Package org.neuroml.model.util

Class NeuroMLConverter

java.lang.Object

org.neuroml.model.util.NeuroMLConverter

public class NeuroMLConverter
extends Object

Field Summary

Fields

Modifier and Type	Field	Description
protected static JAXBContext	jaxb
protected static Marshaller	marshaller
protected static Unmarshaller	unmarshaller

Constructor Summary

Constructors

Constructor	Description
NeuroMLConverter()

Method Summary

Modifier and Type	Method	Description
static void	addElementToDocument(NeuroMLDocument nmlDocument, Standalone nmlElement)
static String	connectionInfo(BaseConnectionNewFormat c)
static String	connectionInfo(BaseConnectionOldFormat c)
static String	convertNeuroML2ToLems(String nml2string)
static LinkedHashMap<String,Standalone>	getAllStandaloneElements(NeuroMLDocument nmlDocument)
static float	getFractionAlong(Input i)
static int	getPostCellId(BaseConnection c)
static int	getPreCellId(BaseConnection c)
static int	getSegmentId(Input i)
static int	getTargetCellId(Input i)
NeuroMLDocument	loadNeuroML(File xmlFile)
NeuroMLDocument	loadNeuroML(File xmlFile, boolean includeIncludes)
NeuroMLDocument	loadNeuroML(File xmlFile, boolean includeIncludes, boolean failOnMissingIncludes)
NeuroMLDocument	loadNeuroML(File xmlFile, boolean includeIncludes, boolean failOnMissingIncludes, ArrayList<String> alreadyIncluded)
NeuroMLDocument	loadNeuroML(String nml2Contents)
NeuroMLDocument	loadNeuroML(String nml2Contents, boolean includeIncludes, File baseDirectoryForIncludes)
NeuroMLDocument	loadNeuroML(String nml2Contents, boolean includeIncludes, File baseDirectoryForIncludes, ArrayList<String> alreadyIncluded)
NetworkHelper	loadNeuroMLOptimized(File xmlOrH5File)
NetworkHelper	loadNeuroMLOptimized(File xmlOrH5File, boolean includeIncludes)
NetworkHelper	loadNeuroMLOptimized(String xml)
static void	main(String[] args)
String	neuroml2ToXml(NeuroMLDocument nml2)
File	neuroml2ToXml(NeuroMLDocument nml2, String filename)
static String	summary(NeuroMLDocument nmlDocument)
static String	summary(NeuroMLDocument nmlDocument, boolean full)
NeuroMLDocument	urlToNeuroML(URL url)
Morphology	xmlToMorphology(String xmlFile)

Methods inherited from class java.lang.Object

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

Field Details

jaxb

protected static JAXBContext jaxb

marshaller

protected static Marshaller marshaller

unmarshaller

protected static Unmarshaller unmarshaller

Constructor Details

NeuroMLConverter

public NeuroMLConverter()
                 throws NeuroMLException

Throws:

NeuroMLException

Method Details

xmlToMorphology

public Morphology xmlToMorphology(String xmlFile)
                           throws FileNotFoundException,
NeuroMLException

Throws:

FileNotFoundException

NeuroMLException

loadNeuroMLOptimized

public NetworkHelper loadNeuroMLOptimized(String xml)
                                   throws NeuroMLException

Throws:

NeuroMLException

loadNeuroMLOptimized

public NetworkHelper loadNeuroMLOptimized(File xmlOrH5File)
                                   throws NeuroMLException

Throws:

NeuroMLException

loadNeuroMLOptimized

public NetworkHelper loadNeuroMLOptimized(File xmlOrH5File,
 boolean includeIncludes)
                                   throws NeuroMLException

Throws:

NeuroMLException

loadNeuroML

public NeuroMLDocument loadNeuroML(File xmlFile)
                            throws IOException,
NeuroMLException

Throws:

IOException

NeuroMLException

loadNeuroML

public NeuroMLDocument loadNeuroML(File xmlFile,
 boolean includeIncludes)
                            throws IOException,
NeuroMLException

Throws:

IOException

NeuroMLException

loadNeuroML

public NeuroMLDocument loadNeuroML(File xmlFile,
 boolean includeIncludes,
 boolean failOnMissingIncludes)
                            throws IOException,
NeuroMLException

Throws:

IOException

NeuroMLException

loadNeuroML

public NeuroMLDocument loadNeuroML(File xmlFile,
 boolean includeIncludes,
 boolean failOnMissingIncludes,
 ArrayList<String> alreadyIncluded)
                            throws NeuroMLException,
IOException

Throws:

NeuroMLException

IOException

loadNeuroML

public NeuroMLDocument loadNeuroML(String nml2Contents)
                            throws NeuroMLException

Throws:

NeuroMLException

loadNeuroML

public NeuroMLDocument loadNeuroML(String nml2Contents,
 boolean includeIncludes,
 File baseDirectoryForIncludes)
                            throws NeuroMLException

Throws:

NeuroMLException

loadNeuroML

public NeuroMLDocument loadNeuroML(String nml2Contents,
 boolean includeIncludes,
 File baseDirectoryForIncludes,
 ArrayList<String> alreadyIncluded)
                            throws NeuroMLException

Throws:

NeuroMLException

urlToNeuroML

public NeuroMLDocument urlToNeuroML(URL url)
                             throws NeuroMLException

Throws:

NeuroMLException

summary

public static String summary(NeuroMLDocument nmlDocument)
                      throws NeuroMLException

Throws:

NeuroMLException

summary

public static String summary(NeuroMLDocument nmlDocument,
 boolean full)
                      throws NeuroMLException

Throws:

NeuroMLException

getPreCellId

public static int getPreCellId(BaseConnection c)

getPostCellId

public static int getPostCellId(BaseConnection c)

connectionInfo

public static String connectionInfo(BaseConnectionOldFormat c)

connectionInfo

public static String connectionInfo(BaseConnectionNewFormat c)

getTargetCellId

public static int getTargetCellId(Input i)

getSegmentId

public static int getSegmentId(Input i)

getFractionAlong

public static float getFractionAlong(Input i)

getAllStandaloneElements

public static LinkedHashMap<String,Standalone> getAllStandaloneElements(NeuroMLDocument nmlDocument)
                                                                 throws NeuroMLException

Throws:

NeuroMLException

addElementToDocument

public static void addElementToDocument(NeuroMLDocument nmlDocument,
 Standalone nmlElement)
                                 throws NeuroMLException

Throws:

NeuroMLException

neuroml2ToXml

public String neuroml2ToXml(NeuroMLDocument nml2)
                     throws NeuroMLException

Throws:

NeuroMLException

neuroml2ToXml

public File neuroml2ToXml(NeuroMLDocument nml2,
 String filename)
                   throws NeuroMLException,
IOException

Throws:

NeuroMLException

IOException

convertNeuroML2ToLems

public static String convertNeuroML2ToLems(String nml2string)

main

public static void main(String[] args)
                 throws Exception

Throws:

Exception