Merge pull request #110 from holtgrewe/hotfix/empty_line_write_fasta

[FIX] Not writing out empty lines to FASTA any more.
[FEATURE] Trac plugin for dox-style links.
[DOC,FIX] Improving documentatinon for classes A-C.
[FIX] Moving pos* functions into a group.
Merge pull request #1 from holtgrewe/feature/dox_links_trac

Feature/dox links trac
Merge branch 'dox' of github.com:weese/seqan into dox
[DOC] addToProfile, alignmentEvaluation, alignmentFreeComparison, allPairsShortestPath
[DOC,FIX] Fixing most global functions that should not be global.
[DOC] assignSeq, assignCroppedSeqId, assignQual, assignQualId, appendSeqs
[DOC] Added/edit dox docu.
[DOC] Added more dox docu
[DOC] Added more dox docu.
[FIX] fixed bug that aligned reads with insertions instead of mismatches at the read
 end (wrong sinkPos)
Merge pull request #126 from weese/razers3-hotfix

[FIX] fixed bug that aligned reads with insertions instead of mismatches...
Merge pull request #4 from singerj/dox

[DOC] Added/edit dox docu.
Merge pull request #5 from rrahn/develop

Develop
Merge branch 'dox' of https://github.com/holtgrewe/seqan into holtgrewe-dox

Conflicts:
	core/include/seqan/misc/priority_type_heap.h
	core/include/seqan/pipe/pool_base.h
[DOC] Added more dox docu.
Merge branch 'dox' of https://github.com/skrakau/seqan into skrakau-dox

Conflicts:
	extras/include/seqan/journaled_set/journaled_set_impl.h
[DOC,FIX] Fix in dox of Repeat.