idare.imagenode.internal.DataManagement

Class NodeManager

java.lang.Object

idare.imagenode.internal.DataManagement.NodeManager

All Implemented Interfaces:

IDARENodeManager, DataSetChangeListener

public class NodeManager
extends Object
implements DataSetChangeListener, IDARENodeManager

NodeManager manages the nodes used in the IDARE App.

Author:

Thomas Pfau

Constructor Summary

Constructors

Constructor and Description
NodeManager(org.cytoscape.model.CyNetworkManager cyNetMgr, ActiveNodeManager anm)

Method Summary

Modifier and Type	Method and Description
void	addNodeChangeListener(NodeChangedListener listener) Add a listener that listens to changes in nodes in this manager.
void	datasetChanged(DataSetChangedEvent e) Inform that there was a change in the DataSets
void	datasetsChanged(DataSetsChangedEvent e) Inform that a Collection of DataSets changed.
void	generateLayoutsForNodes(Set<DataSet> datasets, ImageNodeLayout layout) Generate Layouts for All nodes in the DataSets present in the DataSetLayoutInfoBundles provided.
void	generateLayoutsForNodes(Set<DataSet> datasets, ImageNodeLayout layout, org.cytoscape.work.TaskMonitor monitor) Generate Layouts for All nodes in the DataSets present in the DataSetLayoutInfoBundles provided.
Collection<String>	getActiveIDs() Get a Collection of IDs for which layouts exist and which are active.
Collection<String>	getLayoutedIDs() Get a Collection of IDs for which layouts exist.
ImageNodeLayout	getLayoutForNode(String id) Get the layout for a specific id
ImageNodeModel	getNode(String ID) Get the Node corresponding to the given ID
Collection<String>	getNodesForLayout(ImageNodeLayout Layout) Create a Collection of IDs that are associated with a specific Layout.
Collection<String>	getNodesWithData() Get all nodes, that have associated data.
void	handleEvent(org.cytoscape.session.events.SessionAboutToBeSavedEvent arg0, IDAREImageNodeApp app) Handle a SessionAboutToBeSavedEvent.
void	handleEvent(org.cytoscape.session.events.SessionLoadedEvent arg0, IDAREImageNodeApp app) Restore the data of this nodemanager.
boolean	isNodeActive(String id) Check whether the node with the given ID is layouted and needs an image.
boolean	isNodeLayouted(String id) Check whether a tge node with the given ID is layouted
void	readNodeLayouts(File LayoutFile, IDAREImageNodeApp app) Read Layout data saved in a given File to restore old nodemanager data.
void	removeNodeChangeListener(NodeChangedListener listener) Remove a listener that had listened to changes in nodes in this manager.
void	reset() Reset this NodeManager clearing fields
void	setDataSetManager(DataSetManager dsm) Set the DatasetManager used by this NodeManager.
void	update(DataSet ds, boolean added) Update the Manager/Nodes with the new DataSet, either adding it or removing it form the nodes.
void	updateActiveNodes(Collection<String> updatedIDs)
void	updateNetworkNodes() Update the set of NetworkNode IDs.
void	writeNodeLayouts(File LayoutFile, IDAREImageNodeApp app) Write a structure that can be read again by a nodemanager to restore the current state of the manager.

Methods inherited from class java.lang.Object

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

Constructor Detail

NodeManager

public NodeManager(org.cytoscape.model.CyNetworkManager cyNetMgr,
                   ActiveNodeManager anm)

Method Detail

addNodeChangeListener

public void addNodeChangeListener(NodeChangedListener listener)

Add a listener that listens to changes in nodes in this manager.

Parameters:

listener - the NodeChangeListener to add

removeNodeChangeListener

public void removeNodeChangeListener(NodeChangedListener listener)

Remove a listener that had listened to changes in nodes in this manager.

Parameters:

listener - the NodeChangeListener to remove

setDataSetManager

public void setDataSetManager(DataSetManager dsm)

Set the DatasetManager used by this NodeManager. This is mainly to allow nodelayouts to listen to changes in Datasets.

Parameters:

dsm - the DataSetManager to assign

reset

public void reset()

Reset this NodeManager clearing fields

updateActiveNodes

public void updateActiveNodes(Collection<String> updatedIDs)

updateNetworkNodes

public void updateNetworkNodes()

Description copied from interface: IDARENodeManager

Update the set of NetworkNode IDs. This is to allow a minimal number of updates for graphics.

Specified by:

updateNetworkNodes in interface IDARENodeManager

datasetChanged

public void datasetChanged(DataSetChangedEvent e)

Description copied from interface: DataSetChangeListener

Inform that there was a change in the DataSets

Specified by:

datasetChanged in interface DataSetChangeListener

Parameters:

e - the DataSetChangedEvent to process

datasetsChanged

public void datasetsChanged(DataSetsChangedEvent e)

Description copied from interface: DataSetChangeListener

Inform that a Collection of DataSets changed.

Specified by:

datasetsChanged in interface DataSetChangeListener

Parameters:

e - The DataSetsChangedEvent to process

update

public void update(DataSet ds,
                   boolean added)

Update the Manager/Nodes with the new DataSet, either adding it or removing it form the nodes.

