Merge pull request #33 from raymond301/master

Colorized & Unhideable additions
Fixing problems with submitting searches.
Issue with the view.
More view fixes. 'file' is a reserved keyword.
Fixed regression where quameter pre and post blanks were not getting filtered.
Fixing broken build.
Simplifying the dao.
Unhide shows file path.
Initial, most trivial test of protein group counting passes.
Upgrade of the database schema
Extra table for storing spectral counts for Quameter output.
Only show 1 year of data.
Fixing unhide jsp
Darker colors that are more readable.
Need to loop within the open transaction so data can be accessed.
Need to loop within the open transaction so data can be accessed.
Unhide.jsp fixes.
Merge remote-tracking branch 'origin/master'

Conflicts:
	swift/web/src/main/webapp/quameter/unhide.jsp
Unhide.jsp fixes.
Quameter does not crash if an annotation is not assigned to actual data point (e.g. it is too old)