parameters of RenumberChain function.

with the requested editor. Attention: Interface of RenumberChain has slightly
changed.

Conflicts:
	CMakeLists.txt

The feasibility check flag in the profile was ignored until now

Conflicts:

	modules/io/doc/mmcif.rst

Mainly written by Valerio, with a few tweaks by me

Conflicts:
	CMakeLists.txt

to be modified, since old blast versions (e.g. 2.2.16) find 27 hits
in the created testdatabase and new blastversions (e.g. 2.2.27+) find 28
hits. The only check now is, wether the created database works/something
can be found in it.

environment. The problem is, that wu-blast gets called when calling blastp.

as the old ones. It is now possible to create new blastdatabases and
the property seqid has been added to the aligned patches.

The gnu c++ size() implementation for stl containers has O(n) complexity
while empty() has O(1) complexity