cytoscape.data
Class GraphObjAttributes

java.lang.Object
  cytoscape.data.GraphObjAttributes

Deprecated. Use CyAttributes instead.

public class GraphObjAttributes
extends Object

GraphObjAttributes provides access to node and edge attributes within Cytoscape.

GraphObjAttributes will be replaced by CyAttributes, and will be officially removed from the Cytoscape core in September, 2006.

Field Summary

static String

DEFAULT_CATEGORY Deprecated.

Constructor Summary

GraphObjAttributes(CyAttributes cyAttrs)
Deprecated. Constructor.

Method Summary

void	add(GraphObjAttributes attributes) Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.
boolean	add(String graphObjectName, HashMap bundle) Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.
boolean	add(String attributeName, String id, double value) Deprecated. Use CyAttributes.setAttribute(String, String, Double) instead.
boolean	add(String attributeName, String id, Object value) Deprecated. Storing arbitrary Java objects as attribute values will no longer be supported in CyAttributes. However, you will be able to store arbitrarily complex trees of Boolean, Integer, Double, and String Objects. For details, refer to CyAttributes.
void	addClassMap(HashMap newClassMap) Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.
void	addNameMap(HashMap nameMapping) Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.
void	addNameMapping(String canonicalName, Object graphObject) Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.
void	addObjectMap(HashMap objectMapping) Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.
boolean	append(String attributeName, String id, Object value) Deprecated. Use CyAttributes.setAttributeList(String, String, java.util.List) for equivalent functionality.
void	clearNameMap() Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.
void	clearObjectMap() Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.
int	countIdentical(String graphObjName) Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.
static Class	deduceClass(String string) Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.
void	deleteAttribute(String attributeName) Deprecated. Use CyAttributes.deleteAttribute(String) instead.
void	deleteAttribute(String attributeName, String id) Deprecated. Use CyAttributes.deleteAttribute(String, String) instead.
void	deleteAttributeValue(String attributeName, String graphObjName, Object value) Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.
Object	get(String attributeName, String id) Deprecated. Use CyAttributes instead. It provides several getter methods for retrieving Boolean, Integer, Double and String values.
Object[]	getArrayValues(String attributeName, String graphObjectName) Deprecated. There is no one method in CyAttributes that provides this functionality, but it can be recreated via several calls.
HashMap	getAttribute(String attributeName) Deprecated. Use CyAttributesUtils.getAttribute(String, CyAttributes) instead.
String[]	getAttributeNames() Deprecated. Use CyAttributes.getAttributeNames() instead.
HashMap	getAttributes(String canonicalName) Deprecated. use CyAttributeUtils.getAttributes(String,CyAttributes).
String	getCanonicalName(Object graphObj) Deprecated. Use CyNode.getIdentifier() or CyEdge.getIdentifier() instead.
String	getCategory(String attributeName) Deprecated. Gets a category for the specified attribute.
Class	getClass(String attributeName) Deprecated. Use CyAttributesUtils.getClass(String,CyAttributes) instead.
HashMap	getClassMap() Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.
Double	getDoubleValue(String attributeName, String id) Deprecated. Use CyAttributes.getDoubleAttribute(String, String) instead.
Object	getGraphObject(String canonicalName) Deprecated. Use Cytoscape.getCyNode(String) or Cytoscape.getCyEdge(String, String, String, String) instead.
Integer	getIntegerValue(String attributeName, String id) Deprecated. Use CyAttributes.getIntegerAttribute(String, String) instead.
List	getList(String attributeName, String id) Deprecated. Use CyAttributes.getAttributeList(String, String) instead.
HashMap	getNameMap() Deprecated. Use GraphPerspective.nodesIterator() or GraphPerspective.edgesIterator() instead.
int	getObjectCount(String attributeName) Deprecated. There is no one method in CyAttributes that provides this functionality, but it can be recreated via several calls.
HashMap	getObjectMap() Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.
String[]	getObjectNames(String attributeName) Deprecated. Use MultiHashMap.getObjectKeys(String) instead.
String[]	getStringArrayValues(String attributeName, String id) Deprecated. Use CyAttributes.getAttributeList(String, String) instead.
String	getStringValue(String attributeName, String id) Deprecated. Use CyAttributes.getStringAttribute(String, String) instead.
HashMap	getSummary() Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.
String[]	getUniqueStringValues(String attributeName) Deprecated. There is no one method in CyAttributes that provides this functionality, but it can be recreated via several calls.
Object[]	getUniqueValues(String attributeName) Deprecated. There is no one method in CyAttributes that provides this functionality, but it can be recreated via several calls.
Object	getValue(String attributeName, String id) Deprecated. Use CyAttributes instead. It provides several getter methods for retrieving Boolean, Integer, Double and String values.
boolean	hasAttribute(String attributeName) Deprecated. Use CyAttributes.getType(String) instead.
boolean	hasAttribute(String attributeName, String id) Deprecated. Use CyAttributes.hasAttribute(String, String) instead.
int	numberOfAttributes() Deprecated. Use CyAttributes.getAttributeNames().length instead.
String	processFileHeader(String text) Deprecated. Use CyAttributesReader instead.
void	readAttributesFromFile(File file) Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.
void	readAttributesFromFile(String filename) Deprecated. Use CyAttributesReader instead.
void	removeNameMapping(String canonicalName) Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.
void	removeObjectMapping(Object graphObj) Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.
void	set(GraphObjAttributes attributes) Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.
boolean	set(String graphObjName, HashMap bundle) Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.
boolean	set(String attributeName, String id, double value) Deprecated. Use CyAttributes.setAttribute(String, String, Double) instead.
boolean	set(String attributeName, String id, Object value) Deprecated. Storing arbitrary Java objects as attribute values will no longer be supported in CyAttributes. However, you will be able to store arbitrarily complex trees of Boolean, Integer, Double, and String Objects. For details, refer to CyAttributes.
void	setCategory(String attributeName, String newValue) Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.
boolean	setClass(String attributeName, Class attributeClass) Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.
void	setTaskMonitor(cytoscape.task.TaskMonitor taskMonitor) Deprecated.
String	toString() Deprecated.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_CATEGORY

