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revision 1.2, Sun Jan 23 22:31:29 2005 UTC revision 1.48, Thu Oct 20 12:33:00 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 ($actualUser, $function) = _ParseAssignment($user, $text);
1180                  if ($user) {          if ($actualUser && ! exists $retVal{$actualUser}) {
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                $retVal{$actualUser} = $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 = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1263                                   "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1264                                   [$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, $user) = $annotation->Values(['Annotation(annotation)',
1270                  # Check to see if this is a functional assignment for the desired user.                                                       'Annotation(time)', 'MadeAnnotation(from-link)']);
1271                  my ($user, $type, $function) = split(/\n/, $text);              # Check to see if this is a functional assignment for a trusted user.
1272                  if ($type =~ m/^set $userID function to$/i) {              my ($actualUser, $function) = _ParseAssignment($user, $text);
1273                          # Here it is, so we check the time and save the assignment value.              if ($actualUser) {
1274                          if ($time > $timeSelected) {                  # Here it is a functional assignment. Check the time and the user
1275                    # name. The time must be recent and the user must be trusted.
1276                    if ((exists $trusteeTable{$user}) && ($time > $timeSelected)) {
1277                                  $retVal = $function;                                  $retVal = $function;
1278                                  $timeSelected = $time;                                  $timeSelected = $time;
1279                          }                          }
1280                  }                  }
1281          }          }
1282        } else {
1283            # Here we have a non-FIG feature ID. In this case the user ID does not
1284            # matter. We simply get the information from the External Alias Function
1285            # table.
1286            ($retVal) = $self->GetEntityValues('ExternalAliasFunc', $featureID, ['ExternalAliasFunc(func)']);
1287        }
1288          # Return the assignment found.          # Return the assignment found.
1289          return $retVal;          return $retVal;
1290  }  }
1291    
1292    =head3 FunctionsOf
1293    
1294    C<< my @functionList = $sprout->FunctionOf($featureID, $userID); >>
1295    
1296    Return the functional assignments of a particular feature.
1297    
1298    The functional assignment is handled differently depending on the type of feature. If
1299    the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional
1300    assignment is a type of annotation. The format of an assignment is described in
1301    L</ParseAssignment>. Its worth noting that we cannot filter on the content of the
1302    annotation itself because it's a text field; however, this is not a big problem because
1303    most features only have a small number of annotations.
1304    
1305    If the feature is B<not> identified by a FIG ID, then the functional assignment
1306    information is taken from the B<ExternalAliasFunc> table. If the table does
1307    not contain an entry for the feature, an empty list is returned.
1308    
1309    =over 4
1310    
1311    =item featureID
1312    
1313    ID of the feature whose functional assignments are desired.
1314    
1315    =item RETURN
1316    
1317    Returns a list of 2-tuples, each consisting of a user ID and the text of an assignment by
1318    that user.
1319    
1320    =back
1321    
1322    =cut
1323    #: Return Type @@;
1324    sub FunctionsOf {
1325        # Get the parameters.
1326        my ($self, $featureID) = @_;
1327        # Declare the return value.
1328        my @retVal = ();
1329        # Determine the ID type.
1330        if ($featureID =~ m/^fig\|/) {
1331            # Here we have a FIG feature ID. We must build the list of trusted
1332            # users.
1333            my %trusteeTable = ();
1334            # Build a query for all of the feature's annotations, sorted by date.
1335            my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1336                                   "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1337                                   [$featureID]);
1338            my $timeSelected = 0;
1339            # Loop until we run out of annotations.
1340            while (my $annotation = $query->Fetch()) {
1341                # Get the annotation text.
1342                my ($text, $time, $user) = $annotation->Values(['Annotation(annotation)',
1343                                                                'Annotation(time)',
1344                                                                'MadeAnnotation(user)']);
1345                # Check to see if this is a functional assignment for a trusted user.
1346                my ($actualUser, $function) = _ParseAssignment($user, $text);
1347                if ($actualUser) {
1348                    # Here it is a functional assignment.
1349                    push @retVal, [$actualUser, $function];
1350                }
1351            }
1352        } else {
1353            # Here we have a non-FIG feature ID. In this case the user ID does not
1354            # matter. We simply get the information from the External Alias Function
1355            # table.
1356            my @assignments = $self->GetEntityValues('ExternalAliasFunc', $featureID,
1357                                                     ['ExternalAliasFunc(func)']);
1358            push @retVal, map { ['master', $_] } @assignments;
1359        }
1360        # Return the assignments found.
1361        return @retVal;
1362    }
1363    
1364  =head3 BBHList  =head3 BBHList
1365    
1366  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>
# Line 1120  Line 1380 
1380    
1381  =item RETURN  =item RETURN
1382    
1383  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
1384  their best hits.  on the target genome.
1385    
1386  =back  =back
1387    
1388  =cut  =cut
1389    #: Return Type %;
1390  sub BBHList {  sub BBHList {
1391          # Get the parameters.          # Get the parameters.
1392          my $self = shift @_;      my ($self, $genomeID, $featureList) = @_;
         my ($genomeID, $featureList) = @_;  
1393          # Create the return structure.          # Create the return structure.
1394          my %retVal = ();          my %retVal = ();
1395          # Loop through the incoming features.          # Loop through the incoming features.
# Line 1139  Line 1398 
1398                  my $query = $self->Get(['IsBidirectionalBestHitOf'],                  my $query = $self->Get(['IsBidirectionalBestHitOf'],
1399                                                             "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",                                                             "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",
1400                                                             [$featureID, $genomeID]);                                                             [$featureID, $genomeID]);
1401                  # Look for the best hit.          # Peel off the BBHs found.
1402                  my $bbh = $query->Fetch;          my @found = ();
1403                  if ($bbh) {          while (my $bbh = $query->Fetch) {
1404                          my ($targetFeature) = $bbh->Value('IsBidirectionalBestHitOf(to-link)');              push @found, $bbh->Value('IsBidirectionalBestHitOf(to-link)');
                         $retVal{$featureID} = $targetFeature;  
1405                  }                  }
1406            $retVal{$featureID} = \@found;
1407          }          }
1408          # Return the mapping.          # Return the mapping.
1409          return \%retVal;          return \%retVal;
1410  }  }
1411    
1412    =head3 SimList
1413    
1414    C<< my %similarities = $sprout->SimList($featureID, $count); >>
1415    
1416    Return a list of the similarities to the specified feature.
1417    
1418    Sprout does not support real similarities, so this method just returns the bidirectional
1419    best hits.
