Cytoscape bugfix for SIF files

[anuprulez]

This PR includes a bug fix for SIF to JSON file conversion for Cytoscape charts plugin.

• Nodes are now correctly arranged according to SIF file specification

For the following SIF description:

nodeA xx nodeB
nodeB xx nodeC
nodeC xx nodeD
nodeD xx nodeA nodeB nodeC
nodeB xx nodeD
nodeZ

the resulting graph is:

[dannon]

@anuprulez You should not need to do those dev merges like that, for what it's worth. This looks much better, though.

[dannon]

+1, works well now. Thanks for fixing it up @anuprulez.

[anuprulez]

@dannon I pushed my changes and then did the merge with dev. Should I do the other way?

[dannon]

@anuprulez Unless there's actually a conflict, there is no need to do either -- the only merge in many situations will be the one that happens when a committer merges this back into dev (like what happens when "merge pull request" is clicked).

Even if there are conflicts, as long as they're just build artifacts, those are also trivial to resolve by the committer at merge time.

[martenson]

Please watch milestone and label presence when merging. Or give @galaxybot a chance to catch that (he ignores closed issues).