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Uses of OntologyEntry in gov.nih.nci.caarray.services.arraydesign |
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Methods in gov.nih.nci.caarray.services.arraydesign that return OntologyEntry | |
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OntologyEntry |
DbArrayDesignDataSource.getOntologyEntry(java.lang.String category,
java.lang.String value)
|
OntologyEntry |
ArrayDesignDataSource.getOntologyEntry(java.lang.String category,
java.lang.String value)
Returns the entry corresponding to the data given or null if not found. |
Uses of OntologyEntry in gov.nih.nci.caarray.services.biomaterial |
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Methods in gov.nih.nci.caarray.services.biomaterial that return OntologyEntry | |
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OntologyEntry[] |
BioMaterialManagerDB.getCharacteristicsFromSourceBioSourcesOf(long bioMaterialId,
java.lang.Class objectClass)
Retrieves a list of distinct characteristics of the source BioSource 's
that are used to produce the specified product BioSample or
LabeledExtract . |
static OntologyEntry[] |
BioMaterialUtils.toOntologyEntries(VocabData[] characteristics)
|
Methods in gov.nih.nci.caarray.services.biomaterial with parameters of type OntologyEntry | |
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static VocabData[] |
BioMaterialUtils.toVocabData(OntologyEntry[] characteristics)
|
void |
BioMaterialManagerDB.updateBioMaterialCharacteristics(long bioMaterialId,
java.lang.Class bioMaterialClass,
OntologyEntry[] characteristics)
Save the specified BioMaterial with the specified
characteristics. |
Uses of OntologyEntry in gov.nih.nci.caarray.services.experiment |
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Methods in gov.nih.nci.caarray.services.experiment that return OntologyEntry | |
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OntologyEntry |
ExperimentManagerDB.getAdditionalQualifier(long id)
|
Methods in gov.nih.nci.caarray.services.experiment with parameters of type OntologyEntry | |
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long |
ExperimentManagerDB.addAdditionalQualifier(long experimentId,
OntologyEntry qualifier)
|
static void |
ExperimentUtils.copy(AdditionalQualifierData source,
OntologyEntry target)
|
static void |
ExperimentUtils.copy(OntologyEntry source,
AdditionalQualifierData target)
|
void |
ExperimentManagerDB.updateAdditionalQualifier(OntologyEntry qualifier)
|
Uses of OntologyEntry in gov.nih.nci.caarray.services.mageloader |
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Methods in gov.nih.nci.caarray.services.mageloader that return OntologyEntry | |
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OntologyEntry |
MAGEMLImportManagerDB.matchOntologyEntry(OntologyEntry entry)
|
Methods in gov.nih.nci.caarray.services.mageloader with parameters of type OntologyEntry | |
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OntologyEntry |
MAGEMLImportManagerDB.matchOntologyEntry(OntologyEntry entry)
|
Uses of OntologyEntry in gov.nih.nci.caarray.services.protocol |
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Methods in gov.nih.nci.caarray.services.protocol that return OntologyEntry | |
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OntologyEntry[] |
ProtocolManagerDB.getProtocolTypes()
Get available protocol types. |
Uses of OntologyEntry in gov.nih.nci.caarray.services.util |
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Methods in gov.nih.nci.caarray.services.util that return OntologyEntry | |
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static OntologyEntry |
DBUtils.matchOntologyEntry(OntologyEntry entry,
org.apache.ojb.broker.PersistenceBroker broker)
|
Methods in gov.nih.nci.caarray.services.util with parameters of type OntologyEntry | |
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static OntologyEntry |
DBUtils.matchOntologyEntry(OntologyEntry entry,
org.apache.ojb.broker.PersistenceBroker broker)
|
Uses of OntologyEntry in gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers |
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Methods in gov.nih.nci.caarray.services.util.dataconverter.mapper.fieldmappers that return OntologyEntry | |
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static OntologyEntry |
VocabDataFieldMapper.getOntologyEntry(java.lang.Object bean,