1420    
1421    =over 4
1422    
1423    =item featureID
1424    
1425    ID of the feature whose similarities are desired.
1426    
1427    =item count
1428    
1429    Maximum number of similar features to be returned, or C<0> to return them all.
1430    
1431    =back
1432    
1433    =cut
1434    #: Return Type %;
1435    sub SimList {
1436        # Get the parameters.
1437        my ($self, $featureID, $count) = @_;
1438        # Ask for the best hits.
1439        my @lists = $self->GetAll(['IsBidirectionalBestHitOf'],
1440                                  "IsBidirectionalBestHitOf(from-link) = ? ORDER BY IsBidirectionalBestHitOf(score) DESC",
1441                                  [$featureID], ['IsBidirectionalBestHitOf(to-link)', 'IsBidirectionalBestHitOf(score)'],
1442                                  $count);
1443        # Create the return value.
1444        my %retVal = ();
1445        for my $tuple (@lists) {
1446            $retVal{$tuple->[0]} = $tuple->[1];
1447        }
1448        # Return the result.
1449        return %retVal;
1450    }
1451    
1452    
1453    
1454    =head3 IsComplete
1455    
1456    C<< my $flag = $sprout->IsComplete($genomeID); >>
1457    
1458    Return TRUE if the specified genome is complete, else FALSE.
1459    
1460    =over 4
1461    
1462    =item genomeID
1463    
1464    ID of the genome whose completeness status is desired.
1465    
1466    =item RETURN
1467    
1468    Returns TRUE if the genome is complete, FALSE if it is incomplete, and C<undef> if it is
1469    not found.
1470    
1471    =back
1472    
1473    =cut
1474    #: Return Type $;
1475    sub IsComplete {
1476        # Get the parameters.
1477        my ($self, $genomeID) = @_;
1478        # Declare the return variable.
1479        my $retVal;
1480        # Get the genome's data.
1481        my $genomeData = $self->GetEntity('Genome', $genomeID);
1482        if ($genomeData) {
1483            # The genome exists, so get the completeness flag.
1484            ($retVal) = $genomeData->Value('complete');
1485        }
1486        # Return the result.
1487        return $retVal;
1488    }
1489    
1490  =head3 FeatureAliases  =head3 FeatureAliases
1491    
1492  C<< my @aliasList = $sprout->FeatureAliases($featureID); >>  C<< my @aliasList = $sprout->FeatureAliases($featureID); >>
# Line 1170  Line 1507 
1507  =back  =back
1508    
1509  =cut  =cut
1510    #: Return Type @;
1511  sub FeatureAliases {  sub FeatureAliases {
1512          # Get the parameters.          # Get the parameters.
1513          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
1514          # Get the desired feature's aliases          # Get the desired feature's aliases
1515          my @retVal = $self->GetEntityValues('Feature', $featureID, ['Feature(alias)']);          my @retVal = $self->GetEntityValues('Feature', $featureID, ['Feature(alias)']);
1516          # Return the result.          # Return the result.
# Line 1201  Line 1537 
1537  =back  =back
1538    
1539  =cut  =cut
1540    #: Return Type $;
1541  sub GenomeOf {  sub GenomeOf {
1542          # Get the parameters.          # Get the parameters.
1543          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
1544          # Create a query to find the genome associated with the feature.          # Create a query to find the genome associated with the feature.
1545          my $query = $self->Get(['IsLocatedIn', 'HasContig'], "IsLocatedIn(from-link) = ?", [$featureID]);          my $query = $self->Get(['IsLocatedIn', 'HasContig'], "IsLocatedIn(from-link) = ?", [$featureID]);
1546          # Declare the return value.          # Declare the return value.
# Line 1238  Line 1573 
1573  =back  =back
1574    
1575  =cut  =cut
1576    #: Return Type %;
1577  sub CoupledFeatures {  sub CoupledFeatures {
1578          # Get the parameters.          # Get the parameters.
1579          my $self = shift @_;      my ($self, $featureID) = @_;
1580          my ($featureID) = @_;      # Create a query to retrieve the functionally-coupled features.
1581          # Create a query to retrieve the functionally-coupled features. Note that we depend on the      my $query = $self->Get(['ParticipatesInCoupling', 'Coupling'],
1582          # fact that the functional coupling is physically paired. If (A,B) is in the database, then                             "ParticipatesInCoupling(from-link) = ?", [$featureID]);
         # (B,A) will also be found.  
         my $query = $self->Get(['IsClusteredOnChromosomeWith'],  
                                                    "IsClusteredOnChromosomeWith(from-link) = ?", [$featureID]);  
1583          # 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.
1584          my $found = 0;          my $found = 0;
1585          # Create the return hash.          # Create the return hash.
1586          my %retVal = ();          my %retVal = ();
1587          # Retrieve the relationship records and store them in the hash.          # Retrieve the relationship records and store them in the hash.
1588          while (my $clustering = $query->Fetch()) {          while (my $clustering = $query->Fetch()) {
1589                  my ($otherFeatureID, $score) = $clustering->Values(['IsClusteredOnChromosomeWith(to-link)',          # Get the ID and score of the coupling.
1590                                                                      'IsClusteredOnChromosomeWith(score)']);          my ($couplingID, $score) = $clustering->Values(['Coupling(id)',
1591                                                            'Coupling(score)']);
1592            # The coupling ID contains the two feature IDs separated by a space. We use
1593            # this information to find the ID of the other feature.
1594            my ($fid1, $fid2) = split / /, $couplingID;
1595            my $otherFeatureID = ($featureID eq $fid1 ? $fid2 : $fid1);
1596            # Attach the other feature's score to its ID.
1597                  $retVal{$otherFeatureID} = $score;                  $retVal{$otherFeatureID} = $score;
1598                  $found = 1;                  $found = 1;
1599          }          }
# Line 1268  Line 1606 
1606          return %retVal;          return %retVal;
1607  }  }
1608    
1609    =head3 CouplingEvidence
1610    
1611    C<< my @evidence = $sprout->CouplingEvidence($peg1, $peg2); >>
1612    
1613    Return the evidence for a functional coupling.
1614    
1615    A pair of features is considered evidence of a coupling between two other
1616    features if they occur close together on a contig and both are similar to
1617    the coupled features. So, if B<A1> and B<A2> are close together on a contig,
1618    B<B1> and B<B2> are considered evidence for the coupling if (1) B<B1> and
1619    B<B2> are close together, (2) B<B1> is similar to B<A1>, and (3) B<B2> is
1620    similar to B<A2>.
