Fix for Bug #2936, now Split.pm/flip_strand sets guide_strand according to
sublocation strands. Also initialize the sublocations strand values
if necessary to perform the flip. Tests added.
Initialize the Strand value if missing before performing a "flip_strand"
for an Atomic location, or it will silently fail
Split/flip_strand now makes a strand consistency check in all sublocations,
and sets Guide Strand accordingly. In case of mixed strands (trans-splicing),
it reverse the sublocations order to produce the correct revcom transcript
Split/guide_strand now makes a consistency check of the sublocations
strand values to set its own value, giving undef for mixed strands
Split/to_FTstring don't need to reverse sublocations order anymore
PrimarySeq/subseq now uses "guide_strand" for Split locations to know
when to reverse the sublocations order to produce the correct sequence
Added extensive testing for the introduced changes, with many locations
and subsequences tests in t/Seq/PrimarySeq.t
Expanded some comments
Merge remote branch 'upstream/master'
Merge remote branch 'upstream/master'
PrimarySeq.pm/new: Changed $is_circular test to use "define",
since it fails to add is_circular attribute if the argument is 0
PrimarySeqI.pm: use Bio::Root::clone to make sure that copied objects
get all attributes from the original. Implemented in revcom(), trunc(),
translate(), transcribe() and rev_transcribe()
PrimarySeq.t: TODO tests are now fixed. All the other tests also pass
Merge remote branch 'upstream/master' into test
PrimarySeqI.pm: Avoid using Bio::Root::clone when object
is 'Bio::Seq::LargePrimarySeq' or 'Bio::Seq::LargeSeq'.
This fix fails in t/Seq/LargePSeq.t and t/SeqIO/largefasta.t
FTLocationFactory.pm: Fix in from_string() for some complex
location tests that failed in LocationFactory.t
Fix typing errors
Bio/SeqUtils: trunc_with_features() and revcom_with_features()
now explicitly removes all annotations/features before adding some back,
so they don't conflict with trunc() and revcom() object cloning
Merge remote branch 'upstream/master' into test
Bio/PrimarySeq.pm: Fixed some 'uninitialized value' warnings