idare.Properties

Class IDARESettingsManager

java.lang.Object

idare.Properties.IDARESettingsManager

public class IDARESettingsManager
extends Object

Class to keep track of IDARE IDs and complain (throw exceptions) if duplicate IDs are found. hopefully there wont be any instances with > max(long) nodes in one network...

Author:

thomas

Constructor Summary

Constructors

Constructor and Description
IDARESettingsManager() Initialize the IDare Manager

Method Summary

Modifier and Type	Method and Description
void	addIDs(Collection<Long> ids) Add all IDs of the collection to this manager.
static Set<String>	getNetworkIDAREIDs(org.cytoscape.model.CyNetwork network, String IDCol) Get the set of nodeIDs present in the provided network
long	getNextGeneID() Get the next gene ID which is the largest current ID + 1 This Id should be used otherwise it will be blocked for this manager.
long	getNextNetworkID() Get the next network ID which is the largest current ID + 1 This Id should be used otherwise it will be blocked for this manager.
long	getNextNodeID() Get the next ID which is the largest current ID + 1 This Id should be used otherwise it will be blocked for this manager.
long	getNextProteinComplexID() Get the nextprotein Complex ID which is the largest current ID + 1 This Id should be used otherwise it will be blocked for this manager.
long	getNextProteinID() Get the next protein ID which is the largest current ID + 1 This Id should be used otherwise it will be blocked for this manager.
String	getSubNetworkType(String targetType) Get the IDAREType associated with a specific Target Type for the subnetwork generation.
String	getType(String name) Get the Type associated with a specific Name.
void	handleSessionLoadedEvent(org.cytoscape.session.events.SessionLoadedEvent arg0) Handle the loading of a session
static void	initNetwork(org.cytoscape.model.CyNetwork network) Set up the provided network using the Provided IDCol for the IDARE Names and the NodeTypesCol for the IDARE Node Types
static boolean	isSetupNetwork(org.cytoscape.model.CyNetwork network) Test whether a Network has the table Columns required for usage in IDARE
static void	resetNetworks(Collection<org.cytoscape.model.CyNetwork> networks)
void	resetSubNetworkTypes() Reset the SubNetworkTypes.
static void	setIDARENames(org.cytoscape.model.CyNetwork network, Collection<String> IDs, String ColForNames) Set the matching IDARENames to the values set in the Selected Column(except that Strings will be used in the IDARE_NAME column
static void	SetNetworkData(org.cytoscape.model.CyNetwork network, IDARESettingsManager IDAREIdmgr, String NodeTypeCol, String IDCol, boolean overwrite, NodeManager nm) Set up the provided network using the Provided IDCol for the IDARE Names and the NodeTypesCol for the IDARE Node Types
void	setSubNetworkType(String IDAREType, String targetType) Set the IDAREType associated with a specific Target Type for subnetwork generation.
void	setType(String IDAREType, String targetType) Set the IDAREType associated with a specific Target Type.
static void	SetupNetwork(org.cytoscape.model.CyNetwork network, IDARESettingsManager IDAREIdmgr, String NodeTypeCol, String IDCol) Set up the provided network using the Provided IDCol for the IDARE Names and the NodeTypesCol for the IDARE Node Types

Methods inherited from class java.lang.Object

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

Constructor Detail

IDARESettingsManager

public IDARESettingsManager()

Initialize the IDare Manager

Method Detail

getNextProteinID

public long getNextProteinID()

Get the next protein ID which is the largest current ID + 1 This Id should be used otherwise it will be blocked for this manager.

Returns:

a valid IDARE identifier

getNextGeneID

public long getNextGeneID()

Get the next gene ID which is the largest current ID + 1 This Id should be used otherwise it will be blocked for this manager.

Returns:

a valid IDARE identifier

getNextProteinComplexID

public long getNextProteinComplexID()

Get the nextprotein Complex ID which is the largest current ID + 1 This Id should be used otherwise it will be blocked for this manager.

Returns:

a valid IDARE identifier

getNextNodeID

public long getNextNodeID()

Get the next ID which is the largest current ID + 1 This Id should be used otherwise it will be blocked for this manager.

Returns:

a valid IDARE identifier

getNextNetworkID

public long getNextNetworkID()

Get the next network ID which is the largest current ID + 1 This Id should be used otherwise it will be blocked for this manager.

