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revision 1.59, Wed Jun 7 01:53:03 2006 UTC revision 1.71, Sun Jun 25 00:07:22 2006 UTC
# Line 12  Line 12 
12      use DBObject;      use DBObject;
13      use Tracer;      use Tracer;
14      use FIGRules;      use FIGRules;
15        use FidCheck;
16      use Stats;      use Stats;
17      use POSIX qw(strftime);      use POSIX qw(strftime);
18    
# Line 375  Line 376 
376      # Get the genomes.      # Get the genomes.
377      my @genomes = $self->GetAll(['Genome'], $filterString, $params, ['Genome(id)',      my @genomes = $self->GetAll(['Genome'], $filterString, $params, ['Genome(id)',
378                                                                       'Genome(genus)',                                                                       'Genome(genus)',
379                                                                       'Genome(species)']);                                                                       'Genome(species)',
380                                                                         'Genome(unique-characterization)']);
381      # Sort them by name.      # Sort them by name.
382      my @sorted = sort { lc("$a->[1] $a->[2]") cmp lc("$b->[1] $b->[2]") } @genomes;      my @sorted = sort { lc("$a->[1] $a->[2]") cmp lc("$b->[1] $b->[2]") } @genomes;
383      # Loop through the genomes, creating the option tags.      # Loop through the genomes, creating the option tags.
384      for my $genomeData (@sorted) {      for my $genomeData (@sorted) {
385          # Get the data for this genome.          # Get the data for this genome.
386          my ($genomeID, $genus, $species) = @{$genomeData};          my ($genomeID, $genus, $species, $strain) = @{$genomeData};
387          # Get the contig count.          # Get the contig count.
388          my $count = $self->ContigCount($genomeID);          my $count = $self->ContigCount($genomeID);
389          my $counting = ($count == 1 ? "contig" : "contigs");          my $counting = ($count == 1 ? "contig" : "contigs");
390          # Build the option tag.          # Build the option tag.
391          $retVal .= "<option value=\"$genomeID\">$genus $species ($genomeID) [$count $counting]</option>\n";          $retVal .= "<option value=\"$genomeID\">$genus $species $strain ($genomeID) [$count $counting]</option>\n";
392            Trace("Option tag built for $genomeID: $genus $species $strain.") if T(3);
393      }      }
394      # Close the SELECT tag.      # Close the SELECT tag.
395      $retVal .= "</select>\n";      $retVal .= "</select>\n";
# Line 793  Line 796 
796      return @retVal;      return @retVal;
797  }  }
798    
799    =head3 GenomeLength
800    
801    C<< my $length = $sprout->GenomeLength($genomeID); >>
802    
803    Return the length of the specified genome in base pairs.
804    
805    =over 4
806    
807    =item genomeID
808    
809    ID of the genome whose base pair count is desired.
810    
811    =item RETURN
812    
813    Returns the number of base pairs in all the contigs of the specified
814    genome.
815    
816    =back
817    
818    =cut
819    
820    sub GenomeLength {
821        # Get the parameters.
822        my ($self, $genomeID) = @_;
823        # Declare the return variable.
824        my $retVal = 0;
825        # Get the genome's contig sequence lengths.
826        my @lens = $self->GetFlat(['HasContig', 'IsMadeUpOf'], 'HasContig(from-link) = ?',
827                           [$genomeID], 'IsMadeUpOf(len)');
828        # Sum the lengths.
829        map { $retVal += $_ } @lens;
830        # Return the result.
831        return $retVal;
832    }
833    
834    =head3 FeatureCount
835    
836    C<< my $count = $sprout->FeatureCount($genomeID, $type); >>
837    
838    Return the number of features of the specified type in the specified genome.
839    
840    =over 4
841    
842    =item genomeID
843    
844    ID of the genome whose feature count is desired.
845    
846    =item type
847    
848    Type of feature to count (eg. C<peg>, C<rna>, etc.).
849    
850    =item RETURN
851    
852    Returns the number of features of the specified type for the specified genome.
853    
854    =back
855    
