Package org.neuroml.export.neuron

Class NeuronWriter

java.lang.Object

org.lemsml.export.base.ABaseWriter

org.neuroml.export.base.ANeuroMLBaseWriter

org.neuroml.export.neuron.NeuronWriter

All Implemented Interfaces:

IBaseWriter

public class NeuronWriter
extends ANeuroMLBaseWriter

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	NeuronWriter.ChannelConductanceOption
class	NeuronWriter.CompInfo
static class	NeuronWriter.SupportedUnits

Field Summary

Fields

Modifier and Type	Field	Description
HashMap<String,Integer>	modWarnings
HashMap<String,String>	modWritten
static String	NEURON_HOME_ENV_VAR

Fields inherited from class org.neuroml.export.base.ANeuroMLBaseWriter

nmlDocument

Fields inherited from class org.lemsml.export.base.ABaseWriter

format, lems, sli

Constructor Summary

Constructors

Constructor	Description
NeuronWriter(org.lemsml.jlems.core.type.Lems lems)
NeuronWriter(org.lemsml.jlems.core.type.Lems lems, File outputFolder, String outputFileName)

Method Summary

Modifier and Type	Method	Description
protected void	addComment(StringBuilder sb, String comment)
protected void	addComment(StringBuilder sb, String comment, String indent)
List<File>	convert()
org.neuroml.model.IntracellularProperties	convertCellWithMorphology(org.lemsml.jlems.core.type.Component cellComponent)
static String	formatDefault(float num)
List<File>	generateAndRun(boolean nogui, boolean compileMods, boolean run)
List<File>	generateAndRun(boolean nogui, boolean compileMods, boolean run, boolean useNrnivForNoGui)
static String	generateCellFile(org.neuroml.model.Cell cell)
void	generateFilesForNeuroMLElements(boolean compileMods)
List<File>	generateMainScriptAndMods()
String	generateModFile(org.lemsml.jlems.core.type.Component comp)
String	generateModFile(org.lemsml.jlems.core.type.Component comp, NeuronWriter.ChannelConductanceOption condOption)
String	getMainScript()
org.neuroml.model.MembraneProperties	getMembraneProperties(org.neuroml.model.Cell cell)
boolean	isNoGui()
static void	main(String[] args)
File	saveModToFile(org.lemsml.jlems.core.type.Component comp, String mod)
void	setGenerateAlphabetical(boolean generateAlphabetical)
void	setNoGui(boolean nogui)
void	setParallelMode(boolean parallel)
void	setSupportedFeatures()
static void	writeModBlock(StringBuilder main, String blockName, String contents)

Methods inherited from class org.lemsml.export.base.ABaseWriter

getOutputFileName, getOutputFolder, setOutputFileName, setOutputFolder

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

NEURON_HOME_ENV_VAR

public static final String NEURON_HOME_ENV_VAR

See Also:

Constant Field Values

modWritten

public HashMap<String,String> modWritten

modWarnings

public HashMap<String,Integer> modWarnings

Constructor Detail

NeuronWriter

public NeuronWriter(org.lemsml.jlems.core.type.Lems lems)
             throws ModelFeatureSupportException,
                    org.lemsml.jlems.core.sim.LEMSException,
                    org.neuroml.model.util.NeuroMLException

Throws:

ModelFeatureSupportException

org.lemsml.jlems.core.sim.LEMSException

org.neuroml.model.util.NeuroMLException

NeuronWriter

public NeuronWriter(org.lemsml.jlems.core.type.Lems lems,
                    File outputFolder,
                    String outputFileName)
             throws ModelFeatureSupportException,
                    org.neuroml.model.util.NeuroMLException,
                    org.lemsml.jlems.core.sim.LEMSException

Throws:

ModelFeatureSupportException

org.neuroml.model.util.NeuroMLException

org.lemsml.jlems.core.sim.LEMSException

Method Detail

setSupportedFeatures

public void setSupportedFeatures()

generateAndRun

public List<File> generateAndRun(boolean nogui,
                                 boolean compileMods,
                                 boolean run)
                          throws org.lemsml.jlems.core.sim.LEMSException,
                                 GenerationException,
                                 org.neuroml.model.util.NeuroMLException,
                                 IOException,
                                 ModelFeatureSupportException

