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revision 1.2, Sun Jan 23 22:31:29 2005 UTC revision 1.47, Thu Oct 20 12:02:43 2005 UTC
# Line 11  Line 11 
11          use Tracer;          use Tracer;
12          use FIGRules;          use FIGRules;
13          use Stats;          use Stats;
14        use POSIX qw(strftime);
15    
16    
17  =head1 Sprout Database Manipulation Object  =head1 Sprout Database Manipulation Object
# Line 33  Line 34 
34    
35  =cut  =cut
36    
37  #  #: Constructor SFXlate->new_sprout_only();
38    
39  =head2 Public Methods  =head2 Public Methods
40    
# Line 69  Line 70 
70    
71  * B<maxSequenceLength> maximum number of residues per sequence, (default C<8000>)  * B<maxSequenceLength> maximum number of residues per sequence, (default C<8000>)
72    
73    * B<noDBOpen> suppresses the connection to the database if TRUE, else FALSE
74    
75  =back  =back
76    
77  For example, the following constructor call specifies a database named I<Sprout> and a user name of  For example, the following constructor call specifies a database named I<Sprout> and a user name of
# Line 85  Line 88 
88          # Compute the options. We do this by starting with a table of defaults and overwriting with          # Compute the options. We do this by starting with a table of defaults and overwriting with
89          # the incoming data.          # the incoming data.
90          my $optionTable = Tracer::GetOptions({          my $optionTable = Tracer::GetOptions({
91                                             dbType               => 'mysql',                     # database type                         dbType       => $FIG_Config::dbms,
92                                             dataDir              => 'Data',                      # data file directory                                                          # database type
93                                             xmlFileName  => 'SproutDBD.xml', # database definition file name                         dataDir      => $FIG_Config::sproutData,
94                                             userData             => 'root/',                     # user name and password                                                          # data file directory
95                                             port                 => 0,                           # database connection port                         xmlFileName  => "$FIG_Config::sproutData/SproutDBD.xml",
96                                                            # database definition file name
97                           userData     => "$FIG_Config::dbuser/$FIG_Config::dbpass",
98                                                            # user name and password
99                           port         => $FIG_Config::dbport,
100                                                            # database connection port
101                                             maxSegmentLength => 4500,            # maximum feature segment length                                             maxSegmentLength => 4500,            # maximum feature segment length
102                                             maxSequenceLength => 8000,           # maximum contig sequence length                                             maxSequenceLength => 8000,           # maximum contig sequence length
103                           noDBOpen     => 0,               # 1 to suppress the database open
104                                            }, $options);                                            }, $options);
105          # Get the data directory.          # Get the data directory.
106          my $dataDir = $optionTable->{dataDir};          my $dataDir = $optionTable->{dataDir};
# Line 99  Line 108 
108          $optionTable->{userData} =~ m!([^/]*)/(.*)$!;          $optionTable->{userData} =~ m!([^/]*)/(.*)$!;
109          my ($userName, $password) = ($1, $2);          my ($userName, $password) = ($1, $2);
110          # Connect to the database.          # Connect to the database.
111          my $dbh = DBKernel->new($optionTable->{dbType}, $dbName, $userName, $password, $optionTable->{port});      my $dbh;
112        if (! $optionTable->{noDBOpen}) {
113            $dbh = DBKernel->new($optionTable->{dbType}, $dbName, $userName,
114                                    $password, $optionTable->{port});
115        }
116          # Create the ERDB object.          # Create the ERDB object.
117          my $xmlFileName = "$optionTable->{xmlFileName}";          my $xmlFileName = "$optionTable->{xmlFileName}";
118          my $erdb = ERDB->new($dbh, $xmlFileName);          my $erdb = ERDB->new($dbh, $xmlFileName);
# Line 121  Line 134 
134  and 10999.  and 10999.
135    
136  =cut  =cut
137    #: Return Type $;
138  sub MaxSegment {  sub MaxSegment {
139          my $self = shift @_;      my ($self) = @_;
140          return $self->{_options}->{maxSegmentLength};          return $self->{_options}->{maxSegmentLength};
141  }  }
142    
# Line 136  Line 149 
149  we generally only need a few sequences in memory rather than the entire contig.  we generally only need a few sequences in memory rather than the entire contig.
150    
151  =cut  =cut
152    #: Return Type $;
153  sub MaxSequence {  sub MaxSequence {
154          my $self = shift @_;      my ($self) = @_;
155          return $self->{_options}->{maxSequenceLength};          return $self->{_options}->{maxSequenceLength};
156  }  }
157    
# Line 231  Line 244 
244    
245  sub Get {  sub Get {
246          # Get the parameters.          # Get the parameters.
247          my $self = shift @_;      my ($self, $objectNames, $filterClause, $parameterList) = @_;
         my ($objectNames, $filterClause, $parameterList) = @_;  
248          # We differ from the ERDB Get method in that the parameter list is passed in as a list reference          # We differ from the ERDB Get method in that the parameter list is passed in as a list reference
249          # rather than a list of parameters. The next step is to convert the parameters from a reference          # rather than a list of parameters. The next step is to convert the parameters from a reference
250          # to a real list. We can only do this if the parameters have been specified.          # to a real list. We can only do this if the parameters have been specified.
# Line 268  Line 280 
280    
281  sub GetEntity {  sub GetEntity {
282          # Get the parameters.          # Get the parameters.
283          my $self = shift @_;      my ($self, $entityType, $ID) = @_;
284          my ($entityType, $ID) = @_;      # Call the ERDB method.
285          # Create a query.      return $self->{_erdb}->GetEntity($entityType, $ID);
         my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);  
         # Get the first (and only) object.  
         my $retVal = $query->Fetch();  
         # Return the result.  
         return $retVal;  
286  }  }
287    
288  =head3 GetEntityValues  =head3 GetEntityValues
# Line 305  Line 312 
312  =back  =back
313    
314  =cut  =cut
315    #: Return Type @;
316  sub GetEntityValues {  sub GetEntityValues {
317          # Get the parameters.          # Get the parameters.
318          my $self = shift @_;      my ($self, $entityType, $ID, $fields) = @_;
319          my ($entityType, $ID, $fields) = @_;      # Call the ERDB method.
320          # Get the specified entity.      return $self->{_erdb}->GetEntityValues($entityType, $ID, $fields);
         my $entity = $self->GetEntity($entityType, $ID);  
         # Declare the return list.  
         my @retVal = ();  
         # If we found the entity, push the values into the return list.  
         if ($entity) {  
                 push @retVal, $entity->Values($fields);  
         }  
         # Return the result.  
         return @retVal;  
321  }  }
322    
323  =head3 ShowMetaData  =head3 ShowMetaData
# Line 340  Line 338 
338    
339  sub ShowMetaData {  sub ShowMetaData {
340          # Get the parameters.          # Get the parameters.
341          my $self = shift @_;      my ($self, $fileName) = @_;
         my ($fileName) = @_;  
342          # Compute the file name.          # Compute the file name.
343          my $options = $self->{_options};          my $options = $self->{_options};
344          # Call the show method on the underlying ERDB object.          # Call the show method on the underlying ERDB object.
# Line 378  Line 375 
375  =back  =back
376    
377  =cut  =cut
378    #: Return Type %;
379  sub Load {  sub Load {
380          # Get the parameters.          # Get the parameters.
381          my $self = shift @_;      my ($self, $rebuild) = @_;
         my ($rebuild) = @_;  
382          # Get the database object.          # Get the database object.
383          my $erdb = $self->{_erdb};          my $erdb = $self->{_erdb};
384          # Load the tables from the data directory.          # Load the tables from the data directory.
# Line 393  Line 389 
389    
390  =head3 LoadUpdate  =head3 LoadUpdate
391    
392  C<< my %stats = $sprout->LoadUpdate($truncateFlag, \@tableList); >>  C<< my $stats = $sprout->LoadUpdate($truncateFlag, \@tableList); >>
393    
394  Load updates to one or more database tables. This method enables the client to make changes to one  Load updates to one or more database tables. This method enables the client to make changes to one
395  or two tables without reloading the whole database. For each table, there must be a corresponding  or two tables without reloading the whole database. For each table, there must be a corresponding
# Line 422  Line 418 
418  =back  =back
419    
420  =cut  =cut
421    #: Return Type $%;
422  sub LoadUpdate {  sub LoadUpdate {
423          # Get the parameters.          # Get the parameters.
424          my $self = shift @_;      my ($self, $truncateFlag, $tableList) = @_;
         my ($truncateFlag, $tableList) = @_;  
425          # Get the database object.          # Get the database object.
426          my $erdb = $self->{_erdb};          my $erdb = $self->{_erdb};
427          # Declare the return value.          # Declare the return value.
# Line 437  Line 432 
432          # Loop through the incoming table names.          # Loop through the incoming table names.
433          for my $tableName (@{$tableList}) {          for my $tableName (@{$tableList}) {
434                  # Find the table's file.                  # Find the table's file.
435                  my $fileName = "$dataDir/$tableName";          my $fileName = LoadFileName($dataDir, $tableName);
436                  if (! -e $fileName) {          if (! $fileName) {
437                          $fileName = "$fileName.dtx";              Trace("No load file found for $tableName in $dataDir.") if T(0);
438                  }          } else {
439                  # Attempt to load this table.                  # Attempt to load this table.
440                  my $result = $erdb->LoadTable($fileName, $tableName, $truncateFlag);                  my $result = $erdb->LoadTable($fileName, $tableName, $truncateFlag);
441                  # Accumulate the resulting statistics.                  # Accumulate the resulting statistics.
442                  $retVal->Accumulate($result);                  $retVal->Accumulate($result);
443          }          }
444        }
445          # Return the statistics.          # Return the statistics.
446          return $retVal;          return $retVal;
447  }  }
# Line 459  Line 455 
455  changed.  changed.
456    
457  =cut  =cut
458    #: Return Type ;
459  sub Build {  sub Build {
460          # Get the parameters.          # Get the parameters.
461          my $self = shift @_;      my ($self) = @_;
462          # Create the tables.          # Create the tables.
463          $self->{_erdb}->CreateTables;          $self->{_erdb}->CreateTables;
464  }  }
# Line 474  Line 470 
470  Return a list of all the genome IDs.  Return a list of all the genome IDs.
471    
472  =cut  =cut
473    #: Return Type @;
474  sub Genomes {  sub Genomes {
475          # Get the parameters.          # Get the parameters.
476          my $self = shift @_;      my ($self) = @_;
477          # Get all the genomes.          # Get all the genomes.
478          my @retVal = $self->GetFlat(['Genome'], "", [], 'Genome(id)');          my @retVal = $self->GetFlat(['Genome'], "", [], 'Genome(id)');
479          # Return the list of IDs.          # Return the list of IDs.
# Line 504  Line 500 
500  =back  =back
501    
502  =cut  =cut
503    #: Return Type $;
504  sub GenusSpecies {  sub GenusSpecies {
505          # Get the parameters.          # Get the parameters.
506          my $self = shift @_;      my ($self, $genomeID) = @_;
         my ($genomeID) = @_;  
507          # Get the data for the specified genome.          # Get the data for the specified genome.
508          my @values = $self->GetEntityValues('Genome', $genomeID, ['Genome(genus)', 'Genome(species)',          my @values = $self->GetEntityValues('Genome', $genomeID, ['Genome(genus)', 'Genome(species)',
509                                                                                                                            'Genome(unique-characterization)']);                                                                                                                            'Genome(unique-characterization)']);
# Line 541  Line 536 
536  =back  =back
537    
538  =cut  =cut
539    #: Return Type @;
540  sub FeaturesOf {  sub FeaturesOf {
541          # Get the parameters.          # Get the parameters.
542          my $self = shift @_;      my ($self, $genomeID,$ftype) = @_;
         my ($genomeID,$ftype) = @_;  
543          # Get the features we want.          # Get the features we want.
544          my @features;          my @features;
545          if (!$ftype) {          if (!$ftype) {
# Line 589  Line 583 
583  =item RETURN  =item RETURN
584    
585  Returns a list of the feature's contig segments. The locations are returned as a list in a list  Returns a list of the feature's contig segments. The locations are returned as a list in a list
586  context and as a space-delimited string in a scalar context.  context and as a comma-delimited string in a scalar context.
