Package org.neuroml.export.utils

Class Utils

java.lang.Object

org.neuroml.export.utils.Utils

public class Utils
extends Object

Field Summary

Fields

Modifier and Type	Field	Description
static String	ARCH_64BIT
static String	ARCH_I386
static String	ARCH_I686
static String	ARCH_POWERPC
static String	ARCH_UMAC
static String	DIR_64BIT
static String	DIR_I386
static String	DIR_I686
static String	DIR_POWERPC
static String	DIR_UMAC
static String	LEMS_EXAMPLES_RESOURCES_DIR
static String	NEUROML_COMPTYPR_RESOURCES_DIR
static String	NEUROML_EXAMPLES_RESOURCES_DIR
static String	ORG_NEUROML_EXPORT_VERSION

Constructor Summary

Constructors

Constructor	Description
Utils()

Method Summary

Modifier and Type	Method	Description
static LinkedHashMap<String,org.neuroml.model.Standalone>	convertLemsComponentToNeuroML(org.lemsml.jlems.core.type.Component comp, boolean fixExternalMorphsBiophys, org.lemsml.jlems.core.type.Lems lems)
static org.neuroml.model.NeuroMLDocument	convertLemsComponentToNeuroMLDocument(org.lemsml.jlems.core.type.Component comp)
static String	convertLemsToNeuroMLLikeXml(org.lemsml.jlems.core.type.Lems lems, String onlyNetwork)
static org.lemsml.jlems.core.type.Component	convertNeuroMLToComponent(org.neuroml.model.Standalone nmlElement)
static org.lemsml.jlems.core.sim.Sim	convertNeuroMLToSim(org.neuroml.model.Standalone nmlElement)
static File	copyFromJarToTempLocation(String filename)
static String	extractLemsSimulationXml(org.lemsml.jlems.core.type.Lems lems, String externalFiletoInclude)
static String	extractLemsSimulationXml(org.lemsml.jlems.core.type.Lems lems, String externalFiletoInclude, String reportFile)
static String	getArchSpecificDir()
static org.neuroml.model.Cell	getCellFromComponent(org.lemsml.jlems.core.type.Component comp, org.lemsml.jlems.core.type.Lems lems)
static org.lemsml.jlems.core.type.Dimension	getDimension(String nml2Quantity)
static String	getHeaderComment(Format format)
static float	getMagnitudeInSI(String nml2Quantity)
static org.lemsml.jlems.core.type.Unit	getSIUnitInNeuroML(org.lemsml.jlems.core.type.Dimension dim)
static boolean	is64bitPlatform()
static boolean	isLinuxBasedPlatform()
static boolean	isMacBasedPlatform()
static boolean	isVersionControlDir(File dir)
static boolean	isVersionControlDir(String dirname)
static boolean	isWindowsBasedPlatform()
static void	loadLemsFile(File lemsFile, boolean run, boolean showGui)
static void	main(String[] args)
static int	parseCellRefStringForCellNum(String cellRef)
static String	parseCellRefStringForPopulation(String cellRef)
static org.lemsml.jlems.core.sim.Sim	readLemsNeuroMLFile(File f)
static org.lemsml.jlems.core.sim.Sim	readLemsNeuroMLFile(File f, boolean includeConnectionsFromHDF5)
static org.lemsml.jlems.core.sim.Sim	readLemsNeuroMLFile(String contents)
static org.lemsml.jlems.core.sim.Sim	readNeuroMLFile(File f)
static org.lemsml.jlems.core.sim.Sim	readNeuroMLFile(File f, boolean includeConnectionsFromHDF5)
static org.lemsml.jlems.core.sim.Sim	readNeuroMLFile(String contents)
static void	removeAllFiles(File directory, boolean removeDirToo, boolean removeVC)
static AbstractList	reorderAlphabetically(AbstractList list, boolean ascending)
static String	replaceInExpression(String expression, String oldVal, String newVal)
static void	runLemsFile(File f, boolean showGui)
static String	sysEnvInfo(String indent)

Methods inherited from class java.lang.Object

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

Field Detail

ORG_NEUROML_EXPORT_VERSION

public static String ORG_NEUROML_EXPORT_VERSION

ARCH_I686

public static final String ARCH_I686

See Also:

Constant Field Values

ARCH_I386

public static final String ARCH_I386

See Also:

Constant Field Values

ARCH_64BIT

public static final String ARCH_64BIT

See Also:

Constant Field Values

ARCH_POWERPC

public static final String ARCH_POWERPC

See Also:

Constant Field Values

ARCH_UMAC

public static final String ARCH_UMAC

See Also:

Constant Field Values

DIR_I386

public static final String DIR_I386

See Also:

Constant Field Values

DIR_I686

public static final String DIR_I686

See Also:

Constant Field Values

DIR_64BIT

public static final String DIR_64BIT

See Also:

