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

A

AkdEquation - Class in neuroml.channel
Definition of a type of rate constant equation which takes parameters A, k, d and maps to either exponential, sigmoidal or linoidal.
AkdEquation() - Constructor for class neuroml.channel.AkdEquation
 
allToAll - Variable in class neuroml.network.ConnectivityPattern
 
alpha - Variable in class neuroml.channel.VoltageConcGate
 
alpha - Variable in class neuroml.channel.VoltageGate
 
annotation - Variable in class neuroml.channel.ChannelML
 
annotation - Variable in class neuroml.channel.ChannelType
 
annotation - Variable in class neuroml.channel.DoubleExponentialSynapse
 
annotation - Variable in class neuroml.channel.Ion
 
annotation - Variable in class neuroml.channel.IonConcentration
 
annotation - Variable in class neuroml.channel.Parameter
 
annotation - Variable in class neuroml.channel.SynapseType
 
Annotation - Class in neuroml.meta
Concise processing directives for downstream applications.
Annotation() - Constructor for class neuroml.meta.Annotation
 
annotation - Variable in class neuroml.morph.Cable
 
annotation - Variable in class neuroml.morph.Cell
 
annotation - Variable in class neuroml.morph.Cell.Cables
 
annotation - Variable in class neuroml.morph.Cell.CellBody
 
annotation - Variable in class neuroml.morph.Cell.Segments
 
annotation - Variable in class neuroml.morph.Cell.Spines
 
annotation - Variable in class neuroml.morph.Feature
 
annotation - Variable in class neuroml.morph.Morphology
 
annotation - Variable in class neuroml.morph.Morphology.Features
 
annotation - Variable in class neuroml.network.CellInstance
 
annotation - Variable in class neuroml.network.Connections
 
annotation - Variable in class neuroml.network.GridArrangement
 
annotation - Variable in class neuroml.network.Instances
 
annotation - Variable in class neuroml.network.NetworkML
 
annotation - Variable in class neuroml.network.Population
 
annotation - Variable in class neuroml.network.PopulationLocation
 
annotation - Variable in class neuroml.network.Populations
 
annotation - Variable in class neuroml.network.Projection
 
annotation - Variable in class neuroml.network.Projections
 
annotation - Variable in class neuroml.network.RandomArrangement
 
annotation - Variable in class neuroml.network.SynapseProperties
 
annotation - Variable in class neuroml.NeuroMLLevel3
 
any - Variable in class neuroml.meta.Annotation
 
authorList - Variable in class neuroml.channel.ChannelType
 
authorList - Variable in class neuroml.channel.IonConcentration
 
authorList - Variable in class neuroml.channel.SynapseType
 
authorList - Variable in class neuroml.morph.Cell
 
authorList - Variable in class neuroml.NeuroMLLevel3
 
Authors - Class in neuroml.meta
A reference to an author Note: This element will most likely change when a new set of schema files is adopted for adding references, authors, citations, etc.
Authors() - Constructor for class neuroml.meta.Authors
 

B

beta - Variable in class neuroml.channel.VoltageConcGate
 
beta - Variable in class neuroml.channel.VoltageGate
 
Biophysics - Class in neuroml.bio
Description of biophysical properties of a cell.
Biophysics() - Constructor for class neuroml.bio.Biophysics
 
biophysics - Variable in class neuroml.Level3Cell
 
Block - Class in neuroml.channel
Specification for the influence of a blocking species on the conductance of a BlockingSynapse.
Block() - Constructor for class neuroml.channel.Block
 
block - Variable in class neuroml.channel.BlockingSynapse
 
blockingSyn - Variable in class neuroml.channel.SynapseType
 
BlockingSynapse - Class in neuroml.channel
A synaptic mechanism whose conductance can be blocked by the presence of a specific species (ion/molecule).
BlockingSynapse() - Constructor for class neuroml.channel.BlockingSynapse
 

C

Cable - Class in neuroml.morph
Definition of a cable.
Cable() - Constructor for class neuroml.morph.Cable
 
cable - Variable in class neuroml.morph.CableGroup
 
cable - Variable in class neuroml.morph.Cell.Cables
 
cable - Variable in class neuroml.morph.Segment
 
CableGroup - Class in neuroml.morph
Definition of a cable group.
CableGroup() - Constructor for class neuroml.morph.CableGroup
 
cablegroup - Variable in class neuroml.morph.Cell.Cables
 
CableGroup.Cable - Class in neuroml.morph
Java class for anonymous complex type.
CableGroup.Cable() - Constructor for class neuroml.morph.CableGroup.Cable
 
cables - Variable in class neuroml.morph.Cell
 
Cell - Class in neuroml.morph
Definition of a cell.
Cell() - Constructor for class neuroml.morph.Cell
 
cell - Variable in class neuroml.morph.Cells
 
cell - Variable in class neuroml.NeuroMLLevel3.Cells
 
Cell.Cables - Class in neuroml.morph
Java class for anonymous complex type.
Cell.Cables() - Constructor for class neuroml.morph.Cell.Cables
 
Cell.CellBody - Class in neuroml.morph
Java class for anonymous complex type.
Cell.CellBody() - Constructor for class neuroml.morph.Cell.CellBody
 
Cell.Segments - Class in neuroml.morph
Java class for anonymous complex type.
Cell.Segments() - Constructor for class neuroml.morph.Cell.Segments
 
Cell.Spines - Class in neuroml.morph
Java class for anonymous complex type.
Cell.Spines() - Constructor for class neuroml.morph.Cell.Spines
 
cellBody - Variable in class neuroml.morph.Cell
 
cellId - Variable in class neuroml.network.SynapticLocation
 
CellInstance - Class in neuroml.network
An instance of a cell at a the specified location
CellInstance() - Constructor for class neuroml.network.CellInstance
 
Cells - Class in neuroml.morph
Collection of all cells.
Cells() - Constructor for class neuroml.morph.Cells
 
cells - Variable in class neuroml.morph.Morphology
 
cells - Variable in class neuroml.NeuroMLLevel3
 
cellType - Variable in class neuroml.network.Population
 
center - Variable in class neuroml.meta.Sphere
 
ChannelML - Class in neuroml.channel
Root element containing the ions used in the channel mechanism, the unit system of the file (as attribute), and information on channels and/or ion concentration dynamics
ChannelML() - Constructor for class neuroml.channel.ChannelML
 
channels - Variable in class neuroml.NeuroMLLevel3
 
channelToXml(ChannelML, String) - Method in class neuroml.util.NeuroMLConverter
 
channelType - Variable in class neuroml.channel.ChannelML
 
ChannelType - Class in neuroml.channel
Definition of a voltage/concentration dependent cell membrane conductance
ChannelType() - Constructor for class neuroml.channel.ChannelType
 
charge - Variable in class neuroml.channel.Ion
 
comment - Variable in class neuroml.channel.ImplementationPrefs
 
conc - Variable in class neuroml.channel.Block
 
ConcDependence - Class in neuroml.channel
Specification of what a gate is dependent on the concentration of
ConcDependence() - Constructor for class neuroml.channel.ConcDependence
 
concDependence - Variable in class neuroml.channel.VoltageConcGate
 
conductance - Variable in class neuroml.channel.Ohmic
 
Connection - Class in neuroml.network
A network connection
Connection() - Constructor for class neuroml.network.Connection
 
connection - Variable in class neuroml.network.Connections
 
Connection.InternalProperties - Class in neuroml.network
 
Connection.InternalProperties(SynapseInternalProperties) - Constructor for class neuroml.network.Connection.InternalProperties
 
Connections - Class in neuroml.network
The list of cell connections
Connections() - Constructor for class neuroml.network.Connections
 
connections - Variable in class neuroml.network.Projection
 
ConnectivityPattern - Class in neuroml.network
Information on the number of target cells connected to source cells, etc.
ConnectivityPattern() - Constructor for class neuroml.network.ConnectivityPattern
 
connectivityPattern - Variable in class neuroml.network.Projection
 
ConnectivityPattern.AllToAll - Class in neuroml.network
Java class for anonymous complex type.
ConnectivityPattern.AllToAll() - Constructor for class neuroml.network.ConnectivityPattern.AllToAll
 
ConnectivityPattern.FixedProbability - Class in neuroml.network
Java class for anonymous complex type.
ConnectivityPattern.FixedProbability() - Constructor for class neuroml.network.ConnectivityPattern.FixedProbability
 
content - Variable in class neuroml.network.Connection
 
content - Variable in class neuroml.network.PotentialSynapticLocation
 
CoreEquationType - Enum in neuroml.channel
Java class for CoreEquationType.
corner - Variable in class neuroml.meta.RectangularBox
 
createAkdEquation() - Method in class neuroml.channel.ObjectFactory
Create an instance of AkdEquation
createAnnotation() - Method in class neuroml.meta.ObjectFactory
Create an instance of Annotation
createAuthors() - Method in class neuroml.meta.ObjectFactory
Create an instance of Authors
createBiophysics() - Method in class neuroml.bio.ObjectFactory
Create an instance of Biophysics
createBiophysics(Biophysics) - Method in class neuroml.bio.ObjectFactory
Create an instance of JAXBElement<Biophysics>}
createBlock() - Method in class neuroml.channel.ObjectFactory
Create an instance of Block
createBlockingSynapse() - Method in class neuroml.channel.ObjectFactory
Create an instance of BlockingSynapse
createCable() - Method in class neuroml.morph.ObjectFactory
Create an instance of Cable
createCableGroup() - Method in class neuroml.morph.ObjectFactory
Create an instance of CableGroup
createCableGroupCable() - Method in class neuroml.morph.ObjectFactory
Create an instance of CableGroup.Cable
createCell() - Method in class neuroml.morph.ObjectFactory
Create an instance of Cell
createCellCables() - Method in class neuroml.morph.ObjectFactory
Create an instance of Cell.Cables
createCellCellBody() - Method in class neuroml.morph.ObjectFactory
Create an instance of Cell.CellBody
createCellInstance() - Method in class neuroml.network.ObjectFactory
Create an instance of CellInstance
createCells() - Method in class neuroml.morph.ObjectFactory
Create an instance of Cells
createCellSegments() - Method in class neuroml.morph.ObjectFactory
Create an instance of Cell.Segments
createCellSpines() - Method in class neuroml.morph.ObjectFactory
Create an instance of Cell.Spines
createChannelML() - Method in class neuroml.channel.ObjectFactory
Create an instance of ChannelML
createChannelml(ChannelML) - Method in class neuroml.channel.ObjectFactory
Create an instance of JAXBElement<ChannelML>}
createChannelType() - Method in class neuroml.channel.ObjectFactory
Create an instance of ChannelType
createConcDependence() - Method in class neuroml.channel.ObjectFactory
Create an instance of ConcDependence
createConnection() - Method in class neuroml.network.ObjectFactory
Create an instance of Connection
createConnectionAnnotation(Annotation) - Method in class neuroml.network.ObjectFactory
Create an instance of JAXBElement<Annotation>}
createConnectionGroup(String) - Method in class neuroml.network.ObjectFactory
Create an instance of JAXBElement<String>}
createConnectionInternalProperties(SynapseInternalProperties) - Method in class neuroml.network.ObjectFactory
Create an instance of Connection.InternalProperties}
createConnectionNotes(String) - Method in class neuroml.network.ObjectFactory
Create an instance of JAXBElement<String>}
createConnectionPost(SynapticLocation) - Method in class neuroml.network.ObjectFactory
Create an instance of JAXBElement<SynapticLocation>}
createConnectionPre(SynapticLocation) - Method in class neuroml.network.ObjectFactory
Create an instance of JAXBElement<SynapticLocation>}
createConnectionProperties(Properties) - Method in class neuroml.network.ObjectFactory
Create an instance of JAXBElement<Properties>}
createConnections() - Method in class neuroml.network.ObjectFactory
Create an instance of Connections
createConnectivityPattern() - Method in class neuroml.network.ObjectFactory
Create an instance of ConnectivityPattern
createConnectivityPatternAllToAll() - Method in class neuroml.network.ObjectFactory
Create an instance of ConnectivityPattern.AllToAll
createConnectivityPatternFixedProbability() - Method in class neuroml.network.ObjectFactory
Create an instance of ConnectivityPattern.FixedProbability
createCurrentVoltageRelation() - Method in class neuroml.channel.ObjectFactory
Create an instance of CurrentVoltageRelation
createDecayingPoolModel() - Method in class neuroml.channel.ObjectFactory
Create an instance of DecayingPoolModel
createDoubleExponentialSynapse() - Method in class neuroml.channel.ObjectFactory
Create an instance of DoubleExponentialSynapse
createFeature() - Method in class neuroml.morph.ObjectFactory
Create an instance of Feature
createFreePoints() - Method in class neuroml.morph.ObjectFactory
Create an instance of FreePoints
createGate() - Method in class neuroml.channel.ObjectFactory
Create an instance of Gate
createGateState() - Method in class neuroml.channel.ObjectFactory
Create an instance of Gate.State
createGenericEquation() - Method in class neuroml.channel.ObjectFactory
Create an instance of GenericEquation
createGridArrangement() - Method in class neuroml.network.ObjectFactory
Create an instance of GridArrangement
createGridArrangementSpacing() - Method in class neuroml.network.ObjectFactory
Create an instance of GridArrangement.Spacing
createGroupDetail() - Method in class neuroml.meta.ObjectFactory
Create an instance of GroupDetail
createHHGate() - Method in class neuroml.channel.ObjectFactory
Create an instance of HHGate
createImplementationPrefs() - Method in class neuroml.channel.ObjectFactory
Create an instance of ImplementationPrefs
createImplementationPrefsTableSettings() - Method in class neuroml.channel.ObjectFactory
Create an instance of ImplementationPrefs.TableSettings
createInhomogeneousParam() - Method in class neuroml.morph.ObjectFactory
Create an instance of InhomogeneousParam
createInhomogeneousParamDistal() - Method in class neuroml.morph.ObjectFactory
Create an instance of InhomogeneousParam.Distal
createInhomogeneousParamProximal() - Method in class neuroml.morph.ObjectFactory
Create an instance of InhomogeneousParam.Proximal
createInhomogeneousValue() - Method in class neuroml.bio.ObjectFactory
Create an instance of InhomogeneousValue
createInitialMembPotential() - Method in class neuroml.bio.ObjectFactory
Create an instance of InitialMembPotential
createInstances() - Method in class neuroml.network.ObjectFactory
Create an instance of Instances
createIon() - Method in class neuroml.channel.ObjectFactory
Create an instance of Ion
createIonConcentration() - Method in class neuroml.channel.ObjectFactory
Create an instance of IonConcentration
createIonProperties() - Method in class neuroml.bio.ObjectFactory
Create an instance of IonProperties
createKSGate() - Method in class neuroml.channel.ObjectFactory
Create an instance of KSGate
createKSState() - Method in class neuroml.channel.ObjectFactory
Create an instance of KSState
createLevel3Biophysics() - Method in class neuroml.ObjectFactory
Create an instance of Level3Biophysics
createLevel3Cell() - Method in class neuroml.ObjectFactory
Create an instance of Level3Cell
createManifold() - Method in class neuroml.meta.ObjectFactory
Create an instance of Manifold
createMechanism() - Method in class neuroml.bio.ObjectFactory
Create an instance of Mechanism
createMorphml(Morphology) - Method in class neuroml.morph.ObjectFactory
Create an instance of JAXBElement<Morphology>}
createMorphology() - Method in class neuroml.morph.ObjectFactory
Create an instance of Morphology
createMorphologyFeatures() - Method in class neuroml.morph.ObjectFactory
Create an instance of Morphology.Features
createMorphologyGroupDetails() - Method in class neuroml.morph.ObjectFactory
Create an instance of Morphology.GroupDetails
createMorphologyPropertyDetails() - Method in class neuroml.morph.ObjectFactory
Create an instance of Morphology.PropertyDetails
createNamedParameter() - Method in class neuroml.bio.ObjectFactory
Create an instance of NamedParameter
createNetworkML() - Method in class neuroml.network.ObjectFactory
Create an instance of NetworkML
createNetworkml(NetworkML) - Method in class neuroml.network.ObjectFactory
Create an instance of JAXBElement<NetworkML>}
createNeuroml(NeuroMLLevel3) - Method in class neuroml.ObjectFactory
Create an instance of JAXBElement<NeuroMLLevel3>}
createNeuroMLLevel3() - Method in class neuroml.ObjectFactory
Create an instance of NeuroMLLevel3
createNeuroMLLevel3Cells() - Method in class neuroml.ObjectFactory
Create an instance of NeuroMLLevel3.Cells
createNeuronDBReference() - Method in class neuroml.meta.ObjectFactory
Create an instance of NeuronDBReference
createOhmic() - Method in class neuroml.channel.ObjectFactory
Create an instance of Ohmic
createOhmicConductance() - Method in class neuroml.channel.ObjectFactory
Create an instance of Ohmic.Conductance
createParameter() - Method in class neuroml.channel.ObjectFactory
Create an instance of Parameter
createPath() - Method in class neuroml.morph.ObjectFactory
Create an instance of Path
createPerCellConnection() - Method in class neuroml.network.ObjectFactory
Create an instance of PerCellConnection
createPerson() - Method in class neuroml.meta.ObjectFactory
Create an instance of Person
createPoint() - Method in class neuroml.meta.ObjectFactory
Create an instance of Point
createPoints() - Method in class neuroml.meta.ObjectFactory
Create an instance of Points
createPolygon() - Method in class neuroml.meta.ObjectFactory
Create an instance of Polygon
createPolyhedron() - Method in class neuroml.meta.ObjectFactory
Create an instance of Polyhedron
createPolyhedronPolygons() - Method in class neuroml.meta.ObjectFactory
Create an instance of Polyhedron.Polygons
createPoolVolumeInfo() - Method in class neuroml.channel.ObjectFactory
Create an instance of PoolVolumeInfo
createPopulation() - Method in class neuroml.network.ObjectFactory
Create an instance of Population
createPopulationLocation() - Method in class neuroml.network.ObjectFactory
Create an instance of PopulationLocation
createPopulations() - Method in class neuroml.network.ObjectFactory
Create an instance of Populations
createPotentialSynapticLocation() - Method in class neuroml.network.ObjectFactory
Create an instance of PotentialSynapticLocation
createPotentialSynapticLocationAllowedGroups(String) - Method in class neuroml.network.ObjectFactory
Create an instance of PotentialSynapticLocation.AllowedGroups}
createPotentialSynapticLocationAnnotation(Annotation) - Method in class neuroml.network.ObjectFactory
Create an instance of JAXBElement<Annotation>}
createPotentialSynapticLocationGroup(String) - Method in class neuroml.network.ObjectFactory
Create an instance of JAXBElement<String>}
createPotentialSynapticLocationNotes(String) - Method in class neuroml.network.ObjectFactory
Create an instance of JAXBElement<String>}
createPotentialSynapticLocationProperties(Properties) - Method in class neuroml.network.ObjectFactory
Create an instance of JAXBElement<Properties>}
createPotentialSynapticLocationSynapseDirection(SynapseDirection) - Method in class neuroml.network.ObjectFactory
Create an instance of JAXBElement<SynapseDirection>}
createPotentialSynapticLocationSynapseType(String) - Method in class neuroml.network.ObjectFactory
Create an instance of JAXBElement<String>}
createProjection() - Method in class neuroml.network.ObjectFactory
Create an instance of Projection
createProjections() - Method in class neuroml.network.ObjectFactory
Create an instance of Projections
createProperties() - Method in class neuroml.meta.ObjectFactory
Create an instance of Properties
createProperty() - Method in class neuroml.meta.ObjectFactory
Create an instance of Property
createPropertyDetail() - Method in class neuroml.meta.ObjectFactory
Create an instance of PropertyDetail
createPublication() - Method in class neuroml.meta.ObjectFactory
Create an instance of Publication
createRandomArrangement() - Method in class neuroml.network.ObjectFactory
Create an instance of RandomArrangement
createRateAdjustments() - Method in class neuroml.channel.ObjectFactory
Create an instance of RateAdjustments
createRateAdjustmentsOffset() - Method in class neuroml.channel.ObjectFactory
Create an instance of RateAdjustments.Offset
createRateAdjustmentsQ10Settings() - Method in class neuroml.channel.ObjectFactory
Create an instance of RateAdjustments.Q10Settings
createRateConstantEqn() - Method in class neuroml.channel.ObjectFactory
Create an instance of RateConstantEqn
createRateConstantEqnChoice() - Method in class neuroml.channel.ObjectFactory
Create an instance of RateConstantEqnChoice
createRateConstVoltConcDep() - Method in class neuroml.channel.ObjectFactory
Create an instance of RateConstVoltConcDep
createRectangularBox() - Method in class neuroml.meta.ObjectFactory
Create an instance of RectangularBox
createRectangularBoxSize() - Method in class neuroml.meta.ObjectFactory
Create an instance of RectangularBox.Size
createSegment() - Method in class neuroml.morph.ObjectFactory
Create an instance of Segment
createSpecAxialResistance() - Method in class neuroml.bio.ObjectFactory
Create an instance of SpecAxialResistance
createSpecCapacitance() - Method in class neuroml.bio.ObjectFactory
Create an instance of SpecCapacitance
createSphere() - Method in class neuroml.meta.ObjectFactory
Create an instance of Sphere
createSpine() - Method in class neuroml.morph.ObjectFactory
Create an instance of Spine
createSynapseInternalProperties() - Method in class neuroml.network.ObjectFactory
Create an instance of SynapseInternalProperties
createSynapseProperties() - Method in class neuroml.network.ObjectFactory
Create an instance of SynapseProperties
createSynapseType() - Method in class neuroml.channel.ObjectFactory
Create an instance of SynapseType
createSynapticLocation() - Method in class neuroml.network.ObjectFactory
Create an instance of SynapticLocation
createTransition() - Method in class neuroml.channel.ObjectFactory
Create an instance of Transition
createUnnamedParameter() - Method in class neuroml.bio.ObjectFactory
Create an instance of UnnamedParameter
createVariableNamedParameter() - Method in class neuroml.bio.ObjectFactory
Create an instance of VariableNamedParameter
createVariableParameter() - Method in class neuroml.bio.ObjectFactory
Create an instance of VariableParameter
createVoltageConcGate() - Method in class neuroml.channel.ObjectFactory
Create an instance of VoltageConcGate
createVoltageGate() - Method in class neuroml.channel.ObjectFactory
Create an instance of VoltageGate
currentVoltageRelation - Variable in class neuroml.channel.ChannelType
 