587    
588  =back  =back
589    
590  =cut  =cut
591    #: Return Type @;
592    #: Return Type $;
593  sub FeatureLocation {  sub FeatureLocation {
594          # Get the parameters.          # Get the parameters.
595          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
596          # Create a query for the feature locations.          # Create a query for the feature locations.
597          my $query = $self->Get(['IsLocatedIn'], "IsLocatedIn(from-link) = ? ORDER BY IsLocatedIn(locN)",          my $query = $self->Get(['IsLocatedIn'], "IsLocatedIn(from-link) = ? ORDER BY IsLocatedIn(locN)",
598                                                     [$featureID]);                                                     [$featureID]);
# Line 616  Line 610 
610                  if ($prevContig eq $contigID && $dir eq $prevDir) {                  if ($prevContig eq $contigID && $dir eq $prevDir) {
611                          # Here the new segment is in the same direction on the same contig. Insure the                          # Here the new segment is in the same direction on the same contig. Insure the
612                          # new segment's beginning is next to the old segment's end.                          # new segment's beginning is next to the old segment's end.
613                          if (($dir eq "-" && $beg == $prevBeg - $prevLen) ||              if ($dir eq "-" && $beg + $len == $prevBeg) {
614                                  ($dir eq "+" && $beg == $prevBeg + $prevLen)) {                  # Here we're merging two backward blocks, so we keep the new begin point
615                                  # Here we need to merge two segments. Adjust the beginning and length values                  # and adjust the length.
616                                  # to include both segments.                  $len += $prevLen;
617                    # Pop the old segment off. The new one will replace it later.
618                    pop @retVal;
619                } elsif ($dir eq "+" && $beg == $prevBeg + $prevLen) {
620                    # Here we need to merge two forward blocks. Adjust the beginning and
621                    # length values to include both segments.
622                                  $beg = $prevBeg;                                  $beg = $prevBeg;
623                                  $len += $prevLen;                                  $len += $prevLen;
624                                  # Pop the old segment off. The new one will replace it later.                                  # Pop the old segment off. The new one will replace it later.
# Line 628  Line 627 
627                  }                  }
628                  # Remember this specifier for the adjacent-segment test the next time through.                  # Remember this specifier for the adjacent-segment test the next time through.
629                  ($prevContig, $prevBeg, $prevDir, $prevLen) = ($contigID, $beg, $dir, $len);                  ($prevContig, $prevBeg, $prevDir, $prevLen) = ($contigID, $beg, $dir, $len);
630            # Compute the initial base pair.
631            my $start = ($dir eq "+" ? $beg : $beg + $len - 1);
632                  # Add the specifier to the list.                  # Add the specifier to the list.
633                  push @retVal, "${contigID}_$beg$dir$len";          push @retVal, "${contigID}_$start$dir$len";
634          }          }
635          # Return the list in the format indicated by the context.          # Return the list in the format indicated by the context.
636          return (wantarray ? @retVal : join(' ', @retVal));      return (wantarray ? @retVal : join(',', @retVal));
637  }  }
638    
639  =head3 ParseLocation  =head3 ParseLocation
# Line 656  Line 657 
657  =back  =back
658    
659  =cut  =cut
660    #: Return Type @;
661  sub ParseLocation {  sub ParseLocation {
662          # Get the parameter.      # Get the parameter. Note that if we're called as an instance method, we ignore
663        # the first parameter.
664        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
665          my ($location) = @_;          my ($location) = @_;
666          # Parse it into segments.          # Parse it into segments.
667          $location =~ /^(.*)_(\d*)([+-_])(\d*)$/;      $location =~ /^(.+)_(\d+)([+\-_])(\d+)$/;
668          my ($contigID, $start, $dir, $len) = ($1, $2, $3, $4);          my ($contigID, $start, $dir, $len) = ($1, $2, $3, $4);
669          # If the direction is an underscore, convert it to a + or -.          # If the direction is an underscore, convert it to a + or -.
670          if ($dir eq "_") {          if ($dir eq "_") {
# Line 677  Line 680 
680          return ($contigID, $start, $dir, $len);          return ($contigID, $start, $dir, $len);
681  }  }
682    
683    =head3 PointLocation
684    
685    C<< my $found = Sprout::PointLocation($location, $point); >>
686    
687    Return the offset into the specified location of the specified point on the contig. If
688    the specified point is before the location, a negative value will be returned. If it is
689    beyond the location, an undefined value will be returned. It is assumed that the offset
690    is for the location's contig. The location can either be new-style (using a C<+> or C<->
691    and a length) or old-style (using C<_> and start and end positions.
692    
693    =over 4
694    
695    =item location
696    
697    A location specifier (see L</FeatureLocation> for a description).
698    
699    =item point
700    
701    The offset into the contig of the point in which we're interested.
702    
703    =item RETURN
704    
705    Returns the offset inside the specified location of the specified point, a negative
706    number if the point is before the location, or an undefined value if the point is past
707    the location. If the length of the location is 0, this method will B<always> denote
708    that it is outside the location. The offset will always be relative to the left-most
709    position in the location.
710    
711    =back
712    
713    =cut
714    #: Return Type $;
715    sub PointLocation {
716        # Get the parameter. Note that if we're called as an instance method, we ignore
717        # the first parameter.
718        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
719        my ($location, $point) = @_;
720        # Parse out the location elements. Note that this works on both old-style and new-style
721        # locations.
722        my ($contigID, $start, $dir, $len) = ParseLocation($location);
723        # Declare the return variable.
724        my $retVal;
725        # Compute the offset. The computation is dependent on the direction of the location.
726        my $offset = (($dir == '+') ? $point - $start : $point - ($start - $len + 1));
727        # Return the offset if it's valid.
728        if ($offset < $len) {
729            $retVal = $offset;
730        }
731        # Return the offset found.
732        return $retVal;
733    }
734    
735  =head3 DNASeq  =head3 DNASeq
736    
737  C<< my $sequence = $sprout->DNASeq(\@locationList); >>  C<< my $sequence = $sprout->DNASeq(\@locationList); >>
# Line 699  Line 754 
754  =back  =back
755    
756  =cut  =cut
757    #: Return Type $;
758  sub DNASeq {  sub DNASeq {
759          # Get the parameters.          # Get the parameters.
760          my $self = shift @_;      my ($self, $locationList) = @_;
         my ($locationList) = @_;  
761          # Create the return string.          # Create the return string.
762          my $retVal = "";          my $retVal = "";
763          # Loop through the locations.          # Loop through the locations.
# Line 718  Line 772 
772                  # the start point is the ending. Note that in the latter case we must reverse the DNA string                  # the start point is the ending. Note that in the latter case we must reverse the DNA string
773                  # before putting it in the return value.                  # before putting it in the return value.
774                  my ($start, $stop);                  my ($start, $stop);
775            Trace("Parse of \"$location\" is $beg$dir$len.") if T(SDNA => 4);
776                  if ($dir eq "+") {                  if ($dir eq "+") {
777                          $start = $beg;                          $start = $beg;
778                          $stop = $beg + $len - 1;                          $stop = $beg + $len - 1;
779                  } else {                  } else {
780                          $start = $beg + $len + 1;              $start = $beg - $len + 1;
781                          $stop = $beg;                          $stop = $beg;
782                  }                  }
783            Trace("Looking for sequences containing $start through $stop.") if T(SDNA => 4);
784                  my $query = $self->Get(['IsMadeUpOf','Sequence'],                  my $query = $self->Get(['IsMadeUpOf','Sequence'],
785                          "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .                          "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .
786                          " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",                          " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",
# Line 736  Line 792 
792                                  $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)',                                  $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)',
793                                                                     'IsMadeUpOf(len)']);                                                                     'IsMadeUpOf(len)']);
794                          my $stopPosition = $startPosition + $sequenceLength;                          my $stopPosition = $startPosition + $sequenceLength;
795                Trace("Sequence is from $startPosition to $stopPosition.") if T(SDNA => 4);
796                          # Figure out the start point and length of the relevant section.                          # Figure out the start point and length of the relevant section.
797                          my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);                          my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);
798                          my $len = ($stopPosition <= $stop ? $stopPosition : $stop) - $startPosition - $pos1;              my $len1 = ($stopPosition < $stop ? $stopPosition : $stop) + 1 - $startPosition - $pos1;
799                Trace("Position is $pos1 for length $len1.") if T(SDNA => 4);
800                          # Add the relevant data to the location data.                          # Add the relevant data to the location data.
801                          $locationDNA .= substr($sequenceData, $pos1, $len);              $locationDNA .= substr($sequenceData, $pos1, $len1);
802                  }                  }
803                  # Add this location's data to the return string. Note that we may need to reverse it.                  # Add this location's data to the return string. Note that we may need to reverse it.
804                  if ($dir eq '+') {                  if ($dir eq '+') {
805                          $retVal .= $locationDNA;                          $retVal .= $locationDNA;
806                  } else {                  } else {
807                          $locationDNA = join('', reverse split //, $locationDNA);              $retVal .= FIG::reverse_comp($locationDNA);
                         $retVal .= $locationDNA;  
808                  }                  }
809          }          }
810          # Return the result.          # Return the result.
# Line 773  Line 830 
830  =back  =back
831    
832  =cut  =cut
833    #: Return Type @;
834  sub AllContigs {  sub AllContigs {
835          # Get the parameters.          # Get the parameters.
836          my $self = shift @_;      my ($self, $genomeID) = @_;
         my ($genomeID) = @_;  
837          # Ask for the genome's Contigs.          # Ask for the genome's Contigs.
838          my @retVal = $self->GetFlat(['HasContig'], "HasContig(from-link) = ?", [$genomeID],          my @retVal = $self->GetFlat(['HasContig'], "HasContig(from-link) = ?", [$genomeID],
839                                                                  'HasContig(to-link)');                                                                  'HasContig(to-link)');
# Line 797  Line 853 
853    
854  ID of the contig whose length is desired.  ID of the contig whose length is desired.
855    
856    =item RETURN
857    
858    Returns the number of positions in the contig.
859    
860  =back  =back
861    
862  =cut  =cut
863    #: Return Type $;
864  sub ContigLength {  sub ContigLength {
865          # Get the parameters.          # Get the parameters.
866          my $self = shift @_;      my ($self, $contigID) = @_;
         my ($contigID) = @_;  
867          # Get the contig's last sequence.          # Get the contig's last sequence.
868          my $query = $self->Get(['IsMadeUpOf'],          my $query = $self->Get(['IsMadeUpOf'],
869                  "IsMadeUpOf(from-link) = ? ORDER BY IsMadeUpOf(start-position) DESC",                  "IsMadeUpOf(from-link) = ? ORDER BY IsMadeUpOf(start-position) DESC",
# Line 815  Line 874 
874          # Set it from the sequence data, if any.          # Set it from the sequence data, if any.
875          if ($sequence) {          if ($sequence) {
876                  my ($start, $len) = $sequence->Values(['IsMadeUpOf(start-position)', 'IsMadeUpOf(len)']);                  my ($start, $len) = $sequence->Values(['IsMadeUpOf(start-position)', 'IsMadeUpOf(len)']);
877                  $retVal = $start + $len;          $retVal = $start + $len - 1;
878        }
879        # Return the result.
880        return $retVal;
881    }
882    
883    =head3 ClusterPEGs
884    
885    C<< my $clusteredList = $sprout->ClusterPEGs($sub, \@pegs); >>
886    
887    Cluster the PEGs in a list according to the cluster coding scheme of the specified
888    subsystem. In order for this to work properly, the subsystem object must have
889    been used recently to retrieve the PEGs using the B<get_pegs_from_cell> method.
890    This causes the cluster numbers to be pulled into the subsystem's color hash.
891    If a PEG is not found in the color hash, it will not appear in the output
892    sequence.
893    
894    =over 4
895    
896    =item sub
897    
898    Sprout subsystem object for the relevant subsystem, from the L</get_subsystem>
899    method.
900    
901    =item pegs
902    
903    Reference to the list of PEGs to be clustered.
904    
905    =item RETURN
906    
907    Returns a list of the PEGs, grouped into smaller lists by cluster number.
908    
909    =back
910    
911    =cut
912    #: Return Type $@@;
913    sub ClusterPEGs {
914        # Get the parameters.
915        my ($self, $sub, $pegs) = @_;
916        # Declare the return variable.
917        my $retVal = [];
918        # Loop through the PEGs, creating arrays for each cluster.