java.lang.String fieldName,
java.util.List annotations)
|
static OntologyEntry |
VocabDataFieldMapper.getOntologyEntryByCategory(java.lang.String category,
java.util.List annotations)
Get from the specified list of OntologyEntry s the element
whose category matches the specified category. |
Uses of OntologyEntry in gov.nih.nci.caarray.services.util.dataconverter.test |
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Methods in gov.nih.nci.caarray.services.util.dataconverter.test with parameters of type OntologyEntry | |
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static void |
TestExperimentConversion.compare(OntologyEntry entry,
AdditionalQualifierData data)
|
static void |
TestVocabConversion.compare(OntologyEntry entry,
VocabData vocabData)
|
Uses of OntologyEntry in gov.nih.nci.caarray.services.vocab |
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Methods in gov.nih.nci.caarray.services.vocab that return OntologyEntry | |
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OntologyEntry[] |
VocabManagerDB.getOntologies(long parentVocabId)
|
OntologyEntry[] |
VocabManagerDB.getOntologies(VocabSearchCriteria criteria)
|
OntologyEntry |
VocabManagerDB.getOntology(long id)
|
OntologyEntry |
VocabManagerDB.getOntology(java.lang.String category,
java.lang.String value)
|
OntologyEntry |
VocabManagerDB.getOntologyEntryOrNull(java.lang.String category,
java.lang.String value)
Returns the requested OntologyEntry or null if not found. |
OntologyEntry[] |
VocabManagerDB.getProtocolTypes(long actionId)
Retrieves the list of protocol types that are mapped to the specified action. |
static OntologyEntry[] |
VocabUtils.getVisibleEntries(javax.ejb.SessionContext ctx,
OntologyEntry[] entries)
|
Methods in gov.nih.nci.caarray.services.vocab with parameters of type OntologyEntry | |
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long |
VocabManagerDB.addOntology(OntologyEntry entry)
|
long |
VocabManagerDB.addOntology(OntologyEntry entry,
long parentOntologyEntryId)
|
static void |
VocabUtils.copy(OntologyEntry entry,
VocabData vocab)
|
static void |
VocabUtils.copy(OntologyEntry entry,
VocabDesc vocabDesc)
|
static void |
VocabUtils.copy(VocabData vocab,
OntologyEntry entry)
|
static OntologyEntry[] |
VocabUtils.getVisibleEntries(javax.ejb.SessionContext ctx,
OntologyEntry[] entries)
|
void |
VocabManagerDB.updateOntology(OntologyEntry entry)
|
Uses of OntologyEntry in org.biomage.Array |
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Fields in org.biomage.Array declared as OntologyEntry | |
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protected OntologyEntry |
ZoneDefect.defectType
Indicates the type of defect (e.g. |
protected OntologyEntry |
FeatureDefect.defectType
Indicates the type of defect (e.g. |
protected OntologyEntry |
Fiducial.fiducialType
A descriptive string that indicates the type of a fiducial (e.g. |
protected OntologyEntry |
ArrayGroup.substrateType
Commonly, arrays will be spotted on 1x3 glass microscope slides but there is nothing that says this must be the case. |
Methods in org.biomage.Array that return OntologyEntry | |
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OntologyEntry |
ZoneDefect.getDefectType()
Get method for defectType |
OntologyEntry |
FeatureDefect.getDefectType()
Get method for defectType |
OntologyEntry |
Fiducial.getFiducialType()
Get method for fiducialType |
OntologyEntry |
ArrayGroup.getSubstrateType()
Get method for substrateType |
Methods in org.biomage.Array with parameters of type OntologyEntry | |
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void |
ZoneDefect.setDefectType(OntologyEntry defectType)
Set method for defectType |
void |
FeatureDefect.setDefectType(OntologyEntry defectType)
Set method for defectType |
void |
Fiducial.setFiducialType(OntologyEntry fiducialType)
Set method for fiducialType |
void |
ArrayGroup.setSubstrateType(OntologyEntry substrateType)
Set method for substrateType |
Uses of OntologyEntry in org.biomage.ArrayDesign |
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Fields in org.biomage.ArrayDesign declared as OntologyEntry | |
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protected OntologyEntry |
FeatureGroup.featureShape
The expected shape of the feature on the array: circular, oval, square, etc. |
protected OntologyEntry |
DesignElementGroup.species
