[Biopython-dev] Re: plans for next release

Cayte katel at worldpath.net
Wed Dec 6 01:40:50 EST 2000

> and nice snorkling too :-)
> >

   Do you have pictures of Egypt to post on the web?

> >   Have you ever considered wxPython?  I have a tool, SeqGui.py, in
> > that's sort of like xbbtools.py  I find it easier to work with than
> > Back in May, we had a thread about Gui support. Its in the archives.
> The main reasons for my sticking to Tkinter are the fact that I have used
> Tcl/Tk a lot before I discovered python - I have tons of Tk snippets from
> my previous bioinformatic work (Biowish, GRS, XBbtools, CapDB etc.) which
> is very easy to convert into shorter, cleaner and more efficient python Tk
> code. Maybe the biggest advantage in using Tkinter is the powerful Tk
> Canvas, as far as I know neither wxPython or Gtk python have anything
> to the canvas widget.

  I think the Windows version is a wrapper around the Windows Gui and that
wxPython attempts to provide equivalent functionality in Linux.
> >
> >   I'd like the gui to eventually support color highlighting of features,
> > example, regions of high consensus.
> >
> I don't know how this works in wxPython, but in Tkinter it is already
> there from the beginning. Every line, rectangle etc. you draw in the
> canvas is an unique object and gets an id. You can very easy bind any
> (e.g. MouseOver, DoubleClickButton1 etc.) to any function. To highlight
> different genes or sequence regions is just to group the according id's
> bind a color-change on a MouseOver event.

> e.g. my recently accepted paper about phylogenomics with python (NAR nr2
> 2001) deals with the interactive display of all genes, phylogenetic
> trees, blast results for a microbial genome (between 1000 and 5000 times
> 3).
> I have no fancy webpage yet but you can check a screenshot of the
> phylome of the Bacteria Thermotoga maritima
> at http://www.cbs.dtu.dk/thomas/pyphy/pyphy.png
> (Phylome = set of all phylogenetic trees for a genome.
>  color coding for the kingdom of the closest neighbor in the phylogenetic
>  tree: blue = Bacteria, yellow = Archaea, red = Eukarya)
> Here the phylome map is an interactive display of all phylogenetic trees
> and genes (colored lines in the circle), where each line/gene is sensitive
> to mouse movement. A MouseOver event displays gene information in the top
> Entry, Button1Click shows the phylogenetic tree, Button3 shows a gene
> specific popupmenu for blastresults, alignments etc.
> Each gene can be a member of a metabolic pathway, where selecting a
> in the right listbox changes the width and the arrow shape of each gene
> associated (canvas tag) with the pathway.
> The advantage here is zooming, resizing, moving and event grabbing is part
> of the canvas widget so we only need to redraw single objects.
Does it support colorization with enough flexibility, to support research on
the fly, as in this scenario?

   Ed Enzyme is doing some detective work on  an alignment.  First he
highlights the start and stop codons in red and green.  Then Ed zooms in on
an interesting sequence.  He first highights the hydrophilic regions in
magenta.  Then Ed backtracks and highlights the acidic regions.

> I have never worked with wxPython - what is exactly the strength of
> wxWindows ? I guess it is faster than Tkinter, are there any special
> features not found in the rest of the GUI family ?

  I found it was easier to work with.  With wxPython I could write more code
in the same time and fewer problems, like panels that don't quite line up.


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