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.
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