Throws:

org.lemsml.jlems.core.sim.LEMSException

GenerationException

org.neuroml.model.util.NeuroMLException

IOException

ModelFeatureSupportException

generateAndRun

public List<File> generateAndRun(boolean nogui,
                                 boolean compileMods,
                                 boolean run,
                                 boolean useNrnivForNoGui)
                          throws org.lemsml.jlems.core.sim.LEMSException,
                                 GenerationException,
                                 org.neuroml.model.util.NeuroMLException,
                                 IOException,
                                 ModelFeatureSupportException

Throws:

org.lemsml.jlems.core.sim.LEMSException

GenerationException

org.neuroml.model.util.NeuroMLException

IOException

ModelFeatureSupportException

addComment

protected void addComment(StringBuilder sb,
                          String comment)

Specified by:

addComment in class ABaseWriter

addComment

protected void addComment(StringBuilder sb,
                          String comment,
                          String indent)

setParallelMode

public void setParallelMode(boolean parallel)

setNoGui

public void setNoGui(boolean nogui)

isNoGui

public boolean isNoGui()

setGenerateAlphabetical

public void setGenerateAlphabetical(boolean generateAlphabetical)

generateMainScriptAndMods

public List<File> generateMainScriptAndMods()
                                     throws org.lemsml.jlems.core.sim.LEMSException,
                                            GenerationException,
                                            org.neuroml.model.util.NeuroMLException

Throws:

org.lemsml.jlems.core.sim.LEMSException

GenerationException

org.neuroml.model.util.NeuroMLException

getMainScript

public String getMainScript()
                     throws GenerationException,
                            org.neuroml.model.util.NeuroMLException

Throws:

GenerationException

org.neuroml.model.util.NeuroMLException

saveModToFile

public File saveModToFile(org.lemsml.jlems.core.type.Component comp,
                          String mod)
                   throws org.lemsml.jlems.core.sim.ContentError

Throws:

org.lemsml.jlems.core.sim.ContentError

getMembraneProperties

public org.neuroml.model.MembraneProperties getMembraneProperties(org.neuroml.model.Cell cell)

convertCellWithMorphology

public org.neuroml.model.IntracellularProperties convertCellWithMorphology(org.lemsml.jlems.core.type.Component cellComponent)
                                                                    throws org.lemsml.jlems.core.sim.LEMSException,
                                                                           org.neuroml.model.util.NeuroMLException

Throws:

org.lemsml.jlems.core.sim.LEMSException

org.neuroml.model.util.NeuroMLException

generateCellFile

public static String generateCellFile(org.neuroml.model.Cell cell)
                               throws org.lemsml.jlems.core.sim.LEMSException,
                                      org.neuroml.model.util.NeuroMLException

Throws:

org.lemsml.jlems.core.sim.LEMSException

org.neuroml.model.util.NeuroMLException

formatDefault

public static String formatDefault(float num)

generateModFile

public String generateModFile(org.lemsml.jlems.core.type.Component comp)
                       throws org.lemsml.jlems.core.sim.LEMSException

Throws:

org.lemsml.jlems.core.sim.LEMSException

generateModFile

public String generateModFile(org.lemsml.jlems.core.type.Component comp,
                              NeuronWriter.ChannelConductanceOption condOption)
                       throws org.lemsml.jlems.core.sim.LEMSException

Throws:

org.lemsml.jlems.core.sim.LEMSException

writeModBlock

public static void writeModBlock(StringBuilder main,
                                 String blockName,
                                 String contents)

generateFilesForNeuroMLElements

public void generateFilesForNeuroMLElements(boolean compileMods)
                                     throws org.lemsml.jlems.core.sim.LEMSException,
                                            org.neuroml.model.util.NeuroMLException,
                                            IOException

Throws:

org.lemsml.jlems.core.sim.LEMSException

org.neuroml.model.util.NeuroMLException

IOException

main

public static void main(String[] args)
                 throws Exception

Throws:

Exception

convert

public List<File> convert()
                   throws GenerationException

Throws:

GenerationException