1621    
1622    The score of a coupling is determined by the number of pieces of evidence
1623    that are considered I<representative>. If several evidence items belong to
1624    a group of genomes that are close to each other, only one of those items
1625    is considered representative. The other evidence items are presumed to be
1626    there because of the relationship between the genomes rather than because
1627    the two proteins generated by the features have a related functionality.
1628    
1629    Each evidence item is returned as a three-tuple in the form C<[>I<$peg1a>C<,>
1630    I<$peg2a>C<,> I<$rep>C<]>, where I<$peg1a> is similar to I<$peg1>, I<$peg2a>
1631    is similar to I<$peg2>, and I<$rep> is TRUE if the evidence is representative
1632    and FALSE otherwise.
1633    
1634    =over 4
1635    
1636    =item peg1
1637    
1638    ID of the feature of interest.
1639    
1640    =item peg2
1641    
1642    ID of a feature functionally coupled to the feature of interest.
1643    
1644    =item RETURN
1645    
1646    Returns a list of 3-tuples. Each tuple consists of a feature similar to the feature
1647    of interest, a feature similar to the functionally coupled feature, and a flag
1648    that is TRUE for a representative piece of evidence and FALSE otherwise.
1649    
1650    =back
1651    
1652    =cut
1653    #: Return Type @@;
1654    sub CouplingEvidence {
1655        # Get the parameters.
1656        my ($self, $peg1, $peg2) = @_;
1657        # Declare the return variable.
1658        my @retVal = ();
1659        # Our first task is to find out the nature of the coupling: whether or not
1660        # it exists, its score, and whether the features are stored in the same
1661        # order as the ones coming in.
1662        my ($couplingID, $inverted, $score) = $self->GetCoupling($peg1, $peg2);
1663        # Only proceed if a coupling exists.
1664        if ($couplingID) {
1665            # Determine the ordering to place on the evidence items. If we're
1666            # inverted, we want to see feature 2 before feature 1 (descending); otherwise,
1667            # we want feature 1 before feature 2 (normal).
1668            Trace("Coupling evidence for ($peg1, $peg2) with inversion flag $inverted.") if T(Coupling => 4);
1669            my $ordering = ($inverted ? "DESC" : "");
1670            # Get the coupling evidence.
1671            my @evidenceList = $self->GetAll(['IsEvidencedBy', 'PCH', 'UsesAsEvidence'],
1672                                              "IsEvidencedBy(from-link) = ? ORDER BY PCH(id), UsesAsEvidence(pos) $ordering",
1673                                              [$couplingID],
1674                                              ['PCH(used)', 'UsesAsEvidence(to-link)']);
1675            # Loop through the evidence items. Each piece of evidence is represented by two
1676            # positions in the evidence list, one for each feature on the other side of the
1677            # evidence link. If at some point we want to generalize to couplings with
1678            # more than two positions, this section of code will need to be re-done.
1679            while (@evidenceList > 0) {
1680                my $peg1Data = shift @evidenceList;
1681                my $peg2Data = shift @evidenceList;
1682                Trace("Peg 1 is " . $peg1Data->[1] . " and Peg 2 is " . $peg2Data->[1] . ".") if T(Coupling => 4);
1683                push @retVal, [$peg1Data->[1], $peg2Data->[1], $peg1Data->[0]];
1684            }
1685            Trace("Last index in evidence result is is $#retVal.") if T(Coupling => 4);
1686        }
1687        # Return the result.
1688        return @retVal;
1689    }
1690    
1691    =head3 GetCoupling
1692    
1693    C<< my ($couplingID, $inverted, $score) = $sprout->GetCoupling($peg1, $peg2); >>
1694    
1695    Return the coupling (if any) for the specified pair of PEGs. If a coupling
1696    exists, we return the coupling ID along with an indicator of whether the
1697    coupling is stored as C<(>I<$peg1>C<, >I<$peg2>C<)> or C<(>I<$peg2>C<, >I<$peg1>C<)>.
1698    In the second case, we say the coupling is I<inverted>. The importance of an
1699    inverted coupling is that the PEGs in the evidence will appear in reverse order.
1700    
1701    =over 4
1702    
1703    =item peg1
1704    
1705    ID of the feature of interest.
1706    
1707    =item peg2
1708    
1709    ID of the potentially coupled feature.
1710    
1711    =item RETURN
1712    
1713    Returns a three-element list. The first element contains the database ID of
1714    the coupling. The second element is FALSE if the coupling is stored in the
1715    database in the caller specified order and TRUE if it is stored in the
1716    inverted order. The third element is the coupling's score. If the coupling
1717    does not exist, all three list elements will be C<undef>.
1718    
1719    =back
1720    
1721    =cut
1722    #: Return Type $%@;
1723    sub GetCoupling {
1724        # Get the parameters.
1725        my ($self, $peg1, $peg2) = @_;
1726        # Declare the return values. We'll start with the coupling ID and undefine the
1727        # flag and score until we have more information.
1728        my ($retVal, $inverted, $score) = (CouplingID($peg1, $peg2), undef, undef);
1729        # Find the coupling data.
1730        my @pegs = $self->GetAll(['Coupling', 'ParticipatesInCoupling'],
1731                                     "Coupling(id) = ? ORDER BY ParticipatesInCoupling(pos)",
1732                                     [$retVal], ["ParticipatesInCoupling(from-link)", "Coupling(score)"]);
1733        # Check to see if we found anything.
1734        if (!@pegs) {
1735            Trace("No coupling found.") if T(Coupling => 4);
1736            # No coupling, so undefine the return value.
1737            $retVal = undef;
1738        } else {
1739            # We have a coupling! Get the score and check for inversion.
1740            $score = $pegs[0]->[1];
1741            my $firstFound = $pegs[0]->[0];
1742            $inverted = ($firstFound ne $peg1);
1743            Trace("Coupling score is $score. First peg is $firstFound, peg 1 is $peg1.") if T(Coupling => 4);
1744        }
1745        # Return the result.
