Id.

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 Codonchange.

setConsequence(String) - Method in class org.molgenis.omx.xgap.Variant

Set the Consequence.

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..

setDescription(String) - Method in class org.molgenis.omx.xgap.Variant

Set the Description.

setDetailsForMutation(String) - Method in class org.molgenis.omx.xgap.Variant

Set the DetailsForMutation.

setEffectOnSplicing(Boolean) - Method in class org.molgenis.omx.xgap.Variant

Set the EffectOnSplicing.

setEvent(String) - Method in class org.molgenis.omx.xgap.Variant

Set the Event.

setExon(String) - Method in class org.molgenis.omx.xgap.Variant

Set the Exon.

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 GdnaNotation.

setGene(Gene) - Method in class org.molgenis.omx.xgap.Protein

Set the The gene that produces this protein.

setGene(Integer) - Method in class org.molgenis.omx.xgap.Protein

setGene(Gene) - Method in class org.molgenis.omx.xgap.Transcript

Set the The gene that produces this protein.

setGene(Integer) - Method in class org.molgenis.omx.xgap.Transcript

setGene(String) - Method in class org.molgenis.omx.xgap.Variant

Set the Gene.

setGene_Id(Integer) - Method in class org.molgenis.omx.xgap.Protein

Set foreign key for field gene.

setGene_Id(Integer) - Method in class org.molgenis.omx.xgap.Transcript

Set foreign key for field gene.

setGene_Identifier(String) - Method in class org.molgenis.omx.xgap.Protein

Set a pretty label for cross reference Gene to Gene.Id.

setGene_Identifier(String) - Method in class org.molgenis.omx.xgap.Transcript

Set a pretty label for cross reference Gene to Gene.Id.

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 IdMutation.

setIndividual(Individual) - Method in class org.molgenis.omx.xgap.Sample

Set the The individual from which this sample was taken..

setIndividual(Integer) - Method in class org.molgenis.omx.xgap.Sample

setIndividual_Id(Integer) - Method in class org.molgenis.omx.xgap.Sample

Set foreign key for field individual.

setIndividual_Identifier(String) - Method in class org.molgenis.omx.xgap.Sample

Set a pretty label for cross reference Individual to Individual.Id.

setInheritance(String) - Method in class org.molgenis.omx.xgap.Variant

Set the Inheritance.

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.

setLabel1(Integer) - Method in class org.molgenis.omx.xgap.PairedSample

setLabel1_Id(Integer) - Method in class org.molgenis.omx.xgap.PairedSample

Set foreign key for field label1.

setLabel1_Identifier(String) - Method in class org.molgenis.omx.xgap.PairedSample

Set a pretty label for cross reference Label1 to OntologyTerm.Id.

setLabel2(OntologyTerm) - Method in class org.molgenis.omx.xgap.PairedSample

Set the Which channel or Fluorescent labeling is associated with the second subject.

setLabel2(Integer) - Method in class org.molgenis.omx.xgap.PairedSample

setLabel2_Id(Integer) - Method in class org.molgenis.omx.xgap.PairedSample

Set foreign key for field label2.

setLabel2_Identifier(String) - Method in class org.molgenis.omx.xgap.PairedSample

Set a pretty label for cross reference Label2 to OntologyTerm.Id.

setMarker(Marker) - Method in class org.molgenis.omx.xgap.Marker_ReportsFor

Set the .

setMarker(Integer) - Method in class org.molgenis.omx.xgap.Marker_ReportsFor

setMarker_Id(Integer) - Method in class org.molgenis.omx.xgap.Marker_ReportsFor

Set foreign key for field marker.

setMarker_Identifier(String) - Method in class org.molgenis.omx.xgap.Marker_ReportsFor

Set a pretty label for cross reference Marker to Marker.Id.

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 MutationPosition.

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 NtChange.

setOrderNr(Integer) - Method in class org.molgenis.omx.xgap.Chromosome

Set the orderNr.

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 Pathogenicity.

setPheno(String) - Method in class org.molgenis.omx.patient.Patient

Set the Pheno.

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

setPolymorphism(Polymorphism) - Method in class org.molgenis.omx.xgap.SNP_Polymorphism

Set the .

setPolymorphism(Integer) - Method in class org.molgenis.omx.xgap.SNP_Polymorphism

setPolymorphism_Id(Integer...) - Method in class org.molgenis.omx.xgap.SNP

setPolymorphism_Id(List<Integer>) - Method in class org.molgenis.omx.xgap.SNP

Set foreign key for field polymorphism.

setPolymorphism_Id(Integer) - Method in class org.molgenis.omx.xgap.SNP_Polymorphism

Set foreign key for field polymorphism.

setPolymorphism_Identifier(List<String>) - Method in class org.molgenis.omx.xgap.SNP

Update the foreign key Polymorphism This sets polymorphism to null until next database transaction.

setPolymorphism_Identifier(String) - Method in class org.molgenis.omx.xgap.SNP_Polymorphism

Set a pretty label for cross reference Polymorphism to Polymorphism.Id.

