ucl.physiol.neuroconstruct.cell.converters
Class NeuronMorphReader

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

public class NeuronMorphReader
extends FormatImporter

A class for importing Neuron morphology files (.nrn/.hoc files), and creating Cells which can be used by the rest of the application. Note: hoc files should be "passed through" ucl.physiol.neuroconstruct.neuron.NeuronFileConverter before being used by this class

Author:
Padraig Gleeson

Constructor Summary
NeuronMorphReader()
           
 
Method Summary
static String getBetterSectionName(String origSecName)
           
 String getIgnoredLines()
           
 Cell loadFromMorphologyFile(File oldFile, String name)
          Creates a Cell based on the contents of the NEURON morphology file Note: hoc files should be "passed through" ucl.physiol.neuroconstruct.hoc.NeuronFileConverter before being used by this class
 Cell loadFromMorphologyFile(File morphologyFile, String name, boolean moveSomaToOrigin, boolean moveDendsToConnectionPoint)
          Creates a Cell based on the contents of the NEURON morphology file Note: hoc files should be "passed through" ucl.physiol.neuroconstruct.hoc.NeuronFileConverter before being used by this class
static void main(String[] args)
           
 
Methods inherited from class ucl.physiol.neuroconstruct.cell.converters.FormatImporter
getDesc, getFileExtensions, getName, getWarnings, toString
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

NeuronMorphReader

public NeuronMorphReader()
Method Detail

loadFromMorphologyFile

public Cell loadFromMorphologyFile(File morphologyFile,
                                   String name,
                                   boolean moveSomaToOrigin,
                                   boolean moveDendsToConnectionPoint)
                            throws MorphologyException
Creates a Cell based on the contents of the NEURON morphology file Note: hoc files should be "passed through" ucl.physiol.neuroconstruct.hoc.NeuronFileConverter before being used by this class

Throws:
MorphologyException

getBetterSectionName

public static String getBetterSectionName(String origSecName)

loadFromMorphologyFile

public Cell loadFromMorphologyFile(File oldFile,
                                   String name)
                            throws MorphologyException
Creates a Cell based on the contents of the NEURON morphology file Note: hoc files should be "passed through" ucl.physiol.neuroconstruct.hoc.NeuronFileConverter before being used by this class

Specified by:
loadFromMorphologyFile in class FormatImporter
Throws:
MorphologyException

getIgnoredLines

public String getIgnoredLines()

main

public static void main(String[] args)