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revision 1.3, Sun Aug 14 23:53:25 2005 UTC revision 1.4, Tue Aug 16 20:35:03 2005 UTC
# Line 126  Line 126 
126      if (! defined $subsysFile || $subsysFile eq '') {      if (! defined $subsysFile || $subsysFile eq '') {
127          # Here we want all the subsystems.          # Here we want all the subsystems.
128          %subsystems = map { $_ => 1 } $fig->all_subsystems();          %subsystems = map { $_ => 1 } $fig->all_subsystems();
129      } elsif (ref $subsysFile eq 'ARRAY') {      } else {
130            my $type = ref $subsysFile;
131            if ($type eq 'ARRAY') {
132          # Here the user passed in a list of subsystems.          # Here the user passed in a list of subsystems.
133          %subsystems = map { $_ => 1 } @{$subsysFile};          %subsystems = map { $_ => 1 } @{$subsysFile};
134      } elsif (ref $subsysFile eq 'SCALAR') {          } elsif (! $type || $type eq 'SCALAR') {
135          # Here the list of subsystems is in a file.          # Here the list of subsystems is in a file.
136          if (! -e $subsysFile) {          if (! -e $subsysFile) {
137              # It's an error if the file does not exist.              # It's an error if the file does not exist.
# Line 142  Line 144 
144      } else {      } else {
145          Confess("Invalid subsystem parameter in SproutLoad constructor.");          Confess("Invalid subsystem parameter in SproutLoad constructor.");
146      }      }
147        }
148      # Get the data directory from the Sprout object.      # Get the data directory from the Sprout object.
149      my ($directory) = $sprout->LoadInfo();      my ($directory) = $sprout->LoadInfo();
150      # Create the Sprout load object.      # Create the Sprout load object.
# Line 219  Line 222 
222          # Get the genus, species, and strain from the scientific name. Note that we append          # Get the genus, species, and strain from the scientific name. Note that we append
223          # the genome ID to the strain. In some cases this is the totality of the strain name.          # the genome ID to the strain. In some cases this is the totality of the strain name.
224          my ($genus, $species, @extraData) = split / /, $self->{fig}->genus_species($genomeID);          my ($genus, $species, @extraData) = split / /, $self->{fig}->genus_species($genomeID);
225          my $extra = join " ", @extraData, "[genomeID]";          my $extra = join " ", @extraData, "[$genomeID]";
226          # Get the full taxonomy.          # Get the full taxonomy.
227          my $taxonomy = $fig->taxonomy_of($genomeID);          my $taxonomy = $fig->taxonomy_of($genomeID);
228          # Output the genome record.          # Output the genome record.
# Line 430  Line 433 
433              # Split the tuple.              # Split the tuple.
434              my ($featureID, $locations, $aliases, $type) = @{$featureData};              my ($featureID, $locations, $aliases, $type) = @{$featureData};
435              # Create the feature record.              # Create the feature record.
436              $loadFeature->Put($featureID, 1, $type);              $loadFeature->Put("$genomeID:$featureID", 1, $type);
437              # Create the aliases.              # Create the aliases.
438              for my $alias (split /\s*,\s*/, $aliases) {              for my $alias (split /\s*,\s*/, $aliases) {
439                  $loadFeatureAlias->Put($featureID, $alias);                  $loadFeatureAlias->Put($featureID, $alias);

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