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revision 1.85, Tue Sep 19 00:14:04 2006 UTC revision 1.88, Wed Sep 27 12:34:46 2006 UTC
# Line 2679  Line 2679 
2679      return $retVal;      return $retVal;
2680  }  }
2681    
2682    =head3 PropertyID
2683    
2684    C<< my $id = $sprout->PropertyID($propName, $propValue); >>
2685    
2686    Return the ID of the specified property name and value pair, if the
2687    pair exists.
2688    
2689    =over 4
2690    
2691    =item propName
2692    
2693    Name of the desired property.
2694    
2695    =item propValue
2696    
2697    Value expected for the desired property.
2698    
2699    =item RETURN
2700    
2701    Returns the ID of the name/value pair, or C<undef> if the pair does not exist.
2702    
2703    =back
2704    
2705    =cut
2706    
2707    sub PropertyID {
2708        # Get the parameters.
2709        my ($self, $propName, $propValue) = @_;
2710        # Try to find the ID.
2711        my ($retVal) = $self->GetFlat(['Property'],
2712                                      "Property(property-name) = ? AND Property(property-value) = ?",
2713                                      [$propName, $propValue]);
2714        # Return the result.
2715        return $retVal;
2716    }
2717    
2718  =head3 MergedAnnotations  =head3 MergedAnnotations
2719    
2720  C<< my @annotationList = $sprout->MergedAnnotations(\@list); >>  C<< my @annotationList = $sprout->MergedAnnotations(\@list); >>
# Line 2876  Line 2912 
2912      # Get the parameters.      # Get the parameters.
2913      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
2914      # Get the list of names.      # Get the list of names.
2915      my @retVal = $self->GetFlat(['ContainsFeature', 'HasSSCell'], "ContainsFeature(to-link) = ?",      my @retVal = $self->GetFlat(['HasRoleInSubsystem'], "HasRoleInSubsystem(from-link) = ?",
2916                                  [$featureID], 'HasSSCell(from-link)');                                  [$featureID], 'HasRoleInSubsystem(to-link)');
2917      # Return the result.      # Return the result, sorted.
2918      return @retVal;      return sort @retVal;
2919  }  }
2920    
2921  =head3 GenomeSubsystemData  =head3 GenomeSubsystemData
# Line 3274  Line 3310 
3310          # Here we have a group list. Loop through them individually,          # Here we have a group list. Loop through them individually,
3311          # getting a list of the relevant genomes.          # getting a list of the relevant genomes.
3312          for my $group (@{$groupList}) {          for my $group (@{$groupList}) {
3313              my @genomeIDs = $self->GetFlat(['Genome'], "Genome(group-name) = ?",              my @genomeIDs = $self->GetFlat(['Genome'], "Genome(primary-group) = ?",
3314                  [$group], "Genome(id)");                  [$group], "Genome(id)");
3315              $retVal{$group} = \@genomeIDs;              $retVal{$group} = \@genomeIDs;
3316          }          }
# Line 3282  Line 3318 
3318          # Here we need all of the groups. In this case, we run through all          # Here we need all of the groups. In this case, we run through all
3319          # of the genome records, putting each one found into the appropriate          # of the genome records, putting each one found into the appropriate
3320          # group. Note that we use a filter clause to insure that only genomes          # group. Note that we use a filter clause to insure that only genomes
3321          # in groups are included in the return set.          # in real NMPDR groups are included in the return set.
3322          my @genomes = $self->GetAll(['Genome'], "Genome(group-name) > ' '", [],          my @genomes = $self->GetAll(['Genome'], "Genome(primary-group) <> ?",
3323                                      ['Genome(id)', 'Genome(group-name)']);                                      [$FIG_Config::otherGroup], ['Genome(id)', 'Genome(primary-group)']);
3324          # Loop through the genomes found.          # Loop through the genomes found.
3325          for my $genome (@genomes) {          for my $genome (@genomes) {
3326              # Pop this genome's ID off the current list.              # Pop this genome's ID off the current list.

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