----- Original Message -----
From: "R. Joseph Newton" <[EMAIL PROTECTED]>
To: "Öznur Tastan" <[EMAIL PROTECTED]>
Cc: "Charles K. Clarkson" <[EMAIL PROTECTED]>; "'Perl Lists'"
<[EMAIL PROTECTED]>
Sent: Tuesday, February 24, 2004 7:16 PM
Subject: Re: how to push a double dimensional array
> Öznur Tastan wrote:
>
>
> At the beginning of this thread, you indicated that you needed to store
> alignments. You said this in a way that assumed there was some standard
for
> what an alignment is. There are an infinite number of alignments
arrangements
> in the world, and each might take a somewhat different treatment.
Alignment of
> what with what, in what cooridnate system?
> It is very important that you express these things carefully outside of
code
> first. I suspect that you are using an inappropriate data structure for
the
> type of data and relationships among the data, that you are dealing with.
>
>
>
> > I didn't know that was a problem.
>
> I think you are right in trying to keep the focus narrow. We need better
> understanding of the real-world situation that you are trying to describe,
> though.
>
> Can we step back a bit, focus on one problem at a time, and you tell us:
>
> What information you have going into the problem
> What you want out of the data
Ok: I am starting from the beginning.
The alignment is alignment of two strings so that similiar characters
according to a scoring system(this is out of scope I think) should be in the
same register and there can be gaps in one of the strings denotes as a dash.
so my alignments has three features(seq1 seq2 and the score of the
alignments)
seq1: AADALLL
seq2: - - EVLLL
score:12
There are groups of alignments that I want to keep sperated
say I have 15 alignments (the numbers and distributions can be change with
different input strings)
3 of the alignments belong to first group
4 of them second belong to 2nd group.
5 of them belong to 3rd
2 of them belong to 4th
1 of them belong to 5th)
Since later on I am going to build longer alignments by taking one alignment
from each group in order and concenating them ( all combinations), I need to
store the alignments group by group. Note I know the group numbers in
advance.
So what approach and what data structures would you recommend me to use?
thanks in advance
cheers
oznur
>
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