Package org.cytoscape.session
Class CySession
- java.lang.Object
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- org.cytoscape.session.CySession
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public final class CySession extends Object
A session is an immutable snapshot of the data contents of Cytoscape. Sessions are only meant for saving and restoring the state of Cytoscape and are not meant to be used interactively for anything besides writing, reading, and restoring from session files.
Using the data returned from the various methods in a CySession object should be sufficient to recreate all aspects of Cytoscape at the time the session was created.
Creating an instance of CySession is done following the builder pattern. For example, the following code creates a session that only includes a list of networkViews and Cytoscape properties, but nothing else.
CySession session = new CySession.Builder().networkViews(viewList).cytoscapeProperties(cyProps).build();
Module:
session-api
To use this in your app, include the following dependency in your POM:
<dependency> <groupId>org.cytoscape</groupId> <artifactId>session-api</artifactId> </dependency>
Cytoscape Backwards Compatibility (Final Class): This class is final and therefore can't be extended by users. This means that we may add methods for minor version updates. Methods will only be removed for major version updates.
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
CySession.Builder
A implementation of the builder pattern used to construct immutable instances of CySession objects.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Map<String,List<File>>
getAppFileListMap()
Returns a map of app names to lists of File objects that are stored as part of the session for the specified app.Set<CyNetwork>
getNetworks()
Returns a set of all CyNetwork objects contained in this Session.Set<CyNetworkView>
getNetworkViews()
Returns a set of all CyNetworkView objects contained in this Session.<T extends CyIdentifiable>
TgetObject(Long oldSUID, Class<T> type)
When a session is restored, Cytoscape automatically generates new SUIDs.<T extends CyIdentifiable>
TgetObject(String oldId, Class<T> type)
When a session is restored, Cytoscape automatically generates new SUIDs.Set<CyProperty<?>>
getProperties()
Returns a set ofCyProperty
objects defined for this session.Set<CyTableMetadata>
getTables()
Returns a set of all CyTable objects contained in this Session.Map<CyNetworkView,String>
getViewVisualStyleMap()
Returns a map of CyNetworkViews to the names of the VisualStyle applied to that network view in this session.Set<VisualStyle>
getVisualStyles()
Returns a set containing all VisualStyles defined for this session.
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Method Detail
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getNetworks
public Set<CyNetwork> getNetworks()
Returns a set of all CyNetwork objects contained in this Session.- Returns:
- A set of all CyNetwork objects contained in this Session.
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getNetworkViews
public Set<CyNetworkView> getNetworkViews()
Returns a set of all CyNetworkView objects contained in this Session.- Returns:
- A set of all CyNetworkView objects contained in this Session.
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getTables
public Set<CyTableMetadata> getTables()
Returns a set of all CyTable objects contained in this Session.- Returns:
- A set of all CyTable objects contained in this Session.
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getViewVisualStyleMap
public Map<CyNetworkView,String> getViewVisualStyleMap()
Returns a map of CyNetworkViews to the names of the VisualStyle applied to that network view in this session.- Returns:
- A map of CyNetworkViews to the names of the VisualStyle applied to that network view in this session.
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getProperties
public Set<CyProperty<?>> getProperties()
Returns a set ofCyProperty
objects defined for this session.- Returns:
- A set of session related
CyProperty
objects. defined for this session.
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getVisualStyles
public Set<VisualStyle> getVisualStyles()
Returns a set containing all VisualStyles defined for this session.- Returns:
- A Set of
VisualStyle
objects
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getAppFileListMap
public Map<String,List<File>> getAppFileListMap()
Returns a map of app names to lists of File objects that are stored as part of the session for the specified app.- Returns:
- A map of app names to lists of File objects that are stored as part of the session for the specified app.
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getObject
public <T extends CyIdentifiable> T getObject(Long oldSUID, Class<T> type)
When a session is restored, Cytoscape automatically generates new SUIDs. This method returns an object (CyNode
,CyEdge
,CyNetwork
orCyNetworkView
) given its former SUID.
Use this method if the version of the loaded session is 3.0 or higher.- Parameters:
oldSUID
- The former SUID.type
- The Class of the object to be returned (CyNode
,CyEdge
,CyNetwork
orCyNetworkView
).- Returns:
- An object (
CyNode
,CyEdge
,CyNetwork
orCyNetworkView
) given its former SUID.
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getObject
public <T extends CyIdentifiable> T getObject(String oldId, Class<T> type)
When a session is restored, Cytoscape automatically generates new SUIDs. This method returns an object (CyNode
,CyEdge
,CyNetwork
orCyNetworkView
) given its former identifier.
Use this method if the version of the loaded session is 2.x, because older versions of Cytoscape save String IDs, such as node names and the network titles.- Parameters:
oldId
- The former ID, from Cytocape versions prior than 3.0.type
- The Class of the object to be returned (CyNode
,CyEdge
,CyNetwork
orCyNetworkView
).- Returns:
- An object (
CyNode
,CyEdge
,CyNetwork
orCyNetworkView
) given its former identifier.
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