[EMBOSS] is it possible to use emboss without writing a full application?

[Mahmut Uludag]

Hi Jeff,

Further to Peter's email, i have checked the needle inputs that only the 
sequence and the matrix parameters are emboss specific types.

You can set your sequence inputs using the ajSeqNewNameC function which 
use basic C types.

   AjPSeq ajSeqNewNameC(const char* txt, const char* name)

First parameter is the text of the input sequence.

If you are not aligning one sequence with multiple sequences than the 
algorithm can be simplified, such as you can delete the while-loop and 
the seqall parameter.

For the matrix parameter you can use the ajMatrixNewFile function as in 
the following example.

ajMatrixNewFile(ajStrNewC("/myembossinstall/share/EMBOSS/data/EBLOSUM80"))

If you are doing many alignments and not using the end gap penalties you 
may consider using the emboss stretcher program instead. stretcher uses 
a more advanced algorithm, its memory consumption is less and also it is 
sometimes faster than needle.

--mahmut

> I have a completely different way of gathering command-line user input that doesn’t use Ajax/ACD, can I still use emboss for sequence alignment?  That’s the kind of example I need.