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revision 1.32, Thu Dec 6 13:59:34 2007 UTC revision 1.33, Tue May 6 16:45:37 2008 UTC
# Line 1  Line 1 
1    # -*- perl -*-
2  ########################################################################  ########################################################################
3  #  #
4  # Copyright (c) 2003-2006 University of Chicago and Fellowship  # Copyright (c) 2003-2006 University of Chicago and Fellowship
# Line 81  Line 82 
82  ########################################################################  ########################################################################
83  use strict;  use strict;
84  use FIG;  use FIG;
85    use FIGV;
86  use FIG_Config;  use FIG_Config;
87  use SFXlate;  use SFXlate;
88  use SproutFIG;  use SproutFIG;
# Line 105  Line 107 
107    
108  =item USAGE:  =item USAGE:
109    
110      my $figo = FIGO->new();           #...Subclass defaults to FIG      my $figO = FIGO->new();                    #...Subclass defaults to FIG
111    
112      my $figo = FIGO->new('SPROUT');   #...Subclass is a SPROUT object      my $figO = FIGO->new('SPROUT');            #...Subclass is a SPROUT object
113    
114        my $figO = FIGO->new($orgdir);             #...Subclass includes $orgdir as a "Virtual" SEED genome
115    
116        my $figO = FIGO->new($orgdir, 'SPROUT');   #...Subclass includes $orgdir as a "Virtual" SPROUT genome
117    
118  =back  =back
119    
120  =cut  =cut
121    
122  sub new {  sub new {
123      my($class,$low_level) = @_;      my ($class, @argv) = @_;
124    
125      my $fig;      my $fig;
126      if ($low_level && ($low_level =~ /sprout/i))      if (@argv) {
127      {          if (-d $argv[0]) {
128          $fig = new SproutFIG($FIG_Config::sproutDB, $FIG_Config::sproutData);              print STDERR ("FIGO using FIGV, argv = ( ",
129                              join(qq(, ), @argv),
130                              " )\n",
131                              ) if $ENV{FIG_DEBUG};
132    
133                $fig = FIGV->new(@argv);
134            }
135            else {
136    
137                if ($argv[0] =~ /sprout/io) {
138                    print STDERR "FIGO using SPROUT\n";
139                    $fig = SproutFIG->new($FIG_Config::sproutDB, $FIG_Config::sproutData);
140      }      }
141      else          }
142      {      }
143          $fig = new FIG;      else {
144            print STDERR "FIGO using FIG with installed orgs\n";
145            $fig = FIG->new();
146      }      }
147    
148      my $self = {};      my $self = {};
# Line 288  Line 307 
307  sub all_figfams {  sub all_figfams {
308      my($self) = @_;      my($self) = @_;
309      my $fig = $self->{_fig};      my $fig = $self->{_fig};
310      my $fams = new FigFams($fig);      my $fams = FigFams->new($fig);
311      return map { &FigFamO::new('FigFamO',$self,$_) } $fams->all_families;      return map { &FigFamO::new('FigFamO',$self,$_) } $fams->all_families;
312  }  }
313    
# Line 322  Line 341 
341      my($self,$seq) = @_;      my($self,$seq) = @_;
342    
343      my $fig = $self->{_fig};      my $fig = $self->{_fig};
344      my $fams = new FigFams($fig);      my $fams = FigFams->new($fig);
345      my($fam,$sims) = $fams->place_in_family($seq);      my($fam,$sims) = $fams->place_in_family($seq);
346      if ($fam)      if ($fam)
347      {      {