CurrentVoltageRelation - Class in neuroml.channel
How the current through the channel depends on the conductance of the channel.
CurrentVoltageRelation() - Constructor for class neuroml.channel.CurrentVoltageRelation
 

D

decayConstant - Variable in class neuroml.channel.DecayingPoolModel
 
DecayingPoolModel - Class in neuroml.channel
Element for parameters in a decaying pool model of ion concentration (e.g.
DecayingPoolModel() - Constructor for class neuroml.channel.DecayingPoolModel
 
decayingPoolModel - Variable in class neuroml.channel.IonConcentration
 
decayTime - Variable in class neuroml.channel.DoubleExponentialSynapse
 
defaultErev - Variable in class neuroml.channel.Ion
 
defaultGmax - Variable in class neuroml.channel.Ohmic.Conductance
 
defaultValues - Variable in class neuroml.network.SynapseProperties
 
density - Variable in class neuroml.channel.ChannelType
 
density - Variable in class neuroml.channel.SynapseType
 
depth - Variable in class neuroml.meta.RectangularBox.Size
 
description - Variable in class neuroml.meta.GroupDetail
 
description - Variable in class neuroml.meta.PropertyDetail
 
diameter - Variable in class neuroml.meta.Point
 
direction - Variable in class neuroml.network.PerCellConnection
 
distal - Variable in class neuroml.morph.InhomogeneousParam
 
distal - Variable in class neuroml.morph.Segment
 
distal - Variable in class neuroml.morph.Spine
 
doubExpSyn - Variable in class neuroml.channel.SynapseType
 
DoubleExponentialSynapse - Class in neuroml.channel
A basic synaptic mechanism with a double exponential conductance time course.
DoubleExponentialSynapse() - Constructor for class neuroml.channel.DoubleExponentialSynapse
 

E

email - Variable in class neuroml.meta.Person
 
eta - Variable in class neuroml.channel.Block
 
experimentalTemp - Variable in class neuroml.channel.RateAdjustments.Q10Settings
 
expr - Variable in class neuroml.channel.GenericEquation
 
expr - Variable in class neuroml.channel.RateConstantEqn
 

F

Feature - Class in neuroml.morph
The group of things allowed in features.
Feature() - Constructor for class neuroml.morph.Feature
 
feature - Variable in class neuroml.morph.Morphology.Features
 
features - Variable in class neuroml.morph.Morphology
 
fixedProbability - Variable in class neuroml.network.ConnectivityPattern
 
fractAlongParent - Variable in class neuroml.morph.Cable
 
fraction - Variable in class neuroml.channel.Gate.State
 
fractionAlong - Variable in class neuroml.network.SynapticLocation
 
freePoints - Variable in class neuroml.morph.Cell
 
freePoints - Variable in class neuroml.morph.Feature
 
FreePoints - Class in neuroml.morph
A set of varicosities or synaptic connections.
FreePoints() - Constructor for class neuroml.morph.FreePoints
 
fromValue(String) - Static method in enum neuroml.bio.MechanismType
 
fromValue(String) - Static method in enum neuroml.bio.Units
 
fromValue(String) - Static method in enum neuroml.channel.CoreEquationType
 
fromValue(String) - Static method in enum neuroml.channel.IonRole
 
fromValue(String) - Static method in enum neuroml.channel.Units
 
fromValue(String) - Static method in enum neuroml.meta.LengthUnits
 
fromValue(String) - Static method in enum neuroml.meta.VolumeUnits
 
fromValue(String) - Static method in enum neuroml.meta.YesNo
 
fromValue(String) - Static method in enum neuroml.morph.SpineShape
 
fromValue(String) - Static method in enum neuroml.network.SynapseDirection
 
fullTitle - Variable in class neuroml.meta.Publication
 

G

gamma - Variable in class neuroml.channel.Block
 
Gate - Class in neuroml.channel
Definition of a single voltage/concentration dependent gate
Gate() - Constructor for class neuroml.channel.Gate
 
gate - Variable in class neuroml.channel.Ohmic.Conductance
 
Gate.State - Class in neuroml.channel
Java class for anonymous complex type.
Gate.State() - Constructor for class neuroml.channel.Gate.State
 
GenericEquation - Class in neuroml.channel
Definition of a type of rate constant equation
GenericEquation() - Constructor for class neuroml.channel.GenericEquation
 
