[FIX] Fixed a warning concerning a possible uninitialized variable.

git-svn-id: http://svn.seqan.de/seqan/trunk@13697 e6417c60-b987-48fd-844e-b20f0fcc1017
[FIX] Fixed a warning concerning a possible uninitialized variable.

git-svn-id: http://svn.seqan.de/seqan/trunk@13698 e6417c60-b987-48fd-844e-b20f0fcc1017
[FIX] Fixing CTD setup in case SeqAn does not come from Subversion.


git-svn-id: http://svn.seqan.de/seqan/trunk@13699 e6417c60-b987-48fd-844e-b20f0fcc1017
[DOC] Fixed commas within documentation of bandedChainAlignment function

git-svn-id: http://svn.seqan.de/seqan/trunk@13700 e6417c60-b987-48fd-844e-b20f0fcc1017
[FIX] project for extras/tests renamed as seqan_extras_tests

git-svn-id: http://svn.seqan.de/seqan/trunk@13701 e6417c60-b987-48fd-844e-b20f0fcc1017
[FIX] Fixing pair_align tests.

git-svn-id: http://svn.seqan.de/seqan/trunk@13702 e6417c60-b987-48fd-844e-b20f0fcc1017
[FIX] Fixing RazerS 3 with no output parameter.


git-svn-id: http://svn.seqan.de/seqan/trunk@13703 e6417c60-b987-48fd-844e-b20f0fcc1017
[FIX] Fixing RazerS 2 without output file name parameter.


git-svn-id: http://svn.seqan.de/seqan/trunk@13704 e6417c60-b987-48fd-844e-b20f0fcc1017
[FIX] Fixing file type detection in RazerS 2.


git-svn-id: http://svn.seqan.de/seqan/trunk@13705 e6417c60-b987-48fd-844e-b20f0fcc1017
[FIX] Fixing file type detection in RazerS 3.


git-svn-id: http://svn.seqan.de/seqan/trunk@13706 e6417c60-b987-48fd-844e-b20f0fcc1017
[FIX] Splitting index tests a bit more to remove warning in 32 bit g++ 4.7.

git-svn-id: http://svn.seqan.de/seqan/trunk@13707 e6417c60-b987-48fd-844e-b20f0fcc1017
[API, INTERNAL] Refactored seeds2 module. Changed order of input parameters of constructors of the seed class. Adapted orientation to the new alignment implementation. Removed unused functions. 

git-svn-id: http://svn.seqan.de/seqan/trunk@13709 e6417c60-b987-48fd-844e-b20f0fcc1017
[API] Removing chaining module (multi-dimensional chaining).

2D chaining is still in the seeds module.

The chaining module was hard to maintain and has found no use so far.
Furthermore, it used range trees where practical implementations prefer kd-trees.


git-svn-id: http://svn.seqan.de/seqan/trunk@13710 e6417c60-b987-48fd-844e-b20f0fcc1017
[API] The module seeds2 becomes seeds.

git-svn-id: http://svn.seqan.de/seqan/trunk@13711 e6417c60-b987-48fd-844e-b20f0fcc1017
[DOC] Adding examples for Seed-and-Extend tutorial.

git-svn-id: http://svn.seqan.de/seqan/trunk@13712 e6417c60-b987-48fd-844e-b20f0fcc1017
[DOC] Solution 1 for seed and extend tutorial.

git-svn-id: http://svn.seqan.de/seqan/trunk@13713 e6417c60-b987-48fd-844e-b20f0fcc1017
[DOC] More solutions for seed and extend tutorial.

git-svn-id: http://svn.seqan.de/seqan/trunk@13714 e6417c60-b987-48fd-844e-b20f0fcc1017
[DOC] Adding example and solution for global chaining tutorial.

git-svn-id: http://svn.seqan.de/seqan/trunk@13715 e6417c60-b987-48fd-844e-b20f0fcc1017
[DOC] More seed-and-extend tutorial code.

git-svn-id: http://svn.seqan.de/seqan/trunk@13716 e6417c60-b987-48fd-844e-b20f0fcc1017
[DOC] Fixed documentation of new seeds module.

git-svn-id: http://svn.seqan.de/seqan/trunk@13717 e6417c60-b987-48fd-844e-b20f0fcc1017