[BioPython] plans for next release

[Cayte]

----- Original Message -----
From: "Thomas Sicheritz-Ponten" <thomas@cbs.dtu.dk>
To: "Cayte" <katel@worldpath.net>
Cc: "Brad Chapman" <chapmanb@arches.uga.edu>; "Jeffrey Chang"
<jchang@smi.stanford.edu>; <biopython@biopython.org>
Sent: Saturday, December 02, 2000 4:26 AM
Subject: Re: [BioPython] plans for next release


> >
> > > Jeff:
> > > > > Thomas Sicheritz-Ponten is working on visualization with his
xbbtools,
> > > > > using Tk instead of wx, though.
> > > > >
> > >
> > > Cayte:
> > > >    I'm not sure its supported on Windows.  The web description
mentioned
> > > > Linux but didn't mention Windows.  It imports posix.
> > >
> > > Hi Cayte -- I just looked at this using my little bit of
Windows/python
> > > knowledge. It looks like Thomas is importing posix/posixpath in all of
> > > the different modules in xbbtools, but never actually using them. I
> > > commented out all of the imports, installed Pmw, and xbbtools seems to
> > > run okay on the machine I was playing on (vanilla Windows 98).
> > >
> > > I'm not sure if there is a good reason to import the posix stuff
> > > (Thomas?) but maybe if not, it might be good to get rid of the imports
> > > so it'll run nicely on Windows as well.
> > >
> >   I ran it and it displayed a Fasta file.  But when I selected
> > Translations->6 Frames, it caused this trace.
> >
> > C:\biopython-0.90d04\Scripts\xbbtools>python xbbtools.py lupine.nu
> > Exception in Tkinter callback
> > Traceback (most recent call last):
> >   File "c:\python20\lib\lib-tk\Tkinter.py", line 1287, in __call__
> >     return apply(self.func, args)
> >   File ".\xbb_widget.py", line 333, in gcframe
> >     np = NotePad()
> >   File ".\xbb_utils.py", line 24, in __init__
> >     self.tid = Pmw.ScrolledText(self)
> > AttributeError: ScrolledText
> >
> >   The menu items barely show up, because in Windows, they're xdark green
on
> > black, unless thry're highlighted.
> >
> >   It would be efficient to coordinate different GUIs if its feasable?
On
> > the other hand, if I experiment, I don't want to mess up someone elses'
> > code.
>
> Ok - I just came back from egypt. Of course there is no need at all for
> using posix.posixpath - thats still left from my novice days :-)
> I fix that and try to remove all Pmw widgets (its easy to implement the
> scrolled things in pure Tk)
>
> I do not run python in windows, so could anybody send me correct color
> configurations for windows ?
> I have not worked on xbbtools for a time because of the question about how
> to start one or more blast searches (threaded ?) without freezing the
whole
> Tk mainloop until the blast run is finished. To start a search
(Blast,Fasta
> Clustal etc) from within biopython is definitely a frequent task for which
> there should exist a seperate module/class ... IMHO
>
> c ya
> -thomas
>
> --
> Sicheritz Ponten Thomas E.  CBS, Department of Biotechnology
> thomas@biopython.org        The Technical University of Denmark
> CBS:  +45 45 252489         Building 208, DK-2800 Lyngby
> Fax   +45 45 931585         http://www.cbs.dtu.dk/thomas
>
> De Chelonian Mobile ... The Turtle Moves ...
>
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