genericEquationHh - Variable in class neuroml.channel.RateConstantEqnChoice
 
genericEquationHh - Variable in class neuroml.channel.RateConstVoltConcDep
 
getAllToAll() - Method in class neuroml.network.ConnectivityPattern
Gets the value of the allToAll property.
getAlpha() - Method in class neuroml.channel.VoltageConcGate
Gets the value of the alpha property.
getAlpha() - Method in class neuroml.channel.VoltageGate
Gets the value of the alpha property.
getAnnotation() - Method in class neuroml.channel.ChannelML
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.channel.ChannelType
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.channel.DoubleExponentialSynapse
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.channel.Ion
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.channel.IonConcentration
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.channel.Parameter
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.channel.SynapseType
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.morph.Cable
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.morph.Cell.Cables
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.morph.Cell.CellBody
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.morph.Cell
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.morph.Cell.Segments
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.morph.Cell.Spines
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.morph.Feature
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.morph.Morphology.Features
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.morph.Morphology
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.network.CellInstance
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.network.Connections
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.network.GridArrangement
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.network.Instances
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.network.NetworkML
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.network.Population
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.network.PopulationLocation
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.network.Populations
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.network.Projection
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.network.Projections
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.network.RandomArrangement
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.network.SynapseProperties
Gets the value of the annotation property.
getAnnotation() - Method in class neuroml.NeuroMLLevel3
Gets the value of the annotation property.
getAny() - Method in class neuroml.meta.Annotation
Gets the value of the any property.
getAuthorList() - Method in class neuroml.channel.ChannelType
Gets the value of the authorList property.
getAuthorList() - Method in class neuroml.channel.IonConcentration
Gets the value of the authorList property.
getAuthorList() - Method in class neuroml.channel.SynapseType
Gets the value of the authorList property.
getAuthorList() - Method in class neuroml.morph.Cell
Gets the value of the authorList property.
getAuthorList() - Method in class neuroml.NeuroMLLevel3
Gets the value of the authorList property.
getBeta() - Method in class neuroml.channel.VoltageConcGate
Gets the value of the beta property.
getBeta() - Method in class neuroml.channel.VoltageGate
Gets the value of the beta property.
getBiophysics() - Method in class neuroml.Level3Cell
Gets the value of the biophysics property.
getBlock() - Method in class neuroml.channel.BlockingSynapse
Gets the value of the block property.
getBlockingSyn() - Method in class neuroml.channel.SynapseType
Gets the value of the blockingSyn property.
getCable() - Method in class neuroml.morph.CableGroup
Gets the value of the cable property.
getCable() - Method in class neuroml.morph.Cell.Cables
Gets the value of the cable property.
getCable() - Method in class neuroml.morph.Segment
Gets the value of the cable property.
getCablegroup() - Method in class neuroml.morph.Cell.Cables
Gets the value of the cablegroup property.
getCableList() - Method in class neuroml.morph.Cell
Get the list of cables for this Cell.
getCables() - Method in class neuroml.morph.Cell
Gets the value of the cables property.
getCell() - Method in class neuroml.morph.Cells
Gets the value of the cell property.
getCell() - Method in class neuroml.NeuroMLLevel3.Cells
Gets the value of the cell property.
getCellBody() - Method in class neuroml.morph.Cell
Gets the value of the cellBody property.
getCellId() - Method in class neuroml.network.SynapticLocation
Gets the value of the cellId property.
getCellList() - Method in class neuroml.morph.Morphology
Gets the list of cells for this Morphology.
getCellList() - Method in class neuroml.NeuroMLLevel3
Get the list of cells in this NeuroML file
getCells() - Method in class neuroml.morph.Morphology
Gets the value of the cells property.
getCells() - Method in class neuroml.NeuroMLLevel3
Gets the value of the cells property.
getCellType() - Method in class neuroml.network.Population
Gets the value of the cellType property.
getCenter() - Method in class neuroml.meta.Sphere
Gets the value of the center property.
getChannels() - Method in class neuroml.NeuroMLLevel3
Gets the value of the channels property.
getChannelType() - Method in class neuroml.channel.ChannelML
Gets the value of the channelType property.
getChannelTypeByName(String) - Method in class neuroml.channel.ChannelML
Gets a channel type by name, or null if no such channel exists.
getCharge() - Method in class neuroml.channel.Ion
Gets the value of the charge property.
getComment() - Method in class neuroml.channel.ImplementationPrefs
Gets the value of the comment property.
getConc() - Method in class neuroml.channel.Block
Gets the value of the conc property.
getConcDependence() - Method in class neuroml.channel.VoltageConcGate
Gets the value of the concDependence property.
getConductance() - Method in class neuroml.channel.Ohmic
Gets the value of the conductance property.
getConnection() - Method in class neuroml.network.Connections
Gets the value of the connection property.
getConnections() - Method in class neuroml.network.Projection
Gets the value of the connections property.
getConnectivityPattern() - Method in class neuroml.network.Projection
Gets the value of the connectivityPattern property.
getContent() - Method in class neuroml.network.Connection
Gets the rest of the content model.
getContent() - Method in class neuroml.network.PotentialSynapticLocation
Gets the rest of the content model.
getCorner() - Method in class neuroml.meta.RectangularBox
Gets the value of the corner property.
getCurrentVoltageRelation() - Method in class neuroml.channel.ChannelType
Gets the value of the currentVoltageRelation property.
getDecayConstant() - Method in class neuroml.channel.DecayingPoolModel
Gets the value of the decayConstant property.
getDecayingPoolModel() - Method in class neuroml.channel.IonConcentration
Gets the value of the decayingPoolModel property.
getDecayTime() - Method in class neuroml.channel.DoubleExponentialSynapse
Gets the value of the decayTime property.
getDefaultErev() - Method in class neuroml.channel.Ion
Gets the value of the defaultErev property.
getDefaultGmax() - Method in class neuroml.channel.Ohmic.Conductance
Gets the value of the defaultGmax property.
getDefaultValues() - Method in class neuroml.network.SynapseProperties
Gets the value of the defaultValues property.
getDensity() - Method in class neuroml.channel.ChannelType
Gets the value of the density property.
getDensity() - Method in class neuroml.channel.SynapseType
Gets the value of the density property.
getDepth() - Method in class neuroml.meta.RectangularBox.Size
Gets the value of the depth property.
getDescription() - Method in class neuroml.meta.GroupDetail
Gets the value of the description property.
getDescription() - Method in class neuroml.meta.PropertyDetail
Gets the value of the description property.
getDiameter() - Method in class neuroml.meta.Point
Gets the value of the diameter property.
getDirection() - Method in class neuroml.network.PerCellConnection
Gets the value of the direction property.
getDistal() - Method in class neuroml.morph.InhomogeneousParam
Gets the value of the distal property.
getDistal() - Method in class neuroml.morph.Segment
Gets the value of the distal property.
getDistal() - Method in class neuroml.morph.Spine
Gets the value of the distal property.
getDoubExpSyn() - Method in class neuroml.channel.SynapseType
Gets the value of the doubExpSyn property.
getEmail() - Method in class neuroml.meta.Person
Gets the value of the email property.
getEta() - Method in class neuroml.channel.Block
Gets the value of the eta property.
getExperimentalTemp() - Method in class neuroml.channel.RateAdjustments.Q10Settings
Gets the value of the experimentalTemp property.
getExpr() - Method in class neuroml.channel.GenericEquation
Gets the value of the expr property.
getExpr() - Method in class neuroml.channel.RateConstantEqn
Gets the value of the expr property.
getFeature() - Method in class neuroml.morph.Morphology.Features
Gets the value of the feature property.
getFeatures() - Method in class neuroml.morph.Morphology
Gets the value of the features property.
getFixedProbability() - Method in class neuroml.network.ConnectivityPattern
Gets the value of the fixedProbability property.
getFractAlongParent() - Method in class neuroml.morph.Cable
Gets the value of the fractAlongParent property.
getFraction() - Method in class neuroml.channel.Gate.State
Gets the value of the fraction property.
getFractionAlong() - Method in class neuroml.network.SynapticLocation
Gets the value of the fractionAlong property.
getFreePoints() - Method in class neuroml.morph.Cell
Gets the value of the freePoints property.
getFreePoints() - Method in class neuroml.morph.Feature
Gets the value of the freePoints property.
getFullTitle() - Method in class neuroml.meta.Publication
Gets the value of the fullTitle property.
getGamma() - Method in class neuroml.channel.Block
Gets the value of the gamma property.
getGate() - Method in class neuroml.channel.Ohmic.Conductance
Gets the value of the gate property.
getGenericEquationHh() - Method in class neuroml.channel.RateConstantEqnChoice
Gets the value of the genericEquationHh property.
getGenericEquationHh() - Method in class neuroml.channel.RateConstVoltConcDep
Gets the value of the genericEquationHh property.
getGridArrangement() - Method in class neuroml.network.PopulationLocation
Gets the value of the gridArrangement property.
getGroup() - Method in class neuroml.bio.NamedParameter
Gets the value of the group property.
getGroup() - Method in class neuroml.bio.UnnamedParameter
Gets the value of the group property.
getGroup() - Method in class neuroml.bio.VariableNamedParameter
Gets the value of the group property.
getGroup() - Method in class neuroml.bio.VariableParameter
Gets the value of the group property.
getGroup() - Method in class neuroml.channel.ChannelML
Gets the value of the group property.
getGroup() - Method in class neuroml.channel.ChannelType
Gets the value of the group property.
getGroup() - Method in class neuroml.channel.DoubleExponentialSynapse
Gets the value of the group property.
getGroup() - Method in class neuroml.channel.Ion
Gets the value of the group property.
getGroup() - Method in class neuroml.channel.IonConcentration
Gets the value of the group property.
getGroup() - Method in class neuroml.channel.Parameter
Gets the value of the group property.
getGroup() - Method in class neuroml.channel.SynapseType
Gets the value of the group property.
getGroup() - Method in class neuroml.meta.GroupDetail
Gets the value of the group property.
getGroup() - Method in class neuroml.morph.Cable
Gets the value of the group property.
getGroup() - Method in class neuroml.morph.Cell.Cables
Gets the value of the group property.
getGroup() - Method in class neuroml.morph.Cell.CellBody
Gets the value of the group property.
getGroup() - Method in class neuroml.morph.Cell
Gets the value of the group property.
getGroup() - Method in class neuroml.morph.Cell.Segments
Gets the value of the group property.
getGroup() - Method in class neuroml.morph.Cell.Spines
Gets the value of the group property.
getGroup() - Method in class neuroml.morph.Feature
Gets the value of the group property.
getGroup() - Method in class neuroml.morph.Morphology.Features
Gets the value of the group property.
getGroup() - Method in class neuroml.morph.Morphology
Gets the value of the group property.
getGroup() - Method in class neuroml.network.CellInstance
Gets the value of the group property.
getGroup() - Method in class neuroml.network.Connections
Gets the value of the group property.
getGroup() - Method in class neuroml.network.GridArrangement
Gets the value of the group property.
getGroup() - Method in class neuroml.network.Instances
Gets the value of the group property.
getGroup() - Method in class neuroml.network.NetworkML
Gets the value of the group property.
getGroup() - Method in class neuroml.network.Population
Gets the value of the group property.
getGroup() - Method in class neuroml.network.PopulationLocation
Gets the value of the group property.
getGroup() - Method in class neuroml.network.Populations
Gets the value of the group property.
getGroup() - Method in class neuroml.network.Projection
Gets the value of the group property.
getGroup() - Method in class neuroml.network.Projections
Gets the value of the group property.
getGroup() - Method in class neuroml.network.RandomArrangement
Gets the value of the group property.
getGroup() - Method in class neuroml.network.SynapseProperties
Gets the value of the group property.
getGroup() - Method in class neuroml.NeuroMLLevel3
Gets the value of the group property.
getGroupDetail() - Method in class neuroml.morph.Morphology.GroupDetails
Gets the value of the groupDetail property.
getGroupDetails() - Method in class neuroml.morph.Morphology
Gets the value of the groupDetails property.
getHeight() - Method in class neuroml.meta.RectangularBox.Size
Gets the value of the height property.
getHhGate() - Method in class neuroml.channel.ChannelType
Gets the value of the hhGate property.
getId() - Method in class neuroml.morph.Cable
Gets the value of the id property.
getId() - Method in class neuroml.morph.CableGroup.Cable
Gets the value of the id property.
getId() - Method in class neuroml.morph.Path
Gets the value of the id property.
getId() - Method in class neuroml.morph.Segment
Gets the value of the id property.
getId() - Method in class neuroml.network.CellInstance
Gets the value of the id property.
getId() - Method in class neuroml.network.Connection
Gets the value of the id property.
getImplPrefs() - Method in class neuroml.channel.ChannelType
Gets the value of the implPrefs property.
getInf() - Method in class neuroml.channel.VoltageConcGate
Gets the value of the inf property.
getInf() - Method in class neuroml.channel.VoltageGate
Gets the value of the inf property.
getInhomogeneousParam() - Method in class neuroml.morph.CableGroup
Gets the value of the inhomogeneousParam property.
getInhomogeneousValue() - Method in class neuroml.bio.VariableNamedParameter
Gets the value of the inhomogeneousValue property.
getInhomogeneousValue() - Method in class neuroml.bio.VariableParameter
Gets the value of the inhomogeneousValue property.
getInitialMembPotential() - Method in class neuroml.bio.Biophysics
Gets the value of the initialMembPotential property.
getInstance() - Method in class neuroml.network.Instances
Gets the value of the instance property.
getInstances() - Method in class neuroml.network.Population
Gets the value of the instances property.
getInstitution() - Method in class neuroml.meta.Person
Gets the value of the institution property.
getInternalDelay() - Method in class neuroml.network.SynapseInternalProperties
Gets the value of the internalDelay property.
getIon() - Method in class neuroml.channel.ChannelML
Gets the value of the ion property.
getIon() - Method in class neuroml.channel.ConcDependence
Gets the value of the ion property.
getIon() - Method in class neuroml.channel.Ohmic
Gets the value of the ion property.
getIonByName(String) - Method in class neuroml.channel.ChannelML
Gets the Ion by name, or null if no such ion exists.
getIonConcentration() - Method in class neuroml.channel.ChannelML
Gets the value of the ionConcentration property.
getIonProperties() - Method in class neuroml.bio.Biophysics
Gets the value of the ionProperties property.
getIonSpecies() - Method in class neuroml.channel.IonConcentration
Gets the value of the ionSpecies property.
getKsGate() - Method in class neuroml.channel.ChannelType
Gets the value of the ksGate property.
getLength() - Method in class neuroml.morph.Spine
Gets the value of the length property.
getLengthUnits() - Method in class neuroml.morph.Morphology
Gets the value of the lengthUnits property.
getLengthUnits() - Method in class neuroml.network.NetworkML
Gets the value of the lengthUnits property.
getLengthUnits() - Method in class neuroml.NeuroMLLevel3
Gets the value of the lengthUnits property.
getLocation() - Method in class neuroml.network.CellInstance
Gets the value of the location property.
getManifold() - Method in class neuroml.morph.Feature
Gets the value of the manifold property.
getMaxConc() - Method in class neuroml.channel.ConcDependence
Gets the value of the maxConc property.
getMaxConductance() - Method in class neuroml.channel.DoubleExponentialSynapse
Gets the value of the maxConductance property.
getMaxPerTarget() - Method in class neuroml.network.PerCellConnection
Gets the value of the maxPerTarget property.
getMaxV() - Method in class neuroml.channel.ImplementationPrefs.TableSettings
Gets the value of the maxV property.
getMechanism() - Method in class neuroml.bio.Biophysics
Gets the value of the mechanism property.
getMetric() - Method in class neuroml.morph.InhomogeneousParam
Gets the value of the metric property.
getMinConc() - Method in class neuroml.channel.ConcDependence
Gets the value of the minConc property.
getMinV() - Method in class neuroml.channel.ImplementationPrefs.TableSettings
Gets the value of the minV property.
getModelAuthor() - Method in class neuroml.meta.Authors
Gets the value of the modelAuthor property.
getModelName() - Method in class neuroml.meta.NeuronDBReference
Gets the value of the modelName property.
getModelTranslator() - Method in class neuroml.meta.Authors
Gets the value of the modelTranslator property.
getName() - Method in class neuroml.bio.IonProperties
Gets the value of the name property.
getName() - Method in class neuroml.bio.Mechanism
Gets the value of the name property.
getName() - Method in class neuroml.bio.NamedParameter
Gets the value of the name property.
getName() - Method in class neuroml.bio.VariableNamedParameter
Gets the value of the name property.
getName() - Method in class neuroml.bio.VariableParameter
Gets the value of the name property.
getName() - Method in class neuroml.channel.ChannelType
Gets the value of the name property.
getName() - Method in class neuroml.channel.ConcDependence
Gets the value of the name property.
getName() - Method in class neuroml.channel.CurrentVoltageRelation
Gets the value of the name property.
getName() - Method in class neuroml.channel.Gate.State
Gets the value of the name property.
getName() - Method in class neuroml.channel.Ion
Gets the value of the name property.
getName() - Method in class neuroml.channel.IonConcentration
Gets the value of the name property.
getName() - Method in class neuroml.channel.KSState
Gets the value of the name property.
getName() - Method in class neuroml.channel.Parameter
Gets the value of the name property.
getName() - Method in class neuroml.channel.SynapseType
Gets the value of the name property.
getName() - Method in class neuroml.meta.Person
Gets the value of the name property.
getName() - Method in class neuroml.meta.Points
Gets the value of the name property.
getName() - Method in class neuroml.meta.RectangularBox
Gets the value of the name property.
getName() - Method in class neuroml.meta.Sphere
Gets the value of the name property.
getName() - Method in class neuroml.morph.Cable
Gets the value of the name property.
getName() - Method in class neuroml.morph.CableGroup
Gets the value of the name property.
getName() - Method in class neuroml.morph.Cell
Gets the value of the name property.
getName() - Method in class neuroml.morph.Cell.Segments
Gets the value of the name property.
getName() - Method in class neuroml.morph.Feature
Gets the value of the name property.
getName() - Method in class neuroml.morph.InhomogeneousParam
Gets the value of the name property.
getName() - Method in class neuroml.morph.Morphology
Gets the value of the name property.
getName() - Method in class neuroml.morph.Segment
Gets the value of the name property.
getName() - Method in class neuroml.network.NetworkML
Gets the value of the name property.
getName() - Method in class neuroml.network.Population
Gets the value of the name property.
getName() - Method in class neuroml.network.Projection
Gets the value of the name property.
getName() - Method in class neuroml.NeuroMLLevel3
Gets the value of the name property.
getNeuronDBref() - Method in class neuroml.channel.ChannelType
Gets the value of the neuronDBref property.
getNeuronDBref() - Method in class neuroml.channel.IonConcentration
Gets the value of the neuronDBref property.
getNeuronDBref() - Method in class neuroml.channel.SynapseType
Gets the value of the neuronDBref property.
getNeuronDBref() - Method in class neuroml.morph.Cell
Gets the value of the neuronDBref property.
getNeuronDBref() - Method in class neuroml.NeuroMLLevel3
Gets the value of the neuronDBref property.
getNonSpecific() - Method in class neuroml.channel.Ohmic
Gets the value of the nonSpecific property.
getNormalizationEnd() - Method in class neuroml.morph.InhomogeneousParam.Distal
Gets the value of the normalizationEnd property.
getNotes() - Method in class neuroml.channel.ChannelML
Gets the value of the notes property.
getNotes() - Method in class neuroml.channel.ChannelType
Gets the value of the notes property.
getNotes() - Method in class neuroml.channel.DoubleExponentialSynapse
Gets the value of the notes property.
getNotes() - Method in class neuroml.channel.Ion
Gets the value of the notes property.
getNotes() - Method in class neuroml.channel.IonConcentration
Gets the value of the notes property.
getNotes() - Method in class neuroml.channel.Parameter
Gets the value of the notes property.
getNotes() - Method in class neuroml.channel.SynapseType
Gets the value of the notes property.
getNotes() - Method in class neuroml.morph.Cable
Gets the value of the notes property.
getNotes() - Method in class neuroml.morph.Cell.Cables
Gets the value of the notes property.
getNotes() - Method in class neuroml.morph.Cell.CellBody
Gets the value of the notes property.
getNotes() - Method in class neuroml.morph.Cell
Gets the value of the notes property.
getNotes() - Method in class neuroml.morph.Cell.Segments
Gets the value of the notes property.
getNotes() - Method in class neuroml.morph.Cell.Spines
Gets the value of the notes property.
getNotes() - Method in class neuroml.morph.Feature
Gets the value of the notes property.
getNotes() - Method in class neuroml.morph.Morphology.Features
Gets the value of the notes property.
getNotes() - Method in class neuroml.morph.Morphology
Gets the value of the notes property.
getNotes() - Method in class neuroml.network.CellInstance
Gets the value of the notes property.
getNotes() - Method in class neuroml.network.Connections
Gets the value of the notes property.
getNotes() - Method in class neuroml.network.GridArrangement
Gets the value of the notes property.
getNotes() - Method in class neuroml.network.Instances
Gets the value of the notes property.
getNotes() - Method in class neuroml.network.NetworkML
Gets the value of the notes property.
getNotes() - Method in class neuroml.network.Population
Gets the value of the notes property.
getNotes() - Method in class neuroml.network.PopulationLocation
Gets the value of the notes property.
getNotes() - Method in class neuroml.network.Populations
Gets the value of the notes property.
getNotes() - Method in class neuroml.network.Projection
Gets the value of the notes property.
getNotes() - Method in class neuroml.network.Projections
Gets the value of the notes property.
getNotes() - Method in class neuroml.network.RandomArrangement
Gets the value of the notes property.
getNotes() - Method in class neuroml.network.SynapseProperties
Gets the value of the notes property.
getNotes() - Method in class neuroml.NeuroMLLevel3
Gets the value of the notes property.
getNumPerSource() - Method in class neuroml.network.PerCellConnection
Gets the value of the numPerSource property.
getOffset() - Method in class neuroml.channel.RateAdjustments
Gets the value of the offset property.
getOhmic() - Method in class neuroml.channel.CurrentVoltageRelation
Gets the value of the ohmic property.
getParameter() - Method in class neuroml.bio.InitialMembPotential
Gets the value of the parameter property.
getParameter() - Method in class neuroml.bio.IonProperties
Gets the value of the parameter property.
getParameter() - Method in class neuroml.bio.Mechanism
Gets the value of the parameter property.
getParameter() - Method in class neuroml.bio.SpecAxialResistance
Gets the value of the parameter property.
getParameter() - Method in class neuroml.bio.SpecCapacitance
Gets the value of the parameter property.
getParameter() - Method in class neuroml.channel.RateConstantEqn
Gets the value of the parameter property.
getParameterisedHh() - Method in class neuroml.channel.RateConstantEqnChoice
Gets the value of the parameterisedHh property.
getParamName() - Method in class neuroml.bio.InhomogeneousValue
Gets the value of the paramName property.
getParent() - Method in class neuroml.morph.Cable
Gets the value of the parent property.
getParent() - Method in class neuroml.morph.Path
Gets the value of the parent property.
getParent() - Method in class neuroml.morph.Segment
Gets the value of the parent property.
getParent() - Method in class neuroml.morph.Spine
Gets the value of the parent property.
getPath() - Method in class neuroml.morph.Feature
Gets the value of the path property.
getPerCellConnection() - Method in class neuroml.network.ConnectivityPattern
Gets the value of the perCellConnection property.
getPoint() - Method in class neuroml.meta.Points
Gets the value of the point property.
getPolygon() - Method in class neuroml.meta.Polyhedron.Polygons
Gets the value of the polygon property.
getPolygon() - Method in class neuroml.morph.Cell.CellBody
Gets the value of the polygon property.
getPolygon() - Method in class neuroml.morph.Feature
Gets the value of the polygon property.
getPolygons() - Method in class neuroml.meta.Polyhedron
Gets the value of the polygons property.
getPolyhedron() - Method in class neuroml.morph.Cell.CellBody
Gets the value of the polyhedron property.
getPolyhedron() - Method in class neuroml.morph.Feature
Gets the value of the polyhedron property.
getPoolVolumeInfo() - Method in class neuroml.channel.DecayingPoolModel
Gets the value of the poolVolumeInfo property.
getPopLocation() - Method in class neuroml.network.Population
Gets the value of the popLocation property.
getPopulation() - Method in class neuroml.network.Populations
Gets the value of the population property.
getPopulationList() - Method in class neuroml.NeuroMLLevel3
Get the list of populations in this NeuroML file
getPopulations() - Method in class neuroml.network.NetworkML
Gets the value of the populations property.
getPopulations() - Method in class neuroml.NeuroMLLevel3
Gets the value of the populations property.
getPopulationSize() - Method in class neuroml.network.RandomArrangement
Gets the value of the populationSize property.
getPostDelay() - Method in class neuroml.network.SynapseInternalProperties
Gets the value of the postDelay property.
getPotentialSynapticLocation() - Method in class neuroml.Level3Biophysics
Gets the value of the potentialSynapticLocation property.
getPower() - Method in class neuroml.channel.Gate
Gets the value of the power property.
getPreDelay() - Method in class neuroml.network.SynapseInternalProperties
Gets the value of the preDelay property.
getPreferredPrefix(String, String, boolean) - Method in class neuroml.util.NeuroMLNamespacePrefixMapper
 