Constant Field Values

DIR_POWERPC

public static final String DIR_POWERPC

See Also:

Constant Field Values

DIR_UMAC

public static final String DIR_UMAC

See Also:

Constant Field Values

LEMS_EXAMPLES_RESOURCES_DIR

public static final String LEMS_EXAMPLES_RESOURCES_DIR

See Also:

Constant Field Values

NEUROML_COMPTYPR_RESOURCES_DIR

public static final String NEUROML_COMPTYPR_RESOURCES_DIR

See Also:

Constant Field Values

NEUROML_EXAMPLES_RESOURCES_DIR

public static final String NEUROML_EXAMPLES_RESOURCES_DIR

See Also:

Constant Field Values

Constructor Detail

Utils

public Utils()

Method Detail

getHeaderComment

public static String getHeaderComment(Format format)

getMagnitudeInSI

public static float getMagnitudeInSI(String nml2Quantity)
                              throws org.neuroml.model.util.NeuroMLException

Throws:

org.neuroml.model.util.NeuroMLException

getDimension

public static org.lemsml.jlems.core.type.Dimension getDimension(String nml2Quantity)
                                                         throws org.neuroml.model.util.NeuroMLException

Throws:

org.neuroml.model.util.NeuroMLException

parseCellRefStringForPopulation

public static String parseCellRefStringForPopulation(String cellRef)

parseCellRefStringForCellNum

public static int parseCellRefStringForCellNum(String cellRef)

getSIUnitInNeuroML

public static org.lemsml.jlems.core.type.Unit getSIUnitInNeuroML(org.lemsml.jlems.core.type.Dimension dim)
                                                          throws org.neuroml.model.util.NeuroMLException

Throws:

org.neuroml.model.util.NeuroMLException

readLemsNeuroMLFile

public static org.lemsml.jlems.core.sim.Sim readLemsNeuroMLFile(String contents)
                                                         throws org.lemsml.jlems.core.sim.LEMSException

Throws:

org.lemsml.jlems.core.sim.LEMSException

readNeuroMLFile

public static org.lemsml.jlems.core.sim.Sim readNeuroMLFile(File f)
                                                     throws org.lemsml.jlems.core.sim.LEMSException,
                                                            IOException

Throws:

org.lemsml.jlems.core.sim.LEMSException

IOException

readNeuroMLFile

public static org.lemsml.jlems.core.sim.Sim readNeuroMLFile(File f,
                                                            boolean includeConnectionsFromHDF5)
                                                     throws org.lemsml.jlems.core.sim.LEMSException,
                                                            IOException

Throws:

org.lemsml.jlems.core.sim.LEMSException

IOException

readNeuroMLFile

public static org.lemsml.jlems.core.sim.Sim readNeuroMLFile(String contents)
                                                     throws org.lemsml.jlems.core.sim.LEMSException

Throws:

org.lemsml.jlems.core.sim.LEMSException

copyFromJarToTempLocation

public static File copyFromJarToTempLocation(String filename)
                                      throws org.lemsml.jlems.core.sim.ContentError,
                                             IOException

Throws:

org.lemsml.jlems.core.sim.ContentError

IOException

readLemsNeuroMLFile

public static org.lemsml.jlems.core.sim.Sim readLemsNeuroMLFile(File f)
                                                         throws org.lemsml.jlems.core.sim.LEMSException,
                                                                org.neuroml.model.util.NeuroMLException

Throws:

org.lemsml.jlems.core.sim.LEMSException

org.neuroml.model.util.NeuroMLException

readLemsNeuroMLFile

public static org.lemsml.jlems.core.sim.Sim readLemsNeuroMLFile(File f,
                                                                boolean includeConnectionsFromHDF5)
                                                         throws org.lemsml.jlems.core.sim.LEMSException,
                                                                org.neuroml.model.util.NeuroMLException

Throws:

org.lemsml.jlems.core.sim.LEMSException

org.neuroml.model.util.NeuroMLException

replaceInExpression

public static String replaceInExpression(String expression,
                                         String oldVal,
                                         String newVal)

convertLemsToNeuroMLLikeXml

public static String convertLemsToNeuroMLLikeXml(org.lemsml.jlems.core.type.Lems lems,
                                                 String onlyNetwork)
                                          throws org.lemsml.jlems.core.sim.LEMSException,
                                                 org.neuroml.model.util.NeuroMLException

Throws:

org.lemsml.jlems.core.sim.LEMSException

org.neuroml.model.util.NeuroMLException

extractLemsSimulationXml

public static String extractLemsSimulationXml(org.lemsml.jlems.core.type.Lems lems,
                                              String externalFiletoInclude)
                                       throws org.lemsml.jlems.core.sim.LEMSException,
                                              org.neuroml.model.util.NeuroMLException

