- n - Variable in class neurord.numeric.stochastic.NGoTable
-
- name - Variable in class neurord.model.OutputSpecie
-
- name - Variable in class neurord.model.Reaction
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- name - Variable in class neurord.neuroml.cable
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- name - Variable in class neurord.neuroml.cell
-
- name - Variable in class neurord.neuroml.MetaItem
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- name - Variable in class neurord.neuroml.morphml
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- name - Variable in class neurord.neuroml.MorphMLCableGroup
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- name - Variable in class neurord.neuroml.segment
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- name - Variable in class neurord.numeric.morph.TreePoint
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- NamespaceFiller(HashMap<String, String>...) - Constructor for class neurord.xml.ModelReader.NamespaceFiller
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- NanoMolarity - Class in neurord.model
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- NanoMolarity() - Constructor for class neurord.model.NanoMolarity
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- nbr - Variable in class neurord.numeric.morph.TreePoint
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- ncm(int, int) - Method in class neurord.numeric.stochastic.BinomialTable
-
- ncm_l(int, int) - Method in class neurord.numeric.stochastic.BinomialTable
-
- negate() - Method in class neurord.numeric.math.Matrix
-
- negate(int[]) - Static method in class neurord.util.ArrayUtil
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- neighborize(TreePoint, TreePoint) - Static method in class neurord.numeric.morph.TreePoint
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- neighborize() - Method in class neurord.numeric.morph.VolumeLine
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- nel - Variable in class neurord.inter.SDState
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- nel - Variable in class neurord.numeric.grid.GridCalc
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- NeuroMLBase - Class in neurord.neuroml
-
- NeuroMLBase() - Constructor for class neurord.neuroml.NeuroMLBase
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- neurord - package neurord
-
Stochastic diffusion segments of dendrits with spines.
- neurord.disc - package neurord.disc
-
These are various ways of turning a morphology into a set of elements of constrained volume.
- neurord.examples.branch - package neurord.examples.branch
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- neurord.examples.ictest - package neurord.examples.ictest
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- neurord.examples.morphsurf - package neurord.examples.morphsurf
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- neurord.examples.morphtest - package neurord.examples.morphtest
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- neurord.examples.NOEPAC - package neurord.examples.NOEPAC
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- neurord.examples.plane - package neurord.examples.plane
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- neurord.examples.regions - package neurord.examples.regions
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- neurord.examples.restart - package neurord.examples.restart
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- neurord.examples.smoothvolume - package neurord.examples.smoothvolume
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- neurord.examples.volume - package neurord.examples.volume
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- neurord.geom - package neurord.geom
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Just some geometry - positions, vectors, translations and rotations.
- neurord.inter - package neurord.inter
-
- neurord.model - package neurord.model
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These classes represent the model as it is stored in the input files.
- neurord.neuroml - package neurord.neuroml
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- neurord.numeric - package neurord.numeric
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- neurord.numeric.chem - package neurord.numeric.chem
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Species and reactions
- neurord.numeric.grid - package neurord.numeric.grid
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SteppedStochasticCalc contains the particle number based calculation with fixed timesteps
where a number of diffusion events and reactions is generated for each reaction, volume and
volume-volume connection at each timestep.
- neurord.numeric.math - package neurord.numeric.math
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Just some linear algebra.
- neurord.numeric.morph - package neurord.numeric.morph
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Representation of the morphology and discretized mesh for computational purposes.
- neurord.numeric.pool - package neurord.numeric.pool
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These are deterministic calculations for a single mixed pool.
- neurord.numeric.stochastic - package neurord.numeric.stochastic
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These are the functions for the innner loops of the calculation.
- neurord.phys - package neurord.phys
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- neurord.reduce - package neurord.reduce
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- neurord.util - package neurord.util
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Various utilities todo with file handling, string processing etc.
- neurord.xml - package neurord.xml
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- NEURORD_NS - Static variable in class neurord.xml.ModelReader
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- NextEventQueue - Class in neurord.numeric.grid
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- NextEventQueue(RandomGenerator, StepGenerator, int[][], boolean, double, double) - Constructor for class neurord.numeric.grid.NextEventQueue
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Use create() instead, this is public only for testing.