getProbability() - Method in class neuroml.network.ConnectivityPattern.FixedProbability
Gets the value of the probability property.
getProjection() - Method in class neuroml.network.Projections
Gets the value of the projection property.
getProjectionList() - Method in class neuroml.NeuroMLLevel3
Get the list of projections in this NeuroML file
getProjections() - Method in class neuroml.network.NetworkML
Gets the value of the projections property.
getProjections() - Method in class neuroml.NeuroMLLevel3
Gets the value of the projections property.
getPropDelay() - Method in class neuroml.network.SynapseInternalProperties
Gets the value of the propDelay property.
getProperties() - Method in class neuroml.channel.ChannelML
Gets the value of the properties property.
getProperties() - Method in class neuroml.channel.ChannelType
Gets the value of the properties property.
getProperties() - Method in class neuroml.channel.DoubleExponentialSynapse
Gets the value of the properties property.
getProperties() - Method in class neuroml.channel.Ion
Gets the value of the properties property.
getProperties() - Method in class neuroml.channel.IonConcentration
Gets the value of the properties property.
getProperties() - Method in class neuroml.channel.Parameter
Gets the value of the properties property.
getProperties() - Method in class neuroml.channel.SynapseType
Gets the value of the properties property.
getProperties() - Method in class neuroml.meta.GroupDetail
Gets the value of the properties property.
getProperties() - Method in class neuroml.morph.Cable
Gets the value of the properties property.
getProperties() - Method in class neuroml.morph.Cell.Cables
Gets the value of the properties property.
getProperties() - Method in class neuroml.morph.Cell.CellBody
Gets the value of the properties property.
getProperties() - Method in class neuroml.morph.Cell
Gets the value of the properties property.
getProperties() - Method in class neuroml.morph.Cell.Segments
Gets the value of the properties property.
getProperties() - Method in class neuroml.morph.Cell.Spines
Gets the value of the properties property.
getProperties() - Method in class neuroml.morph.Feature
Gets the value of the properties property.
getProperties() - Method in class neuroml.morph.Morphology.Features
Gets the value of the properties property.
getProperties() - Method in class neuroml.morph.Morphology
Gets the value of the properties property.
getProperties() - Method in class neuroml.morph.Segment
Gets the value of the properties property.
getProperties() - Method in class neuroml.network.CellInstance
Gets the value of the properties property.
getProperties() - Method in class neuroml.network.Connections
Gets the value of the properties property.
getProperties() - Method in class neuroml.network.GridArrangement
Gets the value of the properties property.
getProperties() - Method in class neuroml.network.Instances
Gets the value of the properties property.
getProperties() - Method in class neuroml.network.NetworkML
Gets the value of the properties property.
getProperties() - Method in class neuroml.network.Population
Gets the value of the properties property.
getProperties() - Method in class neuroml.network.PopulationLocation
Gets the value of the properties property.
getProperties() - Method in class neuroml.network.Populations
Gets the value of the properties property.
getProperties() - Method in class neuroml.network.Projection
Gets the value of the properties property.
getProperties() - Method in class neuroml.network.Projections
Gets the value of the properties property.
getProperties() - Method in class neuroml.network.RandomArrangement
Gets the value of the properties property.
getProperties() - Method in class neuroml.network.SynapseProperties
Gets the value of the properties property.
getProperties() - Method in class neuroml.NeuroMLLevel3
Gets the value of the properties property.
getProperty() - Method in class neuroml.meta.Properties
Gets the value of the property property.
getProperty() - Method in class neuroml.meta.PropertyDetail
Gets the value of the property property.
getPropertyDetail() - Method in class neuroml.morph.Morphology.PropertyDetails
Gets the value of the propertyDetail property.
getPropertyDetails() - Method in class neuroml.morph.Morphology
Gets the value of the propertyDetails property.
getProximal() - Method in class neuroml.morph.InhomogeneousParam
Gets the value of the proximal property.
getProximal() - Method in class neuroml.morph.Segment
Gets the value of the proximal property.
getProximal() - Method in class neuroml.morph.Spine
Gets the value of the proximal property.
getPublication() - Method in class neuroml.channel.ChannelType
Gets the value of the publication property.
getPublication() - Method in class neuroml.channel.IonConcentration
Gets the value of the publication property.
getPublication() - Method in class neuroml.channel.SynapseType
Gets the value of the publication property.
getPublication() - Method in class neuroml.morph.Cell
Gets the value of the publication property.
getPublication() - Method in class neuroml.NeuroMLLevel3
Gets the value of the publication property.
getPubmedRef() - Method in class neuroml.meta.Publication
Gets the value of the pubmedRef property.
getQ10Factor() - Method in class neuroml.channel.RateAdjustments.Q10Settings
Gets the value of the q10Factor property.
getQ10Settings() - Method in class neuroml.channel.RateAdjustments
Gets the value of the q10Settings property.
getRandomArrangement() - Method in class neuroml.network.PopulationLocation
Gets the value of the randomArrangement property.
getRateAdjustments() - Method in class neuroml.channel.Ohmic.Conductance
Gets the value of the rateAdjustments property.
getRectangularLocation() - Method in class neuroml.network.GridArrangement
Gets the value of the rectangularLocation property.
getRectangularLocation() - Method in class neuroml.network.RandomArrangement
Gets the value of the rectangularLocation property.
getReference() - Method in class neuroml.network.PopulationLocation
Gets the value of the reference property.
getRestingConc() - Method in class neuroml.channel.DecayingPoolModel
Gets the value of the restingConc property.
getReversalPotential() - Method in class neuroml.channel.DoubleExponentialSynapse
Gets the value of the reversalPotential property.
getRiseTime() - Method in class neuroml.channel.DoubleExponentialSynapse
Gets the value of the riseTime property.
getRole() - Method in class neuroml.channel.Ion
Gets the value of the role property.
getSegment() - Method in class neuroml.morph.Cell.Segments
Gets the value of the segment property.
getSegmentId() - Method in class neuroml.network.SynapticLocation
Gets the value of the segmentId property.
getSegmentList() - Method in class neuroml.morph.Cell
Get the list of segments representing this cell.
getSegmentList(int) - Method in class neuroml.morph.Cell
Get the segment list at the specified index.
getSegments() - Method in class neuroml.morph.Cell
Gets the value of the segments property.
getShape() - Method in class neuroml.morph.Spine
Gets the value of the shape property.
getShellThickness() - Method in class neuroml.channel.PoolVolumeInfo
Gets the value of the shellThickness property.
getSize() - Method in class neuroml.meta.RectangularBox
Gets the value of the size property.
getSource() - Method in class neuroml.network.Projection
Gets the value of the source property.
getSpacing() - Method in class neuroml.network.GridArrangement
Gets the value of the spacing property.
getSpecies() - Method in class neuroml.channel.Block
Gets the value of the species property.
getSpecificAxialResistance() - Method in class neuroml.bio.Biophysics
Gets the value of the specificAxialResistance property.
getSpecificCapacitance() - Method in class neuroml.bio.Biophysics
Gets the value of the specificCapacitance property.
getSphere() - Method in class neuroml.morph.Cell.CellBody
Gets the value of the sphere property.
getSphere() - Method in class neuroml.morph.Feature
Gets the value of the sphere property.
getSphericalLocation() - Method in class neuroml.network.RandomArrangement
Gets the value of the sphericalLocation property.
getSpine() - Method in class neuroml.morph.Cell.Spines
Gets the value of the spine property.
getSpines() - Method in class neuroml.morph.Cell
Gets the value of the spines property.
getSrc() - Method in class neuroml.channel.Transition
Gets the value of the src property.
getState() - Method in class neuroml.channel.Gate
Gets the value of the state property.
getState() - Method in class neuroml.channel.HHGate
Gets the value of the state property.
getState() - Method in class neuroml.channel.KSGate
Gets the value of the state property.
getSynapseProps() - Method in class neuroml.network.Projection
Gets the value of the synapseProps property.
getSynapseType() - Method in class neuroml.channel.ChannelML
Gets the value of the synapseType property.
getSynapseType() - Method in class neuroml.network.SynapseProperties
Gets the value of the synapseType property.
getTableDivisions() - Method in class neuroml.channel.ImplementationPrefs.TableSettings
Gets the value of the tableDivisions property.
getTableSettings() - Method in class neuroml.channel.ImplementationPrefs
Gets the value of the tableSettings property.
getTag() - Method in class neuroml.meta.Property
Gets the value of the tag property.
getTarget() - Method in class neuroml.channel.Transition
Gets the value of the target property.
getTarget() - Method in class neuroml.network.Projection
Gets the value of the target property.
getTau() - Method in class neuroml.channel.VoltageConcGate
Gets the value of the tau property.
getTau() - Method in class neuroml.channel.VoltageGate
Gets the value of the tau property.
getThreshold() - Method in class neuroml.network.SynapseInternalProperties
Gets the value of the threshold property.
getTransition() - Method in class neuroml.channel.HHGate
Gets the value of the transition property.
getTransition() - Method in class neuroml.channel.KSGate
Gets the value of the transition property.
getTranslationStart() - Method in class neuroml.morph.InhomogeneousParam.Proximal
Gets the value of the translationStart property.
getType() - Method in class neuroml.bio.Mechanism
Gets the value of the type property.
getType() - Method in class neuroml.channel.RateConstantEqn
Gets the value of the type property.
getType() - Method in class neuroml.meta.PropertyDetail
Gets the value of the type property.
getUnits() - Method in class neuroml.bio.Biophysics
Gets the value of the units property.
getUnits() - Method in class neuroml.channel.ChannelML
Gets the value of the units property.
getUnits() - Method in class neuroml.network.Projections
Gets the value of the units property.
getUri() - Method in class neuroml.meta.NeuronDBReference
Gets the value of the uri property.
getValue() - Method in class neuroml.bio.InhomogeneousValue
Gets the value of the value property.
getValue() - Method in class neuroml.bio.NamedParameter
Gets the value of the value property.
getValue() - Method in class neuroml.bio.UnnamedParameter
Gets the value of the value property.
getValue() - Method in class neuroml.channel.Parameter
Gets the value of the value property.
getValue() - Method in class neuroml.channel.RateAdjustments.Offset
Gets the value of the value property.
getValue() - Method in class neuroml.meta.Property
Gets the value of the value property.
getVariable() - Method in class neuroml.morph.InhomogeneousParam
Gets the value of the variable property.
getVariableName() - Method in class neuroml.channel.ConcDependence
Gets the value of the variableName property.
getVariableParameter() - Method in class neuroml.bio.InitialMembPotential
Gets the value of the variableParameter property.
getVariableParameter() - Method in class neuroml.bio.Mechanism
Gets the value of the variableParameter property.
getVariableParameter() - Method in class neuroml.bio.SpecAxialResistance
Gets the value of the variableParameter property.
getVariableParameter() - Method in class neuroml.bio.SpecCapacitance
Gets the value of the variableParameter property.
getVoltageConcGate() - Method in class neuroml.channel.Transition
Gets the value of the voltageConcGate property.
getVoltageGate() - Method in class neuroml.channel.Transition
Gets the value of the voltageGate property.
getVolume() - Method in class neuroml.morph.Spine
Gets the value of the volume property.
getVolumeUnits() - Method in class neuroml.morph.Morphology
Gets the value of the volumeUnits property.
getVolumeUnits() - Method in class neuroml.network.NetworkML
Gets the value of the volumeUnits property.
getVolumeUnits() - Method in class neuroml.NeuroMLLevel3
Gets the value of the volumeUnits property.
getWeight() - Method in class neuroml.network.SynapseInternalProperties
Gets the value of the weight property.
getWidth() - Method in class neuroml.meta.RectangularBox.Size
Gets the value of the width property.
getX() - Method in class neuroml.meta.Point
Gets the value of the x property.
getX() - Method in class neuroml.network.GridArrangement.Spacing
Gets the value of the x property.
getY() - Method in class neuroml.meta.Point
Gets the value of the y property.
getY() - Method in class neuroml.network.GridArrangement.Spacing
Gets the value of the y property.
getZ() - Method in class neuroml.meta.Point
Gets the value of the z property.
getZ() - Method in class neuroml.network.GridArrangement.Spacing
Gets the value of the z property.
GridArrangement - Class in neuroml.network
A regular placement of the cells in 1 to 3 dimensions
GridArrangement() - Constructor for class neuroml.network.GridArrangement
 