1746        return ($retVal, $inverted, $score);
1747    }
1748    
1749    =head3 CouplingID
1750    
1751    C<< my $couplingID = Sprout::CouplingID($peg1, $peg2); >>
1752    
1753    Return the coupling ID for a pair of feature IDs.
1754    
1755    The coupling ID is currently computed by joining the feature IDs in
1756    sorted order with a space. Client modules (that is, modules which
1757    use Sprout) should not, however, count on this always being the
1758    case. This method provides a way for abstracting the concept of a
1759    coupling ID. All that we know for sure about it is that it can be
1760    generated easily from the feature IDs and the order of the IDs
1761    in the parameter list does not matter (i.e. C<CouplingID("a1", "b1")>
1762    will have the same value as C<CouplingID("b1", "a1")>.
1763    
1764    =over 4
1765    
1766    =item peg1
1767    
1768    First feature of interest.
1769    
1770    =item peg2
1771    
1772    Second feature of interest.
1773    
1774    =item RETURN
1775    
1776    Returns the ID that would be used to represent a functional coupling of
1777    the two specified PEGs.
1778    
1779    =back
1780    
1781    =cut
1782    #: Return Type $;
1783    sub CouplingID {
1784        return join " ", sort @_;
1785    }
1786    
1787  =head3 GetEntityTypes  =head3 GetEntityTypes
1788    
1789  C<< my @entityList = $sprout->GetEntityTypes(); >>  C<< my @entityList = $sprout->GetEntityTypes(); >>
# Line 1275  Line 1791 
1791  Return the list of supported entity types.  Return the list of supported entity types.
1792    
1793  =cut  =cut
1794    #: Return Type @;
1795  sub GetEntityTypes {  sub GetEntityTypes {
1796          # Get the parameters.          # Get the parameters.
1797          my $self = shift @_;      my ($self) = @_;
1798          # Get the underlying database object.          # Get the underlying database object.
1799          my $erdb = $self->{_erdb};          my $erdb = $self->{_erdb};
1800          # Get its entity type list.          # Get its entity type list.
# Line 1310  Line 1826 
1826  =back  =back
1827    
1828  =cut  =cut
1829    #: Return Type %;
1830  sub ReadFasta {  sub ReadFasta {
1831          # Get the parameters.          # Get the parameters.
1832          my ($fileName, $prefix) = @_;          my ($fileName, $prefix) = @_;
# Line 1329  Line 1845 
1845                  if ($line =~ m/^>\s*(.+?)(\s|\n)/) {                  if ($line =~ m/^>\s*(.+?)(\s|\n)/) {
1846                          # Here we have a new header. Store the current sequence if we have one.                          # Here we have a new header. Store the current sequence if we have one.
1847                          if ($id) {                          if ($id) {
1848                                  $retVal{$id} = $sequence;                  $retVal{$id} = lc $sequence;
1849                          }                          }
1850                          # Clear the sequence accumulator and save the new ID.                          # Clear the sequence accumulator and save the new ID.
1851                          ($id, $sequence) = ("$prefix$1", "");                          ($id, $sequence) = ("$prefix$1", "");
1852                  } else {                  } else {
1853                          # 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.
1854                          # First, we get the actual data out.              # First, we get the actual data out. Note that we normalize to lower
1855                # case.
1856                          $line =~ /^\s*(.*?)(\s|\n)/;                          $line =~ /^\s*(.*?)(\s|\n)/;
1857                          $sequence .= $1;                          $sequence .= $1;
1858                  }                  }
1859          }          }
1860          # Flush out the last sequence (if any).          # Flush out the last sequence (if any).
1861          if ($sequence) {          if ($sequence) {
1862                  $retVal {$id} = $sequence;          $retVal{$id} = lc $sequence;
1863          }          }
1864        # Close the file.
1865        close FASTAFILE;
1866          # Return the hash constructed from the file.          # Return the hash constructed from the file.
1867          return %retVal;          return %retVal;
1868  }  }
# Line 1354  Line 1873 
1873    
1874  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
1875  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
1876  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,
1877    it will not be changed; otherwise, it will be converted. This method can also be used to
1878    perform the reverse task-- insuring that all the locations are in the old format.
1879    
1880  =over 4  =over 4
1881    
# Line 1378  Line 1899 
1899  =back  =back
1900    
1901  =cut  =cut
1902    #: Return Type @;
1903  sub FormatLocations {  sub FormatLocations {
1904          # Get the parameters.          # Get the parameters.
1905          my $self = shift @_;      my ($self, $prefix, $locations, $oldFormat) = @_;
         my ($prefix, $locations, $oldFormat) = @_;  
1906          # Create the return list.          # Create the return list.
1907          my @retVal = ();          my @retVal = ();
1908          # Check to see if any locations were passed in.          # Check to see if any locations were passed in.
1909          if ($locations eq '') {          if ($locations eq '') {
1910              confess "No locations specified.";          Confess("No locations specified.");
1911          } else {          } else {
1912                  # Loop through the locations, converting them to the new format.                  # Loop through the locations, converting them to the new format.
1913                  for my $location (@{$locations}) {                  for my $location (@{$locations}) {
# Line 1422  Line 1942 
1942    
1943  sub DumpData {  sub DumpData {
1944          # Get the parameters.          # Get the parameters.
1945          my $self = shift @_;      my ($self) = @_;
1946          # Get the data directory name.          # Get the data directory name.
1947          my $outputDirectory = $self->{_options}->{dataDir};          my $outputDirectory = $self->{_options}->{dataDir};
1948          # Dump the relations.          # Dump the relations.
# Line 1436  Line 1956 
1956  Return the name of this database's XML definition file.  Return the name of this database's XML definition file.
1957    
1958  =cut  =cut
1959    #: Return Type $;
1960  sub XMLFileName {  sub XMLFileName {
1961          my $self = shift @_;      my ($self) = @_;
1962          return $self->{_xmlName};          return $self->{_xmlName};
1963  }  }
1964    
# Line 1458  Line 1978 
1978  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
1979  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>.
1980    
1981  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'}); >>
1982    
1983  =over 4  =over 4
1984    
# Line 1473  Line 1993 
1993  =back  =back
1994    
1995  =cut  =cut
1996    #: Return Type ;
1997  sub Insert {  sub Insert {
1998          # Get the parameters.          # Get the parameters.
1999          my $self = shift @_;      my ($self, $objectType, $fieldHash) = @_;
         my ($objectType, $fieldHash) = @_;  
2000          # Call the underlying method.          # Call the underlying method.
