Cytoscape 2.8.0 API

cytoscape.data.writers
Class XGMMLWriter

java.lang.Object
  extended by 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)

Cytoscape 2.8.0 API

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