[Pipet Devel] more cvs changes

J.W. Bizzaro bizzaro at geoserve.net
Fri Jan 7 15:02:59 EST 2000

Brad Chapman wrote:
> I think I get the idea that you are talking about here. So when I right
> (button 3) click on a loci,

Actually a double-click from the left (button 1) button.

> I get a "MS file manager type thing" with the
> loci contents in the window and options for the loci at the top (as
> menu-buttons)? Should the window that appears be imbedded in the loci
> window, or in its own X window? Just want to make sure I am completely with
> you on your ideas.

The 'loci window' is what I call a 'windowlet'.  You already have one that
shows up under the container, but it doesn't have any filesystem info.  You
have the filesystem info showing up in its own X-window.  I'd like to have
everything in windowlets if possible (not possible with non-GTK GUI's).

> That sounds great to me. I just didn't know what you plans were for
> changing the main loci-core and didn't want to interfere with them.

I understand.  But I'm not such an Uberhacker that you have to worry about
stepping on my toes.

> I just
> committed some more cvs changes today (see my next message) and modified
> the directory structure a little, but I think I have a "firm" structure for
> now. I'm definately open to changes, and will be very interested to hear
> your ideas on
> how to structure things. They'll probably be lots better than my structure
> since I just ended up building the structure through trial and error.

We've got some major changes to make.  We might as well start a new CVS module
called 'loci'.  Here is the preliminary structure:

    loci*              (currently loci.py)
    (plus some other python scripts) 
        desktop/       (this is currently loci-core - see below)
        nli/           (this will be explained later)
            elements/  (elemental components)
        web/           (this will be the web interface)
            elements/  (elemental components)
    middleware/        (this is where loci XML will be kept)
        bindings/      (bindings to various loci)
    backends/          (this is where shared backends will be kept)

Here is the structure of 'desktop':

    desktop.py         (currently workspace.py)
    (plus other python scripts for desktop) 
    elements/          (elemental GUI widgets in PyGTK)
    pixmaps/           (misc. graphics)
        (some XML preferences here)
        gtkstyles/     (currently styles)
        symbols/       (currently under pixmaps)
        icons/         (currently under pixmaps)

Note that the XML will be managed by the 'middleware' and should not be kept
with the workspace/desktop.

Additions/plugins to Loci will primarily use the elements and bindings
directories.  For example, a plugin for EMBOSS will put things in...


And if you want EMBOSS to run publicly via Loci, you'd put it in the


(if EMBOSS allows this)

> Keep me updated on your thoughts and plans. I'll be continuing to code
> heavily for the next few days (until I have to, ack, get back to classes)
> and then things will lighten up. Thanks much for your comments!

Okay.  Thanks for everything :-)

                      |           J.W. Bizzaro           |
                      |                                  |
                      | http://bioinformatics.org/~jeff/ |
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                      |           THE OPEN LAB           |
                      |    Open Source Bioinformatics    |
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