hmmer3.pm: Fixed a bug where an homology line ending in CS or RF
aminoacids made "next_seq" think it was the consensus structure
track, braking the parser. Added a test that show this
hmmer.t: Fixed minor mistake
hmmmer2 & hmmer3: Complete elimination of the use of '$_'
and removal of trailing whitespaces. Test suite pass.
FTLocationFactory.pm: Adjusted from_string() subroutine to
comply with current GenBank Feature Table Definition, so now
"join(complement(C..D),complement(A..B))" produce the same
result than "complement(join(A..B,C..D))". Added more tests,
and cleaned "LocationFactory.t" format. Also updated outdated
genome test file U58726.gb to its latest version (which complies
with this change), and "Splicedseq.t" (which use it).
FTLocationFactory.pm: Fixed a long-standing issue at "from_string()"
and now "join(A..B,join(C..D,join(E..F,G..H)),I..J)" is
equivalent to "join(A..B,C..D,E..F,G..H,J..I)". Updated test.