Throws:

org.lemsml.jlems.core.sim.LEMSException

org.neuroml.model.util.NeuroMLException

extractLemsSimulationXml

public static String extractLemsSimulationXml(org.lemsml.jlems.core.type.Lems lems,
                                              String externalFiletoInclude,
                                              String reportFile)
                                       throws org.lemsml.jlems.core.sim.LEMSException,
                                              org.neuroml.model.util.NeuroMLException

Throws:

org.lemsml.jlems.core.sim.LEMSException

org.neuroml.model.util.NeuroMLException

convertLemsComponentToNeuroMLDocument

public static org.neuroml.model.NeuroMLDocument convertLemsComponentToNeuroMLDocument(org.lemsml.jlems.core.type.Component comp)
                                                                               throws org.lemsml.jlems.core.sim.LEMSException,
                                                                                      org.neuroml.model.util.NeuroMLException

Throws:

org.lemsml.jlems.core.sim.LEMSException

org.neuroml.model.util.NeuroMLException

convertLemsComponentToNeuroML

public static LinkedHashMap<String,org.neuroml.model.Standalone> convertLemsComponentToNeuroML(org.lemsml.jlems.core.type.Component comp,
                                                                                                     boolean fixExternalMorphsBiophys,
                                                                                                     org.lemsml.jlems.core.type.Lems lems)
                                                                                              throws org.lemsml.jlems.core.sim.LEMSException,
                                                                                                     org.neuroml.model.util.NeuroMLException

Throws:

org.lemsml.jlems.core.sim.LEMSException

org.neuroml.model.util.NeuroMLException

convertNeuroMLToComponent

public static org.lemsml.jlems.core.type.Component convertNeuroMLToComponent(org.neuroml.model.Standalone nmlElement)
                                                                      throws org.neuroml.model.util.NeuroMLException,
                                                                             org.lemsml.jlems.core.sim.LEMSException

Throws:

org.neuroml.model.util.NeuroMLException

org.lemsml.jlems.core.sim.LEMSException

getCellFromComponent

public static org.neuroml.model.Cell getCellFromComponent(org.lemsml.jlems.core.type.Component comp,
                                                          org.lemsml.jlems.core.type.Lems lems)
                                                   throws org.lemsml.jlems.core.sim.LEMSException,
                                                          org.neuroml.model.util.NeuroMLException

Throws:

org.lemsml.jlems.core.sim.LEMSException

org.neuroml.model.util.NeuroMLException

convertNeuroMLToSim

public static org.lemsml.jlems.core.sim.Sim convertNeuroMLToSim(org.neuroml.model.Standalone nmlElement)
                                                         throws org.neuroml.model.util.NeuroMLException,
                                                                org.lemsml.jlems.core.sim.LEMSException

Throws:

org.neuroml.model.util.NeuroMLException

org.lemsml.jlems.core.sim.LEMSException

reorderAlphabetically

public static AbstractList reorderAlphabetically(AbstractList list,
                                                 boolean ascending)

runLemsFile

public static void runLemsFile(File f,
                               boolean showGui)
                        throws org.lemsml.jlems.core.sim.LEMSException,
                               ModelFeatureSupportException,
                               org.neuroml.model.util.NeuroMLException

Throws:

org.lemsml.jlems.core.sim.LEMSException

ModelFeatureSupportException

org.neuroml.model.util.NeuroMLException

loadLemsFile

public static void loadLemsFile(File lemsFile,
                                boolean run,
                                boolean showGui)
                         throws org.lemsml.jlems.core.sim.LEMSException,
                                ModelFeatureSupportException,
                                org.neuroml.model.util.NeuroMLException

Throws:

org.lemsml.jlems.core.sim.LEMSException

ModelFeatureSupportException

org.neuroml.model.util.NeuroMLException

isWindowsBasedPlatform

public static boolean isWindowsBasedPlatform()

isLinuxBasedPlatform

public static boolean isLinuxBasedPlatform()

isMacBasedPlatform

public static boolean isMacBasedPlatform()

getArchSpecificDir

public static String getArchSpecificDir()

Returns:

i686 for most, x86_64 if "64" present in system properties os.arch, e.g. amd64. Will need updating as Neuron tested on more platforms...

is64bitPlatform

public static boolean is64bitPlatform()

isVersionControlDir

public static boolean isVersionControlDir(String dirname)

isVersionControlDir

public static boolean isVersionControlDir(File dir)

removeAllFiles

public static void removeAllFiles(File directory,
                                  boolean removeDirToo,
                                  boolean removeVC)

sysEnvInfo

public static String sysEnvInfo(String indent)

main

public static void main(String[] args)
                 throws org.lemsml.jlems.core.sim.ContentError,
                        IOException,
                        org.lemsml.jlems.core.sim.LEMSException,
                        org.neuroml.model.util.NeuroMLException

Throws:

org.lemsml.jlems.core.sim.ContentError

IOException

org.lemsml.jlems.core.sim.LEMSException

org.neuroml.model.util.NeuroMLException