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?