Remove unused hg18.genome
Refactor GenomeBuilder

Make docs more clear, change names to be more meaningful
Add additional, more thorough test in GenomeImporterTest
Add method for checking if a path is fasta (just using extension)
Add whole genome download function

No UI hook yet, but does have unit test

IGV-2036
Refactor GenomeManager.downloadWholeGenome

IGV-2036
Add URLDownloader

This class implements Runnable, intended to allow cancelling of a download

IGV-2036
Modify CancellableProgressDialog so it doesn't keep a collection of instances

The reason for this was to make sure we only searched for one feature at a time. Now we do that with a boolean flag in FeatureTrackUtils. Simpler, and we plan on using CancellableProgressDialog for genome downloading

IGV-2036
Add UI hook for downloading genome

Change downloadWholeGenome to having a direct directory, rather than file

IGV-2036
Reasonably clean UI, have cancellable progress dialog working

IGV-2036
Tweak zip file rewriting so compressed size is set properly (ie not copied)

IGV-2036
Make downloading of genome more fault-tolerant

Show message if genome can't be downloaded, failed, but not if downloading cancelled

IGV-2036
Change from download button to checkbox

Only show checkbox in single selection mode

Make CancellableProgressDialog have settable parent frame (instead of always using IGV)

IGV-2036
Do better job determining what is a "user-defined" genome

When removing a genome from the list, only delete those files if the genome is not user defined.
This will include genomes downloaded with their sequences from the server

IGV-2036
Add hasCustomSequenceLocation property to genomes

when they are fully downloaded from server. Will use this to inform updating from cache

IGV-2036
Change test parameter to account for the fact that hg18.genome no longer present in test directory
Have refreshing a cached genome respect custom sequence locations

When refreshing a cached genome with a custom sequence location, we first download the new version to a tmp file, rewrite the sequenceLocation of that tmp file, and then replace the previous version. Add unit test for same

IGV-2036
Show asterisk next to genome name if it has local sequence

IGV-2020
Fix minor bug in getFileNameFromURL
Remove type parameter from ManageGenomesDialog.GenomeCellRenderer

This is for Java 6 compatibility