856    =cut
857    
858    sub FeatureCount {
859        # Get the parameters.
860        my ($self, $genomeID, $type) = @_;
861        # Compute the count.
862        my $retVal = $self->GetCount(['HasFeature', 'Feature'],
863                                    "HasFeature(from-link) = ? AND Feature(feature-type) = ?",
864                                    [$genomeID, $type]);
865        # Return the result.
866        return $retVal;
867    }
868    
869    =head3 GenomeAssignments
870    
871    C<< my $fidHash = $sprout->GenomeAssignments($genomeID); >>
872    
873    Return a list of a genome's assigned features. The return hash will contain each
874    assigned feature of the genome mapped to the text of its most recent functional
875    assignment.
876    
877    =over 4
878    
879    =item genomeID
880    
881    ID of the genome whose functional assignments are desired.
882    
883    =item RETURN
884    
885    Returns a reference to a hash which maps each feature to its most recent
886    functional assignment.
887    
888    =back
889    
890    =cut
891    
892    sub GenomeAssignments {
893        # Get the parameters.
894        my ($self, $genomeID) = @_;
895        # Declare the return variable.
896        my $retVal = {};
897        # Query the genome's features and annotations. We'll put the oldest annotations
898        # first so that the last assignment to go into the hash will be the correct one.
899        my $query = $self->Get(['HasFeature', 'IsTargetOfAnnotation', 'Annotation'],
900                               "HasFeature(from-link) = ? ORDER BY Annotation(time)",
901                               [$genomeID]);
902        # Loop through the annotations.
903        while (my $data = $query->Fetch) {
904            # Get the feature ID and annotation text.
905            my ($fid, $annotation) = $data->Values(['HasFeature(to-link)',
906                                                    'Annotation(annotation)']);
907            # Check to see if this is an assignment. Note that the user really
908            # doesn't matter to us, other than we use it to determine whether or
909            # not this is an assignment.
910            my ($user, $assignment) = _ParseAssignment('fig', $annotation);
911            if ($user) {
912                # Here it's an assignment. We put it in the return hash, overwriting
913                # any older assignment that might be present.
914                $retVal->{$fid} = $assignment;
915            }
916        }
917        # Return the result.
918        return $retVal;
919    }
920    
921  =head3 ContigLength  =head3 ContigLength
922    
923  C<< my $length = $sprout->ContigLength($contigID); >>  C<< my $length = $sprout->ContigLength($contigID); >>
# Line 1543  Line 1668 
1668          # Get the ID and score of the coupling.          # Get the ID and score of the coupling.
1669          my ($couplingID, $score) = $clustering->Values(['Coupling(id)',          my ($couplingID, $score) = $clustering->Values(['Coupling(id)',
1670                                                          'Coupling(score)']);                                                          'Coupling(score)']);
1671          # The coupling ID contains the two feature IDs separated by a space. We use          # Get the other feature that participates in the coupling.
1672          # this information to find the ID of the other feature.          my ($otherFeatureID) = $self->GetFlat(['ParticipatesInCoupling'],
1673          my ($fid1, $fid2) = split / /, $couplingID;                                             "ParticipatesInCoupling(to-link) = ? AND ParticipatesInCoupling(from-link) <> ?",
1674          my $otherFeatureID = ($featureID eq $fid1 ? $fid2 : $fid1);                                             [$couplingID, $featureID], 'ParticipatesInCoupling(from-link)');
1675          # Attach the other feature's score to its ID.          # Attach the other feature's score to its ID.
1676          $retVal{$otherFeatureID} = $score;          $retVal{$otherFeatureID} = $score;
1677          $found = 1;          $found = 1;
# Line 2094  Line 2219 
2219      return @retVal;      return @retVal;
2220  }  }
2221    
 =head3 Exists  
   
