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revision 1.8, Tue Feb 26 17:44:16 2008 UTC revision 1.9, Sun Mar 23 15:54:41 2008 UTC
# Line 25  Line 25 
25  use FIG;  use FIG;
26  use FigFams;  use FigFams;
27  use FIG_Config;  use FIG_Config;
28    use Tracer;
29    
30  use Time::HiRes qw( usleep ualarm gettimeofday tv_interval );  use Time::HiRes qw( usleep gettimeofday tv_interval );
31    
32  sub pinned_regions {  sub pinned_regions {
33      my($fig, $pin_desc, $fast_color, $sims_from, $map_sz, $add_features) = @_;      my($fig, $pin_desc, $fast_color, $sims_from, $map_sz, $add_features) = @_;
34    
35      # Get list of pegs required by the description in $pin_desc      # Get list of pegs required by the description in $pin_desc
36      my $pinned_pegs = &expand_peg_list($fig, $pin_desc);      my $pinned_pegs = &expand_peg_list($fig, $pin_desc);
37        Trace("Pinned pegs are " . join(", ", @$pinned_pegs) . ".") if T(3);
38      # Get regions around pinned pegs -- boundaries, features, etc.      # Get regions around pinned pegs -- boundaries, features, etc.
39      my $regions = &define_regions($fig, $map_sz, $pinned_pegs);      my $regions = &define_regions($fig, $map_sz, $pinned_pegs);
   
40      # Filter out overlapping regions caused by gene fusions, frame shifts etc. where multiple PEGs      # Filter out overlapping regions caused by gene fusions, frame shifts etc. where multiple PEGs
41      # are pinned (by similarity or PCH) to the input PEG      # are pinned (by similarity or PCH) to the input PEG
42      $regions = &filter_regions_1($pin_desc, $regions);      $regions = &filter_regions_1($pin_desc, $regions);
# Line 47  Line 47 
47      &add_functional_coupling($fig, $pin_desc, $regions, $feature_data);      &add_functional_coupling($fig, $pin_desc, $regions, $feature_data);
48  #    &add_figfams($fig, $feature_data);  #    &add_figfams($fig, $feature_data);
49      &add_subsystem_data($fig, $pin_desc, $feature_data);      &add_subsystem_data($fig, $pin_desc, $feature_data);
50        Trace("Coloring pegs.") if T(3);
51      # Assign a set number to some PEGs through transitive closure based on similarity, from blast scores      # Assign a set number to some PEGs through transitive closure based on similarity, from blast scores
52      &color_pegs($fig, $pin_desc, $pinned_pegs, $regions, $feature_data, $fast_color, $sims_from);      &color_pegs($fig, $pin_desc, $pinned_pegs, $regions, $feature_data, $fast_color, $sims_from);
53    
# Line 60  Line 60 
60    
61      # Add feature data to the regions to make the final maps      # Add feature data to the regions to make the final maps
62      my $maps = &make_maps($fig, $regions, $feature_data);      my $maps = &make_maps($fig, $regions, $feature_data);
   
63      return $maps;      return $maps;
64  }  }
65    
# Line 119  Line 118 
118              unshift @pegs, $peg;              unshift @pegs, $peg;
119          }          }
120       }       }
   
121      return \@pegs      return \@pegs
122  }  }
123    

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