The organism from which the biosequences of this group are from. |
protected OntologyEntry |
PhysicalArrayDesign.surfaceType
The type of surface from a controlled vocabulary that would include terms such as non-absorptive, absorptive, etc. |
protected OntologyEntry |
FeatureGroup.technologyType
The technology type of this design. |
Methods in org.biomage.ArrayDesign that return OntologyEntry | |
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OntologyEntry |
FeatureGroup.getFeatureShape()
Get method for featureShape |
OntologyEntry |
DesignElementGroup.getFromTypes(int position)
Method to get OntologyEntry from Types_list |
OntologyEntry |
DesignProviderRole.getRole()
|
OntologyEntry |
DesignElementGroup.getSpecies()
Get method for species |
OntologyEntry |
PhysicalArrayDesign.getSurfaceType()
Get method for surfaceType |
OntologyEntry |
FeatureGroup.getTechnologyType()
Get method for technologyType |
Methods in org.biomage.ArrayDesign with parameters of type OntologyEntry | |
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void |
DesignElementGroup.addToTypes(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Types_list |
void |
DesignElementGroup.addToTypes(OntologyEntry ontologyEntry)
Method to add OntologyEntry to Types_list |
void |
DesignElementGroup.removeFromTypes(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Types_list |
void |
FeatureGroup.setFeatureShape(OntologyEntry featureShape)
Set method for featureShape |
void |
DesignProviderRole.setRole(OntologyEntry entry)
|
void |
DesignElementGroup.setSpecies(OntologyEntry species)
Set method for species |
void |
PhysicalArrayDesign.setSurfaceType(OntologyEntry surfaceType)
Set method for surfaceType |
void |
FeatureGroup.setTechnologyType(OntologyEntry technologyType)
Set method for technologyType |
Uses of OntologyEntry in org.biomage.AuditAndSecurity |
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Methods in org.biomage.AuditAndSecurity that return OntologyEntry | |
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OntologyEntry |
Contact.getFromRoles(int position)
Method to get OntologyEntry from Roles_list |
Methods in org.biomage.AuditAndSecurity with parameters of type OntologyEntry | |
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void |
Contact.addToRoles(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Roles_list |
void |
Contact.addToRoles(OntologyEntry ontologyEntry)
Method to add OntologyEntry to Roles_list |
void |
Contact.removeFromRoles(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Roles_list |
Uses of OntologyEntry in org.biomage.BioAssay |
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Fields in org.biomage.BioAssay declared as OntologyEntry | |
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protected OntologyEntry |
Image.format
The file format of the image typically a TIF or a JPEG. |
protected OntologyEntry |
DerivedBioAssay.type
The derivation type, for instance collapsed spot replicate, ratio, averaged intensity, bioassay replicates, etc. |
Methods in org.biomage.BioAssay that return OntologyEntry | |
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OntologyEntry |
Image.getFormat()
Get method for format |
OntologyEntry |
DerivedBioAssay.getType()
Get method for type |
Methods in org.biomage.BioAssay with parameters of type OntologyEntry | |
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void |
Image.setFormat(OntologyEntry format)
Set method for format |
void |
DerivedBioAssay.setType(OntologyEntry type)
Set method for type |
Uses of OntologyEntry in org.biomage.BioMaterial |
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Fields in org.biomage.BioMaterial declared as OntologyEntry | |
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protected OntologyEntry |
Treatment.action
The event that occurred (e.g. |
protected OntologyEntry |
BioMaterial.materialType
The type of material used, i.e. |
protected OntologyEntry |
BioSample.type
The Type attribute describes the role the BioSample holds in the treatment hierarchy. |
Methods in org.biomage.BioMaterial that return OntologyEntry | |
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OntologyEntry |
Treatment.getAction()
Get method for action |
OntologyEntry |
ActionProtocolTypeMap.getAction()
|
OntologyEntry |
BioMaterial.getFromCharacteristics(int position)
Method to get OntologyEntry from Characteristics_list |
