Initial import.
Initial import.
initial import of compiled version of plugin
revised code for goslimmer cytopanel, and associated changes to controller code and initialization code in goslimmer controller and goslimpanelaction
refactoring of code to use enums for GO namespace, and custom overides of JLabel setText method for the coverage statistic label, so that it is autoformatted
changed enum modifier to public
various refactorings of code, changes to visual style to fix rectangle bug
created new version of expandNode method which takes an integer parameter specifying the depth to which the DAG should be expanded.  Removed obsolete commented out actionlistener method.
added new method for getting the namespace specific covered gene IDs by GONamespace enum element
added new public static field 'ontologyName' for storing the name of the ontology which GOSlimmer is to work on.  
This is needed by code which instantiates GeneAssociationReaderUtil, since it requires the ontology which is associated with 
the gene association file to be parsed.
copied a few methods from GOSlimPanelAction to be static methods here, since that is more appropriate.
abstracted nodeAppearance modification code into a new method called 'modifyNodeAppearance', which is called by the two node appearance calculation methods.
Also, added code to set the size of the nodes and their labels based on the value of fields in GOSlimmerGUIViewSettings
These new panels in the goslimmer main panel are used for setting the gene association file to be used and for changing 
view settings.
This class will store, through its static field values, the settings which are to be applied to view appearances in the graphs 
being managed by GOSlimmer, such as how node's are labelled and how their sizes are calculated.
revised removeCoverageAttributes method so that it only deletes the coverage attributes from the nodes which are controlled by this controller.
Added methodds assignCoverageAttributes and resetAndRecalculateCoverageStatistics, which, respectively, 
assign coverage attribute values to nodes managed by this controller and reinitializes and calculates the coverage
 statistics for the graph based on the current attributes.
 
 These methods are used by the newly refactored gene association annotation functionality, which will allow the user 
 to change the gene association data which is being applied to the graph as they wish.
modified main action handler to record the name of the go ontology network to the "GOSlimmer.ontologyName" field, and to use 
the value of that field when instantiating GeneAssociationReaderUtil.  Also, add the new AdvancedViewSettingsPanel and 
GOSlimmerGeneAssociationDialog panels to the goSlimPanel main cytopanel for the plugin, such that users can modify 
advanced view settings, and apply different gene association data to their GO Dag.
added new checkbox for enabling/disabling labelling of nodes with their ontology term name instead of the ID
enabled redrawing of the graph after such a view settings change.
added methods and fields for setting a finite node depth expansion limit, as well as methods for enabling and disabling that behaviour.
added new components and associated actions for specifying the limited node expansion, as well as the associated actions event 
responses for when such controls are manipulated.

Removed several of the constructors and added a new one which takes a Collection of GOSlimmerControllers as input, which will 
be used for modifying said behaviour.
removed obsolete code for setting up the gene association reader, controller, nodecontextmenulistener and statbean for the parent GO graph, since 
the subgraphs now handle all that information;  if we need to re-enable that behaviour, it would be better done in the 
same way which the subgraphs are initialized.

Also, revised instantiation of AdvancedViewSettingsPanel in accord with it's new constructor set.