919        for my $pegID (@{$pegs}) {
920            my $clusterNumber = $sub->get_cluster_number($pegID);
921            # Only proceed if the PEG is in a cluster.
922            if ($clusterNumber >= 0) {
923                # Push this PEG onto the sub-list for the specified cluster number.
924                push @{$retVal->[$clusterNumber]}, $pegID;
925            }
926          }          }
927          # Return the result.          # Return the result.
928          return $retVal;          return $retVal;
# Line 846  Line 953 
953  Returns a three-element list. The first element is a list of feature IDs for the features that  Returns a three-element list. The first element is a list of feature IDs for the features that
954  overlap the region of interest. The second and third elements are the minimum and maximum  overlap the region of interest. The second and third elements are the minimum and maximum
955  locations of the features provided on the specified contig. These may extend outside  locations of the features provided on the specified contig. These may extend outside
956  the start and stop values.  the start and stop values. The first element (that is, the list of features) is sorted
957    roughly by location.
958    
959  =back  =back
960    
961  =cut  =cut
962    #: Return Type @@;
963  sub GenesInRegion {  sub GenesInRegion {
964          # Get the parameters.          # Get the parameters.
965          my $self = shift @_;      my ($self, $contigID, $start, $stop) = @_;
         my ($contigID, $start, $stop) = @_;  
966          # Get the maximum segment length.          # Get the maximum segment length.
967          my $maximumSegmentLength = $self->MaxSegment;          my $maximumSegmentLength = $self->MaxSegment;
968          # Create a hash to receive the feature list. We use a hash so that we can eliminate          # Create a hash to receive the feature list. We use a hash so that we can eliminate
969          # duplicates easily.      # duplicates easily. The hash key will be the feature ID. The value will be a two-element
970        # containing the minimum and maximum offsets. We will use the offsets to sort the results
971        # when we're building the result set.
972          my %featuresFound = ();          my %featuresFound = ();
973          # Prime the values we'll use for the returned beginning and end.          # Prime the values we'll use for the returned beginning and end.
974          my ($min, $max) = ($self->ContigLength($contigID), 0);      my @initialMinMax = ($self->ContigLength($contigID), 0);
975        my ($min, $max) = @initialMinMax;
976          # Create a table of parameters for each query. Each query looks for features travelling in          # Create a table of parameters for each query. Each query looks for features travelling in
977          # a particular direction. The query parameters include the contig ID, the feature direction,          # a particular direction. The query parameters include the contig ID, the feature direction,
978          # the lowest possible start position, and the highest possible start position. This works          # the lowest possible start position, and the highest possible start position. This works
# Line 892  Line 1002 
1002                                          $found = 1;                                          $found = 1;
1003                                  }                                  }
1004                          } elsif ($dir eq '-') {                          } elsif ($dir eq '-') {
1005                                  $end = $beg - $len;                  # Note we switch things around so that the beginning is to the left of the
1006                                  if ($end <= $stop) {                  # ending.
1007                    ($beg, $end) = ($beg - $len, $beg);
1008                    if ($beg <= $stop) {
1009                                          # Denote we found a useful feature.                                          # Denote we found a useful feature.
1010                                          $found = 1;                                          $found = 1;
1011                                  }                                  }
1012                          }                          }
1013                          if ($found) {                          if ($found) {
1014                                  # Here we need to record the feature and update the minimum and maximum.                  # Here we need to record the feature and update the minima and maxima. First,
1015                                  $featuresFound{$featureID} = 1;                  # get the current entry for the specified feature.
1016                                  if ($beg < $min) { $min = $beg; }                  my ($loc1, $loc2) = (exists $featuresFound{$featureID} ? @{$featuresFound{$featureID}} :
1017                                  if ($end < $min) { $min = $end; }                                       @initialMinMax);
1018                                  if ($beg > $max) { $max = $beg; }                  # Merge the current segment's begin and end into the feature begin and end and the
1019                                  if ($end > $max) { $max = $end; }                  # global min and max.
1020                    if ($beg < $loc1) {
1021                        $loc1 = $beg;
1022                        $min = $beg if $beg < $min;
1023                    }
1024                    if ($end > $loc2) {
1025                        $loc2 = $end;
1026                        $max = $end if $end > $max;
1027                    }
1028                    # Store the entry back into the hash table.
1029                    $featuresFound{$featureID} = [$loc1, $loc2];
1030                          }                          }
1031                  }                  }
1032          }          }
1033          # Compute a list of the IDs for the features found.      # Now we must compute the list of the IDs for the features found. We start with a list
1034          my @list = (sort (keys %featuresFound));      # of midpoints / feature ID pairs. (It's not really a midpoint, it's twice the midpoint,
1035        # but the result of the sort will be the same.)
1036        my @list = map { [$featuresFound{$_}->[0] + $featuresFound{$_}->[1], $_] } keys %featuresFound;
1037        # Now we sort by midpoint and yank out the feature IDs.
1038        my @retVal = map { $_->[1] } sort { $a->[0] <=> $b->[0] } @list;
1039          # Return it along with the min and max.          # Return it along with the min and max.
1040          return (\@list, $min, $max);      return (\@retVal, $min, $max);
1041  }  }
1042    
1043  =head3 FType  =head3 FType
# Line 934  Line 1060 
1060  =back  =back
1061    
1062  =cut  =cut
1063    #: Return Type $;
1064  sub FType {  sub FType {
1065          # Get the parameters.          # Get the parameters.
1066          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
1067          # Get the specified feature's type.          # Get the specified feature's type.
1068          my ($retVal) = $self->GetEntityValues('Feature', $featureID, ['Feature(feature-type)']);          my ($retVal) = $self->GetEntityValues('Feature', $featureID, ['Feature(feature-type)']);
1069          # Return the result.          # Return the result.
# Line 947  Line 1072 
1072    
1073  =head3 FeatureAnnotations  =head3 FeatureAnnotations
1074    
1075  C<< my @descriptors = $sprout->FeatureAnnotations($featureID); >>  C<< my @descriptors = $sprout->FeatureAnnotations($featureID, $rawFlag); >>
1076    
1077  Return the annotations of a feature.  Return the annotations of a feature.
1078    
# Line 957  Line 1082 
1082    
1083  ID of the feature whose annotations are desired.  ID of the feature whose annotations are desired.
1084    
1085    =item rawFlag
1086    
1087    If TRUE, the annotation timestamps will be returned in raw form; otherwise, they
1088    will be returned in human-readable form.
1089    
1090  =item RETURN  =item RETURN
1091    
1092  Returns a list of annotation descriptors. Each descriptor is a hash with the following fields.  Returns a list of annotation descriptors. Each descriptor is a hash with the following fields.
# Line 972  Line 1102 
1102  =back  =back
1103    
1104  =cut  =cut
1105    #: Return Type @%;
1106  sub FeatureAnnotations {  sub FeatureAnnotations {
1107          # Get the parameters.          # Get the parameters.
1108          my $self = shift @_;      my ($self, $featureID, $rawFlag) = @_;
         my ($featureID) = @_;  
1109          # Create a query to get the feature's annotations and the associated users.          # Create a query to get the feature's annotations and the associated users.
1110          my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],          my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1111                                                     "IsTargetOfAnnotation(from-link) = ?", [$featureID]);                                                     "IsTargetOfAnnotation(from-link) = ?", [$featureID]);
# Line 989  Line 1118 
1118                          $annotation->Values(['IsTargetOfAnnotation(from-link)',                          $annotation->Values(['IsTargetOfAnnotation(from-link)',
1119                                                                   'Annotation(time)', 'MadeAnnotation(from-link)',                                                                   'Annotation(time)', 'MadeAnnotation(from-link)',
1120                                                                   'Annotation(annotation)']);                                                                   'Annotation(annotation)']);
1121            # Convert the time, if necessary.
1122            if (! $rawFlag) {
1123                $timeStamp = FriendlyTimestamp($timeStamp);
1124            }
1125                  # Assemble them into a hash.                  # Assemble them into a hash.
1126                  my $annotationHash = { featureID => $featureID, timeStamp => $timeStamp,          my $annotationHash = { featureID => $featureID,
1127                                   timeStamp => $timeStamp,
1128                                                             user => $user, text => $text };                                                             user => $user, text => $text };
1129                  # Add it to the return list.                  # Add it to the return list.
1130                  push @retVal, $annotationHash;                  push @retVal, $annotationHash;
# Line 1004  Line 1138 
1138  C<< my %functions = $sprout->AllFunctionsOf($featureID); >>  C<< my %functions = $sprout->AllFunctionsOf($featureID); >>
1139    
1140  Return all of the functional assignments for a particular feature. The data is returned as a  Return all of the functional assignments for a particular feature. The data is returned as a
1141  hash of functional assignments to user IDs. A functional assignment is a type of annotation.  hash of functional assignments to user IDs. A functional assignment is a type of annotation,
1142  It has the format "XXXX\nset XXXX function to\nYYYYY". In this instance, XXXX is the user ID  Functional assignments are described in the L</ParseAssignment> function. Its worth noting that
1143  and YYYYY is the functional assignment text. Its worth noting that we cannot filter on the content  we cannot filter on the content of the annotation itself because it's a text field; however,
1144  of the annotation itself because it's a text field; however, this is not a big problem because most  this is not a big problem because most features only have a small number of annotations.
1145  features only have a small number of annotations.  Finally, if a single user has multiple functional assignments, we will only keep the most
1146    recent one.
1147    
1148  =over 4  =over 4
1149    
# Line 1016  Line 1151 
1151    
1152  ID of the feature whose functional assignments are desired.  ID of the feature whose functional assignments are desired.
1153    
1154    =item RETURN
1155    
1156    Returns a hash mapping the user IDs to functional assignment IDs.
1157    
1158  =back  =back
1159    
1160  =cut  =cut
1161    #: Return Type %;
1162  sub AllFunctionsOf {  sub AllFunctionsOf {
1163          # Get the parameters.          # Get the parameters.
1164          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
1165          # Get all of the feature's annotations.          # Get all of the feature's annotations.
1166          my @query = $self->GetFlat(['IsTargetOfAnnotation', 'Annotation'],      my @query = $self->GetAll(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1167                                                      "IsTargetOfAnnotation(from-link) = ?",                                                      "IsTargetOfAnnotation(from-link) = ?",
1168                                                          [$featureID], 'Annotation(annotation)');                              [$featureID], ['Annotation(time)', 'Annotation(annotation)',
1169                                               'MadeAnnotation(from-link)']);
1170          # Declare the return hash.          # Declare the return hash.
1171          my %retVal;          my %retVal;
1172        # Now we sort the assignments by timestamp in reverse.
1173        my @sortedQuery = sort { -($a->[0] <=> $b->[0]) } @query;
1174          # Loop until we run out of annotations.          # Loop until we run out of annotations.
1175          for my $text (@query) {      for my $annotation (@sortedQuery) {
1176            # Get the annotation fields.
1177            my ($timeStamp, $text, $user) = @{$annotation};
1178                  # Check to see if this is a functional assignment.                  # Check to see if this is a functional assignment.
1179                  my ($user, $function) = ParseAssignment($text);          my ($type, $function) = _ParseAssignment($text);
1180                  if ($user) {          if ($type && ! exists $retVal{$user}) {
1181                          # Here it is, so stuff it in the return hash.              # Here it is a functional assignment and there has been no
1182                          $retVal{$function} = $user;              # previous assignment for this user, so we stuff it in the
1183                # return hash.
1184                $retVal{$user} = $function;
1185                  }                  }
1186          }          }
1187          # Return the hash of assignments found.          # Return the hash of assignments found.
# Line 1047  Line 1192 
1192    
1193  C<< my $functionText = $sprout->FunctionOf($featureID, $userID); >>  C<< my $functionText = $sprout->FunctionOf($featureID, $userID); >>
1194    
1195  Return the most recently-determined functional assignment of a particular feature. A functional  Return the most recently-determined functional assignment of a particular feature.
1196  assignment is a type of annotation. It has the format "XXXX\nset XXXX function to\nYYYYY". In this  
1197  instance, XXXX is the user ID and YYYYY is the functional assignment text. Its worth noting that  The functional assignment is handled differently depending on the type of feature. If
1198  we cannot filter on the content of the annotation itself because it's a text field; however, this  the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional
1199  is not a big problem because most features only have a small number of annotations.  assignment is a type of annotation. The format of an assignment is described in
1200    L</ParseAssignment>. Its worth noting that we cannot filter on the content of the
1201    annotation itself because it's a text field; however, this is not a big problem because
1202    most features only have a small number of annotations.