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)..

setProbeSet(Integer) - Method in class org.molgenis.omx.xgap.Probe

setProbeSet_Id(Integer) - Method in class org.molgenis.omx.xgap.Probe

Set foreign key for field probeSet.

setProbeSet_Identifier(String) - Method in class org.molgenis.omx.xgap.Probe

Set a pretty label for cross reference ProbeSet to ProbeSet.Id.

setPubMedID(String) - Method in class org.molgenis.omx.patient.Patient

Set the PubMedID.

setReference(String) - Method in class org.molgenis.omx.patient.Patient

Set the Reference.

setReportedSNP(Boolean) - Method in class org.molgenis.omx.xgap.Variant

Set the ReportedSNP.

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

setReportsFor(Marker) - Method in class org.molgenis.omx.xgap.Marker_ReportsFor

Set the .

setReportsFor(Integer) - Method in class org.molgenis.omx.xgap.Marker_ReportsFor

setReportsFor(Gene) - Method in class org.molgenis.omx.xgap.Probe

Set the The gene this probe reports for..

setReportsFor(Integer) - Method in class org.molgenis.omx.xgap.Probe

setReportsFor_Id(Integer...) - Method in class org.molgenis.omx.xgap.Marker

setReportsFor_Id(List<Integer>) - Method in class org.molgenis.omx.xgap.Marker

Set foreign key for field reportsFor.

setReportsFor_Id(Integer) - Method in class org.molgenis.omx.xgap.Marker_ReportsFor

Set foreign key for field reportsFor.

setReportsFor_Id(Integer) - Method in class org.molgenis.omx.xgap.Probe

Set foreign key for field reportsFor.

setReportsFor_Identifier(List<String>) - Method in class org.molgenis.omx.xgap.Marker

Update the foreign key ReportsFor This sets reportsFor to null until next database transaction.

setReportsFor_Identifier(String) - Method in class org.molgenis.omx.xgap.Marker_ReportsFor

Set a pretty label for cross reference ReportsFor to Marker.Id.

setReportsFor_Identifier(String) - Method in class org.molgenis.omx.xgap.Probe

Set a pretty label for cross reference ReportsFor to Gene.Id.

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 .

setSNP(Integer) - Method in class org.molgenis.omx.xgap.SNP_Polymorphism

setSNP_Id(Integer) - Method in class org.molgenis.omx.xgap.SNP_Polymorphism

Set foreign key for field sNP.

setSNP_Identifier(String) - Method in class org.molgenis.omx.xgap.SNP_Polymorphism

Set a pretty label for cross reference SNP to SNP.Id.

setSpecies(OntologyTerm) - Method in class org.molgenis.omx.xgap.Chromosome

Set the Reference to the species this chromosome belongs to..

setSpecies(Integer) - Method in class org.molgenis.omx.xgap.Chromosome

setSpecies_Id(Integer) - Method in class org.molgenis.omx.xgap.Chromosome

Set foreign key for field species.

setSpecies_Identifier(String) - Method in class org.molgenis.omx.xgap.Chromosome

Set a pretty label for cross reference Species to OntologyTerm.Id.

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.

setSubject1(Integer) - Method in class org.molgenis.omx.xgap.PairedSample

setSubject1_Id(Integer) - Method in class org.molgenis.omx.xgap.PairedSample

Set foreign key for field subject1.

setSubject1_Identifier(String) - Method in class org.molgenis.omx.xgap.PairedSample

Set a pretty label for cross reference Subject1 to Individual.Id.

setSubject2(Individual) - Method in class org.molgenis.omx.xgap.PairedSample

Set the The second sample.

setSubject2(Integer) - Method in class org.molgenis.omx.xgap.PairedSample

setSubject2_Id(Integer) - Method in class org.molgenis.omx.xgap.PairedSample

Set foreign key for field subject2.

setSubject2_Identifier(String) - Method in class org.molgenis.omx.xgap.PairedSample

Set a pretty label for cross reference Subject2 to Individual.Id.