OntologyEntry |
Compound.getFromCompoundIndices(int position)
Method to get OntologyEntry from CompoundIndices_list |
OntologyEntry |
BioMaterial.getMaterialType()
Get method for materialType |
OntologyEntry |
BioSample.getType()
Get method for type |
Methods in org.biomage.BioMaterial with parameters of type OntologyEntry | |
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void |
BioMaterial.addToCharacteristics(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Characteristics_list |
void |
BioMaterial.addToCharacteristics(OntologyEntry ontologyEntry)
Method to add OntologyEntry to Characteristics_list |
void |
Compound.addToCompoundIndices(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to CompoundIndices_list |
void |
Compound.addToCompoundIndices(OntologyEntry ontologyEntry)
Method to add OntologyEntry to CompoundIndices_list |
void |
BioMaterial.removeFromCharacteristics(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Characteristics_list |
void |
Compound.removeFromCompoundIndices(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from CompoundIndices_list |
void |
Treatment.setAction(OntologyEntry action)
Set method for action |
void |
ActionProtocolTypeMap.setAction(OntologyEntry entry)
|
void |
BioMaterial.setMaterialType(OntologyEntry materialType)
Set method for materialType |
void |
BioSample.setType(OntologyEntry type)
Set method for type |
Uses of OntologyEntry in org.biomage.BioSequence |
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Fields in org.biomage.BioSequence declared as OntologyEntry | |
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protected OntologyEntry |
BioSequence.polymerType
A choice of protein, RNA, or DNA. |
protected OntologyEntry |
BioSequence.species
The organism from which this sequence was obtained. |
protected OntologyEntry |
BioSequence.type
The type of biosequence, i.e. |
Methods in org.biomage.BioSequence that return OntologyEntry | |
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OntologyEntry |
BioSequence.getFromOntologyEntries(int position)
Method to get OntologyEntry from OntologyEntries_list |
OntologyEntry |
BioSequence.getPolymerType()
Get method for polymerType |
OntologyEntry |
BioSequence.getSpecies()
Get method for species |
OntologyEntry |
BioSequence.getType()
Get method for type |
Methods in org.biomage.BioSequence with parameters of type OntologyEntry | |
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void |
BioSequence.addToOntologyEntries(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to OntologyEntries_list |
void |
BioSequence.addToOntologyEntries(OntologyEntry ontologyEntry)
Method to add OntologyEntry to OntologyEntries_list |
void |
BioSequence.removeFromOntologyEntries(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from OntologyEntries_list |
void |
BioSequence.setPolymerType(OntologyEntry polymerType)
Set method for polymerType |
void |
BioSequence.setSpecies(OntologyEntry species)
Set method for species |
void |
BioSequence.setType(OntologyEntry type)
Set method for type |
Uses of OntologyEntry in org.biomage.BQS |
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Methods in org.biomage.BQS that return OntologyEntry | |
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OntologyEntry |
BibliographicReference.getFromParameters(int position)
Method to get OntologyEntry from Parameters_list |
Methods in org.biomage.BQS with parameters of type OntologyEntry | |
---|---|
void |
BibliographicReference.addToParameters(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Parameters_list |
void |
BibliographicReference.addToParameters(OntologyEntry ontologyEntry)
Method to add OntologyEntry to Parameters_list |
void |
BibliographicReference.removeFromParameters(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Parameters_list |
Uses of OntologyEntry in org.biomage.Description |
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Fields in org.biomage.Description declared as OntologyEntry | |
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protected OntologyEntry |
DatabaseEntry.type
The type of record (e.g. |
Methods in org.biomage.Description that return OntologyEntry | |
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OntologyEntry |
Description.getFromAnnotations(int position)
Method to get OntologyEntry from Annotations_list |
OntologyEntry |
OntologyEntry.getFromAssociations(int position)
