Initial import.
Initial import.
added new internal class which extends EdgeAppearanceCalculator, for determining the appearance of edges (currently does nothing other than the default)

Modified node appearance calculator so that node size is determined to be proportional to the number of input network nodes 
which belong to the theme node (as determined by the attribute recording theme nodes).

Created new method for initializing sub calculators, for use in the constructors.
changed edge generation behaviour so that at most 2 new edges (one for each direction) will be created between theme nodes, rather than one for each input edge 
connecting input node members of the theme node.  A Map is created mapping input edges to the theme edges which they contribute to (the map currently does not survive 
beyond map creation, but could be easily manipulated to do so).

A layout is now applied to the newly created theme graph, using the attribute circle layout.

The ThemeMapVisualStyle is applied to the newly created theme graph.
added several new convenience methods for working with attributes, as well as a method for determining the number of member nodes within a theme node.
added new static final String field for defining the name of the edge attribute which records the input edges which contribute to it.
eliminated creation of 'start' and 'exit' buttons from theme mapper plugins menu, as they are no longer relevant since the plugin is effectively stateless in this respect (its functionality is always available).
refactored code so that view is created by a separate method from the one which creates the thematic map graph.

Attribute circle layout is applied to newly created thematic map views

Only a single edge is created between theme nodes, rather than one for each direction in the input edges which connect theme members.

Beginning implementation of hypergeometric test functionality, though it is mostly prototype code at this point.
revised action code to use the refactored ThematicMapFunctionPrototype code to create the thematic map and it's view.
added new statif final field for defining the name of the theme member count attribute.
added some new convienience methods for manipulating nodes and their attributes.
Code ported from BiNGO plugin for performing hypergeometric tests on annotated networks.  These will be modified to provide hypergeometric test functionality to the thematic map plugin.
added new method for retrieving the number of contributing members to a theme edge.
renamed variable name to be more informative
basic implementation of hypergeometric distribution test code, with informative comments.
prototype classes, not yet incorporated into the thematic map plugin's functionality, but may serve some use to future developers.
this class is imported by several of the classes derived from the BiNGO code for hypergeometric tests.  It is being imported so that those classes can 
compile, though it is not being used directly in the thematic map plugin's code.
Added LGPL license, copyright and authorship header, as well as numerous javadoc comments to explain class, field and method meaning.
removed obsolete classes and packages.  These were related to GO term processing, when thematic map plugin was going to specifically integrate with the Gene 
Ontology.  Now that the plugin is intended to be more general, these are no longer needed.
renamed goslimmer specific CyAttribute names such that the prefix is always 'ThemeMapper'.  This clearly identifies the attributes as being related to ThemeMapper, 
as well as preparing for the eventuality that namespaces are introduced for attributes.