ucl.physiol.neuroconstruct.cell.converters
Class MorphMLConverter

java.lang.Object
  ucl.physiol.neuroconstruct.cell.converters.FormatImporter
      ucl.physiol.neuroconstruct.cell.converters.MorphMLConverter

public class MorphMLConverter
extends FormatImporter

A class for importing XML morphology files, and creating Cells which can be used by the rest of the application

Author:

Padraig Gleeson

Constructor Summary

MorphMLConverter()

Method Summary

static SimpleXMLElement	getCellXMLElement(Cell cell, Project project, NeuroMLConstants.NeuroMLLevel level, NeuroMLConstants.NeuroMLVersion version)
static int	getPreferredExportUnits()
String	getWarnings()
static Cell	loadFromJavaObjFile(File objFile)
static Cell	loadFromJavaXMLFile(File javaXMLFile)
Cell	loadFromMorphologyFile(File morphologyFile, String name)
static void	main(String[] args)
static ArrayList<Cell>	saveAllCellsInNeuroML(Project project, MorphCompartmentalisation mc, NeuroMLConstants.NeuroMLLevel level, NeuroMLConstants.NeuroMLVersion version, SimConfig simConfig, File destDir)
static boolean	saveCellInJavaObjFormat(Cell cell, File javaObjFile)
static boolean	saveCellInJavaXMLFormat(Cell cell, File javaXMLFile)
static void	saveCellInNeuroMLFormat(Cell cell, Project project, File neuroMLFile, NeuroMLConstants.NeuroMLLevel level, NeuroMLConstants.NeuroMLVersion version) Creates NeuroML representations of the cell in the specified file.
static void	setPreferredExportUnits(int prefUnits)

Methods inherited from class ucl.physiol.neuroconstruct.cell.converters.FormatImporter

getDesc, getFileExtensions, getName, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

MorphMLConverter

public MorphMLConverter()

Method Detail

loadFromJavaXMLFile

public static Cell loadFromJavaXMLFile(File javaXMLFile)
                                throws MorphologyException

Throws:

MorphologyException

getWarnings

public String getWarnings()

Overrides:

getWarnings in class FormatImporter

getPreferredExportUnits

public static int getPreferredExportUnits()

setPreferredExportUnits

public static void setPreferredExportUnits(int prefUnits)

loadFromJavaObjFile

public static Cell loadFromJavaObjFile(File objFile)
                                throws MorphologyException

Throws:

MorphologyException

loadFromMorphologyFile

public Cell loadFromMorphologyFile(File morphologyFile,
                                   String name)
                            throws MorphologyException

Specified by:

loadFromMorphologyFile in class FormatImporter

Throws:

MorphologyException

saveCellInJavaXMLFormat

public static boolean saveCellInJavaXMLFormat(Cell cell,
                                              File javaXMLFile)
                                       throws MorphologyException

Throws:

MorphologyException

saveCellInJavaObjFormat

public static boolean saveCellInJavaObjFormat(Cell cell,
                                              File javaObjFile)
                                       throws MorphologyException

Throws:

MorphologyException

getCellXMLElement

public static SimpleXMLElement getCellXMLElement(Cell cell,
                                                 Project project,
                                                 NeuroMLConstants.NeuroMLLevel level,
                                                 NeuroMLConstants.NeuroMLVersion version)
                                          throws NeuroMLException,
                                                 CMLMechNotInitException,
                                                 XMLMechanismException

Throws:

NeuroMLException

CMLMechNotInitException

XMLMechanismException

saveCellInNeuroMLFormat

public static void saveCellInNeuroMLFormat(Cell cell,
                                           Project project,
                                           File neuroMLFile,
                                           NeuroMLConstants.NeuroMLLevel level,
                                           NeuroMLConstants.NeuroMLVersion version)
                                    throws MorphologyException

Creates NeuroML representations of the cell in the specified file. Note: may be better in the neuroml package...

Parameters:

cell - The Cell object to export

neuroMLFile - The file to put the NeuroML in

level - The level (currently 1 for "pure" MorphML, or 2 to include channel distributions, level 3 for net aspects) as defined in NeuroMLConstants

Throws:

MorphologyException

saveAllCellsInNeuroML

public static ArrayList<Cell> saveAllCellsInNeuroML(Project project,
                                                    MorphCompartmentalisation mc,
                                                    NeuroMLConstants.NeuroMLLevel level,
                                                    NeuroMLConstants.NeuroMLVersion version,
                                                    SimConfig simConfig,
                                                    File destDir)
                                             throws MorphologyException

Throws:

MorphologyException

main

public static void main(String[] args)