Parameters:

ds - the dataset to update

added - whether the dataset was added

getNode

public ImageNodeModel getNode(String ID)

Get the Node corresponding to the given ID

Parameters:

ID - The ID of the node

Returns:

a node, if it exists, or null, if the ID is not linked to a known node.

getNodesWithData

public Collection<String> getNodesWithData()

Get all nodes, that have associated data.

Returns:

all nodes that have at least one associated dataset.

generateLayoutsForNodes

public void generateLayoutsForNodes(Set<DataSet> datasets,
                                    ImageNodeLayout layout,
                                    org.cytoscape.work.TaskMonitor monitor)
                             throws TooManyItemsException,
                                    ContainerUnplaceableExcpetion,
                                    DimensionMismatchException,
                                    WrongDatasetTypeException

Generate Layouts for All nodes in the DataSets present in the DataSetLayoutInfoBundles provided. This version is to be used if the created nodes are created by a Task.

Parameters:

datasets - The datasets to create nodes for

layout - the layout to use for the nodes

monitor - The TaskMonitor that keeps track of progress.

Throws:

TooManyItemsException - if there are too many items

ContainerUnplaceableExcpetion - if a container cannot be placed

DimensionMismatchException - if the dimensions dont fit.

WrongDatasetTypeException - if a dataset cannot be layout out with the layout.

generateLayoutsForNodes

public void generateLayoutsForNodes(Set<DataSet> datasets,
                                    ImageNodeLayout layout)
                             throws TooManyItemsException,
                                    ContainerUnplaceableExcpetion,
                                    DimensionMismatchException,
                                    WrongDatasetTypeException

Generate Layouts for All nodes in the DataSets present in the DataSetLayoutInfoBundles provided.

Parameters:

datasets - the datasets t generate layouts for

layout - the layout to use for the nodes

Throws:

TooManyItemsException - if too many items were in the datasets

ContainerUnplaceableExcpetion - if a container could not be placed

DimensionMismatchException - if dimensions could not fit

WrongDatasetTypeException - if a dataset could not be layout out with the selected type of layout

isNodeLayouted

public boolean isNodeLayouted(String id)

Check whether a tge node with the given ID is layouted

Parameters:

id - The node id to check

Returns:

true if there is a layout for the given ID, or false otherwise. THis does not check, whether the node exists at all.

isNodeActive

public boolean isNodeActive(String id)

Check whether the node with the given ID is layouted and needs an image.

Parameters:

id - The node ID to check

Returns:

true if there is a layout for the given ID, and it is needed.false otherwise. THis does not check, whether the node exists at all.

getLayoutForNode

public ImageNodeLayout getLayoutForNode(String id)

Get the layout for a specific id

Parameters:

id - The node ID to get the layout for

Returns:

the layout associated with the ID, or null if the ID has no associated layout.

getLayoutedIDs

public Collection<String> getLayoutedIDs()

Get a Collection of IDs for which layouts exist.

Returns:

A Collection of Strings containing all IDs with an associated Layout

getActiveIDs

public Collection<String> getActiveIDs()

Get a Collection of IDs for which layouts exist and which are active.

Returns:

A Collection of Strings containing all IDs with an associated Layout

handleEvent

public void handleEvent(org.cytoscape.session.events.SessionAboutToBeSavedEvent arg0,
                        IDAREImageNodeApp app)

Handle a SessionAboutToBeSavedEvent. Since the order in which the event is handles by the different components of the app is important, This Object does not itself implement the listener, but requires another function to call the handling operation.

Parameters:

arg0 - the event to handle

app - the IDAREImageNodeApp to use for reference

handleEvent

public void handleEvent(org.cytoscape.session.events.SessionLoadedEvent arg0,
                        IDAREImageNodeApp app)

Restore the data of this nodemanager. Since we need to have a specific order for DataSetManager and NodeManager restoration, this cannot simply be achieved by implementing the SessionLoadedListener interface

Parameters:

arg0 - the event to handle

app - the IDAREImageNodeApp for reference

getNodesForLayout

public Collection<String> getNodesForLayout(ImageNodeLayout Layout)

Create a Collection of IDs that are associated with a specific Layout.

Parameters:

Layout - the layout to get nodes for

Returns:

the Nodes IDs assigned to the provided ImageNodeLayout

writeNodeLayouts

public void writeNodeLayouts(File LayoutFile,
                             IDAREImageNodeApp app)
                      throws IOException

Write a structure that can be read again by a nodemanager to restore the current state of the manager.

Parameters:

LayoutFile - the File to write the lyouts to

app - the IDAREImageNodeApp as reference

Throws:

IOException - if something goes wrong during IO

readNodeLayouts

public void readNodeLayouts(File LayoutFile,
                            IDAREImageNodeApp app)
                     throws IOException

Read Layout data saved in a given File to restore old nodemanager data.

Parameters:

LayoutFile - The File to read the layouts from

app - the IDAREImageNodeApp as reference

Throws:

IOException - if something goes wrong during IO