gridArrangement - Variable in class neuroml.network.PopulationLocation
 
GridArrangement.Spacing - Class in neuroml.network
Java class for anonymous complex type.
GridArrangement.Spacing() - Constructor for class neuroml.network.GridArrangement.Spacing
 
group - Variable in class neuroml.bio.NamedParameter
 
group - Variable in class neuroml.bio.UnnamedParameter
 
group - Variable in class neuroml.bio.VariableNamedParameter
 
group - Variable in class neuroml.bio.VariableParameter
 
group - Variable in class neuroml.channel.ChannelML
 
group - Variable in class neuroml.channel.ChannelType
 
group - Variable in class neuroml.channel.DoubleExponentialSynapse
 
group - Variable in class neuroml.channel.Ion
 
group - Variable in class neuroml.channel.IonConcentration
 
group - Variable in class neuroml.channel.Parameter
 
group - Variable in class neuroml.channel.SynapseType
 
group - Variable in class neuroml.meta.GroupDetail
 
group - Variable in class neuroml.morph.Cable
 
group - Variable in class neuroml.morph.Cell.Cables
 
group - Variable in class neuroml.morph.Cell.CellBody
 
group - Variable in class neuroml.morph.Cell
 
group - Variable in class neuroml.morph.Cell.Segments
 
group - Variable in class neuroml.morph.Cell.Spines
 
group - Variable in class neuroml.morph.Feature
 
group - Variable in class neuroml.morph.Morphology.Features
 
group - Variable in class neuroml.morph.Morphology
 
group - Variable in class neuroml.network.CellInstance
 
group - Variable in class neuroml.network.Connections
 
group - Variable in class neuroml.network.GridArrangement
 
group - Variable in class neuroml.network.Instances
 
group - Variable in class neuroml.network.NetworkML
 
group - Variable in class neuroml.network.Population
 
group - Variable in class neuroml.network.PopulationLocation
 
group - Variable in class neuroml.network.Populations
 
group - Variable in class neuroml.network.Projection
 
group - Variable in class neuroml.network.Projections
 
group - Variable in class neuroml.network.RandomArrangement
 
group - Variable in class neuroml.network.SynapseProperties
 
group - Variable in class neuroml.NeuroMLLevel3
 
GroupDetail - Class in neuroml.meta
Metadata for each Group.
GroupDetail() - Constructor for class neuroml.meta.GroupDetail
 
groupDetail - Variable in class neuroml.morph.Morphology.GroupDetails
 
groupDetails - Variable in class neuroml.morph.Morphology
 

H

height - Variable in class neuroml.meta.RectangularBox.Size
 
hhGate - Variable in class neuroml.channel.ChannelType
 
HHGate - Class in neuroml.channel
Gate with Hodgkin Huxley like state transitions
HHGate() - Constructor for class neuroml.channel.HHGate
 

I

id - Variable in class neuroml.morph.Cable
 
id - Variable in class neuroml.morph.CableGroup.Cable
 
id - Variable in class neuroml.morph.Path
 
id - Variable in class neuroml.morph.Segment
 
id - Variable in class neuroml.network.CellInstance
 
id - Variable in class neuroml.network.Connection
 
ImplementationPrefs - Class in neuroml.channel
These items ideally shouldn't be in a specification which deals with a description of the physiology of the channel.
ImplementationPrefs() - Constructor for class neuroml.channel.ImplementationPrefs
 
ImplementationPrefs.TableSettings - Class in neuroml.channel
Java class for anonymous complex type.
ImplementationPrefs.TableSettings() - Constructor for class neuroml.channel.ImplementationPrefs.TableSettings
 
implPrefs - Variable in class neuroml.channel.ChannelType
 
inf - Variable in class neuroml.channel.VoltageConcGate
 
inf - Variable in class neuroml.channel.VoltageGate
 
inhomogeneousParam - Variable in class neuroml.morph.CableGroup
 
InhomogeneousParam - Class in neuroml.morph
Definition of a parameter which varies along a cable group.
InhomogeneousParam() - Constructor for class neuroml.morph.InhomogeneousParam
 
InhomogeneousParam.Distal - Class in neuroml.morph
Java class for anonymous complex type.
InhomogeneousParam.Distal() - Constructor for class neuroml.morph.InhomogeneousParam.Distal
 
InhomogeneousParam.Proximal - Class in neuroml.morph
Java class for anonymous complex type.
InhomogeneousParam.Proximal() - Constructor for class neuroml.morph.InhomogeneousParam.Proximal
 
InhomogeneousValue - Class in neuroml.bio
How a value changes over the cable group
InhomogeneousValue() - Constructor for class neuroml.bio.InhomogeneousValue
 
inhomogeneousValue - Variable in class neuroml.bio.VariableNamedParameter
 
inhomogeneousValue - Variable in class neuroml.bio.VariableParameter
 
initialMembPotential - Variable in class neuroml.bio.Biophysics
 
InitialMembPotential - Class in neuroml.bio
This quantity is often required for computational simulations and specifies the potential difference across the membrane at the start of the simulation.
InitialMembPotential() - Constructor for class neuroml.bio.InitialMembPotential
 
instance - Variable in class neuroml.network.Instances
 
Instances - Class in neuroml.network
Cell Instance position information
Instances() - Constructor for class neuroml.network.Instances
 
instances - Variable in class neuroml.network.Population
 
institution - Variable in class neuroml.meta.Person
 
internalDelay - Variable in class neuroml.network.SynapseInternalProperties
 
ion - Variable in class neuroml.channel.ChannelML
 
ion - Variable in class neuroml.channel.ConcDependence
 
Ion - Class in neuroml.channel
Definition of an ion which is involved in this channel mechanism
Ion() - Constructor for class neuroml.channel.Ion
 
ion - Variable in class neuroml.channel.Ohmic
 
ionConcentration - Variable in class neuroml.channel.ChannelML
 
IonConcentration - Class in neuroml.channel
Concentration of a particular ion species, the concentration of which affects some channels
IonConcentration() - Constructor for class neuroml.channel.IonConcentration
 
ionProperties - Variable in class neuroml.bio.Biophysics
 
IonProperties - Class in neuroml.bio
Some properties accociated with an ion type which takes part in the mechanisms on the cell
IonProperties() - Constructor for class neuroml.bio.IonProperties
 
IonRole - Enum in neuroml.channel
Java class for IonRole.
ionSpecies - Variable in class neuroml.channel.IonConcentration
 

J

jaxb - Variable in class neuroml.util.NeuroMLConverter
 

K

ksGate - Variable in class neuroml.channel.ChannelType
 
KSGate - Class in neuroml.channel
Gate with kinetic scheme transitions
KSGate() - Constructor for class neuroml.channel.KSGate
 
KSState - Class in neuroml.channel
Single kinetic scheme state.
KSState() - Constructor for class neuroml.channel.KSState
 

L

length - Variable in class neuroml.morph.Spine
 
LengthUnits - Enum in neuroml.meta
Java class for LengthUnits.
lengthUnits - Variable in class neuroml.morph.Morphology
 
lengthUnits - Variable in class neuroml.network.NetworkML
 
lengthUnits - Variable in class neuroml.NeuroMLLevel3
 
Level3Biophysics - Class in neuroml
Biophysics of Level3 cell, including specification for allowable synaptic locations
Level3Biophysics() - Constructor for class neuroml.Level3Biophysics
 
Level3Cell - Class in neuroml
Cell with extensions for biophysics, and network functionality
Level3Cell() - Constructor for class neuroml.Level3Cell
 
location - Variable in class neuroml.network.CellInstance
 

M

Manifold - Class in neuroml.meta
A surface.
Manifold() - Constructor for class neuroml.meta.Manifold
 
manifold - Variable in class neuroml.morph.Feature
 
marshaller - Variable in class neuroml.util.NeuroMLConverter
 
maxConc - Variable in class neuroml.channel.ConcDependence
 
maxConductance - Variable in class neuroml.channel.DoubleExponentialSynapse
 
maxPerTarget - Variable in class neuroml.network.PerCellConnection
 
maxV - Variable in class neuroml.channel.ImplementationPrefs.TableSettings
 
mechanism - Variable in class neuroml.bio.Biophysics
 
Mechanism - Class in neuroml.bio
Definition of placement of a single electrophysiological mechanism (e.g.
Mechanism() - Constructor for class neuroml.bio.Mechanism
 
MechanismType - Enum in neuroml.bio
Java class for MechanismType.
metric - Variable in class neuroml.morph.InhomogeneousParam
 
minConc - Variable in class neuroml.channel.ConcDependence
 
minV - Variable in class neuroml.channel.ImplementationPrefs.TableSettings
 
modelAuthor - Variable in class neuroml.meta.Authors
 
modelName - Variable in class neuroml.meta.NeuronDBReference
 
modelTranslator - Variable in class neuroml.meta.Authors
 
Morphology - Class in neuroml.morph
The main element which details the neuronal morphology.
Morphology() - Constructor for class neuroml.morph.Morphology
 
Morphology.Features - Class in neuroml.morph
Java class for anonymous complex type.
Morphology.Features() - Constructor for class neuroml.morph.Morphology.Features
 
Morphology.GroupDetails - Class in neuroml.morph
Java class for anonymous complex type.
Morphology.GroupDetails() - Constructor for class neuroml.morph.Morphology.GroupDetails
 
Morphology.PropertyDetails - Class in neuroml.morph
Java class for anonymous complex type.
Morphology.PropertyDetails() - Constructor for class neuroml.morph.Morphology.PropertyDetails
 
morphologyToXml(Morphology, String) - Method in class neuroml.util.NeuroMLConverter
 

N

name - Variable in class neuroml.bio.IonProperties
 
name - Variable in class neuroml.bio.Mechanism
 
name - Variable in class neuroml.bio.NamedParameter
 
name - Variable in class neuroml.bio.VariableNamedParameter
 
name - Variable in class neuroml.bio.VariableParameter
 
name - Variable in class neuroml.channel.ChannelType
 
name - Variable in class neuroml.channel.ConcDependence
 
name - Variable in class neuroml.channel.CurrentVoltageRelation
 
name - Variable in class neuroml.channel.Gate.State
 
name - Variable in class neuroml.channel.Ion
 
name - Variable in class neuroml.channel.IonConcentration
 
name - Variable in class neuroml.channel.KSState
 
name - Variable in class neuroml.channel.Parameter
 
name - Variable in class neuroml.channel.SynapseType
 
name - Variable in class neuroml.meta.Person
 
name - Variable in class neuroml.meta.Points
 
name - Variable in class neuroml.meta.RectangularBox
 
name - Variable in class neuroml.meta.Sphere
 
name - Variable in class neuroml.morph.Cable
 
name - Variable in class neuroml.morph.CableGroup
 
name - Variable in class neuroml.morph.Cell
 
name - Variable in class neuroml.morph.Cell.Segments
 
name - Variable in class neuroml.morph.Feature
 
name - Variable in class neuroml.morph.InhomogeneousParam
 
name - Variable in class neuroml.morph.Morphology
 
name - Variable in class neuroml.morph.Segment
 
NAME - Static variable in class neuroml.network.Connection.InternalProperties
 
name - Variable in class neuroml.network.NetworkML
 
name - Variable in class neuroml.network.Population
 
NAME - Static variable in class neuroml.network.PotentialSynapticLocation.AllowedGroups
 
name - Variable in class neuroml.network.Projection
 
name - Variable in class neuroml.NeuroMLLevel3
 
NamedParameter - Class in neuroml.bio
Definition of a value for a quantity and the associated groups of cables which have this value
NamedParameter() - Constructor for class neuroml.bio.NamedParameter
 
namespaceToPrefixMap - Variable in class neuroml.util.NeuroMLNamespacePrefixMapper
 
NetworkML - Class in neuroml.network
The main elements which make up a NetworkML compliant document.
NetworkML() - Constructor for class neuroml.network.NetworkML
 
neuroml - package neuroml
 
neuroml.bio - package neuroml.bio
 
neuroml.channel - package neuroml.channel
 
neuroml.meta - package neuroml.meta
 
neuroml.morph - package neuroml.morph
 
neuroml.network - package neuroml.network
 
neuroml.util - package neuroml.util
 
NeuroMLConverter - Class in neuroml.util
 
NeuroMLConverter() - Constructor for class neuroml.util.NeuroMLConverter
 
NeuroMLLevel3 - Class in neuroml
Description of neuronal models, including biophysics and channel mechanisms, and network connections (NeuroML Level 3).
NeuroMLLevel3() - Constructor for class neuroml.NeuroMLLevel3
 
NeuroMLLevel3.Cells - Class in neuroml
Java class for anonymous complex type.
NeuroMLLevel3.Cells() - Constructor for class neuroml.NeuroMLLevel3.Cells
 
NeuroMLNamespacePrefixMapper - Class in neuroml.util
 
NeuroMLNamespacePrefixMapper() - Constructor for class neuroml.util.NeuroMLNamespacePrefixMapper
 
neuromlToXml(NeuroMLLevel3, String) - Method in class neuroml.util.NeuroMLConverter
 
neuronDBref - Variable in class neuroml.channel.ChannelType
 
neuronDBref - Variable in class neuroml.channel.IonConcentration
 
neuronDBref - Variable in class neuroml.channel.SynapseType
 
neuronDBref - Variable in class neuroml.morph.Cell
 
neuronDBref - Variable in class neuroml.NeuroMLLevel3
 
NeuronDBReference - Class in neuroml.meta
A reference to an entity in NeuronDB Note: This element will most likely change when a new set of schema files is adopted for adding references, authors, citations, etc.
NeuronDBReference() - Constructor for class neuroml.meta.NeuronDBReference
 
nonSpecific - Variable in class neuroml.channel.Ohmic
 
normalizationEnd - Variable in class neuroml.morph.InhomogeneousParam.Distal
 
notes - Variable in class neuroml.channel.ChannelML
 
notes - Variable in class neuroml.channel.ChannelType
 
notes - Variable in class neuroml.channel.DoubleExponentialSynapse
 
notes - Variable in class neuroml.channel.Ion
 
notes - Variable in class neuroml.channel.IonConcentration
 
notes - Variable in class neuroml.channel.Parameter
 
notes - Variable in class neuroml.channel.SynapseType
 
notes - Variable in class neuroml.morph.Cable
 
notes - Variable in class neuroml.morph.Cell.Cables
 
notes - Variable in class neuroml.morph.Cell.CellBody
 
notes - Variable in class neuroml.morph.Cell
 
notes - Variable in class neuroml.morph.Cell.Segments
 
notes - Variable in class neuroml.morph.Cell.Spines
 
notes - Variable in class neuroml.morph.Feature
 
notes - Variable in class neuroml.morph.Morphology.Features
 
notes - Variable in class neuroml.morph.Morphology
 
notes - Variable in class neuroml.network.CellInstance
 
notes - Variable in class neuroml.network.Connections
 
notes - Variable in class neuroml.network.GridArrangement
 
notes - Variable in class neuroml.network.Instances
 
notes - Variable in class neuroml.network.NetworkML
 
notes - Variable in class neuroml.network.Population
 
notes - Variable in class neuroml.network.PopulationLocation
 
notes - Variable in class neuroml.network.Populations
 
notes - Variable in class neuroml.network.Projection
 
notes - Variable in class neuroml.network.Projections
 
notes - Variable in class neuroml.network.RandomArrangement
 
notes - Variable in class neuroml.network.SynapseProperties
 
notes - Variable in class neuroml.NeuroMLLevel3
 
numPerSource - Variable in class neuroml.network.PerCellConnection
 

O

ObjectFactory - Class in neuroml.bio
This object contains factory methods for each Java content interface and Java element interface generated in the neuroml.bio package.
ObjectFactory() - Constructor for class neuroml.bio.ObjectFactory
Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: neuroml.bio
ObjectFactory - Class in neuroml.channel
This object contains factory methods for each Java content interface and Java element interface generated in the neuroml.channel package.
ObjectFactory() - Constructor for class neuroml.channel.ObjectFactory
Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: neuroml.channel
ObjectFactory - Class in neuroml.meta
This object contains factory methods for each Java content interface and Java element interface generated in the neuroml.meta package.
ObjectFactory() - Constructor for class neuroml.meta.ObjectFactory
Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: neuroml.meta
ObjectFactory - Class in neuroml.morph
This object contains factory methods for each Java content interface and Java element interface generated in the neuroml.morph package.
ObjectFactory() - Constructor for class neuroml.morph.ObjectFactory
Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: neuroml.morph
ObjectFactory - Class in neuroml.network
This object contains factory methods for each Java content interface and Java element interface generated in the neuroml.network package.
ObjectFactory() - Constructor for class neuroml.network.ObjectFactory
Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: neuroml.network
ObjectFactory - Class in neuroml
This object contains factory methods for each Java content interface and Java element interface generated in the neuroml package.
ObjectFactory() - Constructor for class neuroml.ObjectFactory
Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: neuroml
offset - Variable in class neuroml.channel.RateAdjustments
 
ohmic - Variable in class neuroml.channel.CurrentVoltageRelation
 
Ohmic - Class in neuroml.channel
Signifies an ohmic relation; the current is proportional to the potential difference across the channel
Ohmic() - Constructor for class neuroml.channel.Ohmic
 