public static final String DEFAULT_CATEGORY

Deprecated.

See Also:

Constant Field Values

Constructor Detail

GraphObjAttributes

public GraphObjAttributes(CyAttributes cyAttrs)

Deprecated.

Constructor.

Parameters:

cyAttrs - CyAttributes.

Method Detail

deduceClass

public static Class deduceClass(String string)

Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.

Deduces a Class.

set

public boolean set(String attributeName,
                   String id,
                   Object value)

Deprecated. Storing arbitrary Java objects as attribute values will no longer be supported in CyAttributes. However, you will be able to store arbitrarily complex trees of Boolean, Integer, Double, and String Objects. For details, refer to CyAttributes.

Set an attribute of the specified name to the graph object with the specified id. The attribute may be any java type, or an array of any java type; it can be neither a primitive value nor an array of primitves. If this attribute has not previously been assigned a class, either explicitly or implicitly, then the class is deduced from the object (or the first element in the array of objects). once a class has been assigned for this attribute, every subsequent addition must be an object of that same class.

Parameters:

attributeName - Attribute Name.

id - Unique Identifier.

value - The value of this attribute, either a java object or an array of java objects

Returns:

true indicates that the attribute was set.

Throws:

IllegalArgumentException - if the class of obj (or of obj [0], if obj is an array) does not match the already assigned or deduced java class for this attribute.

append

public boolean append(String attributeName,
                      String id,
                      Object value)

Deprecated. Use CyAttributes.setAttributeList(String, String, java.util.List) for equivalent functionality.

Appends to specified object to an implicit list of attribute values.

Parameters:

attributeName - Attribute Name.

id - Unique Identifier.

value - The value of this attribute.

Returns:

true indicates that the attribute was set.

set

public boolean set(String attributeName,
                   String id,
                   double value)

Deprecated. Use CyAttributes.setAttribute(String, String, Double) instead.

Sets an id/attributeName pair of type double

Value will be promoted to Double.

Parameters:

attributeName - Attribute Name.

id - Unique Identifier.

value - Attribute double value.

Returns:

true indicates that the attribute was set.

setTaskMonitor

public void setTaskMonitor(cytoscape.task.TaskMonitor taskMonitor)

Deprecated.

Sets a TaskMonitor for tracking loading of node attribute files.

Parameters:

taskMonitor -

numberOfAttributes

public int numberOfAttributes()

Deprecated. Use CyAttributes.getAttributeNames().length instead.

Gets the number of different attributes currently registered.

getAttributeNames

public String[] getAttributeNames()

Deprecated. Use CyAttributes.getAttributeNames() instead.

Get the names of all registered attributes

hasAttribute

public boolean hasAttribute(String attributeName)

Deprecated. Use CyAttributes.getType(String) instead.

Determines if the specified attribute has been set/registered.

Parameters:

attributeName - Attribute Name.

Returns:

true indicates that the attribute has been set/registered.

hasAttribute

public boolean hasAttribute(String attributeName,
                            String id)

Deprecated. Use CyAttributes.hasAttribute(String, String) instead.

