Re: [Seqan-dev] Gapped Sequence Itertor seems to trim Gaps at Beginning/Ending of a Row

[Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>]

Hi Nikolai,

this weakness of the Gaps data structure is known to us and on our "to 
be fixed" list.

Off the top of my head, I would look into the alignment printing 
function here:

http://trac.seqan.de/browser/trunk/seqan/core/include/seqan/align/align_base.h#L468

It appears that you have to use the iter() function together with 
length() but not the begin() and end functions. :(

The solution to the Task 1 in alignments uses the iter() function as well:

http://trac.seqan.de/wiki/Tutorial/Alignments/AssignmentPairwiseGlobalAlignment1

HTH
Manuel

On 12/21/2011 03:32 PM, Nikola Koch wrote:
> Hi,
> I'm using Seqan for my Bachelor's thesis, which consists of writing an
> alignment window for BALL.
> Since I need to have pointers from the sequences back to the
> corresponding residues, I have to create my own sequence and alignment
> representations that link back to their origins.
> For computing the actual alignment, I want to use Seqan.
> So I have to push my representations into the Seqan structures and
> after computing the alignment, retrieve the alignment from the Seqan
> structures and push it into my own structures. The Seqan structures I
> use, are the same as described in your tutorial (I'm not using an
> alignment graph)
> And here comes my problem:
> When retrieving the Alignment from your structures I use two iterators
> to iterate over the gapped rows (and columns).
> But when there are gaps at the beginning (or the end) of a row, the
> iterator seems to just ignore them and starts with the character right
> after the gap (or ends with the last character in front of the gap).
> For example: ---AL-GI-- then becomes AL-GI.
>
> The length of such a gapped row seems to also be the length of the row
> without starting/ending gaps.
>
> But when using std::cout with the whole alignment, all gaps are, where
> they should be.
>
> I consulted the Seqan documentation but without result.
>
> So is there a possibility to externally gain access to the gaps at the
> beginning/end of each row?
> Or is there a better way to retrieve the alignment than iterating over
> all rows?
>
> Thanks,
> Nikola
>
>
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