Ohmic.Conductance - Class in neuroml.channel
Java class for anonymous complex type.
Ohmic.Conductance() - Constructor for class neuroml.channel.Ohmic.Conductance
 

P

parameter - Variable in class neuroml.bio.InitialMembPotential
 
parameter - Variable in class neuroml.bio.IonProperties
 
parameter - Variable in class neuroml.bio.Mechanism
 
parameter - Variable in class neuroml.bio.SpecAxialResistance
 
parameter - Variable in class neuroml.bio.SpecCapacitance
 
Parameter - Class in neuroml.channel
Generic parameter used in rate equations
Parameter() - Constructor for class neuroml.channel.Parameter
 
parameter - Variable in class neuroml.channel.RateConstantEqn
 
parameterisedHh - Variable in class neuroml.channel.RateConstantEqnChoice
 
paramName - Variable in class neuroml.bio.InhomogeneousValue
 
parent - Variable in class neuroml.morph.Cable
 
parent - Variable in class neuroml.morph.Path
 
parent - Variable in class neuroml.morph.Segment
 
parent - Variable in class neuroml.morph.Spine
 
path - Variable in class neuroml.morph.Feature
 
Path - Class in neuroml.morph
Possibly branching histological structures.
Path() - Constructor for class neuroml.morph.Path
 
perCellConnection - Variable in class neuroml.network.ConnectivityPattern
 
PerCellConnection - Class in neuroml.network
Connection built iteratively from each pre (or post) cell based on a number of parameters
PerCellConnection() - Constructor for class neuroml.network.PerCellConnection
 
Person - Class in neuroml.meta
A generic reference to a person, for authorship, etc
Person() - Constructor for class neuroml.meta.Person
 
Point - Class in neuroml.meta
A 3D point with optional diameter.
Point() - Constructor for class neuroml.meta.Point
 
point - Variable in class neuroml.meta.Points
 
Points - Class in neuroml.meta
A collection of points.
Points() - Constructor for class neuroml.meta.Points
 
Polygon - Class in neuroml.meta
A closed structure represented by a list of points where the first point connects with the last point.
Polygon() - Constructor for class neuroml.meta.Polygon
 
polygon - Variable in class neuroml.meta.Polyhedron.Polygons
 
polygon - Variable in class neuroml.morph.Cell.CellBody
 
polygon - Variable in class neuroml.morph.Feature
 
polygons - Variable in class neuroml.meta.Polyhedron
 
Polyhedron - Class in neuroml.meta
A 3d surface to represent the cell body or histological structure.
Polyhedron() - Constructor for class neuroml.meta.Polyhedron
 
polyhedron - Variable in class neuroml.morph.Cell.CellBody
 
polyhedron - Variable in class neuroml.morph.Feature
 
Polyhedron.Polygons - Class in neuroml.meta
Java class for anonymous complex type.
Polyhedron.Polygons() - Constructor for class neuroml.meta.Polyhedron.Polygons
 
poolVolumeInfo - Variable in class neuroml.channel.DecayingPoolModel
 
PoolVolumeInfo - Class in neuroml.channel
Information on the volume of the ion pool
PoolVolumeInfo() - Constructor for class neuroml.channel.PoolVolumeInfo
 
popLocation - Variable in class neuroml.network.Population
 
Population - Class in neuroml.network
Description of ...
Population() - Constructor for class neuroml.network.Population
 
population - Variable in class neuroml.network.Populations
 
PopulationLocation - Class in neuroml.network
Description of the 3D positioning of cells in the population, in place of giving explicit locations for each cell
PopulationLocation() - Constructor for class neuroml.network.PopulationLocation
 
populations - Variable in class neuroml.network.NetworkML
 
Populations - Class in neuroml.network
The list of cell populations
Populations() - Constructor for class neuroml.network.Populations
 
populations - Variable in class neuroml.NeuroMLLevel3
 
populationSize - Variable in class neuroml.network.RandomArrangement
 
postDelay - Variable in class neuroml.network.SynapseInternalProperties
 
potentialSynapticLocation - Variable in class neuroml.Level3Biophysics
 
PotentialSynapticLocation - Class in neuroml.network
Subset of sections on cell where synaptic connection of a particular type is allowed
PotentialSynapticLocation() - Constructor for class neuroml.network.PotentialSynapticLocation
 
PotentialSynapticLocation.AllowedGroups - Class in neuroml.network
 
PotentialSynapticLocation.AllowedGroups(String) - Constructor for class neuroml.network.PotentialSynapticLocation.AllowedGroups
 
power - Variable in class neuroml.channel.Gate
 
preDelay - Variable in class neuroml.network.SynapseInternalProperties
 
probability - Variable in class neuroml.network.ConnectivityPattern.FixedProbability
 
Projection - Class in neuroml.network
Description of how one cell population makes synaptic connections with another
Projection() - Constructor for class neuroml.network.Projection
 
projection - Variable in class neuroml.network.Projections
 
projections - Variable in class neuroml.network.NetworkML
 
Projections - Class in neuroml.network
The list of projections from one cell population to another
Projections() - Constructor for class neuroml.network.Projections
 
projections - Variable in class neuroml.NeuroMLLevel3
 
propDelay - Variable in class neuroml.network.SynapseInternalProperties
 
properties - Variable in class neuroml.channel.ChannelML
 
properties - Variable in class neuroml.channel.ChannelType
 
properties - Variable in class neuroml.channel.DoubleExponentialSynapse
 
properties - Variable in class neuroml.channel.Ion
 
properties - Variable in class neuroml.channel.IonConcentration
 
properties - Variable in class neuroml.channel.Parameter
 
properties - Variable in class neuroml.channel.SynapseType
 
properties - Variable in class neuroml.meta.GroupDetail
 
Properties - Class in neuroml.meta
A collection of Properties
Properties() - Constructor for class neuroml.meta.Properties
 
properties - Variable in class neuroml.morph.Cable
 
properties - Variable in class neuroml.morph.Cell.Cables
 
properties - Variable in class neuroml.morph.Cell.CellBody
 
properties - Variable in class neuroml.morph.Cell
 
properties - Variable in class neuroml.morph.Cell.Segments
 
properties - Variable in class neuroml.morph.Cell.Spines
 
properties - Variable in class neuroml.morph.Feature
 
properties - Variable in class neuroml.morph.Morphology.Features
 
properties - Variable in class neuroml.morph.Morphology
 
properties - Variable in class neuroml.morph.Segment
 
properties - Variable in class neuroml.network.CellInstance
 
properties - Variable in class neuroml.network.Connections
 
properties - Variable in class neuroml.network.GridArrangement
 
properties - Variable in class neuroml.network.Instances
 
properties - Variable in class neuroml.network.NetworkML
 
properties - Variable in class neuroml.network.Population
 
properties - Variable in class neuroml.network.PopulationLocation
 
properties - Variable in class neuroml.network.Populations
 
properties - Variable in class neuroml.network.Projection
 
properties - Variable in class neuroml.network.Projections
 
properties - Variable in class neuroml.network.RandomArrangement
 
properties - Variable in class neuroml.network.SynapseProperties
 
properties - Variable in class neuroml.NeuroMLLevel3
 
property - Variable in class neuroml.meta.Properties
 
Property - Class in neuroml.meta
A Tag/Value/Type tuple.
Property() - Constructor for class neuroml.meta.Property
 
property - Variable in class neuroml.meta.PropertyDetail
 
PropertyDetail - Class in neuroml.meta
Metadata for each Property.
PropertyDetail() - Constructor for class neuroml.meta.PropertyDetail
 
propertyDetail - Variable in class neuroml.morph.Morphology.PropertyDetails
 
propertyDetails - Variable in class neuroml.morph.Morphology
 
proximal - Variable in class neuroml.morph.InhomogeneousParam
 
proximal - Variable in class neuroml.morph.Segment
 
proximal - Variable in class neuroml.morph.Spine
 
publication - Variable in class neuroml.channel.ChannelType
 
publication - Variable in class neuroml.channel.IonConcentration
 
publication - Variable in class neuroml.channel.SynapseType
 
Publication - Class in neuroml.meta
A reference to a publication Note: This element will most likely change when a new set of schema files is adopted for adding references, authors, citations, etc.
Publication() - Constructor for class neuroml.meta.Publication
 
publication - Variable in class neuroml.morph.Cell
 
publication - Variable in class neuroml.NeuroMLLevel3
 
pubmedRef - Variable in class neuroml.meta.Publication
 

Q

q10Factor - Variable in class neuroml.channel.RateAdjustments.Q10Settings
 
q10Settings - Variable in class neuroml.channel.RateAdjustments
 

R

randomArrangement - Variable in class neuroml.network.PopulationLocation
 
RandomArrangement - Class in neuroml.network
A random arrangement of cells in a 3D location.
RandomArrangement() - Constructor for class neuroml.network.RandomArrangement
 
rateAdjustments - Variable in class neuroml.channel.Ohmic.Conductance
 
RateAdjustments - Class in neuroml.channel
Adjustments necessary to all the rate equations, e.g temperature dependencies, voltage offsets introduced when moving between species, etc.
RateAdjustments() - Constructor for class neuroml.channel.RateAdjustments
 
RateAdjustments.Offset - Class in neuroml.channel
Java class for anonymous complex type.
RateAdjustments.Offset() - Constructor for class neuroml.channel.RateAdjustments.Offset
 
RateAdjustments.Q10Settings - Class in neuroml.channel
Java class for anonymous complex type.
RateAdjustments.Q10Settings() - Constructor for class neuroml.channel.RateAdjustments.Q10Settings
 
RateConstantEqn - Class in neuroml.channel
Definition of a rate constant equation.
RateConstantEqn() - Constructor for class neuroml.channel.RateConstantEqn
 
RateConstantEqnChoice - Class in neuroml.channel
Choice of the various rate constant expressions allowed
RateConstantEqnChoice() - Constructor for class neuroml.channel.RateConstantEqnChoice
 
RateConstVoltConcDep - Class in neuroml.channel
Rate constant expressions allowed for voltage and conc dependent channels.
RateConstVoltConcDep() - Constructor for class neuroml.channel.RateConstVoltConcDep
 
readNeuroML(String) - Method in class neuroml.util.NeuroMLConverter
 
RectangularBox - Class in neuroml.meta
A Rectangular Box for locating cells in 3D.
RectangularBox() - Constructor for class neuroml.meta.RectangularBox
 
RectangularBox.Size - Class in neuroml.meta
Java class for anonymous complex type.
RectangularBox.Size() - Constructor for class neuroml.meta.RectangularBox.Size
 
rectangularLocation - Variable in class neuroml.network.GridArrangement
 
rectangularLocation - Variable in class neuroml.network.RandomArrangement
 
reference - Variable in class neuroml.network.PopulationLocation
 
restingConc - Variable in class neuroml.channel.DecayingPoolModel
 
reversalPotential - Variable in class neuroml.channel.DoubleExponentialSynapse
 
riseTime - Variable in class neuroml.channel.DoubleExponentialSynapse
 
role - Variable in class neuroml.channel.Ion
 

S

segment - Variable in class neuroml.morph.Cell.Segments
 
Segment - Class in neuroml.morph
Defines the smallest unit within a possibly branching structure, such as a dendrite or axon.
Segment() - Constructor for class neuroml.morph.Segment
 
