Protein Family Alignment Annotation Tool svncode

Improvements to website to better support dowloads for different systems and architectures

better handling of unsigned libraries for PC

win-specific comments

1) Improved readability of code for existing methods. 2) Added java doc to methods that lacked it. 3) Added warning message for when user clicks Color -> Seq Names -> By -> Tax ID / Species but there are not values set and coloring is not applied. 4) Consolidated code to handle non-existing values for TAX ID, Species, cluster ID and user-defined seq annots

1) Fixed bugs where color->seq Names-> by -> taxonomy ID and ->species were not working. 2) Removed Color->seq Names-> by -> Bootstrap as it didn't work and it doesn't make sense given that bootstraps are only associated with internal nodes. 3) Added java doc to various methods that didn't have it. 4) Renamed some methods.

1) Added javadoc to various methods. 2) Added an info message saying that no values exist for cluster ID. This is displayed when the user trys to color the tree by cluster ID and no color changes are applied due to the lack of cluster ID values. Prior to this, the user was left wondering why no color changes were applied. 3) Organized the else if statements in actionPerformed so the order is consistent with the order of the MenuItems. This makes it easier to read and interpret the code.

Moved View-> Color Seq Names-> to View-> Color -> Seq Names-> . Renamed JMenus and JMenuItems to be consistent with Hungarian notation used by original developers for swing components.

Create a new sub menu called View-> Color Seq Names-> , and move relevant menu items to it. This paves way for Color Species etc