cytoscape.data.writers
Class XGMMLWriter

java.lang.Object
  cytoscape.data.writers.XGMMLWriter

public class XGMMLWriter
extends Object

Write network and attributes in XGMML format and
marshall it in a streme.

Since:

Cytoscape 2.6

Version:

1.2

Author:

kono, scooter

See Also:

XGMMLReader

Field Summary

static String	BACKGROUND
protected static int	EDGE
static String	ENCODE_PROPERTY
static String	ENCODING
static String	GRAPH_VIEW_CENTER_X
static String	GRAPH_VIEW_CENTER_Y
static String	GRAPH_VIEW_ZOOM
protected static String	METANODE
protected static int	NETWORK
protected static int	NODE
protected static String	NORMAL
protected static String	REFERENCE

Constructor Summary

XGMMLWriter(CyNetwork network, CyNetworkView view)
Constructor.
Initialize data objects to be saved in XGMML file.

XGMMLWriter(CyNetwork network, CyNetworkView view, boolean noCytoscapeGraphics)
Constructor.
Initialize data objects to be saved in XGMML file.

Method Summary

boolean	isDoFullEncoding()
void	setDoFullEncoding(boolean doFullEnc)
void	write(Writer writer) Write the XGMML file. This method creates all JAXB objects from Cytoscape internal data structure, and them marshall it into an XML (XGMML) document.

Methods inherited from class java.lang.Object

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

Field Detail

ENCODING

public static final String ENCODING

See Also:

Constant Field Values

NORMAL

protected static final String NORMAL

See Also:

Constant Field Values

METANODE

protected static final String METANODE

See Also:

Constant Field Values

REFERENCE

protected static final String REFERENCE

See Also:

Constant Field Values

NODE

protected static final int NODE

See Also:

Constant Field Values

EDGE

protected static final int EDGE

See Also:

Constant Field Values

NETWORK

protected static final int NETWORK

See Also:

Constant Field Values

BACKGROUND

public static final String BACKGROUND

See Also:

Constant Field Values

GRAPH_VIEW_ZOOM

public static final String GRAPH_VIEW_ZOOM

See Also:

Constant Field Values

GRAPH_VIEW_CENTER_X

public static final String GRAPH_VIEW_CENTER_X

See Also:

Constant Field Values

GRAPH_VIEW_CENTER_Y

public static final String GRAPH_VIEW_CENTER_Y

See Also:

Constant Field Values

ENCODE_PROPERTY

public static final String ENCODE_PROPERTY

See Also:

Constant Field Values

Constructor Detail

XGMMLWriter

public XGMMLWriter(CyNetwork network,
                   CyNetworkView view)
            throws IOException,
                   URISyntaxException

Constructor.
Initialize data objects to be saved in XGMML file.

Parameters:

network - CyNetwork object to be saved.

view - CyNetworkView for the network.

Throws:

URISyntaxException

JAXBException

IOException

XGMMLWriter

public XGMMLWriter(CyNetwork network,
                   CyNetworkView view,
                   boolean noCytoscapeGraphics)
            throws IOException,
                   URISyntaxException

Constructor.
Initialize data objects to be saved in XGMML file.

Parameters:

network - CyNetwork object to be saved.

view - CyNetworkView for the network.

noCytoscapeGraphics - boolean to indicate whether cytoscape graphics attributes should be written

Throws:

URISyntaxException

JAXBException

IOException

Method Detail

write

public void write(Writer writer)
           throws IOException

Write the XGMML file.
This method creates all JAXB objects from Cytoscape internal
data structure, and them marshall it into an XML (XGMML) document.

Parameters:

writer - Witer to create XGMML file

Throws:

IOException

isDoFullEncoding

public boolean isDoFullEncoding()

setDoFullEncoding

public void setDoFullEncoding(boolean doFullEnc)