Determines if the specified attributeName/id has been set.

Parameters:

attributeName - Attribute Name.

id - Unique Identifier.

Returns:

true indicates that the attributeName/id has been set.

deleteAttribute

public void deleteAttribute(String attributeName)

Deprecated. Use CyAttributes.deleteAttribute(String) instead.

Remove the entire second level Hashmap whose key is the specified attributeName.

Parameters:

attributeName - AttributeName

deleteAttribute

public void deleteAttribute(String attributeName,
                            String id)

Deprecated. Use CyAttributes.deleteAttribute(String, String) instead.

Removes the specified attribute from the specified node or edge.

Parameters:

attributeName - AttributeName

id - Unique Identifier.

getClass

public Class getClass(String attributeName)

Deprecated. Use CyAttributesUtils.getClass(String,CyAttributes) instead.

All attributes are lists (java.lang.Vector) sharing the same base type; discover and return that here.

Parameters:

attributeName - AttributeName

Returns:

Class Object.

getList

public List getList(String attributeName,
                    String id)

Deprecated. Use CyAttributes.getAttributeList(String, String) instead.

Gets all values associated with this graphObjectName and this attributeName.

Parameters:

attributeName - AttributeName.

id - Unique Identifier.

Returns:

a java.util.Vector of size zero or more, containing java objects whose types may be learned via a call to getType

getValue

public Object getValue(String attributeName,
                       String id)

Deprecated. Use CyAttributes instead. It provides several getter methods for retrieving Boolean, Integer, Double and String values.

For backwards compatibility: the value of an attribute used to be strictly a single scalar; now -- even though attributes are all lists of scalars -- we support the old idiom by retrieving the first scalar from the list.

Parameters:

attributeName - AttributeName.

id - Unique Identifier.

Returns:

Java Object.

get

public Object get(String attributeName,
                  String id)

Deprecated. Use CyAttributes instead. It provides several getter methods for retrieving Boolean, Integer, Double and String values.

Equivalent to getValue() method.

Parameters:

attributeName - Attribute Name.

id - Unique Identifier.

Returns:

Java Object.

getDoubleValue

public Double getDoubleValue(String attributeName,
                             String id)

Deprecated. Use CyAttributes.getDoubleAttribute(String, String) instead.

Gets an attribute Double value.

Parameters:

attributeName - Attribute Name.

id - Unique Identifier.

Returns:

Double Object.

getIntegerValue

public Integer getIntegerValue(String attributeName,
                               String id)

Deprecated. Use CyAttributes.getIntegerAttribute(String, String) instead.

Gets an attribute Integer value.

Parameters:

attributeName - Attribute Name.

id - Unique Identifier.

Returns:

Integer Object.

getStringValue

public String getStringValue(String attributeName,
                             String id)

Deprecated. Use CyAttributes.getStringAttribute(String, String) instead.

Gets an attribute String value.

Parameters:

attributeName - Attribute Name.

id - Unique Identifier.

Returns:

Integer Object.

getAttribute

public HashMap getAttribute(String attributeName)

Deprecated. Use CyAttributesUtils.getAttribute(String, CyAttributes) instead.

Return a hash whose keys are graphObjectName Strings, and whose values are a Vector of java objects the class of these objects, and the category of the attribute (annotation, data, URL) may be learned by calling getClass and getCategory.

Parameters:

attributeName - Attribute Name.

Returns:

a HashMap whose keys are graph object names (typically canonical names for nodes and edges) and whose values are Vectors of java objects.

getStringArrayValues

public String[] getStringArrayValues(String attributeName,
                                     String id)

Deprecated. Use CyAttributes.getAttributeList(String, String) instead.

A convenience method, useful if you are certain that the attribute stores Strings; convert the Vector of Objects into an array of Strings

Parameters:

attributeName - Attribute Name.

id - Unique Identifier.

Returns:

Array of Strings.

toString

public String toString()

Deprecated.

Overrides:

toString in class Object

set

public boolean set(String graphObjName,
                   HashMap bundle)

Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.

A convenience method allowing the addition of multiple different attributes for one graphObject at the same time. Deprecation note: This method has 0 usages in the core.

clearNameMap

public void clearNameMap()

Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.

Removes all entries from the nameMap. Deprecation note: This method has 0 usages in the core.

clearObjectMap

public void clearObjectMap()

Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.

Remove all entries in the canonicalToGraphObject map Deprecation note: This method has 0 usages in the core.

getClassMap

public HashMap getClassMap()

Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.

Deprecation note: This method has 0 usages in the core.

addClassMap

public void addClassMap(HashMap newClassMap)

Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.