- NextEventQueue.Happening - Class in neurord.numeric.grid
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- NextEventQueue.NextDiffusion - Class in neurord.numeric.grid
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- NextEventQueue.NextEvent - Class in neurord.numeric.grid
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- NextEventQueue.NextReaction - Class in neurord.numeric.grid
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- NextEventQueue.NextStimulation - Class in neurord.numeric.grid
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- NextEventQueue.Node - Interface in neurord.numeric.grid
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- NextEventQueue.Numbering - Class in neurord.numeric.grid
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- NextEventQueue.PriorityTree<T extends NextEventQueue.Node> - Class in neurord.numeric.grid
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- nextRandom() - Static method in class neurord.numeric.math.NRRandom
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- nGo(int, double, double) - Method in class neurord.numeric.stochastic.DiscretePStepGenerator
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- nGo(int, double) - Method in class neurord.numeric.stochastic.FixedPStepGenerator
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- nGo(int, double, double) - Method in class neurord.numeric.stochastic.InterpolatingStepGenerator
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- nGo(double) - Method in class neurord.numeric.stochastic.NGoTable
-
- nGo(int, double, double) - Method in class neurord.numeric.stochastic.StepGenerator
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- nGo(int, double) - Method in class neurord.numeric.stochastic.StepGenerator
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- nGoBS(double) - Method in class neurord.numeric.stochastic.NGoTable
-
- NGoTable - Class in neurord.numeric.stochastic
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Table of cumulative probabilities of a certain number of successes
from the total number of events when the probability of success is
given.
- NGoTable(int, double, BaseCalc.distribution_t) - Constructor for class neurord.numeric.stochastic.NGoTable
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- NM_PER_PARTICLE_PUV - Static variable in class neurord.numeric.BaseCalc
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- NMAX - Static variable in class neurord.numeric.stochastic.BinomialTable
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- NMAX_STOCHASTIC - Static variable in class neurord.numeric.stochastic.StepGenerator
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- nnbr - Variable in class neurord.numeric.morph.TreePoint
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- notes - Variable in class neurord.neuroml.cell
-
- NOTICE - Static variable in class neurord.util.Logging
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- NP - Static variable in class neurord.numeric.stochastic.StepGenerator
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- NRANGES - Variable in class neurord.numeric.stochastic.InterpolatingStepGenerator
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- nreaction - Variable in class neurord.numeric.chem.ReactionTable
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- NRRandom - Class in neurord.numeric.math
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- NRRandom() - Constructor for class neurord.numeric.math.NRRandom
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- nspec - Variable in class neurord.inter.SDState
-
- nspec - Variable in class neurord.numeric.grid.GridCalc
-
- number - Variable in class neurord.model.NumberDensity
-
- number - Variable in class neurord.numeric.morph.VolumeElement
-
- NumberDensity - Class in neurord.model
-
- NumberDensity() - Constructor for class neurord.model.NumberDensity
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- Numbering() - Constructor for class neurord.numeric.grid.NextEventQueue.Numbering
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- value - Variable in class neurord.model.MaxElementSide
-
- value - Variable in class neurord.model.NanoMolarity
-
- value - Variable in class neurord.model.PicoSD
-
- value - Variable in class neurord.model.Statistics
-
- value - Variable in class neurord.neuroml.meta
-
- value - Variable in class neurord.neuroml.MetaItem
-
- valueOf(String) - Static method in enum neurord.numeric.BaseCalc.algorithm_t
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum neurord.numeric.BaseCalc.distribution_t
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum neurord.numeric.BaseCalc.output_t
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum neurord.numeric.grid.IGridCalc.EventType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum neurord.numeric.grid.IGridCalc.HappeningKind
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum neurord.numeric.morph.VolumeGrid.geometry_t
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum neurord.SDCalcType
-
Returns the enum constant of this type with the specified name.
- values() - Static method in enum neurord.numeric.BaseCalc.algorithm_t
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum neurord.numeric.BaseCalc.distribution_t
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum neurord.numeric.BaseCalc.output_t
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum neurord.numeric.grid.IGridCalc.EventType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum neurord.numeric.grid.IGridCalc.HappeningKind
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum neurord.numeric.morph.VolumeGrid.geometry_t
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum neurord.SDCalcType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- vector(double, double, double) - Static method in class neurord.geom.Geom
-
- Vector - Interface in neurord.geom
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- versatile_ngo(String, int, double) - Method in class neurord.numeric.stochastic.StepGenerator
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Return a random variate from one of the distributions
appropriate for first-order reactions (binomial, gaussian,
poisson, or something in between, based on how large n is,
and also distribution_t mode specified when this object
was created.
- volume - Variable in class neurord.numeric.morph.VolumeElement
-
- VolumeElement - Class in neurord.numeric.morph
-
- VolumeElement(String, String, String, Position[], Position[], double, Position, double, double, double, double, double) - Constructor for class neurord.numeric.morph.VolumeElement
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- VolumeGrid - Class in neurord.numeric.morph
-
- VolumeGrid() - Constructor for class neurord.numeric.morph.VolumeGrid
-
- VolumeGrid.geometry_t - Enum in neurord.numeric.morph
-
- VolumeLine - Class in neurord.numeric.morph
-
- VolumeLine(int, int, double[], double, double) - Constructor for class neurord.numeric.morph.VolumeLine
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- VolumeSlice - Class in neurord.numeric.morph
-
- VolumeSlice(double, double) - Constructor for class neurord.numeric.morph.VolumeSlice
-
- VolumeTest - Class in neurord.examples.volume
-
- VolumeTest() - Constructor for class neurord.examples.volume.VolumeTest
-