Help needed in C++ / seqan issue

[Andreas Tille <andreas@an3as.eu>]

Hi,

I've got some request to package mugsy which I started in Git[1].  The
source contained several code copies.  I think I sorted out the code
copy of mummer by adding the patches contained in mugsy to the Debian
packaged mummer (see my last upload).

I also tried to get rid of the outdated seqan copy but this creates
several issues of kind

In file included from mugsy/mugsy.cpp:36:0:
mugsy/rna_alphabet.h:183:40: error: conflicting declaration 'typedef class seqan::SimpleType<unsigned char, seqan::_Rna> seqan::Rna'
 typedef SimpleType<unsigned char,_Rna> Rna;^M
                                        ^
In file included from /usr/include/seqan/basic/basic_alphabet.h:90:0,
                 from /usr/include/seqan/basic.h:68,
                 from mugsy/mugsy.cpp:29:
/usr/include/seqan/basic/alphabet_residue.h:402:41: note: previous declaration as 'typedef class seqan::SimpleType<unsigned char, seqan::Rna_> seqan::Rna'
 typedef SimpleType<unsigned char, Rna_> Rna;
                                         ^
In file included from mugsy/mugsy.cpp:36:0:
mugsy/rna_alphabet.h:185:20: error: redefinition of 'struct seqan::ValueSize<seqan::SimpleType<unsigned char, seqan::Rna_> >'
 template <> struct ValueSize< Rna > { enum { VALUE = 4 }; };^M
                    ^
In file included from /usr/include/seqan/basic/basic_alphabet.h:90:0,
                 from /usr/include/seqan/basic.h:68,
                 from mugsy/mugsy.cpp:29:
/usr/include/seqan/basic/alphabet_residue.h:405:8: error: previous definition of 'struct seqan::ValueSize<seqan::SimpleType<unsigned char, seqan::Rna_> >'
 struct ValueSize<Rna>
        ^
In file included from mugsy/mugsy.cpp:36:0:
mugsy/rna_alphabet.h:186:20: error: redefinition of 'struct seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::Rna_> >'
 template <> struct BitsPerValue< Rna > { enum { VALUE = 2 }; };^M
                    ^
...


Just use git-buildpackage on [1] to see more of them.  My C++ knowledge
is basically zero so I do not feel able to fix this what seems to be a
simple task for a C++ programmer.  Before I'll direct this question to
debian-mentors I'd like to test whether I can get some help on our list.

Kind regards

         Andreas.

[1] git://anonscm.debian.org/debian-med/mugsy.git

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