Method to get OntologyEntry from Associations_list |
OntologyEntry |
DatabaseEntry.getType()
Get method for type |
Methods in org.biomage.Description with parameters of type OntologyEntry | |
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void |
Description.addToAnnotations(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Annotations_list |
void |
Description.addToAnnotations(OntologyEntry ontologyEntry)
Method to add OntologyEntry to Annotations_list |
void |
OntologyEntry.addToAssociations(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Associations_list |
void |
OntologyEntry.addToAssociations(OntologyEntry ontologyEntry)
Method to add OntologyEntry to Associations_list |
void |
Description.removeFromAnnotations(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Annotations_list |
void |
OntologyEntry.removeFromAssociations(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Associations_list |
void |
DatabaseEntry.setType(OntologyEntry type)
Set method for type |
Uses of OntologyEntry in org.biomage.Description.Ontology |
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Subclasses of OntologyEntry in org.biomage.Description.Ontology | |
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class |
Age
|
class |
Biometrics
|
class |
ChromosomalAberration
|
Methods in org.biomage.Description.Ontology that return OntologyEntry | |
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protected static OntologyEntry |
BioMaterialCharacteristic.createMGEDMeasurementRestriction(java.lang.String restriction,
OntologyEntry value,
OntologyEntry unit)
|
OntologyEntry |
Age.getAgeValue()
|
abstract OntologyEntry |
BioMaterialCharacteristic.getFromAssociations(int position)
Method to get OntologyEntry from Associations_list |
OntologyEntry |
Biometrics.getHeight()
|
OntologyEntry |
Biometrics.getHeightMeasurement()
|
OntologyEntry |
Age.getInitialTimePoint()
|
OntologyEntry |
Age.getMaxMeasurement()
|
OntologyEntry |
Age.getMaxValue()
|
OntologyEntry |
Age.getMeasurement()
|
OntologyEntry |
Age.getMinMeasurement()
|
OntologyEntry |
Age.getMinValue()
|
OntologyEntry |
Biometrics.getWeight()
|
OntologyEntry |
Biometrics.getWeightMeasurement()
|
Methods in org.biomage.Description.Ontology with parameters of type OntologyEntry | |
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abstract void |
BioMaterialCharacteristic.addToAssociations(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Associations_list |
abstract void |
BioMaterialCharacteristic.addToAssociations(OntologyEntry ontologyEntry)
Method to add OntologyEntry to Associations_list |
void |
ChromosomalAberration.addToTypes(OntologyEntry type)
|
protected static OntologyEntry |
BioMaterialCharacteristic.createMGEDMeasurementRestriction(java.lang.String restriction,
OntologyEntry value,
OntologyEntry unit)
|
abstract void |
BioMaterialCharacteristic.removeFromAssociations(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Associations_list |
void |
ChromosomalAberration.removeFromTypes(OntologyEntry type)
|
void |
Age.setAgeValue(OntologyEntry entry)
|
void |
Biometrics.setHeight(OntologyEntry entry)
|
void |
Biometrics.setHeightMeasurement(OntologyEntry entry)
|
void |
Age.setInitialTimePoint(OntologyEntry entry)
|
void |
Age.setMaxMeasurement(OntologyEntry entry)
|
void |
Age.setMaxValue(OntologyEntry entry)
|
void |
Age.setMeasurement(OntologyEntry entry)
|
void |
Age.setMinMeasurement(OntologyEntry entry)
|
void |
Age.setMinValue(OntologyEntry entry)
|
void |
Biometrics.setWeight(OntologyEntry entry)
|
void |
Biometrics.setWeightMeasurement(OntologyEntry entry)
|
Uses of OntologyEntry in org.biomage.DesignElement |
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Fields in org.biomage.DesignElement declared as OntologyEntry | |
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protected OntologyEntry |
DesignElement.controlType
If the design element represents a control, the type of control it is (normalization, deletion, negative, positive, etc.) |
protected OntologyEntry |
Reporter.warningType
Similar to failType but indicates a warning rather than a failure. |
Methods in org.biomage.DesignElement that return OntologyEntry | |
---|---|
OntologyEntry |
DesignElement.getControlType()
Get method for controlType |
OntologyEntry |
Reporter.getFromFailTypes(int position)
Method to get OntologyEntry from FailTypes_list |
