Re: [Seqan-dev] Getting a sequence as a char *

[Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>]

Hi Nick,

Am Mittwoch, 6. September 2017, 03:38:54 schrieb Nick Mapsy:
> Hi, I'm just getting started with SeqAn (and C++), so I'm sure I'm missing
> something simple here.
> 
> I've got a multiple sequence alignment working and producing an
> Align<String<Dna5> > object. Now all I need is to return the aligned
> sequences (with gaps) as C strings (char *) from the function.

Are you sure you want to be passing around these char** ? This is C++ after 
all and we have references :D

> It seems like a simple thing, but after hours reading through the
> documentation of all the types and functions (and yes, Language Entity
> Types), I can't find the path from Align to char *.
> 
> I found toCString(), but it takes a String, and I don't know how to get
> (gapped) Strings out of an Align.
> 
> Thank you for any help, and hopefully I'm able to make use of this great
> library!

You can create a CharString from the alignment row and then call toCString() 
on the CharString. But, like I said, I would really recommend working with 
Strings and StringSets instead of pointers and [].

> P.S. Here's what I've written so far:
> (I'm using SeqAn 1.4.1 on Ubuntu 16.04.)

Please update to SeqAn2 as SeqAn1 has been deprecated for a while now. The 
ubuntu package is called libseqan2-dev. It is available since Ubuntu 17.04, 
but can also be installed manually:
http://seqan.readthedocs.io/en/master/Infrastructure/Use/Install.html#library-package

Best regards,
Hannes
-- 
Hannes Hauswedell

Scientific staff & PhD candidate
Freie Universität Berlin / Max Planck Institute for Molecular Genetics

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