public class SBMLReader
extends java.lang.Object
Warning: This class is not thread safe, so if using several thread to process SBML files in parallel you should make sure to use new instances of SBMLReader in each thread.
Constructor | Description |
---|---|
SBMLReader() |
Modifier and Type | Method | Description |
---|---|---|
void |
initializeAnnotationParsers() |
Initializes the packageParser
HashMap of this class. |
static void |
main(java.lang.String[] args) |
Reads the file that is passed as argument and write it to the console,
using the method
SBMLWriter.write(SBMLDocument, java.io.OutputStream) . |
ASTNode |
readMathML(java.lang.String mathML) |
|
ASTNode |
readMathML(java.lang.String mathML,
TreeNodeChangeListener listener) |
Reads a mathML String into an
ASTNode . |
ASTNode |
readMathML(java.lang.String mathML,
TreeNodeChangeListener listener,
MathContainer parent) |
Reads a mathML
String into an ASTNode . |
XMLNode |
readNotes(java.lang.String notesXHTML) |
|
XMLNode |
readNotes(java.lang.String notesXHTML,
TreeNodeChangeListener listener) |
Reads a notes XML
String into an XMLNode . |
SBMLDocument |
readSBML(java.io.File file) |
|
SBMLDocument |
readSBML(java.io.File file,
TreeNodeChangeListener listener) |
Reads a SBML String from the given file.
|
SBMLDocument |
readSBML(java.lang.String file) |
Reads SBML from a given file.
|
SBMLDocument |
readSBML(javax.xml.stream.XMLEventReader xmlEventReader) |
|
SBMLDocument |
readSBML(javax.xml.stream.XMLEventReader xmlEventReader,
TreeNodeChangeListener listener) |
Reads an
SBMLDocument from the given XMLEventReader |
SBMLDocument |
readSBMLFile(java.lang.String fileName) |
Reads the SBML file 'fileName' and creates/initialises a SBMLDocument
instance.
|
SBMLDocument |
readSBMLFromStream(java.io.InputStream stream) |
|
SBMLDocument |
readSBMLFromStream(java.io.InputStream stream,
TreeNodeChangeListener listener) |
Reads a SBML document from the given
stream . |
SBMLDocument |
readSBMLFromString(java.lang.String xml) |
|
SBMLDocument |
readSBMLFromString(java.lang.String xml,
TreeNodeChangeListener listener) |
Reads a SBML model from the given XML String.
|
public void initializeAnnotationParsers()
HashMap
of this class.public static void main(java.lang.String[] args) throws java.io.IOException, javax.xml.stream.XMLStreamException, SBMLException
SBMLWriter.write(SBMLDocument, java.io.OutputStream)
.args
- the command line arguments, we are taking the first one as
the file name to read.java.io.IOException
- if the file name is not valid.SBMLException
- if there are any problems reading or writing the SBML model.javax.xml.stream.XMLStreamException
- if there are any problems reading or writing the XML file.public SBMLDocument readSBML(java.io.File file) throws java.io.IOException, javax.xml.stream.XMLStreamException
file
- javax.xml.stream.XMLStreamException
java.io.IOException
public SBMLDocument readSBML(java.io.File file, TreeNodeChangeListener listener) throws java.io.IOException, javax.xml.stream.XMLStreamException
file
- A file containing SBML content.listener
- java.io.IOException
javax.xml.stream.XMLStreamException
public SBMLDocument readSBML(java.lang.String file) throws javax.xml.stream.XMLStreamException, java.io.IOException
file
- The path to an SBML file.javax.xml.stream.XMLStreamException
java.io.IOException
public SBMLDocument readSBMLFile(java.lang.String fileName) throws javax.xml.stream.XMLStreamException, java.io.IOException
fileName
- name of the SBML file to read.javax.xml.stream.XMLStreamException
java.io.IOException
public SBMLDocument readSBML(javax.xml.stream.XMLEventReader xmlEventReader, TreeNodeChangeListener listener) throws javax.xml.stream.XMLStreamException
SBMLDocument
from the given XMLEventReader
xmlEventReader
- listener
- javax.xml.stream.XMLStreamException
public SBMLDocument readSBML(javax.xml.stream.XMLEventReader xmlEventReader) throws javax.xml.stream.XMLStreamException
xmlEventReader
- javax.xml.stream.XMLStreamException
public ASTNode readMathML(java.lang.String mathML, TreeNodeChangeListener listener) throws javax.xml.stream.XMLStreamException
ASTNode
.mathML
- listener
- ASTNode
representing the given mathML String.javax.xml.stream.XMLStreamException
public ASTNode readMathML(java.lang.String mathML, TreeNodeChangeListener listener, MathContainer parent) throws javax.xml.stream.XMLStreamException
String
into an ASTNode
.mathML
- listener
- parent
- the parent MathContainer
of the mathML to parseASTNode
representing the given mathML String
.javax.xml.stream.XMLStreamException
public ASTNode readMathML(java.lang.String mathML) throws javax.xml.stream.XMLStreamException
mathML
- javax.xml.stream.XMLStreamException
public XMLNode readNotes(java.lang.String notesXHTML, TreeNodeChangeListener listener) throws javax.xml.stream.XMLStreamException
String
into an XMLNode
.notesXHTML
- listener
- XMLNode
representing the given notes String
.javax.xml.stream.XMLStreamException
public XMLNode readNotes(java.lang.String notesXHTML) throws javax.xml.stream.XMLStreamException
notesXHTML
- javax.xml.stream.XMLStreamException
public SBMLDocument readSBMLFromStream(java.io.InputStream stream, TreeNodeChangeListener listener) throws javax.xml.stream.XMLStreamException
stream
.stream
- listener
- javax.xml.stream.XMLStreamException
public SBMLDocument readSBMLFromStream(java.io.InputStream stream) throws javax.xml.stream.XMLStreamException
stream
- javax.xml.stream.XMLStreamException
public SBMLDocument readSBMLFromString(java.lang.String xml, TreeNodeChangeListener listener) throws javax.xml.stream.XMLStreamException
xml
- listener
- javax.xml.stream.XMLStreamException
public SBMLDocument readSBMLFromString(java.lang.String xml) throws javax.xml.stream.XMLStreamException
xml
- javax.xml.stream.XMLStreamException