GenomeView 1415: Controlling GenomeView with JavaScript

The main new feature we want to highlight in this release is the ability to control the GenomeView applet from the webpage in which it is embedded using JavaScript. The details are laid out in the integration manual. In short you can use JavaScript to load data and move around in GenomeView. In this context we have also made available a minimal applet that has no menu or side bar.

Furthermore, several options to alter the appearance of GenomeView on start-up have been added.

Three new genomes were added to the Genome Explorer: M. tuberculosis and two release of the human genome (hg18 and hg19).

Internally some of the threading was redesigned to have GenomeView exit cleanly without having to call System.exit.

Some bugs were fixed as well:
- global configuration of the pile-up track now works as expected
- paired end reads were able to stack higher than the configured maximum in some cases, this has been corrected
- scroll speed of the vertical scroll bar of the visualization frame has been increased significantly