Protein Family Alignment Annotation Tool svncode

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

add some comments

add more details to report usage

change default sizes for font, node and branch thickness

initial commit