# Line 658  Line 677 
677      my($self) = @_;      my($self) = @_;
678    
679      my $figO = $self->{_figO};      my $figO = $self->{_figO};
680      return new GenomeO($figO,$self->{_genome});      return GenomeO->new($figO,$self->{_genome});
681  }  }
682    
683    
# Line 762  Line 781 
781      my $fig = $figO->{_fig};      my $fig = $figO->{_fig};
782    
783      my($features) = $fig->genes_in_region($self->genome->id,$self->id,$beg,$end);      my($features) = $fig->genes_in_region($self->genome->id,$self->id,$beg,$end);
784      return map { new FeatureO($figO,$_) } @$features;      return map { FeatureO->new($figO,$_) } @$features;
785  }  }
786    
787    
# Line 862  Line 881 
881      my($self) = @_;      my($self) = @_;
882      my $figO = $self->{_figO};      my $figO = $self->{_figO};
883      $self->id =~ /^fig\|(\d+\.\d+)/;      $self->id =~ /^fig\|(\d+\.\d+)/;
884      return new GenomeO($figO,$1);      return GenomeO->new($figO,$1);
885  }  }
886    
887    
# Line 940  Line 959 
959      my $figO = $self->{_figO};      my $figO = $self->{_figO};
960      my $loc      = $self->location;      my $loc      = $self->location;
961      my $genomeID = $self->genome->id;      my $genomeID = $self->genome->id;
962      return ($loc =~ /^(\S+)_\d+_\d+$/) ? new ContigO($figO,$genomeID,$1) : undef;      return (($loc =~ /^(\S+)_\d+_\d+$/) ? ContigO->new($figO,$genomeID,$1) : undef);
963  }  }
964    
965    
# Line 1163  Line 1182 
1182      my $figO = $self->{_figO};      my $figO = $self->{_figO};
1183      my $fig  = $figO->{_fig};      my $fig  = $figO->{_fig};
1184    
1185      return map { new SubsystemO($figO,$_) } $fig->peg_to_subsystems($self->id);      return map { SubsystemO->new($figO,$_) } $fig->peg_to_subsystems($self->id);
1186  }  }
1187    
1188    
# Line 1478  Line 1497 
1497      my($self) = @_;      my($self) = @_;
1498    
1499      my $figO = $self->{_figO};      my $figO = $self->{_figO};
1500      return new FeatureO($figO,$self->{_peg1});      return FeatureO->new($figO, $self->{_peg1});
1501  }  }
1502    
1503  =head3 peg2  =head3 peg2
# Line 1502  Line 1521 
1521      my($self) = @_;      my($self) = @_;
1522    
1523      my $figO = $self->{_figO};      my $figO = $self->{_figO};
1524      return new FeatureO($figO,$self->{_peg2});      return FeatureO->new($figO,$self->{_peg2});
1525  }  }
1526    
1527    
# Line 1854  Line 1873 
1873      my($self) = @_;      my($self) = @_;
1874    
1875      my $figO = $self->{_figO};      my $figO = $self->{_figO};
1876      return new FeatureO($figO,$self->{_peg1});      return FeatureO->new($figO,$self->{_peg1});
1877  }  }
1878    
1879    
# Line 1883  Line 1902 
1902      my($self) = @_;      my($self) = @_;
1903    
1904      my $figO = $self->{_figO};      my $figO = $self->{_figO};
1905      return new FeatureO($figO,$self->{_peg2});      return FeatureO->new($figO,$self->{_peg2});
1906  }  }
1907    
1908    
# Line 2048  Line 2067 
2067    
2068      my $figO = $self->{_figO};      my $figO = $self->{_figO};
2069      my $subO = $self->{_subO};      my $subO = $self->{_subO};
2070      if (! $subO) { $subO = $self->{_subO} = new Subsystem($self->{_id},$figO->{_fig}); }      if (! $subO) {
2071            $subO = $self->{_subO} = Subsystem->new($self->{_id}, $figO->{_fig});
2072        }
2073    
2074      return map { &GenomeO::new('GenomeO',$figO,$_) } $subO->get_genomes;      return map { &GenomeO::new('GenomeO',$figO,$_) } $subO->get_genomes;