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..

setTissue(Integer) - Method in class org.molgenis.omx.xgap.Sample

setTissue_Id(Integer) - Method in class org.molgenis.omx.xgap.Sample

Set foreign key for field tissue.

setTissue_Identifier(String) - Method in class org.molgenis.omx.xgap.Sample

Set a pretty label for cross reference Tissue to OntologyTerm.Id.

setTrack(Track) - Method in class org.molgenis.omx.xgap.Variant

Set the Track.

setTrack(Integer) - Method in class org.molgenis.omx.xgap.Variant

setTrack_Id(Integer) - Method in class org.molgenis.omx.xgap.Variant

Set foreign key for field track.

setTrack_Identifier(String) - Method in class org.molgenis.omx.xgap.Variant

Set a pretty label for cross reference Track to Track.Id.

setTranscript(Transcript) - Method in class org.molgenis.omx.xgap.Protein

Set the The transcript variant that produces this protein.

setTranscript(Integer) - Method in class org.molgenis.omx.xgap.Protein

setTranscript_Id(Integer) - Method in class org.molgenis.omx.xgap.Protein

Set foreign key for field transcript.

setTranscript_Identifier(String) - Method in class org.molgenis.omx.xgap.Protein

Set a pretty label for cross reference Transcript to Transcript.Id.

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 VariantLength.

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(SNP) - Constructor for class org.molgenis.omx.xgap.SNP

copy constructor

SNP - Static variable in class org.molgenis.omx.xgap.SNP_Polymorphism

SNP_IDENTIFIER - 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_Polymorphism(SNP_Polymorphism) - Constructor for class org.molgenis.omx.xgap.SNP_Polymorphism

copy constructor

SNP_PolymorphismEntityImporter - Class in org.molgenis.omx.xgap.db

Reads SNP_Polymorphism from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

SNP_PolymorphismEntityImporter() - Constructor for class org.molgenis.omx.xgap.db.SNP_PolymorphismEntityImporter

SNP_PolymorphismJpaMapper - Class in org.molgenis.omx.xgap.db

SNP_PolymorphismJpaMapper(Database) - Constructor for class org.molgenis.omx.xgap.db.SNP_PolymorphismJpaMapper

SNP_PolymorphismSecurityDecorator<E extends SNP_Polymorphism> - Class in org.molgenis.omx.xgap.db

TODO add column level security filters

SNP_PolymorphismSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.SNP_PolymorphismSecurityDecorator

SNPEntityImporter - Class in org.molgenis.omx.xgap.db

Reads SNP from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

SNPEntityImporter() - Constructor for class org.molgenis.omx.xgap.db.SNPEntityImporter

SNPJpaMapper - Class in org.molgenis.omx.xgap.db

SNPJpaMapper(Database) - Constructor for class org.molgenis.omx.xgap.db.SNPJpaMapper

SNPSecurityDecorator<E extends SNP> - Class in org.molgenis.omx.xgap.db

TODO add column level security filters

SNPSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.SNPSecurityDecorator

SNPService - Class in org.molgenis.service

SNPService() - Constructor for class org.molgenis.service.SNPService

SPECIES - Static variable in class org.molgenis.omx.xgap.Chromosome

SPECIES_IDENTIFIER - Static variable in class org.molgenis.omx.xgap.Chromosome

SpeciesSecurityDecorator<E extends Species> - Class in org.molgenis.omx.observ.target.db

TODO add column level security filters

SpeciesSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.target.db.SpeciesSecurityDecorator

Spot - Class in org.molgenis.omx.xgap

Spot: This is the spot on a microarray.

Spot() - Constructor for class org.molgenis.omx.xgap.Spot

Spot(Spot) - Constructor for class org.molgenis.omx.xgap.Spot

copy constructor

SpotEntityImporter - Class in org.molgenis.omx.xgap.db

Reads Spot from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

SpotEntityImporter() - Constructor for class org.molgenis.omx.xgap.db.SpotEntityImporter

SpotJpaMapper - Class in org.molgenis.omx.xgap.db

SpotJpaMapper(Database) - Constructor for class org.molgenis.omx.xgap.db.SpotJpaMapper

SpotSecurityDecorator<E extends Spot> - Class in org.molgenis.omx.xgap.db

TODO add column level security filters

SpotSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.SpotSecurityDecorator

SpotService - Class in org.molgenis.service

SpotService() - Constructor for class org.molgenis.service.SpotService

STATUS - Static variable in class org.molgenis.omx.xgap.SNP

StringValueSecurityDecorator<E extends StringValue> - Class in org.molgenis.omx.observ.value.db

TODO add column level security filters

StringValueSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.value.db.StringValueSecurityDecorator

