documentation of fetch_by_region-method fixed

WAS :         $slice = $sa->fetch_by_region('x', 100000, 200000);
CHANGED TO :  $slice = $sa->fetch_by_region('chromosome','x', 100000, 200000);

altered Translate so only strips trailing stop codons if they are actually the last full codon

Added strand argument in the slice subseq method call in alignment_strings. If not present did not return the seq in the right strand when it is < 0

Modified the _mask_features and get_repeatmasked_seq methods to take an additional optional argument to allow not default masking on specific repeat classes or names. Consequently added some changes in RepeatMaskedSlice to take this new argumnent into account. This should not affect any existing script or module

bug fix: get_all_Attributes returned undef instead of [] if no attributes were added - fixed by modifying constructor

added regression test: when requested seq_region is ambiguous slice of highest seq_region should be returned

Replaced deprecated ens_genomic_align calls, and also changed genomic_hit seqname to seq_region_name as more reliable