segmentId - Variable in class neuroml.network.SynapticLocation
 
segments - Variable in class neuroml.morph.Cell
 
setAllToAll(ConnectivityPattern.AllToAll) - Method in class neuroml.network.ConnectivityPattern
Sets the value of the allToAll property.
setAlpha(RateConstVoltConcDep) - Method in class neuroml.channel.VoltageConcGate
Sets the value of the alpha property.
setAlpha(RateConstantEqnChoice) - Method in class neuroml.channel.VoltageGate
Sets the value of the alpha property.
setAnnotation(Annotation) - Method in class neuroml.channel.ChannelML
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.channel.ChannelType
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.channel.DoubleExponentialSynapse
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.channel.Ion
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.channel.IonConcentration
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.channel.Parameter
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.channel.SynapseType
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.morph.Cable
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.morph.Cell.Cables
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.morph.Cell.CellBody
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.morph.Cell.Segments
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.morph.Cell
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.morph.Cell.Spines
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.morph.Feature
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.morph.Morphology.Features
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.morph.Morphology
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.network.CellInstance
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.network.Connections
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.network.GridArrangement
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.network.Instances
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.network.NetworkML
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.network.Population
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.network.PopulationLocation
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.network.Populations
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.network.Projection
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.network.Projections
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.network.RandomArrangement
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.network.SynapseProperties
Sets the value of the annotation property.
setAnnotation(Annotation) - Method in class neuroml.NeuroMLLevel3
Sets the value of the annotation property.
setAuthorList(Authors) - Method in class neuroml.channel.ChannelType
Sets the value of the authorList property.
setAuthorList(Authors) - Method in class neuroml.channel.IonConcentration
Sets the value of the authorList property.
setAuthorList(Authors) - Method in class neuroml.channel.SynapseType
Sets the value of the authorList property.
setAuthorList(Authors) - Method in class neuroml.morph.Cell
Sets the value of the authorList property.
setAuthorList(Authors) - Method in class neuroml.NeuroMLLevel3
Sets the value of the authorList property.
setBeta(RateConstVoltConcDep) - Method in class neuroml.channel.VoltageConcGate
Sets the value of the beta property.
setBeta(RateConstantEqnChoice) - Method in class neuroml.channel.VoltageGate
Sets the value of the beta property.
setBiophysics(Level3Biophysics) - Method in class neuroml.Level3Cell
Sets the value of the biophysics property.
setBlock(Block) - Method in class neuroml.channel.BlockingSynapse
Sets the value of the block property.
setBlockingSyn(BlockingSynapse) - Method in class neuroml.channel.SynapseType
Sets the value of the blockingSyn property.
setCable(BigInteger) - Method in class neuroml.morph.Segment
Sets the value of the cable property.
setCables(Cell.Cables) - Method in class neuroml.morph.Cell
Sets the value of the cables property.
setCellBody(Cell.CellBody) - Method in class neuroml.morph.Cell
Sets the value of the cellBody property.
setCellId(BigInteger) - Method in class neuroml.network.SynapticLocation
Sets the value of the cellId property.
setCells(Cells) - Method in class neuroml.morph.Morphology
Sets the value of the cells property.
setCells(NeuroMLLevel3.Cells) - Method in class neuroml.NeuroMLLevel3
Sets the value of the cells property.
setCellType(String) - Method in class neuroml.network.Population
Sets the value of the cellType property.
setCenter(Point) - Method in class neuroml.meta.Sphere
Sets the value of the center property.
setChannels(ChannelML) - Method in class neuroml.NeuroMLLevel3
Sets the value of the channels property.
setCharge(BigInteger) - Method in class neuroml.channel.Ion
Sets the value of the charge property.
setComment(String) - Method in class neuroml.channel.ImplementationPrefs
Sets the value of the comment property.
setConc(double) - Method in class neuroml.channel.Block
Sets the value of the conc property.
setConcDependence(ConcDependence) - Method in class neuroml.channel.VoltageConcGate
Sets the value of the concDependence property.
setConductance(Ohmic.Conductance) - Method in class neuroml.channel.Ohmic
Sets the value of the conductance property.
setConnections(Connections) - Method in class neuroml.network.Projection
Sets the value of the connections property.
setConnectivityPattern(ConnectivityPattern) - Method in class neuroml.network.Projection
Sets the value of the connectivityPattern property.
setCorner(Point) - Method in class neuroml.meta.RectangularBox
Sets the value of the corner property.
setCurrentVoltageRelation(CurrentVoltageRelation) - Method in class neuroml.channel.ChannelType
Sets the value of the currentVoltageRelation property.
setDecayConstant(double) - Method in class neuroml.channel.DecayingPoolModel
Sets the value of the decayConstant property.
setDecayingPoolModel(DecayingPoolModel) - Method in class neuroml.channel.IonConcentration
Sets the value of the decayingPoolModel property.
setDecayTime(double) - Method in class neuroml.channel.DoubleExponentialSynapse
Sets the value of the decayTime property.
setDefaultErev(Double) - Method in class neuroml.channel.Ion
Sets the value of the defaultErev property.
setDefaultGmax(Double) - Method in class neuroml.channel.Ohmic.Conductance
Sets the value of the defaultGmax property.
setDefaultValues(SynapseInternalProperties) - Method in class neuroml.network.SynapseProperties
Sets the value of the defaultValues property.
setDensity(YesNo) - Method in class neuroml.channel.ChannelType
Sets the value of the density property.
setDensity(YesNo) - Method in class neuroml.channel.SynapseType
Sets the value of the density property.
setDepth(Double) - Method in class neuroml.meta.RectangularBox.Size
Sets the value of the depth property.
setDescription(String) - Method in class neuroml.meta.GroupDetail
Sets the value of the description property.
setDescription(String) - Method in class neuroml.meta.PropertyDetail
Sets the value of the description property.
setDiameter(Double) - Method in class neuroml.meta.Point
Sets the value of the diameter property.
setDirection(String) - Method in class neuroml.network.PerCellConnection
Sets the value of the direction property.
setDistal(InhomogeneousParam.Distal) - Method in class neuroml.morph.InhomogeneousParam
Sets the value of the distal property.
setDistal(Point) - Method in class neuroml.morph.Segment
Sets the value of the distal property.
setDistal(Point) - Method in class neuroml.morph.Spine
Sets the value of the distal property.
setDoubExpSyn(DoubleExponentialSynapse) - Method in class neuroml.channel.SynapseType
Sets the value of the doubExpSyn property.
setEmail(String) - Method in class neuroml.meta.Person
Sets the value of the email property.
setEta(double) - Method in class neuroml.channel.Block
Sets the value of the eta property.
setExperimentalTemp(Double) - Method in class neuroml.channel.RateAdjustments.Q10Settings
Sets the value of the experimentalTemp property.
setExpr(String) - Method in class neuroml.channel.GenericEquation
Sets the value of the expr property.
setExpr(String) - Method in class neuroml.channel.RateConstantEqn
Sets the value of the expr property.
setFeatures(Morphology.Features) - Method in class neuroml.morph.Morphology
Sets the value of the features property.
setFixedProbability(ConnectivityPattern.FixedProbability) - Method in class neuroml.network.ConnectivityPattern
Sets the value of the fixedProbability property.
setFractAlongParent(Double) - Method in class neuroml.morph.Cable
Sets the value of the fractAlongParent property.
setFraction(Double) - Method in class neuroml.channel.Gate.State
Sets the value of the fraction property.
setFractionAlong(Double) - Method in class neuroml.network.SynapticLocation
Sets the value of the fractionAlong property.
setFreePoints(FreePoints) - Method in class neuroml.morph.Cell
Sets the value of the freePoints property.
setFullTitle(String) - Method in class neuroml.meta.Publication
Sets the value of the fullTitle property.
setGamma(double) - Method in class neuroml.channel.Block
Sets the value of the gamma property.
setGenericEquationHh(GenericEquation) - Method in class neuroml.channel.RateConstantEqnChoice
Sets the value of the genericEquationHh property.
setGenericEquationHh(GenericEquation) - Method in class neuroml.channel.RateConstVoltConcDep
Sets the value of the genericEquationHh property.
setGridArrangement(GridArrangement) - Method in class neuroml.network.PopulationLocation
Sets the value of the gridArrangement property.
setGroup(String) - Method in class neuroml.meta.GroupDetail
Sets the value of the group property.
setGroupDetails(Morphology.GroupDetails) - Method in class neuroml.morph.Morphology
Sets the value of the groupDetails property.
setHeight(Double) - Method in class neuroml.meta.RectangularBox.Size
Sets the value of the height property.
setId(BigInteger) - Method in class neuroml.morph.Cable
Sets the value of the id property.
setId(BigInteger) - Method in class neuroml.morph.CableGroup.Cable
Sets the value of the id property.
setId(BigInteger) - Method in class neuroml.morph.Path
Sets the value of the id property.
setId(BigInteger) - Method in class neuroml.morph.Segment
Sets the value of the id property.
setId(BigInteger) - Method in class neuroml.network.CellInstance
Sets the value of the id property.
setId(BigInteger) - Method in class neuroml.network.Connection
Sets the value of the id property.
setImplPrefs(ImplementationPrefs) - Method in class neuroml.channel.ChannelType
Sets the value of the implPrefs property.
setInf(RateConstVoltConcDep) - Method in class neuroml.channel.VoltageConcGate
Sets the value of the inf property.
setInf(RateConstantEqnChoice) - Method in class neuroml.channel.VoltageGate
Sets the value of the inf property.
setInitialMembPotential(InitialMembPotential) - Method in class neuroml.bio.Biophysics
Sets the value of the initialMembPotential property.
setInstances(Instances) - Method in class neuroml.network.Population
Sets the value of the instances property.
setInstitution(String) - Method in class neuroml.meta.Person
Sets the value of the institution property.
setInternalDelay(Double) - Method in class neuroml.network.SynapseInternalProperties
Sets the value of the internalDelay property.
setIon(String) - Method in class neuroml.channel.ConcDependence
Sets the value of the ion property.
setIon(String) - Method in class neuroml.channel.Ohmic
Sets the value of the ion property.
setIonProperties(IonProperties) - Method in class neuroml.bio.Biophysics
Sets the value of the ionProperties property.
setIonSpecies(String) - Method in class neuroml.channel.IonConcentration
Sets the value of the ionSpecies property.
setLength(Double) - Method in class neuroml.morph.Spine
Sets the value of the length property.
setLengthUnits(LengthUnits) - Method in class neuroml.morph.Morphology
Sets the value of the lengthUnits property.
setLengthUnits(LengthUnits) - Method in class neuroml.network.NetworkML
Sets the value of the lengthUnits property.
setLengthUnits(LengthUnits) - Method in class neuroml.NeuroMLLevel3
Sets the value of the lengthUnits property.
setLocation(Point) - Method in class neuroml.network.CellInstance
Sets the value of the location property.
setMaxConc(double) - Method in class neuroml.channel.ConcDependence
Sets the value of the maxConc property.
setMaxConductance(double) - Method in class neuroml.channel.DoubleExponentialSynapse
Sets the value of the maxConductance property.
setMaxPerTarget(Double) - Method in class neuroml.network.PerCellConnection
Sets the value of the maxPerTarget property.
setMaxV(Double) - Method in class neuroml.channel.ImplementationPrefs.TableSettings
Sets the value of the maxV property.
setMetric(String) - Method in class neuroml.morph.InhomogeneousParam
Sets the value of the metric property.
setMinConc(double) - Method in class neuroml.channel.ConcDependence
Sets the value of the minConc property.
setMinV(Double) - Method in class neuroml.channel.ImplementationPrefs.TableSettings
Sets the value of the minV property.
setModelName(String) - Method in class neuroml.meta.NeuronDBReference
Sets the value of the modelName property.
setName(String) - Method in class neuroml.bio.IonProperties
Sets the value of the name property.
setName(String) - Method in class neuroml.bio.Mechanism
Sets the value of the name property.
setName(String) - Method in class neuroml.bio.NamedParameter
Sets the value of the name property.
setName(String) - Method in class neuroml.bio.VariableNamedParameter
Sets the value of the name property.
setName(String) - Method in class neuroml.bio.VariableParameter
Sets the value of the name property.
setName(String) - Method in class neuroml.channel.ChannelType
Sets the value of the name property.
setName(String) - Method in class neuroml.channel.ConcDependence
Sets the value of the name property.
setName(String) - Method in class neuroml.channel.CurrentVoltageRelation
Sets the value of the name property.
setName(String) - Method in class neuroml.channel.Gate.State
Sets the value of the name property.
setName(String) - Method in class neuroml.channel.Ion
Sets the value of the name property.
setName(String) - Method in class neuroml.channel.IonConcentration
Sets the value of the name property.
setName(String) - Method in class neuroml.channel.KSState
Sets the value of the name property.
setName(String) - Method in class neuroml.channel.Parameter
Sets the value of the name property.
setName(String) - Method in class neuroml.channel.SynapseType
Sets the value of the name property.
setName(String) - Method in class neuroml.meta.Person
Sets the value of the name property.
setName(String) - Method in class neuroml.meta.Points
Sets the value of the name property.
setName(String) - Method in class neuroml.meta.RectangularBox
Sets the value of the name property.
setName(String) - Method in class neuroml.meta.Sphere
Sets the value of the name property.
setName(String) - Method in class neuroml.morph.Cable
Sets the value of the name property.
setName(String) - Method in class neuroml.morph.CableGroup
Sets the value of the name property.
setName(String) - Method in class neuroml.morph.Cell.Segments
Sets the value of the name property.
setName(String) - Method in class neuroml.morph.Cell
Sets the value of the name property.
setName(String) - Method in class neuroml.morph.Feature
Sets the value of the name property.
setName(String) - Method in class neuroml.morph.InhomogeneousParam
Sets the value of the name property.
setName(String) - Method in class neuroml.morph.Morphology
Sets the value of the name property.
setName(String) - Method in class neuroml.morph.Segment
Sets the value of the name property.
setName(String) - Method in class neuroml.network.NetworkML
Sets the value of the name property.
setName(String) - Method in class neuroml.network.Population
Sets the value of the name property.
setName(String) - Method in class neuroml.network.Projection
Sets the value of the name property.
setName(String) - Method in class neuroml.NeuroMLLevel3
Sets the value of the name property.
setNeuronDBref(NeuronDBReference) - Method in class neuroml.channel.ChannelType
Sets the value of the neuronDBref property.
setNeuronDBref(NeuronDBReference) - Method in class neuroml.channel.IonConcentration
Sets the value of the neuronDBref property.
setNeuronDBref(NeuronDBReference) - Method in class neuroml.channel.SynapseType
Sets the value of the neuronDBref property.
setNeuronDBref(NeuronDBReference) - Method in class neuroml.morph.Cell
Sets the value of the neuronDBref property.
setNeuronDBref(NeuronDBReference) - Method in class neuroml.NeuroMLLevel3
Sets the value of the neuronDBref property.
setNonSpecific(String) - Method in class neuroml.channel.Ohmic
Sets the value of the nonSpecific property.
setNormalizationEnd(Double) - Method in class neuroml.morph.InhomogeneousParam.Distal
Sets the value of the normalizationEnd property.
setNotes(String) - Method in class neuroml.channel.ChannelML
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.channel.ChannelType
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.channel.DoubleExponentialSynapse
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.channel.Ion
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.channel.IonConcentration
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.channel.Parameter
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.channel.SynapseType
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.morph.Cable
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.morph.Cell.Cables
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.morph.Cell.CellBody
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.morph.Cell.Segments
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.morph.Cell
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.morph.Cell.Spines
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.morph.Feature
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.morph.Morphology.Features
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.morph.Morphology
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.network.CellInstance
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.network.Connections
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.network.GridArrangement
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.network.Instances
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.network.NetworkML
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.network.Population
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.network.PopulationLocation
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.network.Populations
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.network.Projection
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.network.Projections
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.network.RandomArrangement
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.network.SynapseProperties
Sets the value of the notes property.
setNotes(String) - Method in class neuroml.NeuroMLLevel3
Sets the value of the notes property.
setNumPerSource(Double) - Method in class neuroml.network.PerCellConnection
Sets the value of the numPerSource property.
setOffset(RateAdjustments.Offset) - Method in class neuroml.channel.RateAdjustments
Sets the value of the offset property.
setOhmic(Ohmic) - Method in class neuroml.channel.CurrentVoltageRelation
Sets the value of the ohmic property.
setParameterisedHh(AkdEquation) - Method in class neuroml.channel.RateConstantEqnChoice
Sets the value of the parameterisedHh property.
setParamName(String) - Method in class neuroml.bio.InhomogeneousValue
Sets the value of the paramName property.
setParent(BigInteger) - Method in class neuroml.morph.Cable
Sets the value of the parent property.
setParent(BigInteger) - Method in class neuroml.morph.Path
Sets the value of the parent property.
setParent(BigInteger) - Method in class neuroml.morph.Segment
Sets the value of the parent property.
setParent(BigInteger) - Method in class neuroml.morph.Spine
Sets the value of the parent property.
setPerCellConnection(PerCellConnection) - Method in class neuroml.network.ConnectivityPattern
Sets the value of the perCellConnection property.
setPolygon(Polygon) - Method in class neuroml.morph.Cell.CellBody
Sets the value of the polygon property.
setPolygons(Polyhedron.Polygons) - Method in class neuroml.meta.Polyhedron
Sets the value of the polygons property.
setPolyhedron(Polyhedron) - Method in class neuroml.morph.Cell.CellBody
Sets the value of the polyhedron property.
setPoolVolumeInfo(PoolVolumeInfo) - Method in class neuroml.channel.DecayingPoolModel
Sets the value of the poolVolumeInfo property.
setPopLocation(PopulationLocation) - Method in class neuroml.network.Population
Sets the value of the popLocation property.
setPopulations(Populations) - Method in class neuroml.network.NetworkML
Sets the value of the populations property.
setPopulations(Populations) - Method in class neuroml.NeuroMLLevel3
Sets the value of the populations property.
setPopulationSize(BigInteger) - Method in class neuroml.network.RandomArrangement
Sets the value of the populationSize property.
setPostDelay(Double) - Method in class neuroml.network.SynapseInternalProperties
Sets the value of the postDelay property.
setPower(BigInteger) - Method in class neuroml.channel.Gate
Sets the value of the power property.
setPreDelay(Double) - Method in class neuroml.network.SynapseInternalProperties
Sets the value of the preDelay property.
setProbability(Double) - Method in class neuroml.network.ConnectivityPattern.FixedProbability
Sets the value of the probability property.
setProjections(Projections) - Method in class neuroml.network.NetworkML
Sets the value of the projections property.
setProjections(Projections) - Method in class neuroml.NeuroMLLevel3
Sets the value of the projections property.
setPropDelay(Double) - Method in class neuroml.network.SynapseInternalProperties
Sets the value of the propDelay property.
setProperties(Properties) - Method in class neuroml.channel.ChannelML
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.channel.ChannelType
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.channel.DoubleExponentialSynapse
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.channel.Ion
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.channel.IonConcentration
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.channel.Parameter
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.channel.SynapseType
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.morph.Cable
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.morph.Cell.Cables
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.morph.Cell.CellBody
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.morph.Cell.Segments
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.morph.Cell
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.morph.Cell.Spines
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.morph.Feature
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.morph.Morphology.Features
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.morph.Morphology
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.morph.Segment
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.network.CellInstance
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.network.Connections
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.network.GridArrangement
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.network.Instances
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.network.NetworkML
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.network.Population
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.network.PopulationLocation
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.network.Populations
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.network.Projection
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.network.Projections
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.network.RandomArrangement
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.network.SynapseProperties
Sets the value of the properties property.
setProperties(Properties) - Method in class neuroml.NeuroMLLevel3
Sets the value of the properties property.
setProperty(String) - Method in class neuroml.meta.PropertyDetail
Sets the value of the property property.
setPropertyDetails(Morphology.PropertyDetails) - Method in class neuroml.morph.Morphology
Sets the value of the propertyDetails property.
setProximal(InhomogeneousParam.Proximal) - Method in class neuroml.morph.InhomogeneousParam
Sets the value of the proximal property.
setProximal(Point) - Method in class neuroml.morph.Segment
Sets the value of the proximal property.
setProximal(Point) - Method in class neuroml.morph.Spine
Sets the value of the proximal property.
setPubmedRef(String) - Method in class neuroml.meta.Publication
Sets the value of the pubmedRef property.
setQ10Factor(Double) - Method in class neuroml.channel.RateAdjustments.Q10Settings
Sets the value of the q10Factor property.
setQ10Settings(RateAdjustments.Q10Settings) - Method in class neuroml.channel.RateAdjustments
Sets the value of the q10Settings property.
setRandomArrangement(RandomArrangement) - Method in class neuroml.network.PopulationLocation
Sets the value of the randomArrangement property.
setRateAdjustments(RateAdjustments) - Method in class neuroml.channel.Ohmic.Conductance
Sets the value of the rateAdjustments property.
setRectangularLocation(RectangularBox) - Method in class neuroml.network.GridArrangement
Sets the value of the rectangularLocation property.
setRectangularLocation(RectangularBox) - Method in class neuroml.network.RandomArrangement
Sets the value of the rectangularLocation property.
setReference(String) - Method in class neuroml.network.PopulationLocation
Sets the value of the reference property.
setRestingConc(double) - Method in class neuroml.channel.DecayingPoolModel
Sets the value of the restingConc property.
setReversalPotential(double) - Method in class neuroml.channel.DoubleExponentialSynapse
Sets the value of the reversalPotential property.
setRiseTime(double) - Method in class neuroml.channel.DoubleExponentialSynapse
Sets the value of the riseTime property.
setRole(IonRole) - Method in class neuroml.channel.Ion
Sets the value of the role property.
setSegmentId(BigInteger) - Method in class neuroml.network.SynapticLocation
Sets the value of the segmentId property.
setShape(SpineShape) - Method in class neuroml.morph.Spine
Sets the value of the shape property.
setShellThickness(double) - Method in class neuroml.channel.PoolVolumeInfo
Sets the value of the shellThickness property.
setSize(RectangularBox.Size) - Method in class neuroml.meta.RectangularBox
Sets the value of the size property.
setSource(String) - Method in class neuroml.network.Projection
Sets the value of the source property.
setSpacing(GridArrangement.Spacing) - Method in class neuroml.network.GridArrangement
Sets the value of the spacing property.
setSpecies(String) - Method in class neuroml.channel.Block
Sets the value of the species property.
setSpecificAxialResistance(SpecAxialResistance) - Method in class neuroml.bio.Biophysics
Sets the value of the specificAxialResistance property.
setSpecificCapacitance(SpecCapacitance) - Method in class neuroml.bio.Biophysics
Sets the value of the specificCapacitance property.
setSphere(Sphere) - Method in class neuroml.morph.Cell.CellBody
Sets the value of the sphere property.
setSphericalLocation(Sphere) - Method in class neuroml.network.RandomArrangement
Sets the value of the sphericalLocation property.
setSpines(Cell.Spines) - Method in class neuroml.morph.Cell
Sets the value of the spines property.
setSrc(String) - Method in class neuroml.channel.Transition
Sets the value of the src property.
setState(String) - Method in class neuroml.channel.HHGate
Sets the value of the state property.
setSynapseType(String) - Method in class neuroml.network.SynapseProperties
Sets the value of the synapseType property.
setTableDivisions(BigInteger) - Method in class neuroml.channel.ImplementationPrefs.TableSettings
Sets the value of the tableDivisions property.
setTableSettings(ImplementationPrefs.TableSettings) - Method in class neuroml.channel.ImplementationPrefs
Sets the value of the tableSettings property.
setTag(String) - Method in class neuroml.meta.Property
Sets the value of the tag property.
setTarget(String) - Method in class neuroml.channel.Transition
Sets the value of the target property.
setTarget(String) - Method in class neuroml.network.Projection
Sets the value of the target property.
setTau(RateConstVoltConcDep) - Method in class neuroml.channel.VoltageConcGate
Sets the value of the tau property.
setTau(RateConstantEqnChoice) - Method in class neuroml.channel.VoltageGate
Sets the value of the tau property.
setThreshold(Double) - Method in class neuroml.network.SynapseInternalProperties
Sets the value of the threshold property.
setTransition(Transition) - Method in class neuroml.channel.HHGate
Sets the value of the transition property.
setTranslationStart(Double) - Method in class neuroml.morph.InhomogeneousParam.Proximal
Sets the value of the translationStart property.
setType(MechanismType) - Method in class neuroml.bio.Mechanism
Sets the value of the type property.
setType(String) - Method in class neuroml.channel.RateConstantEqn
Sets the value of the type property.
setType(Object) - Method in class neuroml.meta.PropertyDetail
Sets the value of the type property.
setUnits(Units) - Method in class neuroml.bio.Biophysics
Sets the value of the units property.
setUnits(Units) - Method in class neuroml.channel.ChannelML
Sets the value of the units property.
setUnits(Units) - Method in class neuroml.network.Projections
Sets the value of the units property.
setUri(String) - Method in class neuroml.meta.NeuronDBReference
Sets the value of the uri property.
setValue(String) - Method in class neuroml.bio.InhomogeneousValue
Sets the value of the value property.
setValue(double) - Method in class neuroml.bio.NamedParameter
Sets the value of the value property.
setValue(double) - Method in class neuroml.bio.UnnamedParameter
Sets the value of the value property.
setValue(double) - Method in class neuroml.channel.Parameter
Sets the value of the value property.
setValue(Double) - Method in class neuroml.channel.RateAdjustments.Offset
Sets the value of the value property.
setValue(String) - Method in class neuroml.meta.Property
Sets the value of the value property.
setVariable(String) - Method in class neuroml.morph.InhomogeneousParam
Sets the value of the variable property.
setVariableName(String) - Method in class neuroml.channel.ConcDependence
Sets the value of the variableName property.
setVoltageConcGate(VoltageConcGate) - Method in class neuroml.channel.Transition
Sets the value of the voltageConcGate property.
setVoltageGate(VoltageGate) - Method in class neuroml.channel.Transition
Sets the value of the voltageGate property.
setVolume(Double) - Method in class neuroml.morph.Spine
Sets the value of the volume property.
setVolumeUnits(VolumeUnits) - Method in class neuroml.morph.Morphology
Sets the value of the volumeUnits property.
setVolumeUnits(VolumeUnits) - Method in class neuroml.network.NetworkML
Sets the value of the volumeUnits property.
setVolumeUnits(VolumeUnits) - Method in class neuroml.NeuroMLLevel3
Sets the value of the volumeUnits property.
setWeight(Double) - Method in class neuroml.network.SynapseInternalProperties
Sets the value of the weight property.
setWidth(Double) - Method in class neuroml.meta.RectangularBox.Size
Sets the value of the width property.
setX(double) - Method in class neuroml.meta.Point
Sets the value of the x property.
setX(Double) - Method in class neuroml.network.GridArrangement.Spacing
Sets the value of the x property.
setY(double) - Method in class neuroml.meta.Point
Sets the value of the y property.
setY(Double) - Method in class neuroml.network.GridArrangement.Spacing
Sets the value of the y property.
setZ(double) - Method in class neuroml.meta.Point
Sets the value of the z property.
setZ(Double) - Method in class neuroml.network.GridArrangement.Spacing
Sets the value of the z property.
shape - Variable in class neuroml.morph.Spine
 
