XPlasMap iconIn case anyone cares, I’m still slowly1 working on making a non-beta version of XPlasMap. (The present release is 0.96 [see comments here], so it’s getting incrementally closer to 1.0.) I’ve squashed a few bugs, and added a few features, but much of what I’ve been doing has been kind of shuffling things behind to scenes to make it a little easier to maintain, and also to prepare for adding a couple of features that would have stepped on the toes of the original setup.

I spent the morning trying to figure out why printing was suddenly low-resolution, a bug I thought I had fixed several iterations ago. Turns out the fix only works with the most recent versions of wxPython, whereas I was still working with the builtin 2.8.4.0 in the hope of making the file more portable on Leopard. There’s nothing in the release notes that I can see, but when I switched back to 2.8.7.1 print resolution was back to the proper level again.

There are a couple of things in the ToDos that probably won’t make it into v. 1.0, but most of them should, I think.

XPlasMap ToDos for v 1.0

  • BUG - Clicking on anything often selects the plasmid rather than the feature itself. (Take the plasmid out of the pathlist)
  • BUG – Changing gene text parameters overrides text position
  • BUG – Fix highlights in Cut Dialog
  • BUG – Split MCS doesn’t work with no downstream sequence/site
  • BUG – Hide/show text in List View is really slow for a batch of genes!
  • BUG – writeXMLFile intermittently throws error at self.recentFilesMenu.Delete(deleteId) – “invalid item in wxMenu.Delete”
  • BUG – Show/hide comment contextual menu doesn’t work
  • BUG – When importing from FastA make sure first save prompts for a name
  • “Info” icon in toolbar
  • Highlight features when selected
  • Flip text orientation manually
  • Insert fragments by restriction site
  • More fine-grained control of fonts
  • Determine PNG and JPG resolution at export time
  • When importing and identifying sequences, put enzyme sequence into “Note”
  • When opening a file, put MCS center (etc) in if missing. Also put in during creation in dialog
  • Convert restriction sites to MCS
  • Magnifying-glass-type zoom
  • Error message if “Import” tries to open an incorrect file type
  • Checkbox – Identify ORFs in Genbank imports (Default on or off in preferences)
  • Annotation menu
  • Add special symbols for Annotations (Arrows, brace-brackets, etc)
  • Status bar – show mouse position in nucleotides
  • Speed up changes in List View
  • Improve batch handling of genes
  • Clean up the code for the copy and cut fragment sections
  • Turn plasmid name and description into a free-standing comment
  • (With special double-click characteristics?)
  • Import from ApE gb files (APE gb files are broken, repair their LOCUS line spacing and then import; or write a less restrictive GenBank interpreter)
  • Import from GB as circular when noted in LOCUS line
  • Report error when ImportFromGB module fails
  • Print from ListView
  • BUG – short gene goes all the way around when crossing the 90o point
  • BUG – Printing more than one page doesn’t work (Use GetVirtualSize instead of GetSizeTuple; But this causes problems for the next page, if it’s smaller)
  • BUG – Printing is low-resolution (again!)
  • BUG – Highlight color is too opaque
  • BUG – “No features are selected” in List View
  • BUG – Text height of new import is off the window
  • BUG – Short genes only show clockwise arrow
  • Grab “Product” from GenBank imports for names
  • Batch entry for restriction sites
  • Batch entry for genes
  • Change “Insert fragment” shortcut from “⌘I” to “⌘V”; change “Edit plasmid info” shortcut to “⌘I”

  1. XPlasMap is lower priority than writing grants, teaching, doing lab work, and taking kids to birthday parties and tobogganing, so that leaves about an hour twice a week, late at night when the kids are asleep, for XPlasMap.[↩]