cytoscape.data
Class NetworkData

java.lang.Object
  cytoscape.data.NetworkData

public abstract class NetworkData
extends Object

There is an event fired anytime that a value is modified, you need to be listener to the attribute name though.

Field Summary

static int	ATTRIBUTE_ALREADY_ASSIGNED
static int	DOUBLE_TYPE
static String	EDGE_ATTRIBUTE_ADDED
static String	EDGE_ATTRIBUTE_REMOVED
static int	INSANE_ATTRIBUTE_ID
static int	INSANE_ATTRIBUTE_TYPE
static int	NO_SUCH_ATTRIBUTE
static String	NODE_ATTRIBUTE_ADDED
static String	NODE_ATTRIBUTE_REMOVED
static int	OBJECT_TYPE
protected static Object	pcsO
static int	STRING_TYPE
static int	VALUE_NOT_A_DOUBLE
static int	WRONG_ATTRIBUTE_TYPE

Constructor Summary

NetworkData()

Method Summary

static int	addNodeAttribute(String attribute_name) Attempts to add a new Attribute name, of Object type for nodes.
static int	addNodeAttribute(String attribute_name, int attribute_type) Attempts to add a new Attribute name, of given type for nodes.
static double	getNodeAttributeDoubleValue(int node_index, String attribute) DOCUMENT ME!
static double	getNodeAttributeDoubleValue(Node node, String attribute) DOCUMENT ME!
static int	getNodeAttributeID(String attribute) DOCUMENT ME!
static Object	getNodeAttributeObjectValue(int node_index, String attribute) DOCUMENT ME!
static Object	getNodeAttributeObjectValue(Node node, String attribute) DOCUMENT ME!
static String[]	getNodeAttributes(int[] node_indices) Returns all Attributes that one or more of the given nodes have values for.
static String	getNodeAttributeStringValue(int node_index, String attribute) DOCUMENT ME!
static String	getNodeAttributeStringValue(Node node, String attribute) DOCUMENT ME!
static int	getNodeAttributeType(String attribute) DOCUMENT ME!
static Object	getNodeAttributeValue(int node_index, int att_id) DOCUMENT ME!
static Object	getNodeAttributeValue(Node node, String attribute) DOCUMENT ME!
static int	setNodeAttributeDoubleValue(int node_index, int att_id, double value) DOCUMENT ME!
static int	setNodeAttributeDoubleValue(int node_index, String attribute, double value) DOCUMENT ME!
static int	setNodeAttributeDoubleValue(Node node, String attribute, double value) DOCUMENT ME!
static int	setNodeAttributeObjectValue(int node_index, int att_id, Object value) DOCUMENT ME!
static int	setNodeAttributeObjectValue(int node_index, String attribute, Object value) DOCUMENT ME!
static int	setNodeAttributeObjectValue(Node node, String attribute, Object value) DOCUMENT ME!
static int	setNodeAttributeStringValue(int node_index, int att_id, String value) DOCUMENT ME!
static int	setNodeAttributeStringValue(int node_index, String attribute, String value) DOCUMENT ME!
static int	setNodeAttributeStringValue(Node node, String attribute, String value) DOCUMENT ME!
static int	setNodeAttributeValue(Node node, String attribute, Object value) DOCUMENT ME!
static int	setNodeAttributeValue(Node node, String attribute, Object value, int attribute_type) Attempts to set the value for a node, for a given attribute.

Methods inherited from class java.lang.Object

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

Field Detail

NODE_ATTRIBUTE_ADDED

public static String NODE_ATTRIBUTE_ADDED

NODE_ATTRIBUTE_REMOVED

public static String NODE_ATTRIBUTE_REMOVED

EDGE_ATTRIBUTE_ADDED

public static String EDGE_ATTRIBUTE_ADDED

EDGE_ATTRIBUTE_REMOVED

public static String EDGE_ATTRIBUTE_REMOVED

DOUBLE_TYPE

public static int DOUBLE_TYPE

STRING_TYPE

public static int STRING_TYPE

OBJECT_TYPE

public static int OBJECT_TYPE

NO_SUCH_ATTRIBUTE

public static int NO_SUCH_ATTRIBUTE

VALUE_NOT_A_DOUBLE

public static int VALUE_NOT_A_DOUBLE

INSANE_ATTRIBUTE_TYPE

public static int INSANE_ATTRIBUTE_TYPE

WRONG_ATTRIBUTE_TYPE

public static int WRONG_ATTRIBUTE_TYPE

INSANE_ATTRIBUTE_ID

public static int INSANE_ATTRIBUTE_ID

ATTRIBUTE_ALREADY_ASSIGNED

public static int ATTRIBUTE_ALREADY_ASSIGNED

pcsO

protected static Object pcsO

Constructor Detail

NetworkData

public NetworkData()

