Initial cufflinks support - parser for genes.fpkm_tracking and genes_exp.diff files, data source, and track.
Bug fix -- precomputed coverage not shown in whole-genome view
Add preference for unloading data upon genome change (or not).
Add menu item to hide/show junction track
Adjust scale threshold at which insertions are shown.
Remember last directory accessed in igvtools gui.
Remove indiscriminate use of anti-aliasing.
Document GenomeSummaryData

No functional changes
Fix bug in GenomeSummaryData

We essentially were ignoring the first data points of a chromosome under some conditions
Add test for latest GenomeSummaryData bugfix

Also improve documentation on some classes
Give IndefiniteProgressMonitor a no-arg constructor

Since we only use default values, this makes sense.

Also improve some documentation/coding standards on Locus & SAMCodec
Add searchIncrement

 searchIncrement can be negative so we can search backwards as well as forwards, also we can have overlapping sliding windows (setter currently prevents this but could easily be changed)
Some refactoring/cleanup of FeatureTrack, GlobalKeyDispatcher
Implement cancellable searching for certain FeatureSources

PluginFeatureSource and SequenceMatchSource, hardset with instanceof right now. The dialog we use is pretty ugly and we should definitely show the user the region being searched, but it seems to work.
Finalize FeatureSearcher UI

CancellableProgressDialog now it's own class, much better looking, includes status text (TODO @jrobinso double check on thread-safety) so user knows which region is getting searched.
TODO Delay in having dialog pop up, right now it comes up and then goes away quickly if feature immediately found, we should have delay.
Move RandomFeatureSource to it's own class.

Not used now, may be useful later
Update CancellableProgressDialog status text on event thread
Account for insertions when sorting alignments by base
Ignore RandomFeatureSource test utility class

Add some scratch code for preventing this in the future, but it won't actually be an improvement
Move labels to the left of the SequenceMatchDialog
Allow SequenceMatchDialog to take general regex

User picks from radio buttons, from either IUPAC ambiguity codes or regex

Refactor conversion of IUPAC -> regex to SeqenceMatchDialog

Move labels to the left of the SequenceMatchDialog