1203    
1204    Each user has an associated list of trusted users. The assignment returned will be the most
1205    recent one by at least one of the trusted users. If no trusted user list is available, then
1206    the specified user and FIG are considered trusted. If the user ID is omitted, only FIG
1207    is trusted.
1208    
1209    If the feature is B<not> identified by a FIG ID, then the functional assignment
1210    information is taken from the B<ExternalAliasFunc> table. If the table does
1211    not contain an entry for the feature, an undefined value is returned.
1212    
1213  =over 4  =over 4
1214    
# Line 1061  Line 1218 
1218    
1219  =item userID (optional)  =item userID (optional)
1220    
1221  ID of the user whose function determination is desired. If omitted, C<FIG> is assumed.  ID of the user whose function determination is desired. If omitted, only the latest
1222    C<FIG> assignment will be returned.
1223    
1224  =item RETURN  =item RETURN
1225    
# Line 1070  Line 1228 
1228  =back  =back
1229    
1230  =cut  =cut
1231    #: Return Type $;
1232  sub FunctionOf {  sub FunctionOf {
1233          # Get the parameters.          # Get the parameters.
1234          my $self = shift @_;      my ($self, $featureID, $userID) = @_;
1235          my ($featureID, $userID) = @_;      # Declare the return value.
         if (!$userID) { $userID = 'FIG'; }  
         # Build a query for all of the feature's annotation, sorted by date.  
         my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation'],  
                                                     "IsTargetOfAnnotation(from-link) = ?", [$featureID]);  
         # Declare the return value. We'll set this to the most recent annotation for the  
         # specified user.  
1236          my $retVal;          my $retVal;
1237        # Determine the ID type.
1238        if ($featureID =~ m/^fig\|/) {
1239            # Here we have a FIG feature ID. We must build the list of trusted
1240            # users.
1241            my %trusteeTable = ();
1242            # Check the user ID.
1243            if (!$userID) {
1244                # No user ID, so only FIG is trusted.
1245                $trusteeTable{FIG} = 1;
1246            } else {
1247                # Add this user's ID.
1248                $trusteeTable{$userID} = 1;
1249                # Look for the trusted users in the database.
1250                my @trustees = $self->GetFlat(['IsTrustedBy'], 'IsTrustedBy(from-link) = ?', [$userID], 'IsTrustedBy(to-link)');
1251                if (! @trustees) {
1252                    # None were found, so build a default list.
1253                    $trusteeTable{FIG} = 1;
1254                } else {
1255                    # Otherwise, put all the trustees in.
1256                    for my $trustee (@trustees) {
1257                        $trusteeTable{$trustee} = 1;
1258                    }
1259                }
1260            }
1261            # Build a query for all of the feature's annotations, sorted by date.
1262            my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation'],
1263                                   "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1264                                   [$featureID]);
1265          my $timeSelected = 0;          my $timeSelected = 0;
1266          # Loop until we run out of annotations.          # Loop until we run out of annotations.
1267          while (my $annotation = $query->Fetch()) {          while (my $annotation = $query->Fetch()) {
1268                  # Get the annotation text.                  # Get the annotation text.
1269                  my ($text, $time) = $annotation->Values(['Annotation(annotation)','Annotation(time)']);                  my ($text, $time) = $annotation->Values(['Annotation(annotation)','Annotation(time)']);
1270                  # Check to see if this is a functional assignment for the desired user.              # Check to see if this is a functional assignment for a trusted user.
1271                  my ($user, $type, $function) = split(/\n/, $text);              my ($user, $function) = _ParseAssignment($text);
1272                  if ($type =~ m/^set $userID function to$/i) {              if ($user) {
1273                          # Here it is, so we check the time and save the assignment value.                  # Here it is a functional assignment. Check the time and the user
1274                          if ($time > $timeSelected) {                  # name. The time must be recent and the user must be trusted.
1275                    if ((exists $trusteeTable{$user}) && ($time > $timeSelected)) {
1276                                  $retVal = $function;                                  $retVal = $function;
1277                                  $timeSelected = $time;                                  $timeSelected = $time;
1278                          }                          }
1279                  }                  }
1280          }          }
1281        } else {
1282            # Here we have a non-FIG feature ID. In this case the user ID does not
1283            # matter. We simply get the information from the External Alias Function
1284            # table.
1285            ($retVal) = $self->GetEntityValues('ExternalAliasFunc', $featureID, ['ExternalAliasFunc(func)']);
1286        }
1287          # Return the assignment found.          # Return the assignment found.
1288          return $retVal;          return $retVal;
1289  }  }
1290    
1291    =head3 FunctionsOf
1292    
1293    C<< my @functionList = $sprout->FunctionOf($featureID, $userID); >>
1294    
1295    Return the functional assignments of a particular feature.
1296    
1297    The functional assignment is handled differently depending on the type of feature. If
1298    the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional
1299    assignment is a type of annotation. The format of an assignment is described in
1300    L</ParseAssignment>. Its worth noting that we cannot filter on the content of the
1301    annotation itself because it's a text field; however, this is not a big problem because
1302    most features only have a small number of annotations.
1303    
1304    If the feature is B<not> identified by a FIG ID, then the functional assignment
1305    information is taken from the B<ExternalAliasFunc> table. If the table does
1306    not contain an entry for the feature, an empty list is returned.
1307    
1308    =over 4
1309    
1310    =item featureID
1311    
1312    ID of the feature whose functional assignments are desired.
1313    
1314    =item RETURN
1315    
1316    Returns a list of 2-tuples, each consisting of a user ID and the text of an assignment by
1317    that user.
1318    
1319    =back
1320    
1321    =cut
1322    #: Return Type @@;
1323    sub FunctionsOf {
1324        # Get the parameters.
1325        my ($self, $featureID) = @_;
1326        # Declare the return value.
1327        my @retVal = ();
1328        # Determine the ID type.
1329        if ($featureID =~ m/^fig\|/) {
1330            # Here we have a FIG feature ID. We must build the list of trusted
1331            # users.
1332            my %trusteeTable = ();
1333            # Build a query for all of the feature's annotations, sorted by date.
1334            my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation'],
1335                                   "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1336                                   [$featureID]);
1337            my $timeSelected = 0;
1338            # Loop until we run out of annotations.
1339            while (my $annotation = $query->Fetch()) {
1340                # Get the annotation text.
1341                my ($text, $time) = $annotation->Values(['Annotation(annotation)','Annotation(time)']);
1342                # Check to see if this is a functional assignment for a trusted user.
1343                my ($user, $function) = _ParseAssignment($text);
1344                if ($user) {
1345                    # Here it is a functional assignment.
1346                    push @retVal, [$user, $function];
1347                }
1348            }
1349        } else {
1350            # Here we have a non-FIG feature ID. In this case the user ID does not
1351            # matter. We simply get the information from the External Alias Function
1352            # table.
1353            push @retVal, $self->GetEntityValues('ExternalAliasFunc', $featureID, ['ExternalAliasFunc(func)']);
1354        }
1355        # Return the assignments found.
1356        return @retVal;
1357    }
1358    
1359  =head3 BBHList  =head3 BBHList
1360    
1361  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>
# Line 1120  Line 1375 
1375    
1376  =item RETURN  =item RETURN
1377    
1378  Returns a reference to a hash that maps the IDs of the incoming features to the IDs of  Returns a reference to a hash that maps the IDs of the incoming features to the best hits
1379  their best hits.  on the target genome.
1380    
1381  =back  =back
1382    
1383  =cut  =cut
1384    #: Return Type %;
1385  sub BBHList {  sub BBHList {
1386          # Get the parameters.          # Get the parameters.
1387          my $self = shift @_;      my ($self, $genomeID, $featureList) = @_;
         my ($genomeID, $featureList) = @_;  
1388          # Create the return structure.          # Create the return structure.
1389          my %retVal = ();          my %retVal = ();
1390          # Loop through the incoming features.          # Loop through the incoming features.
# Line 1139  Line 1393 
1393                  my $query = $self->Get(['IsBidirectionalBestHitOf'],                  my $query = $self->Get(['IsBidirectionalBestHitOf'],
1394                                                             "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",                                                             "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",
1395                                                             [$featureID, $genomeID]);                                                             [$featureID, $genomeID]);
1396                  # Look for the best hit.          # Peel off the BBHs found.
1397                  my $bbh = $query->Fetch;          my @found = ();
1398                  if ($bbh) {          while (my $bbh = $query->Fetch) {
1399                          my ($targetFeature) = $bbh->Value('IsBidirectionalBestHitOf(to-link)');              push @found, $bbh->Value('IsBidirectionalBestHitOf(to-link)');
                         $retVal{$featureID} = $targetFeature;  
1400                  }                  }
1401            $retVal{$featureID} = \@found;
1402          }          }
1403          # Return the mapping.          # Return the mapping.
1404          return \%retVal;          return \%retVal;
1405  }  }
1406    
1407    =head3 SimList
1408    
1409    C<< my %similarities = $sprout->SimList($featureID, $count); >>
1410    
1411    Return a list of the similarities to the specified feature.
1412    
1413    Sprout does not support real similarities, so this method just returns the bidirectional
1414    best hits.
1415    
1416    =over 4
1417    
1418    =item featureID
1419    
1420    ID of the feature whose similarities are desired.
1421    
1422    =item count
1423    
1424    Maximum number of similar features to be returned, or C<0> to return them all.
1425    
1426    =back
1427    
1428    =cut
1429    #: Return Type %;
1430    sub SimList {
1431        # Get the parameters.
1432        my ($self, $featureID, $count) = @_;
1433        # Ask for the best hits.
1434        my @lists = $self->GetAll(['IsBidirectionalBestHitOf'],
1435                                  "IsBidirectionalBestHitOf(from-link) = ? ORDER BY IsBidirectionalBestHitOf(score) DESC",
1436                                  [$featureID], ['IsBidirectionalBestHitOf(to-link)', 'IsBidirectionalBestHitOf(score)'],
1437                                  $count);
1438        # Create the return value.
1439        my %retVal = ();
1440        for my $tuple (@lists) {
1441            $retVal{$tuple->[0]} = $tuple->[1];
1442        }
1443        # Return the result.
1444        return %retVal;
1445    }
1446    
1447    
1448    
1449    =head3 IsComplete
1450    
1451    C<< my $flag = $sprout->IsComplete($genomeID); >>
1452    
1453    Return TRUE if the specified genome is complete, else FALSE.
1454    
1455    =over 4
1456    
1457    =item genomeID
1458    
1459    ID of the genome whose completeness status is desired.
1460    
1461    =item RETURN
1462    
1463    Returns TRUE if the genome is complete, FALSE if it is incomplete, and C<undef> if it is
1464    not found.
1465    
1466    =back
1467    
1468    =cut
1469    #: Return Type $;
1470    sub IsComplete {
1471        # Get the parameters.
1472        my ($self, $genomeID) = @_;
1473        # Declare the return variable.
1474        my $retVal;
1475        # Get the genome's data.
1476        my $genomeData = $self->GetEntity('Genome', $genomeID);
1477        if ($genomeData) {
1478            # The genome exists, so get the completeness flag.
1479            ($retVal) = $genomeData->Value('complete');
1480        }
1481        # Return the result.
1482        return $retVal;
1483    }
1484    
1485  =head3 FeatureAliases  =head3 FeatureAliases
1486    
1487  C<< my @aliasList = $sprout->FeatureAliases($featureID); >>  C<< my @aliasList = $sprout->FeatureAliases($featureID); >>
# Line 1170  Line 1502 
1502  =back  =back
1503    
1504  =cut  =cut
1505    #: Return Type @;
1506  sub FeatureAliases {  sub FeatureAliases {
1507          # Get the parameters.          # Get the parameters.
1508          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
1509          # Get the desired feature's aliases          # Get the desired feature's aliases
1510          my @retVal = $self->GetEntityValues('Feature', $featureID, ['Feature(alias)']);          my @retVal = $self->GetEntityValues('Feature', $featureID, ['Feature(alias)']);
1511          # Return the result.          # Return the result.
# Line 1201  Line 1532 
1532  =back  =back
1533    
1534  =cut  =cut
1535    #: Return Type $;
1536  sub GenomeOf {  sub GenomeOf {
1537          # Get the parameters.          # Get the parameters.
