#331 Generating drop down menu in code, fixed ontology coloration, and have mappings working. The central node has a bug though I know how to fix it. I will likely change from an explicit fetch of mappings to use a conditional expansion in the relation parser instead.
#331 Refactored edge registry, created node expansion registry to facilitate later use of the node expansion functionality, and to clean up the neighborhood expansions I had in place (they were bugged and I saw this would fix it).
#335 Fixed swirling, committing in case my next steps are messy.
#335 Added node registry for REST calls, to prevent duplicates. Have the soft cap working wonderfully, and expanding via the slider bring nodes in and triggers their REST calls. Great stuff.
Merge branch 'issue330_d3layout'
#335 Merging Elena's layout work in concept graph, so I can borrow in the ontology graph. Borrowed menu behavior already.
#335 Making layout update when sliders change nodes present. The force layout seems to be interfering with the circle placement a lot. I need to compare behavior before and after the changes I am committing.
#335 Have the mapping count filter, central layout, and slider all playing nicely. The layout does not recompute positions though. Nodes made visible appear to be mixed in along the circle in a way I don't understand. WIll fix that next.
#355 Fixed problem with the Radlex ontology, and escape-character requiring acronyms in general. Could not use jquery to access any such acronym in an id, no matter what escaping was done or whether array syntax was used for the jquery selector.
#335 Fixed problem with double ontolgy bubbles not having internal circles sometimes. Was likely a race condtion, but I fixed in a different way.
#335 Have nodes being placed in the circle the way I want, like chairs added to a circular table. Also changed jquery version for the concept graph to the version that still supports older IE browsers. A large portion of our user base still runs IE 8 (25% use IE, 48% of those have IE 8 or less, so 12% of users total have IE 8 or less as of this commit).
#335 No more gaps in center layout when changing the displayed nodes. Arcs are also rendering again. I had a bug there, as well as in counts when generating the layout. It is behaving very well now, except for odd label repositioning timing.
#335 Fixed problem with nodes entering graph with odd randomness when the sliders are changed. Had to do with sorting and which container we iterated over. Sometimes more than one node can pass the filter at the same time, when they have tied values. Fixing next.
#335 Fixed node and arc visiblity filtering, and an issue with appengine libs. I broke things with my last commit, but Eclipse was hiding the problems from me...
#335 Fixed timing of node label positioning. It needs to be called when nodes are added to the layout, which is easily done on every layout refresh.
#347 Fixed infinite loop when dragging a node over the central node. In the last commit I actually detected a code smell that was causing this problem. I have fixed up the node highlighting function. I need to go over the link highlighting function as well, and check other related bits for further code smells. I have used my adjacent linsk method rather than trying to detect nodes and edge relations on the basis of their coordinates, which was an approach pasted from the very original D3 example, if I recall.
#347 Fixed other code smells related to last commit. Would have done as one commit but things were working so well before...they work so well now too.
#348 Simple change to add percentage of mapped nodes to the node popups.
#349 I have refactored the ontology overview into typescript classes and files. It does not run from this commit because I want to get it all stored away before implementing a dependency management system. I don't even want to try explicit script elements in the html file.
#350 Sorted out dependency management for TypeScript using require.js. Fixed a couple bugs that were hidden. It now serves things (to typeScript_ontologyMappingOverview.html), and I hit plain old javascript bugs.