Method Detail

addNodeAttribute

public static int addNodeAttribute(String attribute_name)

Attempts to add a new Attribute name, of Object type for nodes.

Parameters:

attribute_name - the name of the new attribute

Returns:

the ID of the attribute, if assinged, or -1 if already assigned/not a good name.

addNodeAttribute

public static int addNodeAttribute(String attribute_name,
                                   int attribute_type)

Attempts to add a new Attribute name, of given type for nodes. Available types are: OBJECT_TYPE, DOUBLE_TYPE, and STRING_TYPE

Parameters:

attribute_name - the name of the new attribute

Returns:

the ID of the attribute, if assinged, or -1 if already assigned/not a good name.

getNodeAttributeType

public static int getNodeAttributeType(String attribute)

DOCUMENT ME!

Parameters:

attribute - DOCUMENT ME!

Returns:

DOCUMENT ME!

getNodeAttributeID

public static int getNodeAttributeID(String attribute)

DOCUMENT ME!

Parameters:

attribute - DOCUMENT ME!

Returns:

DOCUMENT ME!

setNodeAttributeValue

public static int setNodeAttributeValue(Node node,
                                        String attribute,
                                        Object value)

DOCUMENT ME!

Parameters:

node - DOCUMENT ME!

attribute - DOCUMENT ME!

value - DOCUMENT ME!

Returns:

DOCUMENT ME!

setNodeAttributeValue

public static int setNodeAttributeValue(Node node,
                                        String attribute,
                                        Object value,
                                        int attribute_type)

Attempts to set the value for a node, for a given attribute. However, there a few checks that happen along the way. First the Node must be part of the CytoscapeRootGraph, also the value must match the attribute type, which must match the overall attribute type. No problem if the attribute is not initialized, but if has been initialized, and the types don't match, then you have a problem.

Parameters:

node - the node who should be part of Cytoscape

attribute - the name of this attribute

value - the value, which must match the attribute type

attribute_type - if this attribute has been previosly initialized, then this musht match that type. Otherwise the attribute will get initialized with this type.

Returns:

"1" or a positive value if all went well, otherwise a negative value that corresponds to the error. See the "throws" keeping in mind that these are not really exceptions...

Throws:

{@link - VALUE_NOT_A_DOUBLE} if the attribute_type was double and the value could be put into a Double.

{@link - INSANE_ATTRIBUTE_TYPE} if the given attribute_type is not a supported one

{@link - WRONG_ATTRIBUTE_TYPE} if the given attribute_type does not match the attribute_type of the attribute

{@link - INSANE_ATTRIBUTE_ID} if the attribute does not exist

setNodeAttributeObjectValue

public static int setNodeAttributeObjectValue(int node_index,
                                              String attribute,
                                              Object value)

DOCUMENT ME!

Parameters:

node_index - DOCUMENT ME!

attribute - DOCUMENT ME!

value - DOCUMENT ME!

Returns:

DOCUMENT ME!

setNodeAttributeObjectValue

public static int setNodeAttributeObjectValue(Node node,
                                              String attribute,
                                              Object value)

DOCUMENT ME!

Parameters:

node - DOCUMENT ME!

attribute - DOCUMENT ME!

value - DOCUMENT ME!

Returns:

DOCUMENT ME!

setNodeAttributeObjectValue

public static int setNodeAttributeObjectValue(int node_index,
                                              int att_id,
                                              Object value)

DOCUMENT ME!

Parameters:

node_index - DOCUMENT ME!

att_id - DOCUMENT ME!

value - DOCUMENT ME!