1538          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
1539          # Create a query to find the genome associated with the feature.          # Create a query to find the genome associated with the feature.
1540          my $query = $self->Get(['IsLocatedIn', 'HasContig'], "IsLocatedIn(from-link) = ?", [$featureID]);          my $query = $self->Get(['IsLocatedIn', 'HasContig'], "IsLocatedIn(from-link) = ?", [$featureID]);
1541          # Declare the return value.          # Declare the return value.
# Line 1238  Line 1568 
1568  =back  =back
1569    
1570  =cut  =cut
1571    #: Return Type %;
1572  sub CoupledFeatures {  sub CoupledFeatures {
1573          # Get the parameters.          # Get the parameters.
1574          my $self = shift @_;      my ($self, $featureID) = @_;
1575          my ($featureID) = @_;      # Create a query to retrieve the functionally-coupled features.
1576          # Create a query to retrieve the functionally-coupled features. Note that we depend on the      my $query = $self->Get(['ParticipatesInCoupling', 'Coupling'],
1577          # fact that the functional coupling is physically paired. If (A,B) is in the database, then                             "ParticipatesInCoupling(from-link) = ?", [$featureID]);
         # (B,A) will also be found.  
         my $query = $self->Get(['IsClusteredOnChromosomeWith'],  
                                                    "IsClusteredOnChromosomeWith(from-link) = ?", [$featureID]);  
1578          # This value will be set to TRUE if we find at least one coupled feature.          # This value will be set to TRUE if we find at least one coupled feature.
1579          my $found = 0;          my $found = 0;
1580          # Create the return hash.          # Create the return hash.
1581          my %retVal = ();          my %retVal = ();
1582          # Retrieve the relationship records and store them in the hash.          # Retrieve the relationship records and store them in the hash.
1583          while (my $clustering = $query->Fetch()) {          while (my $clustering = $query->Fetch()) {
1584                  my ($otherFeatureID, $score) = $clustering->Values(['IsClusteredOnChromosomeWith(to-link)',          # Get the ID and score of the coupling.
1585                                                                      'IsClusteredOnChromosomeWith(score)']);          my ($couplingID, $score) = $clustering->Values(['Coupling(id)',
1586                                                            'Coupling(score)']);
1587            # The coupling ID contains the two feature IDs separated by a space. We use
1588            # this information to find the ID of the other feature.
1589            my ($fid1, $fid2) = split / /, $couplingID;
1590            my $otherFeatureID = ($featureID eq $fid1 ? $fid2 : $fid1);
1591            # Attach the other feature's score to its ID.
1592                  $retVal{$otherFeatureID} = $score;                  $retVal{$otherFeatureID} = $score;
1593                  $found = 1;                  $found = 1;
1594          }          }
# Line 1268  Line 1601 
1601          return %retVal;          return %retVal;
1602  }  }
1603    
1604    =head3 CouplingEvidence
1605    
1606    C<< my @evidence = $sprout->CouplingEvidence($peg1, $peg2); >>
1607    
1608    Return the evidence for a functional coupling.
1609    
1610    A pair of features is considered evidence of a coupling between two other
1611    features if they occur close together on a contig and both are similar to
1612    the coupled features. So, if B<A1> and B<A2> are close together on a contig,
1613    B<B1> and B<B2> are considered evidence for the coupling if (1) B<B1> and
1614    B<B2> are close together, (2) B<B1> is similar to B<A1>, and (3) B<B2> is
1615    similar to B<A2>.
1616    
1617    The score of a coupling is determined by the number of pieces of evidence
1618    that are considered I<representative>. If several evidence items belong to
1619    a group of genomes that are close to each other, only one of those items
1620    is considered representative. The other evidence items are presumed to be
1621    there because of the relationship between the genomes rather than because
1622    the two proteins generated by the features have a related functionality.
1623    
1624    Each evidence item is returned as a three-tuple in the form C<[>I<$peg1a>C<,>
1625    I<$peg2a>C<,> I<$rep>C<]>, where I<$peg1a> is similar to I<$peg1>, I<$peg2a>
1626    is similar to I<$peg2>, and I<$rep> is TRUE if the evidence is representative
1627    and FALSE otherwise.
1628    
1629    =over 4
1630    
1631    =item peg1
1632    
1633    ID of the feature of interest.
1634    
1635    =item peg2
1636    
1637    ID of a feature functionally coupled to the feature of interest.
1638    
1639    =item RETURN
1640    
1641    Returns a list of 3-tuples. Each tuple consists of a feature similar to the feature
1642    of interest, a feature similar to the functionally coupled feature, and a flag
1643    that is TRUE for a representative piece of evidence and FALSE otherwise.
1644    
1645    =back
1646    
1647    =cut
1648    #: Return Type @@;
1649    sub CouplingEvidence {
1650        # Get the parameters.
1651        my ($self, $peg1, $peg2) = @_;
1652        # Declare the return variable.
1653        my @retVal = ();
1654        # Our first task is to find out the nature of the coupling: whether or not
1655        # it exists, its score, and whether the features are stored in the same
1656        # order as the ones coming in.
1657        my ($couplingID, $inverted, $score) = $self->GetCoupling($peg1, $peg2);
1658        # Only proceed if a coupling exists.
1659        if ($couplingID) {
1660            # Determine the ordering to place on the evidence items. If we're
1661            # inverted, we want to see feature 2 before feature 1 (descending); otherwise,
1662            # we want feature 1 before feature 2 (normal).
1663            Trace("Coupling evidence for ($peg1, $peg2) with inversion flag $inverted.") if T(Coupling => 4);
1664            my $ordering = ($inverted ? "DESC" : "");
1665            # Get the coupling evidence.
1666            my @evidenceList = $self->GetAll(['IsEvidencedBy', 'PCH', 'UsesAsEvidence'],
1667                                              "IsEvidencedBy(from-link) = ? ORDER BY PCH(id), UsesAsEvidence(pos) $ordering",
1668                                              [$couplingID],
1669                                              ['PCH(used)', 'UsesAsEvidence(to-link)']);
1670            # Loop through the evidence items. Each piece of evidence is represented by two
1671            # positions in the evidence list, one for each feature on the other side of the
1672            # evidence link. If at some point we want to generalize to couplings with
1673            # more than two positions, this section of code will need to be re-done.
1674            while (@evidenceList > 0) {
1675                my $peg1Data = shift @evidenceList;
1676                my $peg2Data = shift @evidenceList;
1677                Trace("Peg 1 is " . $peg1Data->[1] . " and Peg 2 is " . $peg2Data->[1] . ".") if T(Coupling => 4);
1678                push @retVal, [$peg1Data->[1], $peg2Data->[1], $peg1Data->[0]];
1679            }
1680            Trace("Last index in evidence result is is $#retVal.") if T(Coupling => 4);
1681        }
1682        # Return the result.
1683        return @retVal;
1684    }
1685    
1686    =head3 GetCoupling
1687    
1688    C<< my ($couplingID, $inverted, $score) = $sprout->GetCoupling($peg1, $peg2); >>
1689    
1690    Return the coupling (if any) for the specified pair of PEGs. If a coupling
1691    exists, we return the coupling ID along with an indicator of whether the
1692    coupling is stored as C<(>I<$peg1>C<, >I<$peg2>C<)> or C<(>I<$peg2>C<, >I<$peg1>C<)>.
1693    In the second case, we say the coupling is I<inverted>. The importance of an
1694    inverted coupling is that the PEGs in the evidence will appear in reverse order.
1695    
1696    =over 4
1697    
1698    =item peg1
1699    
1700    ID of the feature of interest.
1701    
1702    =item peg2
1703    
1704    ID of the potentially coupled feature.
1705    
1706    =item RETURN
1707    
1708    Returns a three-element list. The first element contains the database ID of
1709    the coupling. The second element is FALSE if the coupling is stored in the
1710    database in the caller specified order and TRUE if it is stored in the
1711    inverted order. The third element is the coupling's score. If the coupling
1712    does not exist, all three list elements will be C<undef>.
1713    
1714    =back
1715    
1716    =cut
1717    #: Return Type $%@;
1718    sub GetCoupling {
1719        # Get the parameters.
1720        my ($self, $peg1, $peg2) = @_;
1721        # Declare the return values. We'll start with the coupling ID and undefine the
1722        # flag and score until we have more information.
1723        my ($retVal, $inverted, $score) = (CouplingID($peg1, $peg2), undef, undef);
1724        # Find the coupling data.
1725        my @pegs = $self->GetAll(['Coupling', 'ParticipatesInCoupling'],
1726                                     "Coupling(id) = ? ORDER BY ParticipatesInCoupling(pos)",
1727                                     [$retVal], ["ParticipatesInCoupling(from-link)", "Coupling(score)"]);
1728        # Check to see if we found anything.
1729        if (!@pegs) {
1730            Trace("No coupling found.") if T(Coupling => 4);
1731            # No coupling, so undefine the return value.
1732            $retVal = undef;
1733        } else {
1734            # We have a coupling! Get the score and check for inversion.
1735            $score = $pegs[0]->[1];
1736            my $firstFound = $pegs[0]->[0];
1737            $inverted = ($firstFound ne $peg1);
1738            Trace("Coupling score is $score. First peg is $firstFound, peg 1 is $peg1.") if T(Coupling => 4);
1739        }
1740        # Return the result.
1741        return ($retVal, $inverted, $score);
1742    }
1743    
1744    =head3 CouplingID
1745    
1746    C<< my $couplingID = Sprout::CouplingID($peg1, $peg2); >>
1747    
1748    Return the coupling ID for a pair of feature IDs.
1749    
1750    The coupling ID is currently computed by joining the feature IDs in
1751    sorted order with a space. Client modules (that is, modules which
1752    use Sprout) should not, however, count on this always being the
1753    case. This method provides a way for abstracting the concept of a
1754    coupling ID. All that we know for sure about it is that it can be
1755    generated easily from the feature IDs and the order of the IDs
1756    in the parameter list does not matter (i.e. C<CouplingID("a1", "b1")>
1757    will have the same value as C<CouplingID("b1", "a1")>.
1758    
1759    =over 4
1760    
1761    =item peg1
1762    
1763    First feature of interest.
1764    
1765    =item peg2
1766    
1767    Second feature of interest.
1768    
1769    =item RETURN
1770    
1771    Returns the ID that would be used to represent a functional coupling of
1772    the two specified PEGs.
1773    
1774    =back
1775    
1776    =cut
1777    #: Return Type $;
1778    sub CouplingID {
1779        return join " ", sort @_;
1780    }
1781    
1782  =head3 GetEntityTypes  =head3 GetEntityTypes
1783    
1784  C<< my @entityList = $sprout->GetEntityTypes(); >>  C<< my @entityList = $sprout->GetEntityTypes(); >>
# Line 1275  Line 1786 
1786  Return the list of supported entity types.  Return the list of supported entity types.
1787    
1788  =cut  =cut
1789    #: Return Type @;
1790  sub GetEntityTypes {  sub GetEntityTypes {
1791          # Get the parameters.          # Get the parameters.
1792          my $self = shift @_;      my ($self) = @_;
1793          # Get the underlying database object.          # Get the underlying database object.
1794          my $erdb = $self->{_erdb};          my $erdb = $self->{_erdb};
1795          # Get its entity type list.          # Get its entity type list.
# Line 1310  Line 1821 
1821  =back  =back
1822    
1823  =cut  =cut
1824    #: Return Type %;
1825  sub ReadFasta {  sub ReadFasta {
1826          # Get the parameters.          # Get the parameters.
1827          my ($fileName, $prefix) = @_;          my ($fileName, $prefix) = @_;
# Line 1329  Line 1840 
1840                  if ($line =~ m/^>\s*(.+?)(\s|\n)/) {                  if ($line =~ m/^>\s*(.+?)(\s|\n)/) {
1841                          # Here we have a new header. Store the current sequence if we have one.                          # Here we have a new header. Store the current sequence if we have one.
1842                          if ($id) {                          if ($id) {
1843                                  $retVal{$id} = $sequence;                  $retVal{$id} = lc $sequence;
1844                          }                          }
1845                          # Clear the sequence accumulator and save the new ID.                          # Clear the sequence accumulator and save the new ID.
