[Pipet Devel] libraries - was more nice interfaces

J.W. Bizzaro bizzaro at bc.edu
Tue Mar 2 23:18:48 EST 1999

Thomas.Sicheritz at molbio.uu.se wrote:

>  > What do you mean by "Que"?
> They don't show "Fawlty Towers" oversea ? - ¿Que? is the spanish quote from
> the a "continental cretin" ... (http://www.metronet.co.uk/cultv/fawlty.htm)

I've seen it on Public Television here.  What is the character just before Que? 
I can't read it on Netscape Mail.

>  >
>  > What do you think should be done regarding "namespace"?
> This basic library - "loci" - should we build it as a shared library - load
> on demand, or will it contain all vital structures/functions statically
> linked to the core ... hmm ... in that case what is the core ?

There is no "core" other than Paos, which is called on demand and is not a
single process.

The library of analytical tools (see the glossary) will be shared, only loaded
if and when needed, using "include".  So really, they're Python modules.

To get a better idea, take a look at the modules for Konrad's "Molecular
Modeling Tollkit".  This may be pretty much what Konrad will contribute to Loci:


> A question concerning addon modules:
>   If I am going to write new phylogenomic tools in e.g. pyhton - what do I
>   need to think about to make the programs loci-compatible ?

Good point.  With the development of the first graphical tools for Loci, such as
your sequence editor, we will be constructing a standard for Loci tools.  So,
there will be a certain amount of Python code in each tool that is the same for
all tools, even new ones.  And eventually we should be able to provide other
programmers with a nonfunctioning core to which they can add their code.

What should the standard/core of each graphical tool be able to do?

  (1) Read workflow data from Paos
  (2) Get bio data from Paos or directly from file
  (3) Convert bio data to layout for graphics
  (4) Have drawing capability (links to gnome-canvas)
  (5) Send work flow data to Paos
  (6) Send bio data to Paos or write to file
  (7) Find available tools to use or launch (from Paos?)

Anything else?

>   What should I tell other programmers ? Do we need a "locus style guide" ?

In a sense.  We should have clear instructions on how to add to the core of the
graphical tool, and what the programmer should know about how Loci functions.

This is all very important, because Loci will have to be very easy to expand for
it to get expanded by others at all.

J.W. Bizzaro                  Phone: 617-552-3905
Boston College                mailto:bizzaro at bc.edu
Department of Chemistry       http://www.uml.edu/Dept/Chem/Bizzaro/

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