added functionalities

See merge request !18

-added overlap/distance calculation for domains
-added alignment string calculation for domain arrangements

[SequenceSet] added emplace_back method

See merge request !17

[AlignmentMatrix] added gop/gep return function

See merge request !16

switching back to cmake 2.8 for time beeing

See merge request !15

Develop ck

See merge request !14

Changed from shared_ptr to normal SequenceObject in vector to make iterator usage much simpler

-EditSequence contains both editStrings
-EditSequence contains as well start and end position of the alignment in the sequnce

-run traceback automatically when required
-adapted tests

- added Smith-Waterman algorithm
- added test for Smith-Waterman algorithm
- added test for RASPODOM

- easier handling for the user
- possible to set parameters once and reuse it
git commit -m "adding AlignmentMatrix" -a -m

hmmscan read fix and more tests

See merge request !12

- [BUGFIX] corrected read of evalue and bitscore of hmmscan parsing
- [ADDED] tests for hmmscan/superfamily parsing