1846                          ($id, $sequence) = ("$prefix$1", "");                          ($id, $sequence) = ("$prefix$1", "");
1847                  } else {                  } else {
1848                          # Here we have a data line, so we add it to the sequence accumulator.                          # Here we have a data line, so we add it to the sequence accumulator.
1849                          # First, we get the actual data out.              # First, we get the actual data out. Note that we normalize to lower
1850                # case.
1851                          $line =~ /^\s*(.*?)(\s|\n)/;                          $line =~ /^\s*(.*?)(\s|\n)/;
1852                          $sequence .= $1;                          $sequence .= $1;
1853                  }                  }
1854          }          }
1855          # Flush out the last sequence (if any).          # Flush out the last sequence (if any).
1856          if ($sequence) {          if ($sequence) {
1857                  $retVal {$id} = $sequence;          $retVal{$id} = lc $sequence;
1858          }          }
1859        # Close the file.
1860        close FASTAFILE;
1861          # Return the hash constructed from the file.          # Return the hash constructed from the file.
1862          return %retVal;          return %retVal;
1863  }  }
# Line 1354  Line 1868 
1868    
1869  Insure that a list of feature locations is in the Sprout format. The Sprout feature location  Insure that a list of feature locations is in the Sprout format. The Sprout feature location
1870  format is I<contig>_I<beg*len> where I<*> is C<+> for a forward gene and C<-> for a backward  format is I<contig>_I<beg*len> where I<*> is C<+> for a forward gene and C<-> for a backward
1871  gene. The old format is I<contig>_I<beg>_I<end>.  gene. The old format is I<contig>_I<beg>_I<end>. If a feature is in the new format already,
1872    it will not be changed; otherwise, it will be converted. This method can also be used to
1873    perform the reverse task-- insuring that all the locations are in the old format.
1874    
1875  =over 4  =over 4
1876    
# Line 1378  Line 1894 
1894  =back  =back
1895    
1896  =cut  =cut
1897    #: Return Type @;
1898  sub FormatLocations {  sub FormatLocations {
1899          # Get the parameters.          # Get the parameters.
1900          my $self = shift @_;      my ($self, $prefix, $locations, $oldFormat) = @_;
         my ($prefix, $locations, $oldFormat) = @_;  
1901          # Create the return list.          # Create the return list.
1902          my @retVal = ();          my @retVal = ();
1903          # Check to see if any locations were passed in.          # Check to see if any locations were passed in.
1904          if ($locations eq '') {          if ($locations eq '') {
1905              confess "No locations specified.";          Confess("No locations specified.");
1906          } else {          } else {
1907                  # Loop through the locations, converting them to the new format.                  # Loop through the locations, converting them to the new format.
1908                  for my $location (@{$locations}) {                  for my $location (@{$locations}) {
# Line 1422  Line 1937 
1937    
1938  sub DumpData {  sub DumpData {
1939          # Get the parameters.          # Get the parameters.
1940          my $self = shift @_;      my ($self) = @_;
1941          # Get the data directory name.          # Get the data directory name.
1942          my $outputDirectory = $self->{_options}->{dataDir};          my $outputDirectory = $self->{_options}->{dataDir};
1943          # Dump the relations.          # Dump the relations.
# Line 1436  Line 1951 
1951  Return the name of this database's XML definition file.  Return the name of this database's XML definition file.
1952    
1953  =cut  =cut
1954    #: Return Type $;
1955  sub XMLFileName {  sub XMLFileName {
1956          my $self = shift @_;      my ($self) = @_;
1957          return $self->{_xmlName};          return $self->{_xmlName};
1958  }  }
1959    
# Line 1458  Line 1973 
1973  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
1974  property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.  property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
1975    
1976  C<< $sprout->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence = 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>  C<< $sprout->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>
1977    
1978  =over 4  =over 4
1979    
# Line 1473  Line 1988 
1988  =back  =back
1989    
1990  =cut  =cut
1991    #: Return Type ;
1992  sub Insert {  sub Insert {
1993          # Get the parameters.          # Get the parameters.
1994          my $self = shift @_;      my ($self, $objectType, $fieldHash) = @_;
         my ($objectType, $fieldHash) = @_;  
1995          # Call the underlying method.          # Call the underlying method.
1996          $self->{_erdb}->InsertObject($objectType, $fieldHash);          $self->{_erdb}->InsertObject($objectType, $fieldHash);
1997  }  }
# Line 1515  Line 2029 
2029  =back  =back
2030    
2031  =cut  =cut
2032    #: Return Type $;
2033  sub Annotate {  sub Annotate {
2034          # Get the parameters.          # Get the parameters.
2035          my $self = shift @_;      my ($self, $fid, $timestamp, $user, $text) = @_;
         my ($fid, $timestamp, $user, $text) = @_;  
2036          # Create the annotation ID.          # Create the annotation ID.
2037          my $aid = "$fid:$timestamp";          my $aid = "$fid:$timestamp";
2038          # Insert the Annotation object.          # Insert the Annotation object.
# Line 1539  Line 2052 
2052    
2053  =head3 AssignFunction  =head3 AssignFunction
2054    
2055  C<< my $ok = $sprout->AssignFunction($featureID, $user, $function); >>  C<< my $ok = $sprout->AssignFunction($featureID, $user, $function, $assigningUser); >>
2056    
2057  This method assigns a function to a feature. Functions are a special type of annotation. The general  This method assigns a function to a feature. Functions are a special type of annotation. The general
2058  format is "XXXX\nset XXXX function to\nYYYYY" where XXXX is the feature type and YYYY is the functional  format is described in L</ParseAssignment>.
 assignment text.  
2059    
2060  =over 4  =over 4
2061    
# Line 1553  Line 2065 
2065    
2066  =item user  =item user
2067    
2068  Name of the user making the assignment. This is frequently a group name, like C<kegg> or C<fig>.  Name of the user group making the assignment, such as C<kegg> or C<fig>.
2069    
2070  =item function  =item function
2071    
2072  Text of the function being assigned.  Text of the function being assigned.
2073    
2074    =item assigningUser (optional)
2075    
2076    Name of the individual user making the assignment. If omitted, defaults to the user group.
2077    
2078  =item RETURN  =item RETURN
2079    
2080  Returns 1 if successful, 0 if an error occurred.  Returns 1 if successful, 0 if an error occurred.
# Line 1566  Line 2082 
2082  =back  =back
2083    
2084  =cut  =cut
2085    #: Return Type $;
2086  sub AssignFunction {  sub AssignFunction {
2087          # Get the parameters.          # Get the parameters.
2088          my $self = shift @_;      my ($self, $featureID, $user, $function, $assigningUser) = @_;
2089          my ($featureID, $user, $function) = @_;      # Default the assigning user.
2090        if (! $assigningUser) {
2091            $assigningUser = $user;
2092        }
2093          # Create an annotation string from the parameters.          # Create an annotation string from the parameters.
2094          my $annotationText = "$user\nset $user function to\n$function";      my $annotationText = "$assigningUser\nset $user function to\n$function";
2095          # Get the current time.          # Get the current time.
2096          my $now = time;          my $now = time;
2097          # Declare the return variable.          # Declare the return variable.
# Line 1614  Line 2133 
2133  =back  =back
2134    
2135  =cut  =cut
2136    #: Return Type @;
2137  sub FeaturesByAlias {  sub FeaturesByAlias {
2138          # Get the parameters.          # Get the parameters.
2139          my $self = shift @_;      my ($self, $alias) = @_;
         my ($alias) = @_;  
2140          # Declare the return variable.          # Declare the return variable.
2141          my @retVal = ();          my @retVal = ();
2142          # Parse the alias.          # Parse the alias.
# Line 1657  Line 2175 
2175  =back  =back
2176    
2177  =cut  =cut
2178    #: Return Type $;
2179  sub Exists {  sub Exists {
2180          # Get the parameters.          # Get the parameters.
2181          my $self = shift @_;      my ($self, $entityName, $entityID) = @_;
         my ($entityName, $entityID) = @_;  
2182          # Check for the entity instance.          # Check for the entity instance.
2183        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
2184          my $testInstance = $self->GetEntity($entityName, $entityID);          my $testInstance = $self->GetEntity($entityName, $entityID);
2185          # Return an existence indicator.          # Return an existence indicator.
2186          my $retVal = ($testInstance ? 1 : 0);          my $retVal = ($testInstance ? 1 : 0);
# Line 1688  Line 2206 
2206  =back  =back
2207    
2208  =cut  =cut
2209    #: Return Type $;
2210  sub FeatureTranslation {  sub FeatureTranslation {
2211          # Get the parameters.          # Get the parameters.
2212          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
2213          # Get the specified feature's translation.          # Get the specified feature's translation.
2214          my ($retVal) = $self->GetEntityValues("Feature", $featureID, ['Feature(translation)']);          my ($retVal) = $self->GetEntityValues("Feature", $featureID, ['Feature(translation)']);
2215          return $retVal;          return $retVal;
# Line 1721  Line 2238 
2238  =back  =back
2239    
2240  =cut  =cut
2241    #: Return Type @;
2242  sub Taxonomy {  sub Taxonomy {
2243          # Get the parameters.          # Get the parameters.
2244          my $self = shift @_;      my ($self, $genome) = @_;
         my ($genome) = @_;  
2245          # Find the specified genome's taxonomy string.          # Find the specified genome's taxonomy string.
2246          my ($list) = $self->GetEntityValues('Genome', $genome, ['Genome(taxonomy)']);          my ($list) = $self->GetEntityValues('Genome', $genome, ['Genome(taxonomy)']);
2247          # Declare the return variable.          # Declare the return variable.
# Line 1765  Line 2281 
2281  =back  =back
2282    
2283  =cut  =cut
2284    #: Return Type $;
2285  sub CrudeDistance {  sub CrudeDistance {
2286          # Get the parameters.          # Get the parameters.
2287          my $self = shift @_;      my ($self, $genome1, $genome2) = @_;
         my ($genome1, $genome2) = @_;  
2288          # Insure that the distance is commutative by sorting the genome IDs.          # Insure that the distance is commutative by sorting the genome IDs.
2289          my ($genomeA, $genomeB);          my ($genomeA, $genomeB);
2290          if ($genome2 < $genome2) {          if ($genome2 < $genome2) {
# Line 1813  Line 2328 
2328  =back  =back
2329    
2330  =cut  =cut
2331    #: Return Type $;
2332  sub RoleName {  sub RoleName {
2333          # Get the parameters.          # Get the parameters.
2334          my $self = shift @_;      my ($self, $roleID) = @_;
         my ($roleID) = @_;  
2335          # Get the specified role's name.          # Get the specified role's name.
2336          my ($retVal) = $self->GetEntityValues('Role', $roleID, ['Role(name)']);          my ($retVal) = $self->GetEntityValues('Role', $roleID, ['Role(name)']);
2337          # Use the ID if the role has no name.          # Use the ID if the role has no name.
# Line 1847  Line 2361 
2361  =back  =back
2362    
2363  =cut  =cut
2364    #: Return Type @;
2365  sub RoleDiagrams {  sub RoleDiagrams {
2366          # Get the parameters.          # Get the parameters.
2367          my $self = shift @_;      my ($self, $roleID) = @_;
         my ($roleID) = @_;  
2368          # Query for the diagrams.          # Query for the diagrams.
2369          my @retVal = $self->GetFlat(['RoleOccursIn'], "RoleOccursIn(from-link) = ?", [$roleID],          my @retVal = $self->GetFlat(['RoleOccursIn'], "RoleOccursIn(from-link) = ?", [$roleID],
2370                                                                  'RoleOccursIn(to-link)');                                                                  'RoleOccursIn(to-link)');
# Line 1859  Line 2372 
2372          return @retVal;          return @retVal;
2373  }  }
2374    
2375    =head3 GetProperties
2376    
2377    C<< my @list = $sprout->GetProperties($fid, $key, $value, $url); >>
2378    
2379    Return a list of the properties with the specified characteristics.
2380    
2381    Properties are arbitrary key-value pairs associated with a feature. (At some point they
2382    will also be associated with genomes.) A property value is represented by a 4-tuple of
2383    the form B<($fid, $key, $value, $url)>. These exactly correspond to the parameter
2384    
2385    =over 4
2386    
2387    =item fid
2388    
2389    ID of the feature possessing the property.
2390    
2391    =item key
2392    
2393    Name or key of the property.
2394    
2395    =item value
2396    
2397    Value of the property.
2398    
2399    =item url
2400    
2401    URL of the document that indicated the property should have this particular value, or an
2402    empty string if no such document exists.