2075  }  }
# Line 2064  Line 2085 
2085    
2086      my $figO = $self->{_figO};      my $figO = $self->{_figO};
2087      my $subO = $self->{_subO};      my $subO = $self->{_subO};
2088      if (! $subO) { $subO = $self->{_subO} = new Subsystem($self->{_id},$figO->{_fig}); }      if (! $subO) {
2089            $subO = $self->{_subO} = Subsystem->new($self->{_id}, $figO->{_fig});
2090        }
2091    
2092      return map { &FunctionalRoleO::new('FunctionalRoleO',$figO,$_) }  $subO->get_roles($self->id);      return map { &FunctionalRoleO::new('FunctionalRoleO',$figO,$_) }  $subO->get_roles($self->id);
2093  }  }
# Line 2080  Line 2103 
2103    
2104      my $figO = $self->{_figO};      my $figO = $self->{_figO};
2105      my $subO = $self->{_subO};      my $subO = $self->{_subO};
2106      if (! $subO) { $subO = $self->{_subO} = new Subsystem($self->{_id},$figO->{_fig}); }      if (! $subO) {
2107            $subO = $self->{_subO} = Subsystem->new($self->{_id}, $figO->{_fig});
2108        }
2109    
2110      return $subO->get_curator;      return $subO->get_curator;
2111  }  }
# Line 2097  Line 2122 
2122    
2123      my $figO = $self->{_figO};      my $figO = $self->{_figO};
2124      my $subO = $self->{_subO};      my $subO = $self->{_subO};
2125      if (! $subO) { $subO = $self->{_subO} = new Subsystem($self->{_id},$figO->{_fig}); }      if (! $subO) {
2126            $subO = $self->{_subO} = Subsystem->new($self->{_id},$figO->{_fig});
2127        }
2128    
2129      return $subO->get_variant_code_for_genome($genome->id);      return $subO->get_variant_code_for_genome($genome->id);
2130  }  }
# Line 2113  Line 2140 
2140    
2141      my $figO = $self->{_figO};      my $figO = $self->{_figO};
2142      my $subO = $self->{_subO};      my $subO = $self->{_subO};
2143      if (! $subO) { $subO = $self->{_subO} = new Subsystem($self->{_id},$figO->{_fig}); }      if (! $subO) {
2144            $subO = $self->{_subO} = Subsystem->new($self->{_id},$figO->{_fig});
2145        }
2146    
2147      return $subO->get_pegs_from_cell($genome->id,$role->id);      return $subO->get_pegs_from_cell($genome->id,$role->id);
2148  }  }
# Line 2291  Line 2320 
2320  =head3 Display all complete, prokaryotic genomes  =head3 Display all complete, prokaryotic genomes
2321    
2322  use FIGO;  use FIGO;
2323  my $figO = new FIGO;  my $figO = FIGO->new();
2324    
2325  foreach $genome ($figO->genomes('complete','prokaryotic'))  foreach $genome ($figO->genomes('complete','prokaryotic'))
2326  {  {
# Line 2301  Line 2330 
2330  #---------------------------------------------  #---------------------------------------------
2331    
2332  use FIG;  use FIG;
2333  my $fig = new FIG;  my $fig = FIG->new();
2334    
2335  foreach $genome (grep { $fig->is_prokaryotic($_) } $fig->genomes('complete'))  foreach $genome (grep { $fig->is_prokaryotic($_) } $fig->genomes('complete'))
2336  {  {
# Line 2313  Line 2342 
2342  =head3 Show how to access contigs and extract sequence  =head3 Show how to access contigs and extract sequence
2343    
2344  use FIGO;  use FIGO;
2345  my $figO = new FIGO;  my $figO = FIGO->new();
2346    
2347  $genomeId = '83333.1';  $genomeId = '83333.1';
2348  my $genome = new GenomeO($figO,$genomeId);  my $genome = GenomeO->new($figO, $genomeId);
2349    