OntologyEntry |
Reporter.getWarningType()
Get method for warningType |
Methods in org.biomage.DesignElement with parameters of type OntologyEntry | |
---|---|
void |
Reporter.addToFailTypes(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to FailTypes_list |
void |
Reporter.addToFailTypes(OntologyEntry ontologyEntry)
Method to add OntologyEntry to FailTypes_list |
void |
Reporter.removeFromFailTypes(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from FailTypes_list |
void |
DesignElement.setControlType(OntologyEntry controlType)
Set method for controlType |
void |
Reporter.setWarningType(OntologyEntry warningType)
Set method for warningType |
Uses of OntologyEntry in org.biomage.Experiment |
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Fields in org.biomage.Experiment declared as OntologyEntry | |
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protected OntologyEntry |
ExperimentalFactor.category
The category of an ExperimentalFactor could be biological (time, [glucose]) or a methodological factor (differing cDNA preparation protocols). |
protected OntologyEntry |
FactorValue.value
Allows a more complex value to be specified for a FactorValue than a simple Measurement. |
Methods in org.biomage.Experiment that return OntologyEntry | |
---|---|
OntologyEntry |
ExperimentalFactor.getCategory()
Get method for category |
OntologyEntry |
ExperimentalFactor.getFromAnnotations(int position)
Method to get OntologyEntry from Annotations_list |
OntologyEntry |
ExperimentDesign.getFromTypes(int position)
Method to get OntologyEntry from Types_list |
OntologyEntry |
ExperimentProviderRole.getRole()
|
OntologyEntry |
FactorValue.getValue()
Get method for value |
Methods in org.biomage.Experiment with parameters of type OntologyEntry | |
---|---|
void |
ExperimentalFactor.addToAnnotations(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Annotations_list |
void |
ExperimentalFactor.addToAnnotations(OntologyEntry ontologyEntry)
Method to add OntologyEntry to Annotations_list |
void |
ExperimentDesign.addToTypes(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Types_list |
void |
ExperimentDesign.addToTypes(OntologyEntry ontologyEntry)
Method to add OntologyEntry to Types_list |
void |
ExperimentalFactor.removeFromAnnotations(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Annotations_list |
void |
ExperimentDesign.removeFromTypes(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Types_list |
void |
ExperimentalFactor.setCategory(OntologyEntry category)
Set method for category |
void |
ExperimentProviderRole.setRole(OntologyEntry entry)
|
void |
FactorValue.setValue(OntologyEntry value)
Set method for value |
Uses of OntologyEntry in org.biomage.HigherLevelAnalysis |
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Fields in org.biomage.HigherLevelAnalysis declared as OntologyEntry | |
---|---|
protected OntologyEntry |
NodeValue.dataType
The data type of the any element. |
protected OntologyEntry |
NodeValue.scale
The scale (linear, log10, ln, etc.) of the value. |
protected OntologyEntry |
NodeValue.type
The type of value, distance, etc. |
Methods in org.biomage.HigherLevelAnalysis that return OntologyEntry | |
---|---|
OntologyEntry |
NodeValue.getDataType()
Get method for dataType |
OntologyEntry |
NodeValue.getScale()
Get method for scale |
OntologyEntry |
NodeValue.getType()
Get method for type |
Methods in org.biomage.HigherLevelAnalysis with parameters of type OntologyEntry | |
---|---|
void |
NodeValue.setDataType(OntologyEntry dataType)
Set method for dataType |
void |
NodeValue.setScale(OntologyEntry scale)
Set method for scale |
void |
NodeValue.setType(OntologyEntry type)
Set method for type |
Uses of OntologyEntry in org.biomage.Interface |
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Methods in org.biomage.Interface that return OntologyEntry | |
---|---|
OntologyEntry |
HasAction.getAction()
Get method for action |
OntologyEntry |
HasCategory.getCategory()
Get method for category |
OntologyEntry |
HasControlType.getControlType()
Get method for controlType |
OntologyEntry |
HasDataType.getDataType()
Get method for dataType |
OntologyEntry |
HasDefectType.getDefectType()
Get method for defectType |
OntologyEntry |
HasFeatureShape.getFeatureShape()
Get method for featureShape |
OntologyEntry |
HasFiducialType.getFiducialType()
Get method for fiducialType |
OntologyEntry |
