Package ucl.physiol.neuroconstruct.project

Core neuroConstruct project classes

See:
Description

Interface Summary

GenerationReport	Interface to let the main frame know when the generation of cell positions, network connection, etc.
ProjectEventListener	Interface to add to Main Frame which, when altered, change the info of the project
ProjectEventListner	Interface to add to components in the Main Frame which, when altered, change the info of the project
VoltageEventListener	Interface to add to objects which need updating when the voltage changes during rerun of simulations

Class Summary

ArbourConnectionsInfo	Stores info on volume/arbourisation based connections
BasicProjectInfo	Class containing basic information about the project
CellGroupsInfo	Extension of AbstractTableModel used for storing the Cell Group info
CellInitialiser	Thread to handle initialisation of cells, in the case that initial potential is not fixed
CellManager	Class for storing types of cells in project
CellPositionGenerator	Thread to handle generation of the cell positions based on the project settings
CompNodeGenerator	Thread to handle generation of node ids of the generated cells, possibly based on cell position and network connections
ConicalRegion	Extension of Regions in 3D
ConnectivityConditions	Helper class for storing the conditions on the number of target cells which can be connected to by source cells, and vice versa
ConnSpecificProps	Class for extra info on single connection
CylindricalRegion	Extension of Regions in 3D
ElecInputGenerator	Thread to handle generation of the electrical inputs based on the project settings
ElecInputInfo	Extension of AbstractTableModel for storing info on electrophysiological inputs
Expand	Class for generating HTML representation of neuroConstruct project
GapOption	Options for what to do with gap between pre & post synaptic connection point
GeneralProperties	Storing of general properties associated with the application
GeneratedCellPositions	Storage for the positions generated when the Generate cell positions...
GeneratedElecInputs	Storage for the locations and settings of electrical inputs generated when the Generate cell positions...
GeneratedNetworkConnections	Storage for network connection info generated when "Generate cell positions and network connections" button pressed.
GeneratedPlotSaves	Storage for what variables in the cells to save/plot
GrowMode	Helper class for specifying grow modes, i.e.
IgorNeuroMatic	Class which generates a simple file for easy loading of simulation results into Igor Pro (potentially with the free NeuroMatic set of functions from http://www.neuromatic.thinkrandom.com)
InternalParameter	Parameter used for storing internal variables
InternalPhysicalParameter	Parameter used for storing internal variables containing physical quantities
InternalStringFloatParameter	Parameter used for storing internal variables, in string or float form
MatlabOctave	Class which generates a simple file for easy loading of simulation results into Matlab, or Octave (freely available at http://www.octave.org)
MaxMinLength	Helper class for specifying maximum and minimum lengths for synaptic connections
MorphBasedConnGenerator	Thread to handle generation of the morphology based network connections based on the project settings
MorphologyFileUpdate	Class used to update morphology files when there is a change in the names of classes/fields used
MultiRunManager	Helper class for managing multiple runs
PlotSaveGenerator	Thread to handle generation of what to plot/save during simulation run
PositionedCell	Class for holding the position of a cell, and its cell group
PositionRecord	Single position record
PostSynapticObject	Helper class for specifying a single post synaptic mechanism instance corresponding e.g.
PrePostAllowedLocs	Helper class for storing which of axon, dendrite, soma are allowed for pre or post connections
Project	Main class holding references to the important data objects of the project
ProjectFileUpdate	Class used to update project files when there is a change in the names of classes used, e.g.
ProjectManager	A class for handling interaction with the project All non gui functionality will (eventually) be transferred here, to reduce the size of MainFrame, and to give access to the core functionality via the command line interface
ProjectProperties	A class to contain non 3D related project specific settings
ProjectStructure	Class defining, and if necessary creating, project directories, etc.
RectangularBox	Extension of Regions in 3D
Region	Base class for Regions in 3D.
RegionsInfo	Extension of AbstractTableModel to store the info on the regions
RegionTypeHelper	Helper class for getting list of Region types
SearchPattern	Helper class for specifying search patterns (ways to link up presynaptic connection points on axons with dendritic connection points)
SimConfig	Class containing info on a simulation configuration.
SimConfigInfo	Class containing info on simulation configurations in a single project, which handles the default sim config
SimpleNetworkConnectionsInfo	Implementation of AbstractTableModel used for storing the Network Connections Info
SimPlot	Info on something to plot **and/or save** during a simulation
SimPlotInfo	Extension of AbstractTableModel for storing info on what plots to show during a simulation
SingleElectricalInput	Spec of a single electrical input
SphericalRegion	Extension of Regions in 3D
SynapticProperties	Dialog for entry of synaptic connection properties: type, delay threshold, etc.
VolumeBasedConnGenerator	Thread to handle generation of volume based connections/axonal arbourisations

Exception Summary

CellCreationException	Exception when trying to create new cells
NamingException	Exception thrown when someone tries to name a Cell Group with a name already taken
NoProjectLoadedException	An exception thrown when a method is called which should only be called if a valid project is loaded
ProjectFileParsingException	Exception thrown when the parsing of a project file goes bad

Package ucl.physiol.neuroconstruct.project Description

Core neuroConstruct project classes