Protein Family Alignment Annotation Tool svncode

Make the residue annotation tooltip less in-your-face. Once the tooltip was activated, it was reappearing for every moused-over residue even when the mouse was only passing thru and not spending more than second over the residue. Now it must spend at least one second at a new residue after being moved

Cosmetic. Nos sig change

1) Percent Id scrollpane now displays sequence names with more than 10 chars. Prior to this fix the trailing chars were removed and longer sequence names were impossible to decipher. 3) The pane shows actual %IDs and not fractions. 3) The diagonal of the %ID matrix is displayed as red to help users locate columns and rows of interest

1. Rename some menu items in tree so the expected function is clearer. 2. Report error when the user forgets to select nodes prior to clicking View -> Color Seq names of selected nodes. 3. The pink selection box on the tree now selects the internal nodes within the box in addition the external nodes within the box. 4. After View -> Color seq names of selected nodes is applies ,the selected nodes are de-selected so the names are no longer pink and the applied colour is visible and an obvious change has been mase. 5. Make the vertical bar red, thicker, and nudged slightly to the right so it more obvious to the user. Instructions on how to use the vertical bar and now displayed in red text on the bottom left panel

1. Now reports stats for ancestral nodes that are missing from the tree. The values will be zero. 2. Added example usage. 3 Added a label option to indicate the tree name

1. Found sequences now appear as yellow in MSA and tree. 2. Selected sequences and leaf nodes now appear as bright pink. 3. Random color assignment to tree can no longer use the hue 300-310 as it would class with selected leaves.

1. prevent inclusion of a randomly generated color for a seqname in the tree when it is bright yellow or bright green as they are difficult to see on white background. Instead, get another random color until it is not bright yellow or green. 2. change displayed branch length from 1 decimal point to 2 decimal points. 3. Renamed a bunch of methods that referred to Properties so they refer to SequenceAnnotations instead.

improve help for usage