_compute_gene_distance() tweaked to gracefully ignore S.pombe genes.
Added code to wise() to collect HMM from Allele as necessary.
CHanged handling of LTRs in genbank_tbl(). Minor/debugging changes elsewhere..
Added code to find last codon to _make_genbank_gene_terminii(). Other minor order cahnges to this method also.
Created genbank_coords() method to get/set adjusted coords that are Genbank compliant (determined by  _make_genbank_gene_terminii() ).
Squashed bug in reoptimise related to out-of-range error checking in $exon->_adjust(). Added capability to handle $exon->genbank_coords() to genbank_tbl().
 _make_genbank_gene_terminii() elaborated to more completely handle genbank criteria for STOP coord. Uses new $exon->genbank_coords() method to store newly calculated value.
 Improved wise() ability to get HMM from http://www.saccharomycessensustricto.org
Working code for genbank compliant STOP in _make_genbank_gene_terminii().
genbank_coords() improvements.
Modification to fragment() to get required data. May revert later as inefficient.
Modified merge() method to handle orthogroups if the genes are no in the reference genome (i.e., no direct access to other OG memebers). Ugly but necessary.
Altered _make_genbank_gene_terminii() to improve exection order. Created _genbank_quality_filter() to delete certain pseudogenes that cannot pass Genbank tbl2asn filters.
_make_genbank_compatible() improved to hande more cases and optimize execution order.
_invert_coords() changes to correct very old bug... first exons <1 codon return wrong bases.
Added reoptimize() call with lax intron params. _make_genbank_gene_terminii()
Micro changes.
Micro changes.
Micro changes.