org.colomoto.biolqm.io.ginml

Class AbstractGINMLWriter

java.lang.Object

org.colomoto.biolqm.io.ginml.AbstractGINMLWriter

Direct Known Subclasses:

LogicalModel2GINML

public abstract class AbstractGINMLWriter
extends Object

Some common methods to write a GINML file.

Author:

Aurelien Naldi

Field Summary

Fields

Modifier and Type	Field and Description
static String	DEFAULT_DTD

Constructor Summary

Constructors

Constructor and Description
AbstractGINMLWriter()

Method Summary

Modifier and Type	Method and Description
void	export(OutputStream out) Start the GINML export.
abstract List<String>	getNodes() get the names of the nodes to save in GINML.
protected void	writeEdge(XMLWriter xw, String from, String to, int threshold, String sign) Write an edge to GINML.
abstract void	writeEdges(XMLWriter out) Start writing the edges (interactions).
protected void	writeLogicalParameter(XMLWriter xw, int targetValue, String activeInteractions) Write a logical parameter to GINML.
protected void	writeNodeDecl(XMLWriter xw, String nodeID, int max) Write a node declaration to GINML.
abstract void	writeNodes(XMLWriter out) Start writing the nodes.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_DTD

public static final String DEFAULT_DTD

See Also:

Constant Field Values

Constructor Detail

AbstractGINMLWriter

public AbstractGINMLWriter()

Method Detail

export

public void export(OutputStream out)
            throws IOException

Start the GINML export.

Parameters:

out - an opened output stream to save the result

Throws:

IOException - if writing fails

getNodes

public abstract List<String> getNodes()

get the names of the nodes to save in GINML.

Returns:

the list of node IDs

writeNodes

public abstract void writeNodes(XMLWriter out)
                         throws IOException

Start writing the nodes. This must be implemented by subclasses.

Parameters:

out - an opened XML writer to save the result

Throws:

IOException - if writing fails

writeEdges

public abstract void writeEdges(XMLWriter out)
                         throws IOException

Start writing the edges (interactions). This must be implemented by subclasses.

Parameters:

out - an opened XML writer to save the result

Throws:

IOException - if writing fails

writeEdge

protected void writeEdge(XMLWriter xw,
                         String from,
                         String to,
                         int threshold,
                         String sign)
                  throws IOException

Write an edge to GINML.

Parameters:

xw - an opened XML writer to save the result

from - the name of the source node

to - the name of the target node

threshold - the threshold of this interaction

sign - the sign of this interaction

Throws:

IOException - if writing fails

writeNodeDecl

protected void writeNodeDecl(XMLWriter xw,
                             String nodeID,
                             int max)
                      throws IOException

Write a node declaration to GINML. This method will not close the tag to let the caller add child elements, especially parameters.

Parameters:

xw - an opened XML writer to save the result

nodeID - the ID of the component to save

max - the maximal value of this component (should be at least 1)

Throws:

IOException - if writing fails

writeLogicalParameter

protected void writeLogicalParameter(XMLWriter xw,
                                     int targetValue,
                                     String activeInteractions)
                              throws IOException

Write a logical parameter to GINML.

Parameters:

xw - an opened XML writer to save the result

targetValue - the target value when this parameter is enabled

activeInteractions - the list of associated active interactions

Throws:

IOException - if writing fails