Protein Family Alignment Annotation Tool svncode

Removed "link" as a standard node

Fixed size/position of edit dialog

Fixed uppercase/lowercase bug
Moved Show/hide/Show all/ from edit menu to view menu in treeviewer

Edit REs Ann dialog...reworked color

fix for "sort by seq annotation as STRINg put blanks at BEGINING" bug

Fix for "Tree Zoom by right mouse can bogusly collapse tree in Y"

plus removing some unwanted print statments

Added new features for tree: view->show, meaning now you can
show / hide "user defined properties".

Fixed (hahaha yeah right) the inconsistencies with
"user defined properties" including duplicates and synonyms
for both alignment and tree whether generated or loaded.
As well as various ATVgraphic() draw bugs

Milestone #3 of tree->view->show reached.

This feature is complete except for one bug that
appears to be outside the code altered for this feature.

In particular the user defined proprties for the whole tree that
should be calculated as part of the "propert list" appear to NOT
be set correctly.

This means that in the MENU of view->show no user defined properties
show up...however you can still hide/show user defined properties
for individual nodes by using the checkboxes on the Node Panel.

Milestone #2 in "tree->view->show".

Still as in milestone#1 the functionality has not yet changed. This is
an under-the-hood change.

Now the DRAWING code also uses the new more flexible system
of open eded "show strings" rather than the hard coded "hide flags".
This means all the code refactoring is done and now its time to
move onto milestone #3...add the new fucntionality. This should be
as simple as saying to node panel "hey show hide/show flags for user
defined and synonyms" and "hey menu...allow show hide of same". Under
the hood this functionality is already there.

HIDE flags removed from implementation. SHOW strings used instead. HIDE flags can be READ but SHOW strings are read/written
Rename your test .nhx files to have _readFlags.nhx or something and test reading them, writing them back out with new code, and reading them back in.