Speed improvement - tile ids now sorted in sql query rather than on
client

Change-Id: I9286e9ebf8ea8122be691da3b8c1ec5217d5f572
Fixed bug where required points would get removed before optional,
invalidated ones.
queryBounds for vertices are now the triangle bounds rather than polygon
bounds.

Change-Id: I1356d215061560114b0658f781b7fb8a22b334aa
Minor cleanup and bugfixes for CytoscapeWebTool
addCallback() now gives the option of passing the current state to
the callback function.
Added distanceSquared(), not used.

Change-Id: I82a831a4077bbd286a2623a07fda63d72ae3aa21
added getArea()

Change-Id: I10027f2131ff5e146f0bbde896cd03ddf4d35571
added debugging code

Change-Id: I4f9d06945904776091c0ed519a48d64f17fea68f
Removed unused value from tile descriptors.

Change-Id: I701baae6052aa49c6c7d0c1892495251d81afef0
multiple shp import works again

Change-Id: Ic8707ecc1ed91bb25bc2763d24290520b96a544e
fixed error in printout.
Included MinHeap, not used yet.

Change-Id: I8313ea21ea3490df1269d7a2c0523c87c479d8b2
Polygon markers are now stored in the geometry stream.
No longer pooling Java objects (it made it slower).
GeneralizedGeometry.as now supports adding polygon markers out of order.

Change-Id: Icecb1f1a53ec64e647e94e35286795741ead8f23
fixed bug where part markers weren't decoded correctly.

Change-Id: Ic35acc194e78c152b47a9aa343090db0cfd7a9f9
added check for debug mode

Change-Id: I7a853b051c3ad6b480df514337cf4359024cb5ab
modified eclipse export script
added debugging code
updated docs

Change-Id: I9dfaf39c79aeab75b6f5f34bfde9cbbe6bbddbef
Merge remote-tracking branch 'origin/master' into foo
chnages to Rad Viz plot, and other related changes