2350  foreach $contig ($genome->contigs_of)  foreach $contig ($genome->contigs_of)
2351  {  {
# Line 2328  Line 2357 
2357  #---------------------------------------------  #---------------------------------------------
2358    
2359  use FIG;  use FIG;
2360  my $fig = new FIG;  my $fig = FIG->new();
2361    
2362  $genomeId = '83333.1';  $genomeId = '83333.1';
2363    
# Line 2346  Line 2375 
2375  ### accessing data related to features  ### accessing data related to features
2376    
2377  use FIGO;  use FIGO;
2378  my $figO = new FIGO;  my $figO = FIGO->new();
2379    
2380  my $genome = new GenomeO($figO,"83333.1");  my $genome = GenomeO->new($figO, "83333.1");
2381  my $peg  = "fig|83333.1.peg.4";  my $peg  = "fig|83333.1.peg.4";
2382  my $pegO = new FeatureO($figO,$peg);  my $pegO = FeatureO->new($figO, $peg);
2383    
2384  print join("\t",$pegO->id,$pegO->location,$pegO->function_of),"\n",  print join("\t",$pegO->id,$pegO->location,$pegO->function_of),"\n",
2385        $pegO->dna_seq,"\n",        $pegO->dna_seq,"\n",
# Line 2365  Line 2394 
2394    
2395    
2396  use FIG;  use FIG;
2397  my $fig = new FIG;  my $fig = FIG->new();
2398    
2399  my $genome = "83333.1";  my $genome = "83333.1";
2400  my $peg  = "fig|83333.1.peg.4";  my $peg  = "fig|83333.1.peg.4";
# Line 2384  Line 2413 
2413  ### accessing similarities  ### accessing similarities
2414    
2415  use FIGO;  use FIGO;
2416  my $figO = new FIGO;  my $figO = FIGO->new();
2417    
2418  $peg  = "fig|83333.1.peg.4";  $peg  = "fig|83333.1.peg.4";
2419  $pegO = new FeatureO($figO,$peg);  $pegO = FeatureO->new($figO, $peg);
2420    
2421  @sims = $pegO->sims;  # use sims( -all => 1, -max => 10000, -cutoff => 1.0e-20) to all  @sims = $pegO->sims;  # use sims( -all => 1, -max => 10000, -cutoff => 1.0e-20) to all
2422                        # sims (including non-FIG sequences                        # sims (including non-FIG sequences
2423  foreach $sim (@sims)  foreach $sim (@sims)
2424  {  {
2425      $peg2  = $sim->id2;      $peg2  = $sim->id2;
2426      $pegO2 = new FeatureO($figO,$peg2);      $pegO2 = FeatureO->new($figO, $peg2);
2427      $func  = $pegO2->function_of;      $func  = $pegO2->function_of;
2428      $sc    = $sim->psc;      $sc    = $sim->psc;
2429      print join("\t",($peg2,$sc,$func)),"\n";      print join("\t",($peg2,$sc,$func)),"\n";
# Line 2404  Line 2433 
2433    
2434    
2435  use FIG;  use FIG;
2436  my $fig = new FIG;  my $fig = FIG new;
2437    
2438  $peg  = "fig|83333.1.peg.4";  $peg  = "fig|83333.1.peg.4";
2439    
# Line 2422  Line 2451 
2451  ### accessing BBHs  ### accessing BBHs
2452    
2453  use FIGO;  use FIGO;
2454  my $figO = new FIGO;  my $figO = FIGO new;
2455    
2456  $peg  = "fig|83333.1.peg.4";  $peg  = "fig|83333.1.peg.4";
2457  $pegO = new FeatureO($figO,$peg);  $pegO = FeatureO->new($figO, $peg);
2458    
2459  @bbhs = $pegO->bbhs;  @bbhs = $pegO->bbhs;
2460  foreach $bbh (@bbhs)  foreach $bbh (@bbhs)
2461  {  {
2462      $peg2  = $bbh->peg2;      $peg2  = $bbh->peg2;
2463      $pegO2 = new FeatureO($figO,$peg2);      $pegO2 = FeatureO->new($figO, $peg2);
2464      $func  = $pegO2->function_of;      $func  = $pegO2->function_of;
2465      $sc    = $bbh->psc;      $sc    = $bbh->psc;
2466      print join("\t",($peg2,$sc,$func)),"\n";      print join("\t",($peg2,$sc,$func)),"\n";
# Line 2440  Line 2469 
2469  #---------------------------------------------  #---------------------------------------------