2403    
2404    =back
2405    
2406    The parameters act as a filter for the desired data. Any non-null parameter will
2407    automatically match all the tuples returned. So, specifying just the I<$fid> will
2408    return all the properties of the specified feature; similarly, specifying the I<$key>
2409    and I<$value> parameters will return all the features having the specified property
2410    value.
2411    
2412    A single property key can have many values, representing different ideas about the
2413    feature in question. For example, one paper may declare that a feature C<fig|83333.1.peg.10> is
2414    virulent, and another may declare that it is not virulent. A query about the virulence of
2415    C<fig|83333.1.peg.10> would be coded as
2416    
2417        my @list = $sprout->GetProperties('fig|83333.1.peg.10', 'virulence', '', '');
2418    
2419    Here the I<$value> and I<$url> fields are left blank, indicating that those fields are
2420    not to be filtered. The tuples returned would be
2421    
2422        ('fig|83333.1.peg.10', 'virulence', 'yes', 'http://www.somewhere.edu/first.paper.pdf')
2423        ('fig|83333.1.peg.10', 'virulence', 'no', 'http://www.somewhere.edu/second.paper.pdf')
2424    
2425    =cut
2426    #: Return Type @@;
2427    sub GetProperties {
2428        # Get the parameters.
2429        my ($self, @parms) = @_;
2430        # Declare the return variable.
2431        my @retVal = ();
2432        # Now we need to create a WHERE clause that will get us the data we want. First,
2433        # we create a list of the columns containing the data for each parameter.
2434        my @colNames = ('HasProperty(from-link)', 'Property(property-name)',
2435                        'Property(property-value)', 'HasProperty(evidence)');
2436        # Now we build the WHERE clause and the list of parameter values.
2437        my @where = ();
2438        my @values = ();
2439        for (my $i = 0; $i <= $#colNames; $i++) {
2440            my $parm = $parms[$i];
2441            if (defined $parm && ($parm ne '')) {
2442                push @where, "$colNames[$i] = ?";
2443                push @values, $parm;
2444            }
2445        }
2446        # Format the WHERE clause.
2447        my $filter = (@values > 0 ? (join " AND ", @where) : undef);
2448        # Ask for all the propertie values with the desired characteristics.
2449        my $query = $self->Get(['HasProperty', 'Property'], $filter, \@values);
2450        while (my $valueObject = $query->Fetch()) {
2451            my @tuple = $valueObject->Values(\@colNames);
2452            push @retVal, \@tuple;
2453        }
2454        # Return the result.
2455        return @retVal;
2456    }
2457    
2458  =head3 FeatureProperties  =head3 FeatureProperties
2459    
2460  C<< my @properties = $sprout->FeatureProperties($featureID); >>  C<< my @properties = $sprout->FeatureProperties($featureID); >>
# Line 1885  Line 2481 
2481  =back  =back
2482    
2483  =cut  =cut
2484    #: Return Type @@;
2485  sub FeatureProperties {  sub FeatureProperties {
2486          # Get the parameters.          # Get the parameters.
2487          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
2488          # Get the properties.          # Get the properties.
2489          my @retVal = $self->GetAll(['HasProperty', 'Property'], "HasProperty(from-link) = ?", [$featureID],          my @retVal = $self->GetAll(['HasProperty', 'Property'], "HasProperty(from-link) = ?", [$featureID],
2490                                                          ['Property(property-name)', 'Property(property-value)',                                                          ['Property(property-name)', 'Property(property-value)',
# Line 1917  Line 2512 
2512  =back  =back
2513    
2514  =cut  =cut
2515    #: Return Type $;
2516  sub DiagramName {  sub DiagramName {
2517          # Get the parameters.          # Get the parameters.
2518          my $self = shift @_;      my ($self, $diagramID) = @_;
         my ($diagramID) = @_;  
2519          # Get the specified diagram's name and return it.          # Get the specified diagram's name and return it.
2520          my ($retVal) = $self->GetEntityValues('Diagram', $diagramID, ['Diagram(name)']);          my ($retVal) = $self->GetEntityValues('Diagram', $diagramID, ['Diagram(name)']);
2521          return $retVal;          return $retVal;
# Line 1950  Line 2544 
2544  =back  =back
2545    
2546  =cut  =cut
2547    #: Return Type @;
2548  sub MergedAnnotations {  sub MergedAnnotations {
2549          # Get the parameters.          # Get the parameters.
2550          my $self = shift @_;      my ($self, $list) = @_;
         my ($list) = @_;  
2551          # Create a list to hold the annotation tuples found.          # Create a list to hold the annotation tuples found.
2552          my @tuples = ();          my @tuples = ();
2553          # Loop through the features in the input list.          # Loop through the features in the input list.
# Line 1969  Line 2562 
2562          }          }
2563          # Sort the result list by timestamp.          # Sort the result list by timestamp.
2564          my @retVal = sort { $a->[1] <=> $b->[1] } @tuples;          my @retVal = sort { $a->[1] <=> $b->[1] } @tuples;
2565        # Loop through and make the time stamps friendly.
2566        for my $tuple (@retVal) {
2567            $tuple->[1] = FriendlyTimestamp($tuple->[1]);
2568        }
2569          # Return the sorted list.          # Return the sorted list.
2570          return @retVal;          return @retVal;
2571  }  }
# Line 1995  Line 2592 
2592  =back  =back
2593    
2594  =cut  =cut
2595    #: Return Type @;
2596  sub RoleNeighbors {  sub RoleNeighbors {
2597          # Get the parameters.          # Get the parameters.
2598          my $self = shift @_;      my ($self, $roleID) = @_;
         my ($roleID) = @_;  
2599          # Get all the diagrams containing this role.          # Get all the diagrams containing this role.
2600          my @diagrams = $self->GetFlat(['RoleOccursIn'], "RoleOccursIn(from-link) = ?", [$roleID],          my @diagrams = $self->GetFlat(['RoleOccursIn'], "RoleOccursIn(from-link) = ?", [$roleID],
2601                                                                    'RoleOccursIn(to-link)');                                                                    'RoleOccursIn(to-link)');
# Line 2038  Line 2634 
2634  =back  =back
2635    
2636  =cut  =cut
2637    #: Return Type @;
2638  sub FeatureLinks {  sub FeatureLinks {
2639          # Get the parameters.          # Get the parameters.
2640          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
2641          # Get the feature's links.          # Get the feature's links.
2642          my @retVal = $self->GetEntityValues('Feature', $featureID, ['Feature(link)']);          my @retVal = $self->GetEntityValues('Feature', $featureID, ['Feature(link)']);
2643          # Return the feature's links.          # Return the feature's links.
# Line 2054  Line 2649 
2649  C<< my %subsystems = $sprout->SubsystemsOf($featureID); >>  C<< my %subsystems = $sprout->SubsystemsOf($featureID); >>
2650    
2651  Return a hash describing all the subsystems in which a feature participates. Each subsystem is mapped  Return a hash describing all the subsystems in which a feature participates. Each subsystem is mapped
2652  to the role the feature performs.  to the roles the feature performs.
2653    
2654  =over 4  =over 4
2655    
# Line 2064  Line 2659 
2659    
2660  =item RETURN  =item RETURN
2661    
2662  Returns a hash mapping all the feature's subsystems to the feature's role.  Returns a hash mapping all the feature's subsystems to a list of the feature's roles.
2663    
2664  =back  =back
2665    
2666  =cut  =cut
2667    #: Return Type %@;
2668  sub SubsystemsOf {  sub SubsystemsOf {
2669          # Get the parameters.          # Get the parameters.
2670          my $self = shift @_;      my ($self, $featureID) = @_;
2671          my ($featureID) = @_;      # Get the subsystem list.
         # Use the SSCell to connect features to subsystems.  
2672          my @subsystems = $self->GetAll(['ContainsFeature', 'HasSSCell', 'IsRoleOf'],          my @subsystems = $self->GetAll(['ContainsFeature', 'HasSSCell', 'IsRoleOf'],
2673                                                                          "ContainsFeature(to-link) = ?", [$featureID],                                                                          "ContainsFeature(to-link) = ?", [$featureID],
2674                                                                          ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);                                                                          ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);
2675          # Create the return value.          # Create the return value.
2676          my %retVal = ();          my %retVal = ();
2677        # Build a hash to weed out duplicates. Sometimes the same PEG and role appears
2678        # in two spreadsheet cells.
2679        my %dupHash = ();
2680          # Loop through the results, adding them to the hash.          # Loop through the results, adding them to the hash.
2681          for my $record (@subsystems) {          for my $record (@subsystems) {
2682                  $retVal{$record->[0]} = $record->[1];          # Get this subsystem and role.
2683            my ($subsys, $role) = @{$record};
2684            # Insure it's the first time for both.
2685            my $dupKey = "$subsys\n$role";
2686            if (! exists $dupHash{"$subsys\n$role"}) {
2687                $dupHash{$dupKey} = 1;
2688                push @{$retVal{$subsys}}, $role;
2689            }
2690          }          }
2691          # Return the hash.          # Return the hash.
2692          return %retVal;          return %retVal;
2693  }  }
2694    
2695    =head3 SubsystemList
2696    
2697    C<< my @subsystems = $sprout->SubsystemList($featureID); >>
2698    
2699    Return a list containing the names of the subsystems in which the specified
2700    feature participates. Unlike L</SubsystemsOf>, this method only returns the
2701    subsystem names, not the roles.
2702    
2703    =over 4
2704    
2705    =item featureID
2706    
2707    ID of the feature whose subsystem names are desired.
2708    
2709    =item RETURN
2710    
2711    Returns a list of the names of the subsystems in which the feature participates.
2712    
2713    =back
2714    
2715    =cut
2716    #: Return Type @;
2717    sub SubsystemList {
2718        # Get the parameters.
2719        my ($self, $featureID) = @_;
2720        # Get the list of names.
2721        my @retVal = $self->GetFlat(['ContainsFeature', 'HasSSCell'], "ContainsFeature(to-link) = ?",
2722                                    [$featureID], 'HasSSCell(from-link)');
2723        # Return the result.
2724        return @retVal;
2725    }
2726    
2727  =head3 RelatedFeatures  =head3 RelatedFeatures
2728    
2729  C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>  C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>
# Line 2118  Line 2754 
2754  =back  =back
2755    
2756  =cut  =cut
2757    #: Return Type @;
2758  sub RelatedFeatures {  sub RelatedFeatures {
2759          # Get the parameters.          # Get the parameters.
2760          my $self = shift @_;      my ($self, $featureID, $function, $userID) = @_;
         my ($featureID, $function, $userID) = @_;  
2761          # Get a list of the features that are BBHs of the incoming feature.          # Get a list of the features that are BBHs of the incoming feature.
2762          my @bbhFeatures = $self->GetFlat(['IsBidirectionalBestHitOf'],          my @bbhFeatures = $self->GetFlat(['IsBidirectionalBestHitOf'],
2763                                                                           "IsBidirectionalBestHitOf(from-link) = ?", [$featureID],                                                                           "IsBidirectionalBestHitOf(from-link) = ?", [$featureID],
# Line 2167  Line 2802 
2802  =back  =back
2803    
2804  =cut  =cut
2805    #: Return Type @;
2806  sub TaxonomySort {  sub TaxonomySort {
2807          # Get the parameters.          # Get the parameters.
2808          my $self = shift @_;      my ($self, $featureIDs) = @_;
         my ($featureIDs) = @_;  
2809          # Create the working hash table.          # Create the working hash table.
2810          my %hashBuffer = ();          my %hashBuffer = ();
2811          # Loop through the features.          # Loop through the features.
# Line 2180  Line 2814 
2814                  my ($taxonomy) = $self->GetFlat(['IsLocatedIn', 'HasContig', 'Genome'], "IsLocatedIn(from-link) = ?",                  my ($taxonomy) = $self->GetFlat(['IsLocatedIn', 'HasContig', 'Genome'], "IsLocatedIn(from-link) = ?",
2815                                                                                  [$fid], 'Genome(taxonomy)');                                                                                  [$fid], 'Genome(taxonomy)');
2816                  # Add this feature to the hash buffer.                  # Add this feature to the hash buffer.