Returns:

a valid IDARE identifier

addIDs

public void addIDs(Collection<Long> ids)
            throws IllegalArgumentException

Add all IDs of the collection to this manager. The manager checks whether any ID is already used.

Parameters:

ids - - The ids that need to be checked

Throws:

IllegalArgumentException - - If the provided ID is already present in this Manager this exception is thrown IF an exception is thrown, the Manager is still valid and none of the provided ids has been added.

getType

public String getType(String name)

Get the Type associated with a specific Name.

Parameters:

name - the name to request the type for..

Returns:

the type associated with the given name.

setType

public void setType(String IDAREType,
                    String targetType)

Set the IDAREType associated with a specific Target Type.

Parameters:

IDAREType - The IDAREType for a specified targettype (i.e. entries from IDAREProperties;

targetType - The type to match to the given IDAREType

resetSubNetworkTypes

public void resetSubNetworkTypes()

Reset the SubNetworkTypes. This should be called when new subnetworktypes are being set for a subnetwork generation process.

setSubNetworkType

public void setSubNetworkType(String IDAREType,
                              String targetType)

Set the IDAREType associated with a specific Target Type for subnetwork generation.

Parameters:

IDAREType - The IDAREType to assign a string to

targetType - The string the IDAREType should be assigned to.

getSubNetworkType

public String getSubNetworkType(String targetType)

Get the IDAREType associated with a specific Target Type for the subnetwork generation.

Parameters:

targetType - the type to extract an IDAREType for.

Returns:

the IDARE String associate with the given type

handleSessionLoadedEvent

public void handleSessionLoadedEvent(org.cytoscape.session.events.SessionLoadedEvent arg0)

Handle the loading of a session

Parameters:

arg0 - - The SessionLoadedEvent to use.

resetNetworks

public static void resetNetworks(Collection<org.cytoscape.model.CyNetwork> networks)

SetupNetwork

public static void SetupNetwork(org.cytoscape.model.CyNetwork network,
                                IDARESettingsManager IDAREIdmgr,
                                String NodeTypeCol,
                                String IDCol)

Set up the provided network using the Provided IDCol for the IDARE Names and the NodeTypesCol for the IDARE Node Types

Parameters:

network - the network to set up

IDAREIdmgr - A IDARE ID Manager to set up the IDs of all

NodeTypeCol - The Column indicating the node type.

IDCol - The Column name indicating the node ID

SetNetworkData

public static void SetNetworkData(org.cytoscape.model.CyNetwork network,
                                  IDARESettingsManager IDAREIdmgr,
                                  String NodeTypeCol,
                                  String IDCol,
                                  boolean overwrite,
                                  NodeManager nm)

Set up the provided network using the Provided IDCol for the IDARE Names and the NodeTypesCol for the IDARE Node Types

Parameters:

network - - the network to set up

IDAREIdmgr - - A IDARE ID Manager to set up the IDs of all

NodeTypeCol - The Column indicating the node type.

IDCol - The Column name indicating the node ID

overwrite - Whether to overwrite existing names and types.

nm - The nodemanager, which should be updated according to the overwritten entries.

isSetupNetwork

public static boolean isSetupNetwork(org.cytoscape.model.CyNetwork network)

Test whether a Network has the table Columns required for usage in IDARE

Parameters:

network - The network to test.

Returns:

whether the network is set up to be used with IDARE.

setIDARENames

public static void setIDARENames(org.cytoscape.model.CyNetwork network,
                                 Collection<String> IDs,
                                 String ColForNames)

Set the matching IDARENames to the values set in the Selected Column(except that Strings will be used in the IDARE_NAME column

Parameters:

network - - the network for which to assign the names

IDs - - The IDs which are transferred

ColForNames - - The Column to get the IDs from.

initNetwork

public static void initNetwork(org.cytoscape.model.CyNetwork network)

Set up the provided network using the Provided IDCol for the IDARE Names and the NodeTypesCol for the IDARE Node Types

Parameters:

network - - the network to set up

getNetworkIDAREIDs

public static Set<String> getNetworkIDAREIDs(org.cytoscape.model.CyNetwork network,
                                             String IDCol)

Get the set of nodeIDs present in the provided network

Parameters:

network - - the CyNetwork to retrieve the nodeids from

IDCol - - The column in the networks node CyTable containing the IDs.

Returns:

- a Set of IDs present in the provided network