[Bioperl-l] small question

L.Pollak lorenz@ist.org
Sun, 30 Jul 2000 19:35:14 +0200

> Yup. Annotation objects can't "know" about Sequence objects otherwise we
> have screwed something up (along with nasty memory cycles as well. Lorenz
> - you should make sure you understand about memory cycles).

sure, ok i mean i didn't know the word "memory cycle" but i know what
are talking about. I was thinking about a reference to the parent object
as used in Ian Korf's BPlite. (no recursive function calls ;) )

but i have another problem i would like to discuss:
when reading a comment from a swissprot file there are special
comment blocks that start with "-!-". The last version of
would read the whole CC lines and then replace all "-!-"s and "\n"s with
spaces which is not so good as we now want to write the comment back in
swissprot format.

shall i split up the comment into different comment objects for every
block starting with "-!-" or shall i read the whole comment literally,
store it in one object and let the user handle the special blocks...
(as i have done it for now)

kind regards,

PS: tonight i will commit a swiss.pm that can now write everything 
except the "SQ"-sequence line because i don't know how to calculate the
CRC64 sum ...