ucl.physiol.neuroconstruct.neuron
Class NeuronFileManager

java.lang.Object
  ucl.physiol.neuroconstruct.neuron.NeuronFileManager

public class NeuronFileManager
extends Object

Main file for generating the script files for NEURON

Author:

Padraig Gleeson

Field Summary

static String	CURR_CLAMP_VAR_AMP_EXPR
static String	CURR_CLAMP_VAR_MOD
static String	EXT_CURR_CLAMP_MOD
static String	FORCE_REGENERATE_MODS_FILENAME
static String	RAND_STIM_VAR_MOD
static String	RAND_STIM_VAR_RATE_EXPR
static int	RUN_HOC Various options for running the generated code: Generate hoc
static int	RUN_PYTHON_HDF5 Various options for running the generated code: Generate hoc/Python
static int	RUN_PYTHON_XML Various options for running the generated code: Generate hoc/Python
static int	RUN_VIA_CONDOR Various options for running the generated code: Generate condor code (semi deprecated)

Constructor Summary

NeuronFileManager(Project project)

Method Summary

void	addComment(StringBuilder responseBuffer, String comment)
static boolean	addComments()
static void	addHocComment(StringBuilder responseBuffer, String comment)
static void	addHocComment(StringBuilder responseBuffer, String comment, boolean inclReturn)
static void	addHocComment(StringBuilder responseBuffer, String comment, String preSlashes, boolean inclReturn)
void	addMajorComment(StringBuilder responseBuffer, String comment)
static void	addMajorHocComment(StringBuilder responseBuffer, String comment)
static float	convertToNeuronValue(Float val, String simIndepVarName)
String	convertToNeuronVarName(String simIndepVarName)
void	forceNextModNotRecompile()
void	forceNextModRecompile()
String	generateCellGroups()
String	generateGUIForRerunning()
boolean	generateLinuxBasedScripts()
String	generatePlots()
String	generateRunMechanism()
String	generateShapePlot()
void	generateTheNeuronFiles(SimConfig simConfig, MultiRunManager multiRunManager, int runMode, long randomSeed)
float	getCurrentGenTime()
long	getCurrentRandomSeed()
long	getCurrentRunMode()
Vector	getGeneratedFilenames()
ArrayList<String>	getGeneratedSimReferences()
String	getHocFriendlyFilename(String filename)
static String	getHocSectionName(String secname)
static String	getHocSegmentName(String secname)
File	getMainHocFile()
Vector<String>	getModFilesToCompile()
String	getNextColour(String plotFrame)
static boolean	isRunModePythonBased(int runMode)
static void	main(String[] args)
static String	makePythonFriendly(String name)
void	reset()
void	runNeuronFile(File mainHocFile)
void	setQuitAfterRun(boolean quit)
void	setSuggestedRemoteRunTime(int t)

Methods inherited from class java.lang.Object

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

Field Detail

RUN_HOC

public static final int RUN_HOC

Various options for running the generated code: Generate hoc

See Also:

Constant Field Values

RUN_VIA_CONDOR

public static final int RUN_VIA_CONDOR

Various options for running the generated code: Generate condor code (semi deprecated)

See Also:

Constant Field Values

RUN_PYTHON_XML

public static final int RUN_PYTHON_XML

Various options for running the generated code: Generate hoc/Python

See Also:

Constant Field Values

RUN_PYTHON_HDF5

public static final int RUN_PYTHON_HDF5

Various options for running the generated code: Generate hoc/Python

See Also:

Constant Field Values

EXT_CURR_CLAMP_MOD

public static final String EXT_CURR_CLAMP_MOD

See Also:

Constant Field Values

CURR_CLAMP_VAR_MOD

public static final String CURR_CLAMP_VAR_MOD

See Also:

Constant Field Values

RAND_STIM_VAR_MOD

public static final String RAND_STIM_VAR_MOD

See Also:

Constant Field Values

CURR_CLAMP_VAR_AMP_EXPR

public static final String CURR_CLAMP_VAR_AMP_EXPR

See Also:

Constant Field Values

RAND_STIM_VAR_RATE_EXPR

public static final String RAND_STIM_VAR_RATE_EXPR

See Also:

Constant Field Values

FORCE_REGENERATE_MODS_FILENAME

public static final String FORCE_REGENERATE_MODS_FILENAME

See Also:

Constant Field Values

Constructor Detail

NeuronFileManager

public NeuronFileManager(Project project)

Method Detail

addComments

public static boolean addComments()

reset

public void reset()

generateTheNeuronFiles

public void generateTheNeuronFiles(SimConfig simConfig,
                                   MultiRunManager multiRunManager,
                                   int runMode,
                                   long randomSeed)
                            throws NeuronException,
                                   IOException

Throws:

NeuronException

IOException

forceNextModRecompile

public void forceNextModRecompile()

forceNextModNotRecompile

public void forceNextModNotRecompile()

makePythonFriendly

public static String makePythonFriendly(String name)

setQuitAfterRun

public void setQuitAfterRun(boolean quit)

getGeneratedSimReferences

public ArrayList<String> getGeneratedSimReferences()

getGeneratedFilenames

public Vector getGeneratedFilenames()

getCurrentRandomSeed

public long getCurrentRandomSeed()

getCurrentRunMode

public long getCurrentRunMode()

getCurrentGenTime

public float getCurrentGenTime()

getHocSectionName

public static String getHocSectionName(String secname)

getHocSegmentName

public static String getHocSegmentName(String secname)

getHocFriendlyFilename

public String getHocFriendlyFilename(String filename)

generateCellGroups

public String generateCellGroups()
                          throws NeuronException

Throws:

NeuronException

generatePlots

public String generatePlots()

generateShapePlot

public String generateShapePlot()

getNextColour

public String getNextColour(String plotFrame)

generateLinuxBasedScripts

public boolean generateLinuxBasedScripts()

generateRunMechanism

public String generateRunMechanism()

generateGUIForRerunning

public String generateGUIForRerunning()

isRunModePythonBased

public static boolean isRunModePythonBased(int runMode)

addComment

public void addComment(StringBuilder responseBuffer,
                       String comment)

addHocComment

public static void addHocComment(StringBuilder responseBuffer,
                                 String comment)

addHocComment

public static void addHocComment(StringBuilder responseBuffer,
                                 String comment,
                                 boolean inclReturn)

addHocComment

public static void addHocComment(StringBuilder responseBuffer,
                                 String comment,
                                 String preSlashes,
                                 boolean inclReturn)

addMajorComment

public void addMajorComment(StringBuilder responseBuffer,
                            String comment)

addMajorHocComment

public static void addMajorHocComment(StringBuilder responseBuffer,
                                      String comment)

convertToNeuronValue

public static float convertToNeuronValue(Float val,
                                         String simIndepVarName)

convertToNeuronVarName

public String convertToNeuronVarName(String simIndepVarName)

setSuggestedRemoteRunTime

public void setSuggestedRemoteRunTime(int t)

runNeuronFile

public void runNeuronFile(File mainHocFile)
                   throws NeuronException

Throws:

NeuronException

getMainHocFile

public File getMainHocFile()
                    throws NeuronException

Throws:

NeuronException

main

public static void main(String[] args)

getModFilesToCompile

public Vector<String> getModFilesToCompile()