2817                  if (exists $hashBuffer{$taxonomy}) {          Tracer::AddToListMap(\%hashBuffer, $taxonomy, $fid);
                         push @{$hashBuffer{$taxonomy}}, $fid;  
                 } else {  
                         $hashBuffer{$taxonomy} = [$fid];  
                 }  
2818          }          }
2819          # Sort the keys and get the elements.          # Sort the keys and get the elements.
2820          my @retVal = ();          my @retVal = ();
# Line 2250  Line 2880 
2880  =back  =back
2881    
2882  =cut  =cut
2883    #: Return Type @@;
2884  sub GetAll {  sub GetAll {
2885          # Get the parameters.          # Get the parameters.
2886          my $self = shift @_;      my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
2887          my ($objectNames, $filterClause, $parameterList, $fields, $count) = @_;      # Call the ERDB method.
2888          # Create the query.      my @retVal = $self->{_erdb}->GetAll($objectNames, $filterClause, $parameterList,
2889          my $query = $self->Get($objectNames, $filterClause, $parameterList);                                          $fields, $count);
         # Set up a counter of the number of records read.  
         my $fetched = 0;  
         # Insure the counter has a value.  
         if (!defined $count) {  
                 $count = 0;  
         }  
         # Loop through the records returned, extracting the fields. Note that if the  
         # counter is non-zero, we stop when the number of records read hits the count.  
         my @retVal = ();  
         while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {  
                 my @rowData = $row->Values($fields);  
                 push @retVal, \@rowData;  
                 $fetched++;  
         }  
2890          # Return the resulting list.          # Return the resulting list.
2891          return @retVal;          return @retVal;
2892  }  }
# Line 2312  Line 2928 
2928  =back  =back
2929    
2930  =cut  =cut
2931    #: Return Type @;
2932  sub GetFlat {  sub GetFlat {
2933          # Get the parameters.          # Get the parameters.
2934          my $self = shift @_;      my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
         my ($objectNames, $filterClause, $parameterList, $field) = @_;  
2935          # Construct the query.          # Construct the query.
2936          my $query = $self->Get($objectNames, $filterClause, $parameterList);          my $query = $self->Get($objectNames, $filterClause, $parameterList);
2937          # Create the result list.          # Create the result list.
# Line 2423  Line 3038 
3038  to load the entire database.  to load the entire database.
3039    
3040  =cut  =cut
3041    #: Return Type @;
3042  sub LoadInfo {  sub LoadInfo {
3043          # Get the parameters.          # Get the parameters.
3044          my $self = shift @_;      my ($self) = @_;
3045          # Create the return list, priming it with the name of the data directory.          # Create the return list, priming it with the name of the data directory.
3046          my @retVal = ($self->{_options}->{dataDir});          my @retVal = ($self->{_options}->{dataDir});
3047          # Concatenate the table names.          # Concatenate the table names.
# Line 2460  Line 3075 
3075  =back  =back
3076    
3077  =cut  =cut
3078    #: Return Type %;
3079  sub LowBBHs {  sub LowBBHs {
3080          # Get the parsameters.          # Get the parsameters.
3081          my $self = shift @_;      my ($self, $featureID, $cutoff) = @_;
         my ($featureID, $cutoff) = @_;  
3082          # Create the return hash.          # Create the return hash.
3083          my %retVal = ();          my %retVal = ();
3084          # Create a query to get the desired BBHs.          # Create a query to get the desired BBHs.
# Line 2480  Line 3094 
3094          return %retVal;          return %retVal;
3095  }  }
3096    
3097    =head3 GetGroups
3098    
3099    C<< my %groups = $sprout->GetGroups(\@groupList); >>
3100    
3101    Return a hash mapping each group to the IDs of the genomes in the group.
3102    A list of groups may be specified, in which case only those groups will be
3103    shown. Alternatively, if no parameter is supplied, all groups will be
3104    included. Genomes that are not in any group are omitted.
3105    
3106    =cut
3107    #: Return Type %@;
3108    sub GetGroups {
3109        # Get the parameters.
3110        my ($self, $groupList) = @_;
3111        # Declare the return value.
3112        my %retVal = ();
3113        # Determine whether we are getting all the groups or just some.
3114        if (defined $groupList) {
3115            # Here we have a group list. Loop through them individually,
3116            # getting a list of the relevant genomes.
3117            for my $group (@{$groupList}) {
3118                my @genomeIDs = $self->GetFlat(['Genome'], "Genome(group-name) = ?",
3119                    [$group], "Genome(id)");
3120                $retVal{$group} = \@genomeIDs;
3121            }
3122        } else {
3123            # Here we need all of the groups. In this case, we run through all
3124            # of the genome records, putting each one found into the appropriate
3125            # group. Note that we use a filter clause to insure that only genomes
3126            # in groups are included in the return set.
3127            my @genomes = $self->GetAll(['Genome'], "Genome(group-name) > ' '", [],
3128                                        ['Genome(id)', 'Genome(group-name)']);
3129            # Loop through the genomes found.
3130            for my $genome (@genomes) {
3131                # Pop this genome's ID off the current list.
3132                my @groups = @{$genome};
3133                my $genomeID = shift @groups;
3134                # Loop through the groups, adding the genome ID to each group's
3135                # list.
3136                for my $group (@groups) {
3137                    Tracer::AddToListMap(\%retVal, $group, $genomeID);
3138                }
3139            }
3140        }
3141        # Return the hash we just built.
3142        return %retVal;
3143    }
3144    
3145    =head3 MyGenomes
3146    
3147    C<< my @genomes = Sprout::MyGenomes($dataDir); >>
3148    
3149    Return a list of the genomes to be included in the Sprout.
3150    
3151    This method is provided for use during the Sprout load. It presumes the Genome load file has
3152    already been created. (It will be in the Sprout data directory and called either C<Genome>
3153    or C<Genome.dtx>.) Essentially, it reads in the Genome load file and strips out the genome
3154    IDs.
3155    
3156    =over 4
3157    
3158    =item dataDir
3159    
3160    Directory containing the Sprout load files.
3161    
3162    =back
3163    
3164    =cut
3165    #: Return Type @;
3166    sub MyGenomes {
3167        # Get the parameters.
3168        my ($dataDir) = @_;
3169        # Compute the genome file name.
3170        my $genomeFileName = LoadFileName($dataDir, "Genome");
3171        # Extract the genome IDs from the files.
3172        my @retVal = map { $_ =~ /^(\S+)/; $1 } Tracer::GetFile($genomeFileName);
3173        # Return the result.
3174        return @retVal;
3175    }
3176    
3177    =head3 LoadFileName
3178    
3179    C<< my $fileName = Sprout::LoadFileName($dataDir, $tableName); >>
3180    
3181    Return the name of the load file for the specified table in the specified data
3182    directory.
3183    
3184    =over 4
3185    
3186    =item dataDir
3187    
3188    Directory containing the Sprout load files.
3189    
3190    =item tableName
3191    
3192    Name of the table whose load file is desired.
3193    
3194    =item RETURN
3195    
3196    Returns the name of the file containing the load data for the specified table, or
3197    C<undef> if no load file is present.
3198    
3199    =back
3200    
3201    =cut
3202    #: Return Type $;
3203    sub LoadFileName {
3204        # Get the parameters.
3205        my ($dataDir, $tableName) = @_;
3206        # Declare the return variable.
3207        my $retVal;
3208        # Check for the various file names.
3209        if (-e "$dataDir/$tableName") {
3210            $retVal = "$dataDir/$tableName";
3211        } elsif (-e "$dataDir/$tableName.dtx") {
3212            $retVal = "$dataDir/$tableName.dtx";
3213        }
3214        # Return the result.
3215        return $retVal;
3216    }
3217    
3218  =head2 Internal Utility Methods  =head2 Internal Utility Methods
3219    
3220  =head3 ParseAssignment  =head3 ParseAssignment
3221    
3222  Parse annotation text to determine whether or not it is a functional assignment. If it is,  Parse annotation text to determine whether or not it is a functional assignment. If it is,
3223  the user and function text will be returned as a 2-element list. If it isn't, an empty list  the user, function text, and assigning user will be returned as a 3-element list. If it
3224  will be returned.  isn't, an empty list will be returned.
3225    
3226    A functional assignment is always of the form
3227    
3228        I<XXXX>C<\nset >I<YYYY>C< function to\n>I<ZZZZZ>
3229    
3230    where I<XXXX> is the B<assigning user>, I<YYYY> is the B<user>, and I<ZZZZ> is the
3231    actual functional role. In most cases, the user and the assigning user will be the
3232    same, but that is not always the case.
3233    
3234  This is a static method.  This is a static method.
3235    
# Line 2505  Line 3248 
3248    
3249  =cut  =cut
3250    
3251  sub ParseAssignment {  sub _ParseAssignment {
3252          # Get the parameters.          # Get the parameters.
3253          my ($text) = @_;          my ($text) = @_;
3254          # Declare the return value.          # Declare the return value.
3255          my @retVal = ();          my @retVal = ();
3256          # Check to see if this is a functional assignment.          # Check to see if this is a functional assignment.
3257          my ($user, $type, $function) = split(/\n/, $text);      my ($type, $function) = split(/\n/, $text);
3258          if ($type =~ m/^set $user function to$/i) {      if ($type =~ m/^set ([^ ]+) function to$/i) {
3259                  # Here it is, so we return the user name and function text.          # Here it is, so we return the user name (which is in $1), the functional role text,
3260                  @retVal = ($user, $function);          # and the assigning user.
3261            @retVal = ($1, $function);
3262          }          }
3263          # Return the result list.          # Return the result list.
3264          return @retVal;          return @retVal;
3265  }  }
3266    
3267    =head3 FriendlyTimestamp
3268    
3269    Convert a time number to a user-friendly time stamp for display.
3270    
3271    This is a static method.
3272    
3273    =over 4
3274    
3275    =item timeValue
3276    
3277    Numeric time value.
3278    
3279    =item RETURN
3280    
3281    Returns a string containing the same time in user-readable format.
3282    
3283    =back
3284    
3285    =cut
3286    
3287    sub FriendlyTimestamp {
3288        my ($timeValue) = @_;
3289        my $retVal = localtime($timeValue);
3290        return $retVal;
3291    }
3292    
3293    =head3 AddProperty
3294    
3295    C<< my  = $sprout->AddProperty($featureID, $key, $value, $url); >>
3296    
3297    Add a new attribute value (Property) to a feature. In the SEED system, attributes can
3298    be added to almost any object. In Sprout, they can only be added to features. In
3299    Sprout, attributes are implemented using I<properties>. A property represents a key/value
3300    pair. If the particular key/value pair coming in is not already in the database, a new
3301    B<Property> record is created to hold it.
3302    
3303    =over 4
3304    
3305    =item peg
3306    
3307    ID of the feature to which the attribute is to be replied.
3308    
3309    =item key
3310    
3311    Name of the attribute (key).
3312    
3313    =item value
3314    
3315    Value of the attribute.
3316    
3317    =item url
3318    
3319    URL or text citation from which the property was obtained.
3320    
3321    =back
3322    
3323    =cut
3324    #: Return Type ;
3325    sub AddProperty {
3326        # Get the parameters.
3327        my ($self, $featureID, $key, $value, $url) = @_;
3328        # Declare the variable to hold the desired property ID.
3329        my $propID;
3330        # Attempt to find a property record for this key/value pair.
3331        my @properties = $self->GetFlat(['Property'],
3332                                       "Property(property-name) = ? AND Property(property-value) = ?",
3333                                       [$key, $value], 'Property(id)');
3334        if (@properties) {
3335            # Here the property is already in the database. We save its ID.
3336            $propID = $properties[0];
3337            # Here the property value does not exist. We need to generate an ID. It will be set
3338            # to a number one greater than the maximum value in the database. This call to
3339            # GetAll will stop after one record.
3340            my @maxProperty = $self->GetAll(['Property'], "ORDER BY Property(id) DESC", [], ['Property(id)'],
3341                                            1);
3342            $propID = $maxProperty[0]->[0] + 1;
3343            # Insert the new property value.
3344            $self->Insert('Property', { 'property-name' => $key, 'property-value' => $value, id => $propID });
3345        }
3346        # Now we connect the incoming feature to the property.
3347        $self->Insert('HasProperty', { 'from-link' => $featureID, 'to-link' => $propID, evidence => $url });
3348    }
3349    
3350    
3351    
3352  1;  1;

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