HasFormat.getFormat()
Get method for format |
OntologyEntry |
HasAnnotations.getFromAnnotations(int position)
Method to get OntologyEntry from Annotations_list |
OntologyEntry |
HasAssociations.getFromAssociations(int position)
Method to get OntologyEntry from Associations_list |
OntologyEntry |
HasCharacteristics.getFromCharacteristics(int position)
Method to get OntologyEntry from Characteristics_list |
OntologyEntry |
HasCompoundIndices.getFromCompoundIndices(int position)
Method to get OntologyEntry from CompoundIndices_list |
OntologyEntry |
HasFailTypes.getFromFailTypes(int position)
Method to get OntologyEntry from FailTypes_list |
OntologyEntry |
HasOntologyEntries.getFromOntologyEntries(int position)
Method to get OntologyEntry from OntologyEntries_list |
OntologyEntry |
HasParameters.getFromParameters(int position)
Method to get OntologyEntry from Parameters_list |
OntologyEntry |
HasRoles.getFromRoles(int position)
Method to get OntologyEntry from Roles_list |
OntologyEntry |
HasTypes.getFromTypes(int position)
Method to get OntologyEntry from Types_list |
OntologyEntry |
HasMaterialType.getMaterialType()
Get method for materialType |
OntologyEntry |
HasPolymerType.getPolymerType()
Get method for polymerType |
OntologyEntry |
HasScale.getScale()
Get method for scale |
OntologyEntry |
HasSpecies.getSpecies()
Get method for species |
OntologyEntry |
HasSubstrateType.getSubstrateType()
Get method for substrateType |
OntologyEntry |
HasSurfaceType.getSurfaceType()
Get method for surfaceType |
OntologyEntry |
HasTechnologyType.getTechnologyType()
Get method for technologyType |
OntologyEntry |
HasType.getType()
Get method for type |
OntologyEntry |
HasValue.getValue()
Get method for value |
OntologyEntry |
HasWarningType.getWarningType()
Get method for warningType |
Methods in org.biomage.Interface with parameters of type OntologyEntry | |
---|---|
void |
HasAnnotations.addToAnnotations(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Annotations_list |
void |
HasAnnotations.addToAnnotations(OntologyEntry ontologyEntry)
Method to add OntologyEntry to Annotations_list |
void |
HasAssociations.addToAssociations(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Associations_list |
void |
HasAssociations.addToAssociations(OntologyEntry ontologyEntry)
Method to add OntologyEntry to Associations_list |
void |
HasCharacteristics.addToCharacteristics(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Characteristics_list |
void |
HasCharacteristics.addToCharacteristics(OntologyEntry ontologyEntry)
Method to add OntologyEntry to Characteristics_list |
void |
HasCompoundIndices.addToCompoundIndices(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to CompoundIndices_list |
void |
HasCompoundIndices.addToCompoundIndices(OntologyEntry ontologyEntry)
Method to add OntologyEntry to CompoundIndices_list |
void |
HasFailTypes.addToFailTypes(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to FailTypes_list |
void |
HasFailTypes.addToFailTypes(OntologyEntry ontologyEntry)
Method to add OntologyEntry to FailTypes_list |
void |
HasOntologyEntries.addToOntologyEntries(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to OntologyEntries_list |
void |
HasOntologyEntries.addToOntologyEntries(OntologyEntry ontologyEntry)
Method to add OntologyEntry to OntologyEntries_list |
void |
HasParameters.addToParameters(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Parameters_list |
void |
HasParameters.addToParameters(OntologyEntry ontologyEntry)
Method to add OntologyEntry to Parameters_list |
void |
HasRoles.addToRoles(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Roles_list |
void |
HasRoles.addToRoles(OntologyEntry ontologyEntry)
Method to add OntologyEntry to Roles_list |
void |
HasTypes.addToTypes(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Types_list |
void |
HasTypes.addToTypes(OntologyEntry ontologyEntry)
Method to add OntologyEntry to Types_list |
void |
HasAnnotations.removeFromAnnotations(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Annotations_list |
void |
HasAssociations.removeFromAssociations(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Associations_list |
void |
HasCharacteristics.removeFromCharacteristics(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Characteristics_list |
void |
HasCompoundIndices.removeFromCompoundIndices(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from CompoundIndices_list |