2001          $self->{_erdb}->InsertObject($objectType, $fieldHash);          $self->{_erdb}->InsertObject($objectType, $fieldHash);
2002  }  }
# Line 1515  Line 2034 
2034  =back  =back
2035    
2036  =cut  =cut
2037    #: Return Type $;
2038  sub Annotate {  sub Annotate {
2039          # Get the parameters.          # Get the parameters.
2040          my $self = shift @_;      my ($self, $fid, $timestamp, $user, $text) = @_;
         my ($fid, $timestamp, $user, $text) = @_;  
2041          # Create the annotation ID.          # Create the annotation ID.
2042          my $aid = "$fid:$timestamp";          my $aid = "$fid:$timestamp";
2043          # Insert the Annotation object.          # Insert the Annotation object.
# Line 1539  Line 2057 
2057    
2058  =head3 AssignFunction  =head3 AssignFunction
2059    
2060  C<< my $ok = $sprout->AssignFunction($featureID, $user, $function); >>  C<< my $ok = $sprout->AssignFunction($featureID, $user, $function, $assigningUser); >>
2061    
2062  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
2063  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.  
2064    
2065  =over 4  =over 4
2066    
# Line 1553  Line 2070 
2070    
2071  =item user  =item user
2072    
2073  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>.
2074    
2075  =item function  =item function
2076    
2077  Text of the function being assigned.  Text of the function being assigned.
2078    
2079    =item assigningUser (optional)
2080    
2081    Name of the individual user making the assignment. If omitted, defaults to the user group.
2082    
2083  =item RETURN  =item RETURN
2084    
2085  Returns 1 if successful, 0 if an error occurred.  Returns 1 if successful, 0 if an error occurred.
# Line 1566  Line 2087 
2087  =back  =back
2088    
2089  =cut  =cut
2090    #: Return Type $;
2091  sub AssignFunction {  sub AssignFunction {
2092          # Get the parameters.          # Get the parameters.
2093          my $self = shift @_;      my ($self, $featureID, $user, $function, $assigningUser) = @_;
2094          my ($featureID, $user, $function) = @_;      # Default the assigning user.
2095        if (! $assigningUser) {
2096            $assigningUser = $user;
2097        }
2098          # Create an annotation string from the parameters.          # Create an annotation string from the parameters.
2099          my $annotationText = "$user\nset $user function to\n$function";      my $annotationText = "$assigningUser\nset $user function to\n$function";
2100          # Get the current time.          # Get the current time.
2101          my $now = time;          my $now = time;
2102          # Declare the return variable.          # Declare the return variable.
# Line 1614  Line 2138 
2138  =back  =back
2139    
2140  =cut  =cut
2141    #: Return Type @;
2142  sub FeaturesByAlias {  sub FeaturesByAlias {
2143          # Get the parameters.          # Get the parameters.
2144          my $self = shift @_;      my ($self, $alias) = @_;
         my ($alias) = @_;  
2145          # Declare the return variable.          # Declare the return variable.
2146          my @retVal = ();          my @retVal = ();
2147          # Parse the alias.          # Parse the alias.
# Line 1657  Line 2180 
2180  =back  =back
2181    
2182  =cut  =cut
2183    #: Return Type $;
2184  sub Exists {  sub Exists {
2185          # Get the parameters.          # Get the parameters.
2186          my $self = shift @_;      my ($self, $entityName, $entityID) = @_;
         my ($entityName, $entityID) = @_;  
2187          # Check for the entity instance.          # Check for the entity instance.
2188        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
2189          my $testInstance = $self->GetEntity($entityName, $entityID);          my $testInstance = $self->GetEntity($entityName, $entityID);
2190          # Return an existence indicator.          # Return an existence indicator.
2191          my $retVal = ($testInstance ? 1 : 0);          my $retVal = ($testInstance ? 1 : 0);
# Line 1688  Line 2211 
2211  =back  =back
2212    
2213  =cut  =cut
2214    #: Return Type $;
2215  sub FeatureTranslation {  sub FeatureTranslation {
2216          # Get the parameters.          # Get the parameters.
2217          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
2218          # Get the specified feature's translation.          # Get the specified feature's translation.
2219          my ($retVal) = $self->GetEntityValues("Feature", $featureID, ['Feature(translation)']);          my ($retVal) = $self->GetEntityValues("Feature", $featureID, ['Feature(translation)']);
2220          return $retVal;          return $retVal;
# Line 1721  Line 2243 
2243  =back  =back
2244    
2245  =cut  =cut
2246    #: Return Type @;
2247  sub Taxonomy {  sub Taxonomy {
2248          # Get the parameters.          # Get the parameters.
2249          my $self = shift @_;      my ($self, $genome) = @_;
         my ($genome) = @_;  
2250          # Find the specified genome's taxonomy string.          # Find the specified genome's taxonomy string.
2251          my ($list) = $self->GetEntityValues('Genome', $genome, ['Genome(taxonomy)']);          my ($list) = $self->GetEntityValues('Genome', $genome, ['Genome(taxonomy)']);
2252          # Declare the return variable.          # Declare the return variable.
# Line 1765  Line 2286 
2286  =back  =back
2287    
2288  =cut  =cut
2289    #: Return Type $;
2290  sub CrudeDistance {  sub CrudeDistance {
2291          # Get the parameters.          # Get the parameters.
2292          my $self = shift @_;      my ($self, $genome1, $genome2) = @_;
         my ($genome1, $genome2) = @_;  
2293          # Insure that the distance is commutative by sorting the genome IDs.          # Insure that the distance is commutative by sorting the genome IDs.
2294          my ($genomeA, $genomeB);          my ($genomeA, $genomeB);
2295          if ($genome2 < $genome2) {          if ($genome2 < $genome2) {
# Line 1813  Line 2333 
2333  =back  =back
2334    
2335  =cut  =cut
2336    #: Return Type $;
2337  sub RoleName {  sub RoleName {
2338          # Get the parameters.          # Get the parameters.
2339          my $self = shift @_;      my ($self, $roleID) = @_;
         my ($roleID) = @_;  
2340          # Get the specified role's name.          # Get the specified role's name.
2341          my ($retVal) = $self->GetEntityValues('Role', $roleID, ['Role(name)']);          my ($retVal) = $self->GetEntityValues('Role', $roleID, ['Role(name)']);
2342          # Use the ID if the role has no name.          # Use the ID if the role has no name.
# Line 1847  Line 2366 
2366  =back  =back
2367    
2368  =cut  =cut
2369    #: Return Type @;
2370  sub RoleDiagrams {  sub RoleDiagrams {
2371          # Get the parameters.          # Get the parameters.