Returns:

DOCUMENT ME!

setNodeAttributeDoubleValue

public static int setNodeAttributeDoubleValue(int node_index,
                                              String attribute,
                                              double value)

DOCUMENT ME!

Parameters:

node_index - DOCUMENT ME!

attribute - DOCUMENT ME!

value - DOCUMENT ME!

Returns:

DOCUMENT ME!

setNodeAttributeDoubleValue

public static int setNodeAttributeDoubleValue(Node node,
                                              String attribute,
                                              double value)

DOCUMENT ME!

Parameters:

node - DOCUMENT ME!

attribute - DOCUMENT ME!

value - DOCUMENT ME!

Returns:

DOCUMENT ME!

setNodeAttributeDoubleValue

public static int setNodeAttributeDoubleValue(int node_index,
                                              int att_id,
                                              double value)

DOCUMENT ME!

Parameters:

node_index - DOCUMENT ME!

att_id - DOCUMENT ME!

value - DOCUMENT ME!

Returns:

DOCUMENT ME!

setNodeAttributeStringValue

public static int setNodeAttributeStringValue(int node_index,
                                              String attribute,
                                              String value)

DOCUMENT ME!

Parameters:

node_index - DOCUMENT ME!

attribute - DOCUMENT ME!

value - DOCUMENT ME!

Returns:

DOCUMENT ME!

setNodeAttributeStringValue

public static int setNodeAttributeStringValue(Node node,
                                              String attribute,
                                              String value)

DOCUMENT ME!

Parameters:

node - DOCUMENT ME!

attribute - DOCUMENT ME!

value - DOCUMENT ME!

Returns:

DOCUMENT ME!

setNodeAttributeStringValue

public static int setNodeAttributeStringValue(int node_index,
                                              int att_id,
                                              String value)

DOCUMENT ME!

Parameters:

node_index - DOCUMENT ME!

att_id - DOCUMENT ME!

value - DOCUMENT ME!

Returns:

DOCUMENT ME!

getNodeAttributeValue

public static Object getNodeAttributeValue(Node node,
                                           String attribute)

DOCUMENT ME!

Parameters:

node - DOCUMENT ME!

attribute - DOCUMENT ME!

Returns:

DOCUMENT ME!

getNodeAttributeValue

public static Object getNodeAttributeValue(int node_index,
                                           int att_id)

DOCUMENT ME!

Parameters:

node_index - DOCUMENT ME!

att_id - DOCUMENT ME!

Returns:

DOCUMENT ME!

getNodeAttributeObjectValue

public static Object getNodeAttributeObjectValue(Node node,
                                                 String attribute)

DOCUMENT ME!

Parameters:

node - DOCUMENT ME!

attribute - DOCUMENT ME!

Returns:

DOCUMENT ME!

getNodeAttributeStringValue

public static String getNodeAttributeStringValue(Node node,
                                                 String attribute)

DOCUMENT ME!

Parameters:

node - DOCUMENT ME!

attribute - DOCUMENT ME!

Returns:

DOCUMENT ME!

getNodeAttributeDoubleValue

public static double getNodeAttributeDoubleValue(Node node,
                                                 String attribute)

DOCUMENT ME!

Parameters:

node - DOCUMENT ME!

attribute - DOCUMENT ME!

Returns:

DOCUMENT ME!

getNodeAttributeObjectValue

public static Object getNodeAttributeObjectValue(int node_index,
                                                 String attribute)

DOCUMENT ME!

Parameters:

node_index - DOCUMENT ME!

attribute - DOCUMENT ME!

Returns:

DOCUMENT ME!

getNodeAttributeStringValue

public static String getNodeAttributeStringValue(int node_index,
                                                 String attribute)

DOCUMENT ME!

Parameters:

node_index - DOCUMENT ME!

attribute - DOCUMENT ME!

Returns:

DOCUMENT ME!

getNodeAttributeDoubleValue

public static double getNodeAttributeDoubleValue(int node_index,
                                                 String attribute)

DOCUMENT ME!

Parameters:

node_index - DOCUMENT ME!

attribute - DOCUMENT ME!

Returns:

DOCUMENT ME!

getNodeAttributes

public static String[] getNodeAttributes(int[] node_indices)

Returns all Attributes that one or more of the given nodes have values for.