Deprecation note: This method has 0 usages in the core.

getObjectMap

public HashMap getObjectMap()

Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.

Deprecation note: This method has 0 usages in the core.

addNameMap

public void addNameMap(HashMap nameMapping)

Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.

A wholesale addition of all entries in a -> HashMap. Deprecation note: This method has 0 usages in the core.

addObjectMap

public void addObjectMap(HashMap objectMapping)

Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.

add all entries in the given HashMap (entry: -> ) to the canonicalToGraphObject HashMap. Deprecation note: This method has 0 usages in the core.

set

public void set(GraphObjAttributes attributes)

Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.

copy all attributes in the supplied GraphObjAttributes object into this GraphObjAttributes. any pre-existing attributes survive intact as long as they do not have the same attribute name as the attributes passed in. Deprecation note: This method has 0 usages in the core.

deleteAttributeValue

public void deleteAttributeValue(String attributeName,
                                 String graphObjName,
                                 Object value)

Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.

remove the specified attribute value from the specified node or edge. there may be multiple values associated with the attribute, so search through the list, and if it is found, remove it. Deprecation note: This method has 0 usages in the core.

readAttributesFromFile

public void readAttributesFromFile(File file)
                            throws IOException

Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.

Deprecation note: This method has 0 usages in the core.

Parameters:

file - File Object.

Throws:

IOException

getSummary

public HashMap getSummary()

Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.

Return attributeName/attributeClass pairs, for every known attribute Deprecation note: This method has 0 usages in the core.

countIdentical

public int countIdentical(String graphObjName)

Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.

multiple GraphObj's (edges in particular) may have the same name; this method counts names which begin with the same string. for instance there may be two edges between the same pair of nodes:

    VNG0382G (geneFusion) VNG1230G
    VNG0382G (geneFusion) VNG1232G
  

the first pair encountered may be give the name

    VNG0382G (geneFusion) VNG1230G
  

we may wish to give the second pair the name

    VNG0382G (geneFusion) VNG1230G_1
  

this method provides a count of matches based on String.startsWith ("VNG0382G (geneFusion) VNG1230G") which solves the problem of all subsequent duplicates simply append a number to the base name.

whoever calls this method must construct the new object's name -first- and then is expected to append "_N" where N is the value returned here (and of course, if the result is 0, there is no need to append '_0'. Deprecation note: This method has 0 usages in the core.

getObjectCount

public int getObjectCount(String attributeName)

Deprecated. There is no one method in CyAttributes that provides this functionality, but it can be recreated via several calls.

return the number of graph objects with the specified attribute. Deprecation note: This method has 0 usage in the core.

getCanonicalName

public String getCanonicalName(Object graphObj)

Deprecated. Use CyNode.getIdentifier() or CyEdge.getIdentifier() instead.

Returns the canonical name associated with this graphObject (a node or edge, previously stored with a call to addNameMapping). if no mapping exists, null is returned. Deprecation notes: This method has _62_ usages in the core. Canonical name is now the same thing as node/edge identifier. Calling this method is therefore equivalent to calling: node.getIdentifier(); edge.getIdentifier();

getAttributes

public HashMap getAttributes(String canonicalName)

Deprecated. use CyAttributeUtils.getAttributes(String,CyAttributes).

for the graphObject named by canonicalName, extract and return all attributes. Deprecation note: This method has 18 usages in the core. most of which are in the VizMapper.

addNameMapping

public void addNameMapping(String canonicalName,
                           Object graphObject)

Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.

establish mapping between a java object (a graph node or edge) and its canonical (standard) name.

• clients of this class (view, or cytoscape plugins) usually deal with graph nodes and edges, and only secondarily with names;
• attributes are stored and retrieved by canonical name
• the client must be able to translate from the node or edge object to the name, in order to get at the attributes
• this method allows a new mapping between object and canonical name. Deprecation note: This method has 6 usages in the core.

  See Also:

  getCanonicalName(java.lang.Object)

getGraphObject

public Object getGraphObject(String canonicalName)

Deprecated. Use Cytoscape.getCyNode(String) or Cytoscape.getCyEdge(String, String, String, String) instead.

return the graph object (node or edge) associated with this canonical name, previously stored with a call to addNameMapping. if no mapping exists, null is returned. Deprecation note: This method has 3 usages in the core. Canonical name is now the same thing as node/edge identifier. This method is therefore equivalent to: Cytoscape.getRootGraph().getNode( identifier ); Cytoscape.getRootGraph().getEdge( identifier ); See implementation in Rowan's CytocapeDataImpl for details.

getObjectNames

public String[] getObjectNames(String attributeName)

