Cytoscape 2.6.2 (c) 2006,2007 ISB, MSKCC, UCSD

cytoscape.data.readers
Class CytoscapeSessionReader

java.lang.Object
  extended by cytoscape.data.readers.CytoscapeSessionReader

public class CytoscapeSessionReader
extends Object

Reader to load CYtoscape Session file (.cys).
This class unzip cys file and read all files in the archive.

This class accept input as URL only! If it is a file, use File.toURL() to get platform dependent file URL.

Since:
Cytoscape 2.3
Version:
1.0
Author:
kono
See Also:
XGMMLReader

Field Summary
static String BOOKMARK_PACKAGE_NAME
           
static String CY_PROPS
           
static String CYSESSION
           
static String PACKAGE_NAME
           
static String VIZMAP_PROPS
           
static String XGMML_EXT
           
 
Constructor Summary
CytoscapeSessionReader(String fileName)
          Constructor.
CytoscapeSessionReader(String fileName, TaskMonitor monitor)
          Creates a new CytoscapeSessionReader object.
CytoscapeSessionReader(URL sourceName)
          Creates a new CytoscapeSessionReader object.
CytoscapeSessionReader(URL sourceName, TaskMonitor monitor)
          Constructor for remote file (specified by an URL)
 
Method Summary
 String getCysessionNote()
          Extract Session Note test field in cysession.xml
 void read()
          Read a session file.
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

PACKAGE_NAME

public static final String PACKAGE_NAME
See Also:
Constant Field Values

BOOKMARK_PACKAGE_NAME

public static final String BOOKMARK_PACKAGE_NAME
See Also:
Constant Field Values

CYSESSION

public static final String CYSESSION
See Also:
Constant Field Values

VIZMAP_PROPS

public static final String VIZMAP_PROPS
See Also:
Constant Field Values

CY_PROPS

public static final String CY_PROPS
See Also:
Constant Field Values

XGMML_EXT

public static final String XGMML_EXT
See Also:
Constant Field Values
Constructor Detail

CytoscapeSessionReader

public CytoscapeSessionReader(URL sourceName,
                              TaskMonitor monitor)
                       throws IOException
Constructor for remote file (specified by an URL)

Parameters:
sourceName -
Throws:
IOException - This is for remote session file (URL).

CytoscapeSessionReader

public CytoscapeSessionReader(String fileName,
                              TaskMonitor monitor)
                       throws IOException
Creates a new CytoscapeSessionReader object.

Parameters:
fileName - DOCUMENT ME!
monitor - DOCUMENT ME!
Throws:
IOException - DOCUMENT ME!

CytoscapeSessionReader

public CytoscapeSessionReader(String fileName)
                       throws IOException
Constructor.
Create reader from file name.

Parameters:
fileName -
Throws:
IOException

CytoscapeSessionReader

public CytoscapeSessionReader(URL sourceName)
                       throws IOException
Creates a new CytoscapeSessionReader object.

Parameters:
sourceName - DOCUMENT ME!
Throws:
IOException - DOCUMENT ME!
Method Detail

read

public void read()
          throws IOException,
                 javax.xml.bind.JAXBException,
                 Exception
Read a session file.

Throws:
IOException
javax.xml.bind.JAXBException
Exception

getCysessionNote

public String getCysessionNote()
Extract Session Note test field in cysession.xml

Returns:
Session Note

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