 C<< my $found = $sprout->Exists($entityName, $entityID); >>  
   
 Return TRUE if an entity exists, else FALSE.  
   
 =over 4  
   
 =item entityName  
   
 Name of the entity type (e.g. C<Feature>) relevant to the existence check.  
   
 =item entityID  
   
 ID of the entity instance whose existence is to be checked.  
   
 =item RETURN  
   
 Returns TRUE if the entity instance exists, else FALSE.  
   
 =back  
   
 =cut  
 #: Return Type $;  
 sub Exists {  
     # Get the parameters.  
     my ($self, $entityName, $entityID) = @_;  
     # Check for the entity instance.  
     Trace("Checking existence of $entityName with ID=$entityID.") if T(4);  
     my $testInstance = $self->GetEntity($entityName, $entityID);  
     # Return an existence indicator.  
     my $retVal = ($testInstance ? 1 : 0);  
     return $retVal;  
 }  
   
2222  =head3 FeatureTranslation  =head3 FeatureTranslation
2223    
2224  C<< my $translation = $sprout->FeatureTranslation($featureID); >>  C<< my $translation = $sprout->FeatureTranslation($featureID); >>
# Line 2666  Line 2756 
2756      return @retVal;      return @retVal;
2757  }  }
2758    
   
   
2759  =head3 RelatedFeatures  =head3 RelatedFeatures
2760    
2761  C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>  C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>
# Line 2919  Line 3007 
3007      return %retVal;      return %retVal;
3008  }  }
3009    
3010    =head3 Sims
3011    
3012    C<< my $simList = $sprout->Sims($fid, $maxN, $maxP, $select, $max_expand, $filters); >>
3013    
3014    Get a list of similarities for a specified feature. Similarity information is not kept in the
3015    Sprout database; rather, they are retrieved from a network server. The similarities are
3016    returned as B<Sim> objects. A Sim object is actually a list reference that has been blessed
3017    so that its elements can be accessed by name.
3018    
3019    Similarities can be either raw or expanded. The raw similarities are basic
3020    hits between features with similar DNA. Expanding a raw similarity drags in any
3021    features considered substantially identical. So, for example, if features B<A1>,
3022    B<A2>, and B<A3> are all substatially identical to B<A>, then a raw similarity
3023    B<[C,A]> would be expanded to B<[C,A] [C,A1] [C,A2] [C,A3]>.
3024    
3025    =over 4
3026    
3027    =item fid
3028    
3029    ID of the feature whose similarities are desired.
3030    
3031    =item maxN
3032    
3033    Maximum number of similarities to return.
3034    
3035    =item maxP
3036    
3037    Minumum allowable similarity score.
3038    
3039    =item select
3040    
3041    Selection criterion: C<raw> means only raw similarities are returned; C<fig>
3042    means only similarities to FIG features are returned; C<all> means all expanded
3043    similarities are returned; and C<figx> means similarities are expanded until the
3044    number of FIG features equals the maximum.
3045    
3046    =item max_expand
3047    
3048    The maximum number of features to expand.
3049    
3050    =item filters
3051    
3052    Reference to a hash containing filter information, or a subroutine that can be
3053    used to filter the sims.
3054    
3055    =item RETURN
3056    
3057    Returns a reference to a list of similarity objects, or C<undef> if an error
3058    occurred.
3059    
3060    =back
3061    
3062    =cut
3063    
3064    sub Sims {
3065        # Get the parameters.
3066        my ($self, $fid, $maxN, $maxP, $select, $max_expand, $filters) = @_;
3067        # Create the shim object to test for deleted FIDs.
3068        my $shim = FidCheck->new($self);
3069        # Ask the network for sims.
3070        my $retVal = FIGRules::GetNetworkSims($shim, $fid, {}, $maxN, $maxP, $select, $max_expand, $filters);
3071        # Return the result.
3072        return $retVal;
3073    }
3074    
3075  =head3 GetGroups  =head3 GetGroups
3076    
3077  C<< my %groups = $sprout->GetGroups(\@groupList); >>  C<< my %groups = $sprout->GetGroups(\@groupList); >>

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