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

SUBJECT1 - Static variable in class org.molgenis.omx.xgap.PairedSample

SUBJECT1_IDENTIFIER - Static variable in class org.molgenis.omx.xgap.PairedSample

SUBJECT2 - Static variable in class org.molgenis.omx.xgap.PairedSample

SUBJECT2_IDENTIFIER - 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

TextValueSecurityDecorator<E extends TextValue> - Class in org.molgenis.omx.observ.value.db

TODO add column level security filters

TextValueSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.value.db.TextValueSecurityDecorator

TISSUE - Static variable in class org.molgenis.omx.xgap.Sample

TISSUE_IDENTIFIER - 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(Track) - Constructor for class org.molgenis.omx.xgap.Track

copy constructor

TRACK - Static variable in class org.molgenis.omx.xgap.Variant

TRACK_IDENTIFIER - Static variable in class org.molgenis.omx.xgap.Variant

TrackEntityImporter - Class in org.molgenis.omx.xgap.db

Reads Track from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

TrackEntityImporter() - Constructor for class org.molgenis.omx.xgap.db.TrackEntityImporter

TrackJpaMapper - Class in org.molgenis.omx.xgap.db

TrackJpaMapper(Database) - Constructor for class org.molgenis.omx.xgap.db.TrackJpaMapper

TrackSecurityDecorator<E extends Track> - Class in org.molgenis.omx.xgap.db

TODO add column level security filters

TrackSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.TrackSecurityDecorator

TrackService - Class in org.molgenis.service

TrackService() - Constructor for class org.molgenis.service.TrackService

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

Transcript(Transcript) - Constructor for class org.molgenis.omx.xgap.Transcript

copy constructor

TRANSCRIPT_IDENTIFIER - Static variable in class org.molgenis.omx.xgap.Protein

TranscriptEntityImporter - Class in org.molgenis.omx.xgap.db

Reads Transcript from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

TranscriptEntityImporter() - Constructor for class org.molgenis.omx.xgap.db.TranscriptEntityImporter

TranscriptJpaMapper - Class in org.molgenis.omx.xgap.db

TranscriptJpaMapper(Database) - Constructor for class org.molgenis.omx.xgap.db.TranscriptJpaMapper

TranscriptSecurityDecorator<E extends Transcript> - Class in org.molgenis.omx.xgap.db

TODO add column level security filters

TranscriptSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.TranscriptSecurityDecorator

TranscriptService - Class in org.molgenis.service

TranscriptService() - Constructor for class org.molgenis.service.TranscriptService

U

update(List<E>) - Method in class org.molgenis.omx.auth.db.InstituteSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.auth.db.PersonRoleSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.auth.db.PersonSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.core.db.MolgenisEntitySecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.core.db.MolgenisFileSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.core.db.RuntimePropertySecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.db.CategorySecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.db.CharacteristicSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.db.DataSetSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.db.ObservableFeatureSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.db.ObservationSetSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.db.ObservationTargetSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.db.ObservedValueSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.db.ProtocolSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.target.db.AccessionSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.target.db.IndividualSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.target.db.OntologySecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.target.db.OntologyTermSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.target.db.PanelSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.target.db.PanelSourceSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.target.db.SpeciesSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.value.db.BoolValueSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.value.db.CategoricalValueSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.value.db.DateTimeValueSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.value.db.DateValueSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.value.db.DecimalValueSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.value.db.EmailValueSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.value.db.HtmlValueSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.value.db.HyperlinkValueSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.value.db.IntValueSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.value.db.LongValueSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.value.db.MrefValueSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.value.db.StringValueSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.value.db.TextValueSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.value.db.ValueSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.observ.value.db.XrefValueSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.patient.db.PatientSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.xgap.db.ChromosomeSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.xgap.db.CloneSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.xgap.db.DerivedTraitSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.xgap.db.EnvironmentalFactorSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.xgap.db.GeneSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.xgap.db.Marker_ReportsForSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.xgap.db.MarkerSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.xgap.db.MassPeakSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.xgap.db.MetaboliteSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.xgap.db.NMRBinSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.xgap.db.PairedSampleSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.xgap.db.PolymorphismSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.xgap.db.ProbeSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.xgap.db.ProbeSetSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.xgap.db.ProteinSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.xgap.db.SampleSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.xgap.db.SNP_PolymorphismSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.xgap.db.SNPSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.xgap.db.SpotSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.xgap.db.TrackSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.xgap.db.TranscriptSecurityDecorator

update(List<E>) - Method in class org.molgenis.omx.xgap.db.VariantSecurityDecorator

