[Biophp-dev] New question from the Newbie

[Nico Stuurman]

Hi Fred,
 
> I am planning to do a locuslink-file parser.

That is great!  I am quite interested in using that parser!

> So I read the swissprot parser in order to get some good ideas.
> Since my knowledge in php is not as good as yours I have a newbie question
> concerning the following line of the function parse_swissprot
> 
> while (list($no, $linestr) = each($flines))

I am a little confused where this code comes from. Did you get the code
from the current biophp cvs (it is all quite confusingly organized at
the moment)?

I am asking, because I can not find a function parse_swissprot.  There
is a class parse_swissprot (in file parsers/swissprot_inc.php). 
However, this file only contains the line you mention here embedded in a
comment (on line # 167).  Line #166 reads:

while ( list($no, $linestr) = each($sourcelines) ) {

$sourcelines is an array that contains every line of the actual data as
an item (in the while loop, $no will hold the line number and $linesrt
the line's content).

Somehow, it looks like you are working with an older version of the
code.  

It also looks like Sean and I should do a better job documenting how the
parser classes work (I can barely remember myself!).


Hope this helps, please don't hesitate to ask further questions.


Best,

Nico