2372          my $self = shift @_;      my ($self, $roleID) = @_;
         my ($roleID) = @_;  
2373          # Query for the diagrams.          # Query for the diagrams.
2374          my @retVal = $self->GetFlat(['RoleOccursIn'], "RoleOccursIn(from-link) = ?", [$roleID],          my @retVal = $self->GetFlat(['RoleOccursIn'], "RoleOccursIn(from-link) = ?", [$roleID],
2375                                                                  'RoleOccursIn(to-link)');                                                                  'RoleOccursIn(to-link)');
# Line 1859  Line 2377 
2377          return @retVal;          return @retVal;
2378  }  }
2379    
2380    =head3 GetProperties
2381    
2382    C<< my @list = $sprout->GetProperties($fid, $key, $value, $url); >>
2383    
2384    Return a list of the properties with the specified characteristics.
2385    
2386    Properties are arbitrary key-value pairs associated with a feature. (At some point they
2387    will also be associated with genomes.) A property value is represented by a 4-tuple of
2388    the form B<($fid, $key, $value, $url)>. These exactly correspond to the parameter
2389    
2390    =over 4
2391    
2392    =item fid
2393    
2394    ID of the feature possessing the property.
2395    
2396    =item key
2397    
2398    Name or key of the property.
2399    
2400    =item value
2401    
2402    Value of the property.
2403    
2404    =item url
2405    
2406    URL of the document that indicated the property should have this particular value, or an
2407    empty string if no such document exists.
2408    
2409    =back
2410    
2411    The parameters act as a filter for the desired data. Any non-null parameter will
2412    automatically match all the tuples returned. So, specifying just the I<$fid> will
2413    return all the properties of the specified feature; similarly, specifying the I<$key>
2414    and I<$value> parameters will return all the features having the specified property
2415    value.
2416    
2417    A single property key can have many values, representing different ideas about the
2418    feature in question. For example, one paper may declare that a feature C<fig|83333.1.peg.10> is
2419    virulent, and another may declare that it is not virulent. A query about the virulence of
2420    C<fig|83333.1.peg.10> would be coded as
2421    
2422        my @list = $sprout->GetProperties('fig|83333.1.peg.10', 'virulence', '', '');
2423    
2424    Here the I<$value> and I<$url> fields are left blank, indicating that those fields are
2425    not to be filtered. The tuples returned would be
2426    
2427        ('fig|83333.1.peg.10', 'virulence', 'yes', 'http://www.somewhere.edu/first.paper.pdf')
2428        ('fig|83333.1.peg.10', 'virulence', 'no', 'http://www.somewhere.edu/second.paper.pdf')
2429    
2430    =cut
2431    #: Return Type @@;
2432    sub GetProperties {
2433        # Get the parameters.
2434        my ($self, @parms) = @_;
2435        # Declare the return variable.
2436        my @retVal = ();
2437        # Now we need to create a WHERE clause that will get us the data we want. First,
2438        # we create a list of the columns containing the data for each parameter.
2439        my @colNames = ('HasProperty(from-link)', 'Property(property-name)',
2440                        'Property(property-value)', 'HasProperty(evidence)');
2441        # Now we build the WHERE clause and the list of parameter values.
2442        my @where = ();
2443        my @values = ();
2444        for (my $i = 0; $i <= $#colNames; $i++) {
2445            my $parm = $parms[$i];
2446            if (defined $parm && ($parm ne '')) {
2447                push @where, "$colNames[$i] = ?";
2448                push @values, $parm;
2449            }
2450        }
2451        # Format the WHERE clause.
2452        my $filter = (@values > 0 ? (join " AND ", @where) : undef);
2453        # Ask for all the propertie values with the desired characteristics.
2454        my $query = $self->Get(['HasProperty', 'Property'], $filter, \@values);
2455        while (my $valueObject = $query->Fetch()) {
2456            my @tuple = $valueObject->Values(\@colNames);
2457            push @retVal, \@tuple;
2458        }
2459        # Return the result.
2460        return @retVal;
2461    }
2462    
2463  =head3 FeatureProperties  =head3 FeatureProperties
2464    
2465  C<< my @properties = $sprout->FeatureProperties($featureID); >>  C<< my @properties = $sprout->FeatureProperties($featureID); >>
# Line 1885  Line 2486 
2486  =back  =back
2487    
2488  =cut  =cut
2489    #: Return Type @@;
2490  sub FeatureProperties {  sub FeatureProperties {
2491          # Get the parameters.          # Get the parameters.
2492          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
2493          # Get the properties.          # Get the properties.
2494          my @retVal = $self->GetAll(['HasProperty', 'Property'], "HasProperty(from-link) = ?", [$featureID],          my @retVal = $self->GetAll(['HasProperty', 'Property'], "HasProperty(from-link) = ?", [$featureID],
2495                                                          ['Property(property-name)', 'Property(property-value)',                                                          ['Property(property-name)', 'Property(property-value)',
# Line 1917  Line 2517 
2517  =back  =back
2518    
2519  =cut  =cut
2520    #: Return Type $;
2521  sub DiagramName {  sub DiagramName {
2522          # Get the parameters.          # Get the parameters.
2523          my $self = shift @_;      my ($self, $diagramID) = @_;
         my ($diagramID) = @_;  
2524          # Get the specified diagram's name and return it.          # Get the specified diagram's name and return it.
2525          my ($retVal) = $self->GetEntityValues('Diagram', $diagramID, ['Diagram(name)']);          my ($retVal) = $self->GetEntityValues('Diagram', $diagramID, ['Diagram(name)']);
2526          return $retVal;          return $retVal;
# Line 1950  Line 2549 
2549  =back  =back
2550    
2551  =cut  =cut
2552    #: Return Type @;
2553  sub MergedAnnotations {  sub MergedAnnotations {
2554          # Get the parameters.          # Get the parameters.
2555          my $self = shift @_;      my ($self, $list) = @_;
         my ($list) = @_;  
2556          # Create a list to hold the annotation tuples found.          # Create a list to hold the annotation tuples found.
2557          my @tuples = ();          my @tuples = ();
2558          # Loop through the features in the input list.          # Loop through the features in the input list.
# Line 1969  Line 2567 
2567          }          }
2568          # Sort the result list by timestamp.          # Sort the result list by timestamp.
2569          my @retVal = sort { $a->[1] <=> $b->[1] } @tuples;          my @retVal = sort { $a->[1] <=> $b->[1] } @tuples;
2570        # Loop through and make the time stamps friendly.