update(Chromosome) - Method in class org.molgenis.service.ChromosomeService

update(Clone) - Method in class org.molgenis.service.CloneService

update(DerivedTrait) - Method in class org.molgenis.service.DerivedTraitService

update(EnvironmentalFactor) - Method in class org.molgenis.service.EnvironmentalFactorService

update(Gene) - Method in class org.molgenis.service.GeneService

update(Marker) - Method in class org.molgenis.service.MarkerService

update(MassPeak) - Method in class org.molgenis.service.MassPeakService

update(Metabolite) - Method in class org.molgenis.service.MetaboliteService

update(NMRBin) - Method in class org.molgenis.service.NMRBinService

update(PairedSample) - Method in class org.molgenis.service.PairedSampleService

update(Patient) - Method in class org.molgenis.service.PatientService

update(Polymorphism) - Method in class org.molgenis.service.PolymorphismService

update(Probe) - Method in class org.molgenis.service.ProbeService

update(ProbeSet) - Method in class org.molgenis.service.ProbeSetService

update(Protein) - Method in class org.molgenis.service.ProteinService

update(Sample) - Method in class org.molgenis.service.SampleService

update(SNP) - Method in class org.molgenis.service.SNPService

update(Spot) - Method in class org.molgenis.service.SpotService

update(Track) - Method in class org.molgenis.service.TrackService

update(Transcript) - Method in class org.molgenis.service.TranscriptService

update(Variant) - Method in class org.molgenis.service.VariantService

V

validate() - Method in class org.molgenis.omx.patient.Patient

validate() - Method in class org.molgenis.omx.xgap.Chromosome

validate() - Method in class org.molgenis.omx.xgap.Clone

validate() - Method in class org.molgenis.omx.xgap.DerivedTrait

validate() - Method in class org.molgenis.omx.xgap.EnvironmentalFactor

validate() - Method in class org.molgenis.omx.xgap.Gene

validate() - Method in class org.molgenis.omx.xgap.Marker

validate() - Method in class org.molgenis.omx.xgap.Marker_ReportsFor

validate() - Method in class org.molgenis.omx.xgap.MassPeak

validate() - Method in class org.molgenis.omx.xgap.Metabolite

validate() - Method in class org.molgenis.omx.xgap.NMRBin

validate() - Method in class org.molgenis.omx.xgap.PairedSample

validate() - Method in class org.molgenis.omx.xgap.Polymorphism

validate() - Method in class org.molgenis.omx.xgap.Probe

validate() - Method in class org.molgenis.omx.xgap.ProbeSet

validate() - Method in class org.molgenis.omx.xgap.Protein

validate() - Method in class org.molgenis.omx.xgap.Sample

validate() - Method in class org.molgenis.omx.xgap.SNP

validate() - Method in class org.molgenis.omx.xgap.SNP_Polymorphism

validate() - Method in class org.molgenis.omx.xgap.Spot

validate() - Method in class org.molgenis.omx.xgap.Track

validate() - Method in class org.molgenis.omx.xgap.Transcript

validate() - Method in class org.molgenis.omx.xgap.Variant

VALUE - Static variable in class org.molgenis.omx.xgap.Polymorphism

ValueSecurityDecorator<E extends Value> - Class in org.molgenis.omx.observ.value.db

TODO add column level security filters

ValueSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.value.db.ValueSecurityDecorator

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

Variant(Variant) - Constructor for class org.molgenis.omx.xgap.Variant

copy constructor

VariantEntityImporter - Class in org.molgenis.omx.xgap.db

Reads Variant from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

VariantEntityImporter() - Constructor for class org.molgenis.omx.xgap.db.VariantEntityImporter

VariantJpaMapper - Class in org.molgenis.omx.xgap.db

VariantJpaMapper(Database) - Constructor for class org.molgenis.omx.xgap.db.VariantJpaMapper

VARIANTLENGTH - Static variable in class org.molgenis.omx.xgap.Variant

VariantSecurityDecorator<E extends Variant> - Class in org.molgenis.omx.xgap.db

TODO add column level security filters

VariantSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.xgap.db.VariantSecurityDecorator

VariantService - Class in org.molgenis.service

VariantService() - Constructor for class org.molgenis.service.VariantService

W

WebAppInitializer - Class in org.molgenis.omx.das

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

X

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

XrefValueSecurityDecorator<E extends XrefValue> - Class in org.molgenis.omx.observ.value.db

TODO add column level security filters

XrefValueSecurityDecorator(Mapper<E>) - Constructor for class org.molgenis.omx.observ.value.db.XrefValueSecurityDecorator

Y

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

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