ucl.physiol.neuroconstruct.cell.converters
Class MorphMLConverter

java.lang.Object
  extended by ucl.physiol.neuroconstruct.cell.converters.FormatImporter
      extended by 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)