Merge branch 'master' into issue330_d3layout
#330 Updated root index function
#330 Modified getRootIndex and horizontal tree layout to deal solely with the ontology in question
#330 Refactored layouts
#330 added children function. Still working on calculating depth
#330 Added depth to graph nodes. Added changes to visualize nodes with multiple parents in a tree-based layout
#330 Managed visualizations of more than one ontology for trees
#330 added support for multiple ontologies for vertical tree
#330 added support for multiple ontologies for radial tree
#330 Added handling for multiple nodes with no parents in on eontology
#330 fixed flying nodes issue realted to depth calculations by d3
#330 fixed root issue
Fixing bugs in tree layouts
#330 Tidied up the code, fixed some layout problems
#423 Working on incomplete paths to root problem, but there is a major problem with the visualization locking up. I stashed and retested, but it wasn't in the last commit. Sorting that out then coming back to this.
Merge branch 'master' into issue423_pathsToRoot
#423 Fixed layout timer and layout trigger on mouse over (via temporary edge additions). This was blocking my task of fixing paths to root complete parsing.
Merge issue330_d3layout to solve problems with making tree the default layout. Figured out that the problems occur when new nodes and edges are being added to the graph. Added code to help test and fix this issue.
Merge branch 'issue423_pathsToRoot'