"Catch-all" project for generic helper classes such as tsv reader, etc.

git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/trunk/icb-commons/icb-utils@14200 60cd2ccc-2b05-0410-9566-da273a940bff
Move TSVReader from twease (originally from locusminer) into the general purpose icb utils project.

git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/trunk/icb-commons/icb-utils@14201 60cd2ccc-2b05-0410-9566-da273a940bff
Cleanup the TSVReader a bit and add a few simple tests.  More tests should be added.  It's a simple class, but if useful, coverage should be nearly 100%.

git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/trunk/icb-commons/icb-utils@14213 60cd2ccc-2b05-0410-9566-da273a940bff
Cleanup the TSVReader a bit and add a few simple tests.  More tests should be added.  It's a simple class, but if useful, coverage should be nearly 100%.

git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/trunk/icb-commons/icb-utils@14214 60cd2ccc-2b05-0410-9566-da273a940bff
Move the Fasta Parser into the common utilities project.  This has been on the list of "thinge to do" for some time.

git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/trunk/icb-commons/icb-utils@14293 60cd2ccc-2b05-0410-9566-da273a940bff
Implementation of a class to support Queue classes to limit the size of a queue. Notably useful with a PriorityQueue to have a Prioritized Queue but with a constricted size. Comments welcome.

git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/trunk/icb-commons/icb-utils@14309 60cd2ccc-2b05-0410-9566-da273a940bff
Renamed Limited to Bounded.

git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/trunk/icb-commons/icb-utils@14310 60cd2ccc-2b05-0410-9566-da273a940bff
Reimplementation based on just PriorityQueue as this is what this is really most useful for and is easier to understand and use. This also simplifies implementation.

A reverse method was added.

git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/trunk/icb-commons/icb-utils@14318 60cd2ccc-2b05-0410-9566-da273a940bff
Reimplementation based on just PriorityQueue as this is what this is really most useful for and is easier to understand and use. This also simplifies implementation.

A reverse method was added to obain the elements of the queue in reverse order.

git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/trunk/icb-commons/icb-utils@14319 60cd2ccc-2b05-0410-9566-da273a940bff
Slight change to javadoc. add/addAll/offer ALWAYS return true (per the PriorityQueue javadoc).

git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/trunk/icb-commons/icb-utils@14320 60cd2ccc-2b05-0410-9566-da273a940bff
Removed @date javadoc

git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/trunk/icb-commons/icb-utils@14334 60cd2ccc-2b05-0410-9566-da273a940bff
Removed @date javadoc, moved date to @author tag

git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/trunk/icb-commons/icb-utils@14337 60cd2ccc-2b05-0410-9566-da273a940bff
Moved some methods from Twease-StringFormatting to new class ICBStringUtils (including tests).

git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/trunk/icb-commons/icb-utils@14341 60cd2ccc-2b05-0410-9566-da273a940bff


git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/trunk/icb-commons/icb-utils@14342 60cd2ccc-2b05-0410-9566-da273a940bff
So icb-utils can be standalone

git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/trunk/icb-commons/icb-utils@14386 60cd2ccc-2b05-0410-9566-da273a940bff
Remove empty directories from subversion.

git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/trunk/icb-commons/icb-utils@14400 60cd2ccc-2b05-0410-9566-da273a940bff
Updated icb-utils

git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/trunk/icb-commons/icb-utils@14446 60cd2ccc-2b05-0410-9566-da273a940bff
Not complete - lots more tests to write to check implementation, but the start of the the ConditionsParser.

git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/trunk/icb-commons/icb-utils@14478 60cd2ccc-2b05-0410-9566-da273a940bff
First cut at a conditions parser for Fabien.

git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/trunk/icb-commons/icb-utils@14486 60cd2ccc-2b05-0410-9566-da273a940bff
Minor addition to javadoc

git-svn-id: https://pbtech-vc.med.cornell.edu/public/svn/trunk/icb-commons/icb-utils@14487 60cd2ccc-2b05-0410-9566-da273a940bff