2470    
2471  use FIG;  use FIG;
2472  my $fig = new FIG;  my $fig = FIG->new();
2473    
2474  $peg  = "fig|83333.1.peg.4";  $peg  = "fig|83333.1.peg.4";
2475    
# Line 2457  Line 2486 
2486  ### accessing annotations  ### accessing annotations
2487    
2488  use FIGO;  use FIGO;
2489  my $figO = new FIGO;  my $figO = FIGO->new();
2490    
2491  $peg  = "fig|83333.1.peg.4";  $peg  = "fig|83333.1.peg.4";
2492  $pegO = new FeatureO($figO,$peg);  $pegO = FeatureO->new($figO, $peg);
2493    
2494  @annotations = $pegO->annotations;  @annotations = $pegO->annotations;
2495    
# Line 2472  Line 2501 
2501  #---------------------------------------------  #---------------------------------------------
2502    
2503  use FIG;  use FIG;
2504  my $fig = new FIG;  my $fig = FIG->new();
2505    
2506  $peg = "fig|83333.1.peg.4";  $peg = "fig|83333.1.peg.4";
2507  @annotations = $fig->feature_annotations($peg);  @annotations = $fig->feature_annotations($peg);
# Line 2489  Line 2518 
2518    
2519    
2520  use FIGO;  use FIGO;
2521  my $figO = new FIGO;  my $figO = FIGO->new();
2522    
2523  my $peg  = "fig|83333.1.peg.4";  my $peg  = "fig|83333.1.peg.4";
2524  my $pegO = new FeatureO($figO,$peg);  my $pegO = FeatureO->new($figO, $peg);
2525  foreach $coupled ($pegO->coupled_to)  foreach $coupled ($pegO->coupled_to)
2526  {  {
2527      print join("\t",($coupled->peg1,$coupled->peg2,$coupled->sc)),"\n";      print join("\t",($coupled->peg1,$coupled->peg2,$coupled->sc)),"\n";
# Line 2508  Line 2537 
2537    
2538    
2539  use FIG;  use FIG;
2540  my $fig = new FIG;  my $fig = FIG->new();
2541    
2542  my $peg1  = "fig|83333.1.peg.4";  my $peg1  = "fig|83333.1.peg.4";
2543  foreach $coupled ($fig->coupled_to($peg1))  foreach $coupled ($fig->coupled_to($peg1))
# Line 2528  Line 2557 
2557  =head3 Accessing Subsystem data  =head3 Accessing Subsystem data
2558    
2559  use FIGO;  use FIGO;
2560  my $figO = new FIGO;  my $figO = FIGO->new();
2561    
2562  foreach $sub ($figO->subsystems)  foreach $sub ($figO->subsystems)
2563  {  {
# Line 2562  Line 2591 
2591  #---------------------------------------------  #---------------------------------------------
2592    
2593  use FIG;  use FIG;
2594  my $fig = new FIG;  my $fig = FIG->new();
2595    
2596  foreach $sub (grep { $fig->usable_subsystem($_) } $fig->all_subsystems)  foreach $sub (grep { $fig->usable_subsystem($_) } $fig->all_subsystems)
2597  {  {
2598      $subO = new Subsystem($sub,$fig);      $subO = Subsystem->new($sub, $fig);
2599      $curator = $subO->get_curator;      $curator = $subO->get_curator;
2600      print join("\t",($sub,$curator)),"\n";      print join("\t",($sub,$curator)),"\n";
2601    
# Line 2597  Line 2626 
2626  =head3 Accessing FIGfams  =head3 Accessing FIGfams
2627    
2628  use FIGO;  use FIGO;
2629  my $figO = new FIGO;  my $figO = FIGO->new();
2630    
2631  foreach $fam ($figO->all_figfams)  foreach $fam ($figO->all_figfams)
2632  {  {
# Line 2615  Line 2644 
2644  use FigFam;  use FigFam;
2645  use FigFams;  use FigFams;
2646    
2647  my $fig = new FIG;  my $fig = FIG->new();
2648  my $figfams = new FigFams($fig);  my $figfams = FigFams->new($fig);
2649    
2650  foreach $fam ($figfams->all_families)  foreach $fam ($figfams->all_families)
2651  {  {
2652      my $figfam = new FigFam($fig,$fam);      my $figfam = FigFam->new($fig, $fam);