Deprecated. Use MultiHashMap.getObjectKeys(String) instead.

return the canonical names of all objects with a given attribute. Deprecation note: This method has 3 usages in the core.

removeNameMapping

public void removeNameMapping(String canonicalName)

Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.

removes a mapping between a java object (a graph node or edge) and its canonical (standard) name. Deprecation note: This method has 2 usages in the core.

setClass

public boolean setClass(String attributeName,
                        Class attributeClass)

Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.

specify the class of this attribute. all subsequently added attribute values must be of the exactly this class. Deprecation note: This method has 2 usages in the core.

removeObjectMapping

public void removeObjectMapping(Object graphObj)

Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.

removes a mapping between a canonical name and its graph object Deprecation note: This method has 2 usages in the core.

getArrayValues

public Object[] getArrayValues(String attributeName,
                               String graphObjectName)

Deprecated. There is no one method in CyAttributes that provides this functionality, but it can be recreated via several calls.

a convenience method: convert the Vector of objects into an array. Deprecation note: This method has 2 usages in the core.

readAttributesFromFile

public void readAttributesFromFile(String filename)
                            throws IOException

Deprecated. Use CyAttributesReader instead.

Reads attributes from a file. There is one basic format for attribute files, but a few aspects of the format are flexible.

The simplest form looks like this:

  expresssion ratio
  geneA = 0.1
  geneB = 8.9
  ...
  geneZ = 23.2
  

Deprecation note: This method has 2 usages in the core.

Throws:

IOException

getNameMap

public HashMap getNameMap()

Deprecated. Use GraphPerspective.nodesIterator() or GraphPerspective.edgesIterator() instead.

Deprecation note: This method has 1 usage in the core.

getUniqueValues

public Object[] getUniqueValues(String attributeName)

Deprecated. There is no one method in CyAttributes that provides this functionality, but it can be recreated via several calls.

return the unique values among the values of all objects with a given attribute. Deprecation note: This method has 1 usage in the core.

getUniqueStringValues

public String[] getUniqueStringValues(String attributeName)

Deprecated. There is no one method in CyAttributes that provides this functionality, but it can be recreated via several calls.

return the unique Strings among the values of all objects with a given attribute. Deprecation note: This method has 1 usage in the core.

processFileHeader

public String processFileHeader(String text)

Deprecated. Use CyAttributesReader instead.

deduce attribute name, category, and java class from the first line of the attributes file. the form of the first line is

  attribute name  (category=xxxx) (class=yyyy)
  

category and class are optional; if absent, class will be inferred (see deduceClass), and category set to DEFAULT_CATEGORY every attribute file must have, at minimum, the name attribute in the first line, possibly with embedded spaces in addition, the first line may have category and class information, as in homologene (category=staticWebPage) (class=java.net.URL) the present method extracts the mandatory attribute name, and the optional category and class information.

note: category and class information, if present, are not only parsed here: the information is also stored as appropriate in the current class data members. Deprecation note: This method has 1 usage in the core.

add

public void add(GraphObjAttributes attributes)

Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.

Adds a set of attributes.

Parameters:

attributes - GraphObjAttributes Object. Deprecation note: This method has 0 usages in the core.

add

public boolean add(String attributeName,
                   String id,
                   Object value)

Deprecated. Storing arbitrary Java objects as attribute values will no longer be supported in CyAttributes. However, you will be able to store arbitrarily complex trees of Boolean, Integer, Double, and String Objects. For details, refer to CyAttributes.

Adds a new Attribute.

Parameters:

attributeName - Attribute Name

id - Unique Identifier

value - Value

Returns:

true indicates success.

add

public boolean add(String attributeName,
                   String id,
                   double value)

Deprecated. Use CyAttributes.setAttribute(String, String, Double) instead.

Sets an id/attributeName pair of type double

Value will be promoted to Double.

Parameters:

attributeName - Attribute Name.

id - Unique Identifier.

value - Attribute double value.

Returns:

true indicates that the attribute was set.

add

public boolean add(String graphObjectName,
                   HashMap bundle)

Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.

A convenience method allowing the addition of multiple different attributes for one graphObject at the same time.

Deprecation note: This method has 0 usages in the core.

setCategory

public void setCategory(String attributeName,
                        String newValue)

Deprecated. Method is no longer needed in the Cytoscape core, and no equivalent method will be provided.

Assigns an arbitrary category name to the specified attribute.

Parameters:

attributeName - Attribute name

newValue - New value.

getCategory

public String getCategory(String attributeName)

Deprecated.

Gets a category for the specified attribute.

Parameters:

attributeName - Attribute name

Returns:

Category name.