PAINT v2.29

Fixes dialog problem and
allows for full alphanumeric in the version

Paint-v2.28c

Fix to #44, update the number of rows in the association table when a new node is selected

Paint-v2.28b

The association table now shows all of the experimental annotations for painted annotations (and they are linked out).

Fixed bug #45 (which actually wasn't about notes, but was because of an obsolete, negated term)

Paint-v2.28a

This is first attempt at fixing problem with Taxon and Qualifier dialogs being non-responsive to mouse input.

Paint-v2.28

Fix for #39 (aka #38) where opening 'new' failed
Added scroll to selected node on command-click (for annotation) #40
non-cellular processes are now in yellow in matrix (fixes #42)
added mini-list of withs in annotation table #41

PAINT-v2.27

• This fixes the scrolling problem that Marc (and others presumably) were having.
• It also fixes #32, so the tree no longer is squashed after expanding nodes
• Searching is improved I think. Click on the evidence column at the bottom to see how it works, be nice to include the count of the number of experimental results for each term. Also try out the find utility, much more useful now
• Adding the scripts too with the increased memory and in the correct order
• Last, but not least you now can choose to use either the PANTHER server to obtain the trees or you can load them from the saved tree files. The downside (or upside) is that for older families loading from the files may be older PANTHER releases. The upside is that you could potentially load twice (server and file) to visually compare the changes between panther release.

Logging of retrieval times added

No new features and no bug fixes in terms of functionality. Major thing is to gather more information for debugging the problems loading large protein families.

Under the hood, just incidentally, there is code for exporting to phyloxml.

PAINT-v2.25

Need to set the attr table model up first because the position of the rows is used to determine the position of the nodes on the y axis so these line up

PAINT

1. Found one possible cause for some families not loading. If the annotations being collected for the leaf nodes (experimentally determined) were made to obsolete GO terms then havoc ensued. PAINT now courteously replaces the obsolete term for these experiment annotations with the replacement term. (If there is one and only one replacement).
2. As a by-product while debugging the above the matrix term-column sorting was sped up. Perhaps not an obvious improvement, but slightly less waiting time.
3. Restored the older version of macify. May help with the qualifier dialog box not showing up. Please let me know.