[Bio] / FigKernelPackages / FIG.pm Repository:
ViewVC logotype

Diff of /FigKernelPackages/FIG.pm

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.648, Sun Jan 20 21:33:42 2008 UTC revision 1.649, Fri Jan 25 21:13:50 2008 UTC
# Line 19794  Line 19794 
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    

Legend:
Removed from v.1.648  
changed lines
  Added in v.1.649

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3