[FIX-#561] Splits pair_align into multiple translation units to free compilation resources.
[INTERNAL,NOP] Modifies CMakeLists to reduce number of object files build. Fixes some whitespace issues.
[FIX] Disables OBJECT feature which is not supported by cmake versions less than 2.8.8.
[FIX] Fixes compiler issues with set macros from within cmake.
[FIX] Fixes some compiler issues.

Merge branch 'release/fix/561' of https://github.com/rrahn/seqan into release/fix/561

Conflicts:
	apps/pair_align/lib/CMakeLists.txt
Merge branch 'develop' of github.com:seqan/seqan into release/fix/561
[INTERNAL] Some cosmetic changes.
Merge pull request #753 from rrahn/release/fix/561

[FIX] Makes pair_align compile on travis.