2571        for my $tuple (@retVal) {
2572            $tuple->[1] = FriendlyTimestamp($tuple->[1]);
2573        }
2574          # Return the sorted list.          # Return the sorted list.
2575          return @retVal;          return @retVal;
2576  }  }
# Line 1995  Line 2597 
2597  =back  =back
2598    
2599  =cut  =cut
2600    #: Return Type @;
2601  sub RoleNeighbors {  sub RoleNeighbors {
2602          # Get the parameters.          # Get the parameters.
2603          my $self = shift @_;      my ($self, $roleID) = @_;
         my ($roleID) = @_;  
2604          # Get all the diagrams containing this role.          # Get all the diagrams containing this role.
2605          my @diagrams = $self->GetFlat(['RoleOccursIn'], "RoleOccursIn(from-link) = ?", [$roleID],          my @diagrams = $self->GetFlat(['RoleOccursIn'], "RoleOccursIn(from-link) = ?", [$roleID],
2606                                                                    'RoleOccursIn(to-link)');                                                                    'RoleOccursIn(to-link)');
# Line 2038  Line 2639 
2639  =back  =back
2640    
2641  =cut  =cut
2642    #: Return Type @;
2643  sub FeatureLinks {  sub FeatureLinks {
2644          # Get the parameters.          # Get the parameters.
2645          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
2646          # Get the feature's links.          # Get the feature's links.
2647          my @retVal = $self->GetEntityValues('Feature', $featureID, ['Feature(link)']);          my @retVal = $self->GetEntityValues('Feature', $featureID, ['Feature(link)']);
2648          # Return the feature's links.          # Return the feature's links.
# Line 2054  Line 2654 
2654  C<< my %subsystems = $sprout->SubsystemsOf($featureID); >>  C<< my %subsystems = $sprout->SubsystemsOf($featureID); >>
2655    
2656  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
2657  to the role the feature performs.  to the roles the feature performs.
2658    
2659  =over 4  =over 4
2660    
# Line 2064  Line 2664 
2664    
2665  =item RETURN  =item RETURN
2666    
2667  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.
2668    
2669  =back  =back
2670    
2671  =cut  =cut
2672    #: Return Type %@;
2673  sub SubsystemsOf {  sub SubsystemsOf {
2674          # Get the parameters.          # Get the parameters.
2675          my $self = shift @_;      my ($self, $featureID) = @_;
2676          my ($featureID) = @_;      # Get the subsystem list.
         # Use the SSCell to connect features to subsystems.  
2677          my @subsystems = $self->GetAll(['ContainsFeature', 'HasSSCell', 'IsRoleOf'],          my @subsystems = $self->GetAll(['ContainsFeature', 'HasSSCell', 'IsRoleOf'],
2678                                                                          "ContainsFeature(to-link) = ?", [$featureID],                                                                          "ContainsFeature(to-link) = ?", [$featureID],
2679                                                                          ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);                                                                          ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);
2680          # Create the return value.          # Create the return value.
2681          my %retVal = ();          my %retVal = ();
2682        # Build a hash to weed out duplicates. Sometimes the same PEG and role appears
2683        # in two spreadsheet cells.
2684        my %dupHash = ();
2685          # Loop through the results, adding them to the hash.          # Loop through the results, adding them to the hash.
2686          for my $record (@subsystems) {          for my $record (@subsystems) {
2687                  $retVal{$record->[0]} = $record->[1];          # Get this subsystem and role.
2688            my ($subsys, $role) = @{$record};
2689            # Insure it's the first time for both.
2690            my $dupKey = "$subsys\n$role";
2691            if (! exists $dupHash{"$subsys\n$role"}) {
2692                $dupHash{$dupKey} = 1;
2693                push @{$retVal{$subsys}}, $role;
2694            }
2695          }          }
2696          # Return the hash.          # Return the hash.
2697          return %retVal;          return %retVal;
2698  }  }
2699    
2700    =head3 SubsystemList
2701    
2702    C<< my @subsystems = $sprout->SubsystemList($featureID); >>
2703    
2704    Return a list containing the names of the subsystems in which the specified
2705    feature participates. Unlike L</SubsystemsOf>, this method only returns the
2706    subsystem names, not the roles.
2707    
2708    =over 4
2709    
2710    =item featureID
2711    
2712    ID of the feature whose subsystem names are desired.
2713    
2714    =item RETURN
2715    
2716    Returns a list of the names of the subsystems in which the feature participates.
2717    
2718    =back
2719    
2720    =cut
2721    #: Return Type @;
2722    sub SubsystemList {
2723        # Get the parameters.
2724        my ($self, $featureID) = @_;
2725        # Get the list of names.
2726        my @retVal = $self->GetFlat(['ContainsFeature', 'HasSSCell'], "ContainsFeature(to-link) = ?",
2727                                    [$featureID], 'HasSSCell(from-link)');
2728        # Return the result.
2729        return @retVal;
2730    }
2731    
2732  =head3 RelatedFeatures  =head3 RelatedFeatures
2733    
2734  C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>  C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>
# Line 2118  Line 2759 
2759  =back  =back
2760    
2761  =cut  =cut
2762    #: Return Type @;
2763  sub RelatedFeatures {  sub RelatedFeatures {
2764          # Get the parameters.          # Get the parameters.
2765          my $self = shift @_;      my ($self, $featureID, $function, $userID) = @_;
         my ($featureID, $function, $userID) = @_;  
2766          # 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.
2767          my @bbhFeatures = $self->GetFlat(['IsBidirectionalBestHitOf'],          my @bbhFeatures = $self->GetFlat(['IsBidirectionalBestHitOf'],
2768                                                                           "IsBidirectionalBestHitOf(from-link) = ?", [$featureID],                                                                           "IsBidirectionalBestHitOf(from-link) = ?", [$featureID],
# Line 2167  Line 2807 
2807  =back  =back
2808    
2809  =cut  =cut
2810    #: Return Type @;
2811  sub TaxonomySort {  sub TaxonomySort {
2812          # Get the parameters.          # Get the parameters.
2813          my $self = shift @_;      my ($self, $featureIDs) = @_;
         my ($featureIDs) = @_;  
2814          # Create the working hash table.          # Create the working hash table.
2815          my %hashBuffer = ();          my %hashBuffer = ();
2816          # Loop through the features.          # Loop through the features.
