Update Addresses Issues Caused by Java 1.6 Update 15

Sun and Oracle would do well to test and repair their updates as rigorously as we do! Last week, an update was released for Java, the technology on which QuickGene is based. That update contains a major flaw for Windows users, which prevents QuickGene (or any other Java program) from accessing certain essential information it has stored in the registry. This causes QuickGene 0.5 to crash while starting up.

Unfortunately, this update was released at nearly the same time as the QuickGene update, resulting in a number of computers containing the both the new Java version and QuickGene 0.5. Per chance, none of the four PCs in the office had the update, which caused the problem to go unnoticed until we updated our QuickGene installations at home and received reports from beta testers about mysterious crashes. Of course, we got to work on the problem immediately and, two hours later, we released a new update to version 0.5.1. This temporarily circumvented the problem, avoiding further crashes and allowing people to run QuickGene once again, despite the errors in Java.

Today, we have released an improved version which entirely avoids the current registry access problems currently present in Java. All Windows users should check for updates via the "Help" menu or download and install the latest version (currently 0.5.2) as soon as possible.

QuickGene Beta 0.5 Adds Easy Navigation to Vector Maps

A great deal of work went into the step to QuickGene's update to 0.5, including a complete overhaul of the way in which maps are displayed. Users might recognize the navigation methods from regular map services such as Google Maps, in which smooth scrolling and zooming with intuitive mouse controls were a refreshing innovation. We've adopted this natural feeling navigation method for use in genetic maps, making QuickGene's map controls the most intuitive in existence!

Standard functions such as printing, saving images, toggling the display different elements and many other enhancements have also been added to the map view. This view replaces the previously available linear and circular views, further enhancing the clean, straight-forward interface QuickGene aims for.

One of the most popular requests we receive is the ability to choose which buffers to display, when more than one is available. As always, your wish is our command! Users may now also specify their preferred enzyme supplier in the Enzyme Manager, which will then always display those buffers when available for any given restriction enzyme. This includes the buffers displayed anywhere the Enzyme Manager as well as in tool-tips shown when hovering the mouse over restriction sites in a sequence or map.

Full support for saving files to the GenBank format has also been completed, allowing for extended interaction between QuickGene and any other software tools you use. Furthermore, QuickGene can now open even more file-types and even attempts to recognize sequences in files it doesn't recognize!

We hope you enjoy all the improvements and feel free to give us your opinion.

The full list of changes is as follows:

New features

• Sequence maps have been completely rebuilt and now include:
  
  
  
  • More intuitive navigation using mouse controls
  
  
  • New navigation controls and a mini-map
  
  
  • Ability to print maps and to save maps as image files
  
  
  • Merged linear and circular maps into a single view
  
  
  • Added view options to select topology and visibility of features, enzymes and rulers
  
  
  • Improved map rulers
  
  
  • Improved display speed
• Replaced "Sequence Editor" shelf-menu with more intuitive, view-dependent "View Options"


• Added colorized feature icons, indicating bookmark, feature or search result, including direction and strand, if applicable.


• Full GenBank support with additional support for QuickGene-specific information, such as colors, non-directional features and bookmarks.


• Added the option to select which enzyme producer appears first in tooltips and in the enzyme manager


• Added option to copy a selection as the top or bottom strand in either direction or as a translation in any frame.

Changes

• Added a warning dialog when saving in the Fasta format when data may be lost


• Increased flexibility of opening simple sequence files


• Improved loading speeds of enzyme lists


• Merged the "Sequence" and "Project" menus, introducing a new "Map" menu for newly introduced functionality


• Fixed certain ".seq" files occasionally not being recognized as valid sequences


• Fixed rare cases of missed enzyme cleavage sites with ambiguous, palindromic recognition sequences


• Fixed incorrect and inconsistent frames of translations


• Fixed display of bookmarks in the sequence editor


• Fixed available space in the status bar for base position and selection sizes


• Fixed base number of cursor position to be more logical


• Fixed printing sequence with single-letter translations


• Fixed printing sequence with features