shellThickness - Variable in class neuroml.channel.PoolVolumeInfo
 
size - Variable in class neuroml.meta.RectangularBox
 
source - Variable in class neuroml.network.Projection
 
spacing - Variable in class neuroml.network.GridArrangement
 
SpecAxialResistance - Class in neuroml.bio
Specific axial resistance of a group of sections
SpecAxialResistance() - Constructor for class neuroml.bio.SpecAxialResistance
 
SpecCapacitance - Class in neuroml.bio
Capacitance per unit area of a group of sections
SpecCapacitance() - Constructor for class neuroml.bio.SpecCapacitance
 
species - Variable in class neuroml.channel.Block
 
specificAxialResistance - Variable in class neuroml.bio.Biophysics
 
specificCapacitance - Variable in class neuroml.bio.Biophysics
 
Sphere - Class in neuroml.meta
A spherical structure such as a cell body or cell.
Sphere() - Constructor for class neuroml.meta.Sphere
 
sphere - Variable in class neuroml.morph.Cell.CellBody
 
sphere - Variable in class neuroml.morph.Feature
 
sphericalLocation - Variable in class neuroml.network.RandomArrangement
 
spine - Variable in class neuroml.morph.Cell.Spines
 
Spine - Class in neuroml.morph
A spine with location, shape, and direction.
Spine() - Constructor for class neuroml.morph.Spine
 
spines - Variable in class neuroml.morph.Cell
 
SpineShape - Enum in neuroml.morph
Java class for SpineShape.
src - Variable in class neuroml.channel.Transition
 
state - Variable in class neuroml.channel.Gate
 
state - Variable in class neuroml.channel.HHGate
 
state - Variable in class neuroml.channel.KSGate
 
SynapseDirection - Enum in neuroml.network
Java class for SynapseDirection.
SynapseInternalProperties - Class in neuroml.network
Variables specifying a single synapse or default vlaues for a set of connections
SynapseInternalProperties() - Constructor for class neuroml.network.SynapseInternalProperties
 
SynapseProperties - Class in neuroml.network
Information on the synapse which is used in a connection
SynapseProperties() - Constructor for class neuroml.network.SynapseProperties
 
synapseProps - Variable in class neuroml.network.Projection
 
synapseType - Variable in class neuroml.channel.ChannelML
 
SynapseType - Class in neuroml.channel
Definition of a synaptic process
SynapseType() - Constructor for class neuroml.channel.SynapseType
 
synapseType - Variable in class neuroml.network.SynapseProperties
 
SynapticLocation - Class in neuroml.network
Java class for SynapticLocation complex type.
SynapticLocation() - Constructor for class neuroml.network.SynapticLocation
 

T

tableDivisions - Variable in class neuroml.channel.ImplementationPrefs.TableSettings
 
tableSettings - Variable in class neuroml.channel.ImplementationPrefs
 
tag - Variable in class neuroml.meta.Property
 
target - Variable in class neuroml.channel.Transition
 
target - Variable in class neuroml.network.Projection
 
tau - Variable in class neuroml.channel.VoltageConcGate
 
tau - Variable in class neuroml.channel.VoltageGate
 
threshold - Variable in class neuroml.network.SynapseInternalProperties
 
transition - Variable in class neuroml.channel.HHGate
 
transition - Variable in class neuroml.channel.KSGate
 
Transition - Class in neuroml.channel
What causes the gate to open and close.
Transition() - Constructor for class neuroml.channel.Transition
 
translationStart - Variable in class neuroml.morph.InhomogeneousParam.Proximal
 
type - Variable in class neuroml.bio.Mechanism
 
type - Variable in class neuroml.channel.RateConstantEqn
 
type - Variable in class neuroml.meta.PropertyDetail
 

U

units - Variable in class neuroml.bio.Biophysics
 
Units - Enum in neuroml.bio
Java class for Units.
units - Variable in class neuroml.channel.ChannelML
 
Units - Enum in neuroml.channel
Java class for Units.
units - Variable in class neuroml.network.Projections
 
unmarshaller - Variable in class neuroml.util.NeuroMLConverter
 
UnnamedParameter - Class in neuroml.bio
Definition of a value for a quantity and the associated groups of cables which have this value.
UnnamedParameter() - Constructor for class neuroml.bio.UnnamedParameter
 
uri - Variable in class neuroml.meta.NeuronDBReference
 

V

value - Variable in class neuroml.bio.InhomogeneousValue
 
value() - Method in enum neuroml.bio.MechanismType
 
value - Variable in class neuroml.bio.NamedParameter
 
value() - Method in enum neuroml.bio.Units
 
value - Variable in class neuroml.bio.UnnamedParameter
 
value() - Method in enum neuroml.channel.CoreEquationType
 
value() - Method in enum neuroml.channel.IonRole
 
value - Variable in class neuroml.channel.Parameter
 
value - Variable in class neuroml.channel.RateAdjustments.Offset
 
value() - Method in enum neuroml.channel.Units
 
value() - Method in enum neuroml.meta.LengthUnits
 
value - Variable in class neuroml.meta.Property
 
value() - Method in enum neuroml.meta.VolumeUnits
 
value() - Method in enum neuroml.meta.YesNo
 
value() - Method in enum neuroml.morph.SpineShape
 
value() - Method in enum neuroml.network.SynapseDirection
 
valueOf(String) - Static method in enum neuroml.bio.MechanismType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum neuroml.bio.Units
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum neuroml.channel.CoreEquationType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum neuroml.channel.IonRole
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum neuroml.channel.Units
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum neuroml.meta.LengthUnits
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum neuroml.meta.VolumeUnits
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum neuroml.meta.YesNo
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum neuroml.morph.SpineShape
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum neuroml.network.SynapseDirection
Returns the enum constant of this type with the specified name.
values() - Static method in enum neuroml.bio.MechanismType
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum neuroml.bio.Units
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum neuroml.channel.CoreEquationType
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum neuroml.channel.IonRole
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum neuroml.channel.Units
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum neuroml.meta.LengthUnits
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum neuroml.meta.VolumeUnits
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum neuroml.meta.YesNo
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum neuroml.morph.SpineShape
Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum neuroml.network.SynapseDirection
Returns an array containing the constants of this enum type, in the order they're declared.
variable - Variable in class neuroml.morph.InhomogeneousParam
 
variableName - Variable in class neuroml.channel.ConcDependence
 
VariableNamedParameter - Class in neuroml.bio
Definition of a value for a quantity which varies over a given group of cables
VariableNamedParameter() - Constructor for class neuroml.bio.VariableNamedParameter
 
variableParameter - Variable in class neuroml.bio.InitialMembPotential
 
variableParameter - Variable in class neuroml.bio.Mechanism
 
variableParameter - Variable in class neuroml.bio.SpecAxialResistance
 
variableParameter - Variable in class neuroml.bio.SpecCapacitance
 
VariableParameter - Class in neuroml.bio
Definition of a value for a quantity which varies over a given group of cables
VariableParameter() - Constructor for class neuroml.bio.VariableParameter
 
voltageConcGate - Variable in class neuroml.channel.Transition
 
VoltageConcGate - Class in neuroml.channel
Definition of a mechanics of a gate which depends on voltage and concentration (e.g.
VoltageConcGate() - Constructor for class neuroml.channel.VoltageConcGate
 
voltageGate - Variable in class neuroml.channel.Transition
 
VoltageGate - Class in neuroml.channel
Definition of a voltage gate.
VoltageGate() - Constructor for class neuroml.channel.VoltageGate
 
volume - Variable in class neuroml.morph.Spine
 
VolumeUnits - Enum in neuroml.meta
Java class for VolumeUnits.
volumeUnits - Variable in class neuroml.morph.Morphology
 
volumeUnits - Variable in class neuroml.network.NetworkML
 
volumeUnits - Variable in class neuroml.NeuroMLLevel3
 

W

weight - Variable in class neuroml.network.SynapseInternalProperties
 
width - Variable in class neuroml.meta.RectangularBox.Size
 

X

x - Variable in class neuroml.meta.Point
 
x - Variable in class neuroml.network.GridArrangement.Spacing
 
xmlToChannel(String) - Method in class neuroml.util.NeuroMLConverter
 
xmlToMorphology(String) - Method in class neuroml.util.NeuroMLConverter
 
xmlToNetwork(String) - Method in class neuroml.util.NeuroMLConverter
 

Y

y - Variable in class neuroml.meta.Point
 
y - Variable in class neuroml.network.GridArrangement.Spacing
 
YesNo - Enum in neuroml.meta
Java class for YesNo.

Z

z - Variable in class neuroml.meta.Point
 
z - Variable in class neuroml.network.GridArrangement.Spacing
 

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NeuroML API (v1.4)