[Bio] / Sprout / FeatureSaplingLoader.pm Repository:
ViewVC logotype

Diff of /Sprout/FeatureSaplingLoader.pm

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

revision 1.3, Thu May 28 18:08:56 2009 UTC revision 1.6, Thu Oct 29 18:31:48 2009 UTC
# Line 45  Line 45 
45    
46  =item erdb  =item erdb
47    
48  [[SaplingPm]] object for the database being loaded.  L<Sapling> object for the database being loaded.
49    
50  =item options  =item options
51    
# Line 214  Line 214 
214          my @essentials = $fig->get_attributes($fid, undef, ['essential', 'potential-essential']);          my @essentials = $fig->get_attributes($fid, undef, ['essential', 'potential-essential']);
215          for my $essentialTuple (@essentials) {          for my $essentialTuple (@essentials) {
216              my (undef, undef, $essentialityType, $url) = @$essentialTuple;              my (undef, undef, $essentialityType, $url) = @$essentialTuple;
217                # Only keep this datum if it has a URL. The ones without URLs are
218                # all duplicates.
219                if ($url) {
220              # Form a hyperlink from this essentiality tuple.              # Form a hyperlink from this essentiality tuple.
221              my $link = HyperLink->new($essentialityType, $url);              my $link = HyperLink->new($essentialityType, $url);
222              # Store it as essentiality data for this feature.              # Store it as essentiality data for this feature.
223              $self->PutE(FeatureEssential => $fid, essential => $link);              $self->PutE(FeatureEssential => $fid, essential => $link);
224          }          }
225            }
226          # If this is a PEG, we have a protein sequence.          # If this is a PEG, we have a protein sequence.
227          my $proteinID;          my $proteinID;
228          if ($type eq 'peg') {          if ($type eq 'peg') {
# Line 257  Line 261 
261              my $natural = AliasAnalysis::Type($aliasType => $aliasID) || $aliasID;              my $natural = AliasAnalysis::Type($aliasType => $aliasID) || $aliasID;
262              # Create the identifier record.              # Create the identifier record.
263              $self->PutE(Identifier => $aliasID, natural_form => $natural,              $self->PutE(Identifier => $aliasID, natural_form => $natural,
264                          source => $type);                          source => $aliasType);
265              # Is this a protein alias?              # Is this a protein alias?
266              if ($aliasConf eq 'C' && $proteinID) {              if ($aliasConf eq 'C' && $proteinID) {
267                  # Yes. Connect it using IsNamedBy.                  # Yes. Connect it using IsNamedBy.
# Line 271  Line 275 
275          $self->PutE(Identifier => $fid, natural_form => $fid,          $self->PutE(Identifier => $fid, natural_form => $fid,
276                      source => 'SEED');                      source => 'SEED');
277          $self->PutR(Identifies => $fid, $fid, conf => 'A');          $self->PutR(Identifies => $fid, $fid, conf => 'A');
         if ($proteinID) {  
             $self->PutR(IsNamedBy => $proteinID, $fid);  
         }  
278      }      }
279  }  }
280    

Legend:
Removed from v.1.3  
changed lines
  Added in v.1.6

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3