Package de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml

Class SBML_XML_Reader

java.lang.Object

org.graffiti.plugin.io.AbstractInputSerializer

de.ipk_gatersleben.ag_nw.graffiti.plugins.ios.importers.sbml.SBML_XML_Reader

All Implemented Interfaces:

InputSerializer, Serializer

public class SBML_XML_Reader
extends AbstractInputSerializer

Constructor Summary

Constructors

Constructor	Description
SBML_XML_Reader()

Method Summary

Modifier and Type	Method	Description
static void	doValidateSBMLOnLoad(boolean validate)
String[]	getExtensions()	Implemented method of interface InputSerializer.java Returns the extension of files that can be read in with the SBML importer
String[]	getFileTypeDescriptions()	Implemented method of interface InputSerializer.java Returns the description of the input format
static boolean	isFixPath2Models()
static boolean	isValidatingSBMLOnLoad()
void	read(InputStream in, Graph g)	Reads in a graph from the given input stream.
void	read(Reader reader, Graph g)
void	read(org.sbml.jsbml.SBMLDocument document, Graph g, BackgroundTaskStatusProviderSupportingExternalCallImpl status)	Method controls the import of the SBML document.
static void	setFixPath2Models(boolean fix)
boolean	validFor(InputStream reader)

Methods inherited from class org.graffiti.plugin.io.AbstractInputSerializer

read, read, read

Methods inherited from class java.lang.Object

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

Constructor Details

SBML_XML_Reader

public SBML_XML_Reader()

Method Details

doValidateSBMLOnLoad

public static void doValidateSBMLOnLoad(boolean validate)

isValidatingSBMLOnLoad

public static boolean isValidatingSBMLOnLoad()

setFixPath2Models

public static void setFixPath2Models(boolean fix)

isFixPath2Models

public static boolean isFixPath2Models()

read

public void read(org.sbml.jsbml.SBMLDocument document,
Graph g,
BackgroundTaskStatusProviderSupportingExternalCallImpl status)

Method controls the import of the SBML document.

Parameters:

document - contains the data to be imported.

g - is the data structure for reading in the information.

read

public void read(Reader reader,
Graph g)
          throws Exception

Throws:

Exception

read

public void read(InputStream in,
Graph g)
          throws IOException

Description copied from class: AbstractInputSerializer

Reads in a graph from the given input stream.

Specified by:

read in interface InputSerializer

Specified by:

read in class AbstractInputSerializer

Parameters:

in - The input stream to read the graph from.

g - The graph to add the newly read graph to.

Throws:

IOException - If an IO error occurs.

validFor

public boolean validFor(InputStream reader)

Specified by:

validFor in interface InputSerializer

Overrides:

validFor in class AbstractInputSerializer

Parameters:

reader - Warning: The Inputstream-Length may be limited in size, e.g. may only provide access to the first 5000 bytes.

Returns:

getExtensions

public String[] getExtensions()

Implemented method of interface InputSerializer.java Returns the extension of files that can be read in with the SBML importer

Returns:

DOCUMENT ME!

getFileTypeDescriptions

public String[] getFileTypeDescriptions()

Implemented method of interface InputSerializer.java Returns the description of the input format

Returns:

DOCUMENT ME!