| 19794 |
=cut |
=cut |
| 19795 |
|
|
| 19796 |
sub pick_gene_boundaries { |
sub pick_gene_boundaries { |
| 19797 |
my($self,$genome,$loc,$tran,$genetic_code) = @_; |
my($self, $genome, $loc, $tran, $genetic_code, $search_region) = @_; |
| 19798 |
|
|
| 19799 |
if ($ENV{FIG_VERBOSE}) { |
if ($ENV{FIG_VERBOSE}) { |
| 19800 |
print STDERR "Picking gene boundaries for org=$genome, loc=$loc"; |
print STDERR "Picking gene boundaries for org=$genome, loc=$loc"; |
| 19801 |
print STDERR ", tran=$tran" if $tran; |
print STDERR ", tran=$tran" if $tran; |
| 19802 |
print STDERR ", genetic_code=$genetic_code" if $genetic_code; |
print STDERR ", genetic_code=$genetic_code" if $genetic_code; |
| 19803 |
|
print STDERR ", search_region=$search_region" if $search_region; |
| 19804 |
print STDERR "\n"; |
print STDERR "\n"; |
| 19805 |
} |
} |
| 19806 |
|
|
| 19807 |
my($leftStop, $firstStart, $start, $end, $rightStop); |
my($leftStop, $firstStart, $start, $end, $rightStop); |
| 19808 |
|
|
| 19809 |
my $full_loc = new FullLocation($self, $genome, $loc, $tran, $genetic_code); |
my $full_loc = new FullLocation($self, $genome, $loc, $tran, $genetic_code); |
| 19810 |
if ($full_loc->PickGeneBoundaries()) { |
if ($full_loc->PickGeneBoundaries(-limit => $search_region)) { |
| 19811 |
return ($full_loc->SeedString(), $full_loc->Translation()); |
return ($full_loc->SeedString(), $full_loc->Translation()); |
| 19812 |
} |
} |
| 19813 |
|
|
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