2653      print join("\t",($fam,$figfam->family_function)),"\n";      print join("\t",($fam,$figfam->family_function)),"\n";
2654      foreach $peg ($figfam->list_members)      foreach $peg ($figfam->list_members)
2655      {      {
# Line 2633  Line 2662 
2662  =head3 Placing a sequence into a FIGfam  =head3 Placing a sequence into a FIGfam
2663    
2664  use FIGO;  use FIGO;
2665  my $figO = new FIGO;  my $figO = FIGO->new();
2666    
2667  $seq = "MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILS  $seq = "MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILS
2668  AFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTH  AFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTH
# Line 2663  Line 2692 
2692  use FigFam;  use FigFam;
2693  use FigFams;  use FigFams;
2694    
2695  my $fig = new FIG;  my $fig = FIG->new();
2696  my $figfams = new FigFams($fig);  my $figfams = FigFams->new($fig);
2697    
2698  $seq = "MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILS  $seq = "MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILS
2699  AFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTH  AFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTH
# Line 2693  Line 2722 
2722  =head3 Getting representative sequences for a FIGfam  =head3 Getting representative sequences for a FIGfam
2723    
2724  use FIGO;  use FIGO;
2725  my $figO = new FIGO;  my $figO = FIGO->new();
2726    
2727  $fam         = "FIG102446";  $fam         = "FIG102446";
2728  my $famO     = &FigFamO::new('FigFamO',$figO,$fam);  my $famO     = &FigFamO::new('FigFamO',$figO,$fam);
# Line 2710  Line 2739 
2739  use FigFam;  use FigFam;
2740  use FigFams;  use FigFams;
2741    
2742  my $fig = new FIG;  my $fig = FIG->new();
2743    
2744  $fam         = "FIG102446";  $fam         = "FIG102446";
2745  my $famO     = new FigFam($fig,$fam);  my $famO     = FigFam->new($fig, $fam);
2746  my @rep_seqs = $famO->representatives;  my @rep_seqs = $famO->representatives;
2747    
2748  foreach $seq (@rep_seqs)  foreach $seq (@rep_seqs)
# Line 2728  Line 2757 
2757  =head3 Testing for membership in FIGfam  =head3 Testing for membership in FIGfam
2758    
2759  use FIGO;  use FIGO;
2760  my $figO = new FIGO;  my $figO = FIGO->new();
2761    
2762  $seq = "MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILS  $seq = "MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILS
2763  AFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTH  AFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTH
# Line 2760  Line 2789 
2789  use FigFam;  use FigFam;
2790  use FigFams;  use FigFams;
2791    
2792  my $fig = new FIG;  my $fig = FIG->new();
2793    
2794  $seq = "MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILS  $seq = "MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILS
2795  AFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTH  AFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTH
# Line 2773  Line 2802 
2802  $seq =~ s/\n//gs;  $seq =~ s/\n//gs;
2803    
2804  $fam                  = "FIG102446";  $fam                  = "FIG102446";
2805  my $famO              = new FigFam($fig,$fam);  my $famO              = FigFam->new($fig, $fam);
2806  my($should_be, $sims) = $famO->should_be_member($seq);  my($should_be, $sims) = $famO->should_be_member($seq);
2807    
2808  if ($should_be)  if ($should_be)

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