> Hmm - right now I feel I have time to get familiar with python ... so maybe I > am going to try to build a sequence editor ... any suggestions ? Great! The sequence vis/edit locus should be closely tied to the sequence comparison locus: I think users may open up various sequences (using the file/document translation locus) into the sequence comparison locus and then double-click on a sequence to see it in the vis/edit tool. Users may also load a sequence directly into the vis/edit locus, bypassing the comparison locus. Once in the vis/edit locus, sequences should be treated like an image in the GIMP or Photoshop: Users should be able to click-drag-select segments of a sequence just like an area in an image. I imagine the background of the selected segment would transition from white to black...or maybe a dashed-line box will surround the segment...I'd prefer the former. Once selected, the segments can be cut (^X) copied (^C) pasted (^V) or deleted (^D). The user should also be able to zoom in and out on the sequence...zooming in to the resolution of one residue. The mouse pointer can point out where selections or insertions occur. I'd also like to see a box on the side that shows the start and stop positions of selections, in numerical values. The menu bar should contain a file menu with open, close and exit...and an edit menu with copy, cut, paste and delete...maybe even undo...these are obvious standards. I can't recall exactly how your Tcl/Tk editor works. I may have described much of it already. I think this is a fun tool to be working on. Also. take a look at the graphics on this Web site: http://www.latrobe.edu.au/www/genetics/compmap.96.01.html It is a chromosome map comparison tool (which may be a part of what you're going to do...or another tool?), but I like the graphics. With the gnome-canvas widget (see below) we will be able to make anti-aliased shapes like this. > > I don't know anything about pythons way to handle classes - is there any > reason for me to code the sequence classes in C++ ? - or would it be enough > to let python handle the basic sequence object and code the heavy number > crunching part in C++/C ? >From my experience, Python may be better at handling this sort of thing than even C++, but Konrad is the best person to answer this question right now. By the way, C should be used for number crunching rather than C++. We discussed the "problems" with C++ before you came aboard, and we feel that C is more portable and more directly linked with Python and GTK. So the Tulip core distribution should be all Python and ANSI-C. Third party add-ons can be whatever...we just want the core to be consistent. > > I think I allready know from my Tcl/Tk sequence editor what > solutions/ways I definitely should avoid :-) > - anybody else with tips/hints/critics ? > If not, I am going to bugger my printer with ... some ... pages of python > and GTK manuals/references. > I'm sure you got my message about PyG Tools, but again, you may want to start at my page: http://www.uml.edu/Dept/Chem/BICGroup/PyGTools/ The first widget binding I think you'll want to get familiar with is the gnome-canvas (part of PyGNOME). It is supposed to be similar to the Tk canvas. -- J.W. Bizzaro Phone: 617-552-3905 Boston College mailto:bizzaro at bc.edu Department of Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/ --