void |
HasFailTypes.removeFromFailTypes(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from FailTypes_list |
void |
HasOntologyEntries.removeFromOntologyEntries(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from OntologyEntries_list |
void |
HasParameters.removeFromParameters(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Parameters_list |
void |
HasRoles.removeFromRoles(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Roles_list |
void |
HasTypes.removeFromTypes(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Types_list |
void |
HasAction.setAction(OntologyEntry action)
Set method for action |
void |
HasCategory.setCategory(OntologyEntry category)
Set method for category |
void |
HasControlType.setControlType(OntologyEntry controlType)
Set method for controlType |
void |
HasDataType.setDataType(OntologyEntry dataType)
Set method for dataType |
void |
HasDefectType.setDefectType(OntologyEntry defectType)
Set method for defectType |
void |
HasFeatureShape.setFeatureShape(OntologyEntry featureShape)
Set method for featureShape |
void |
HasFiducialType.setFiducialType(OntologyEntry fiducialType)
Set method for fiducialType |
void |
HasFormat.setFormat(OntologyEntry format)
Set method for format |
void |
HasMaterialType.setMaterialType(OntologyEntry materialType)
Set method for materialType |
void |
HasPolymerType.setPolymerType(OntologyEntry polymerType)
Set method for polymerType |
void |
HasScale.setScale(OntologyEntry scale)
Set method for scale |
void |
HasSpecies.setSpecies(OntologyEntry species)
Set method for species |
void |
HasSubstrateType.setSubstrateType(OntologyEntry substrateType)
Set method for substrateType |
void |
HasSurfaceType.setSurfaceType(OntologyEntry surfaceType)
Set method for surfaceType |
void |
HasTechnologyType.setTechnologyType(OntologyEntry technologyType)
Set method for technologyType |
void |
HasType.setType(OntologyEntry type)
Set method for type |
void |
HasValue.setValue(OntologyEntry value)
Set method for value |
void |
HasWarningType.setWarningType(OntologyEntry warningType)
Set method for warningType |
Uses of OntologyEntry in org.biomage.Protocol |
---|
Fields in org.biomage.Protocol declared as OntologyEntry | |
---|---|
protected OntologyEntry |
Parameter.dataType
The type of data generated by the parameter i.e. |
protected OntologyEntry |
Software.type
The type of a piece of Software. |
protected OntologyEntry |
Protocol.type
The type of a Protocol, a user should provide/use a recommended vocabulary. |
protected OntologyEntry |
Hardware.type
The type of a piece of Hardware. |
Methods in org.biomage.Protocol that return OntologyEntry | |
---|---|
OntologyEntry |
Parameter.getDataType()
Get method for dataType |
OntologyEntry |
Software.getType()
Get method for type |
OntologyEntry |
Protocol.getType()
Get method for type |
OntologyEntry |
Hardware.getType()
Get method for type |
Methods in org.biomage.Protocol with parameters of type OntologyEntry | |
---|---|
void |
Parameter.setDataType(OntologyEntry dataType)
Set method for dataType |
void |
Software.setType(OntologyEntry type)
Set method for type |
void |
Protocol.setType(OntologyEntry type)
Set method for type |
void |
Hardware.setType(OntologyEntry type)
Set method for type |
Uses of OntologyEntry in org.biomage.QuantitationType |
---|
Fields in org.biomage.QuantitationType declared as OntologyEntry | |
---|---|
protected OntologyEntry |
QuantitationType.dataType
The specific type for the quantitations. |
protected OntologyEntry |
QuantitationType.scale
Indication of how to interpret the value. |
Methods in org.biomage.QuantitationType that return OntologyEntry | |
---|---|
OntologyEntry |
QuantitationType.getDataType()
Get method for dataType |
OntologyEntry |
QuantitationType.getScale()
Get method for scale |
Methods in org.biomage.QuantitationType with parameters of type OntologyEntry | |
---|---|
void |
QuantitationType.setDataType(OntologyEntry dataType)
Set method for dataType |
void |
QuantitationType.setScale(OntologyEntry scale)
Set method for scale |
Uses of OntologyEntry in org.biomage.tools.helpers |
---|
Subclasses of OntologyEntry in org.biomage.tools.helpers | |
---|---|
class |
MGEDOntologyClassEntry
|
class |
MGEDOntologyEntry
|
class |
MGEDOntologyPropertyEntry
|
|
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