# Line 2180  Line 2819 
2819                  my ($taxonomy) = $self->GetFlat(['IsLocatedIn', 'HasContig', 'Genome'], "IsLocatedIn(from-link) = ?",                  my ($taxonomy) = $self->GetFlat(['IsLocatedIn', 'HasContig', 'Genome'], "IsLocatedIn(from-link) = ?",
2820                                                                                  [$fid], 'Genome(taxonomy)');                                                                                  [$fid], 'Genome(taxonomy)');
2821                  # Add this feature to the hash buffer.                  # Add this feature to the hash buffer.
2822                  if (exists $hashBuffer{$taxonomy}) {          Tracer::AddToListMap(\%hashBuffer, $taxonomy, $fid);
                         push @{$hashBuffer{$taxonomy}}, $fid;  
                 } else {  
                         $hashBuffer{$taxonomy} = [$fid];  
                 }  
2823          }          }
2824          # Sort the keys and get the elements.          # Sort the keys and get the elements.
2825          my @retVal = ();          my @retVal = ();
# Line 2250  Line 2885 
2885  =back  =back
2886    
2887  =cut  =cut
2888    #: Return Type @@;
2889  sub GetAll {  sub GetAll {
2890          # Get the parameters.          # Get the parameters.
2891          my $self = shift @_;      my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
2892          my ($objectNames, $filterClause, $parameterList, $fields, $count) = @_;      # Call the ERDB method.
2893          # Create the query.      my @retVal = $self->{_erdb}->GetAll($objectNames, $filterClause, $parameterList,
2894          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++;  
         }  
2895          # Return the resulting list.          # Return the resulting list.
2896          return @retVal;          return @retVal;
2897  }  }
# Line 2312  Line 2933 
2933  =back  =back
2934    
2935  =cut  =cut
2936    #: Return Type @;
2937  sub GetFlat {  sub GetFlat {
2938          # Get the parameters.          # Get the parameters.
2939          my $self = shift @_;      my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
         my ($objectNames, $filterClause, $parameterList, $field) = @_;  
2940          # Construct the query.          # Construct the query.
2941          my $query = $self->Get($objectNames, $filterClause, $parameterList);          my $query = $self->Get($objectNames, $filterClause, $parameterList);
2942          # Create the result list.          # Create the result list.
# Line 2423  Line 3043 
3043  to load the entire database.  to load the entire database.
3044    
3045  =cut  =cut
3046    #: Return Type @;
3047  sub LoadInfo {  sub LoadInfo {
3048          # Get the parameters.          # Get the parameters.
3049          my $self = shift @_;      my ($self) = @_;
3050          # 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.
3051          my @retVal = ($self->{_options}->{dataDir});          my @retVal = ($self->{_options}->{dataDir});
3052          # Concatenate the table names.          # Concatenate the table names.
# Line 2460  Line 3080 
3080  =back  =back
3081    
3082  =cut  =cut
3083    #: Return Type %;
3084  sub LowBBHs {  sub LowBBHs {
3085          # Get the parsameters.          # Get the parsameters.
3086          my $self = shift @_;      my ($self, $featureID, $cutoff) = @_;
         my ($featureID, $cutoff) = @_;  
3087          # Create the return hash.          # Create the return hash.
3088          my %retVal = ();          my %retVal = ();
3089          # Create a query to get the desired BBHs.          # Create a query to get the desired BBHs.
# Line 2480  Line 3099 
3099          return %retVal;          return %retVal;
3100  }  }
3101    
3102    =head3 GetGroups
3103    
3104    C<< my %groups = $sprout->GetGroups(\@groupList); >>
3105    
3106    Return a hash mapping each group to the IDs of the genomes in the group.
3107    A list of groups may be specified, in which case only those groups will be
3108    shown. Alternatively, if no parameter is supplied, all groups will be
3109    included. Genomes that are not in any group are omitted.
3110    
3111    =cut
3112    #: Return Type %@;
3113    sub GetGroups {
3114        # Get the parameters.
3115        my ($self, $groupList) = @_;
3116        # Declare the return value.
3117        my %retVal = ();
3118        # Determine whether we are getting all the groups or just some.
3119        if (defined $groupList) {
3120            # Here we have a group list. Loop through them individually,
3121            # getting a list of the relevant genomes.
3122            for my $group (@{$groupList}) {
3123                my @genomeIDs = $self->GetFlat(['Genome'], "Genome(group-name) = ?",
3124                    [$group], "Genome(id)");
3125                $retVal{$group} = \@genomeIDs;
3126            }
3127        } else {
3128            # Here we need all of the groups. In this case, we run through all
3129            # of the genome records, putting each one found into the appropriate
3130            # group. Note that we use a filter clause to insure that only genomes
3131            # in groups are included in the return set.
3132            my @genomes = $self->GetAll(['Genome'], "Genome(group-name) > ' '", [],
3133                                        ['Genome(id)', 'Genome(group-name)']);
3134            # Loop through the genomes found.
3135            for my $genome (@genomes) {
3136                # Pop this genome's ID off the current list.
3137                my @groups = @{$genome};
3138                my $genomeID = shift @groups;
3139                # Loop through the groups, adding the genome ID to each group's
3140                # list.
3141                for my $group (@groups) {
3142                    Tracer::AddToListMap(\%retVal, $group, $genomeID);
3143                }
3144            }
3145        }
3146        # Return the hash we just built.
3147        return %retVal;
3148    }
3149    
3150    =head3 MyGenomes
3151    
3152    C<< my @genomes = Sprout::MyGenomes($dataDir); >>
3153    
3154    Return a list of the genomes to be included in the Sprout.
3155    
3156    This method is provided for use during the Sprout load. It presumes the Genome load file has
3157    already been created. (It will be in the Sprout data directory and called either C<Genome>
3158    or C<Genome.dtx>.) Essentially, it reads in the Genome load file and strips out the genome
3159    IDs.
3160    
3161    =over 4
3162    
3163    =item dataDir
3164    
3165    Directory containing the Sprout load files.
3166    
3167    =back
3168    
3169    =cut
3170    #: Return Type @;
3171    sub MyGenomes {
3172        # Get the parameters.
3173        my ($dataDir) = @_;
3174        # Compute the genome file name.
3175        my $genomeFileName = LoadFileName($dataDir, "Genome");
3176        # Extract the genome IDs from the files.
3177        my @retVal = map { $_ =~ /^(\S+)/; $1 } Tracer::GetFile($genomeFileName);
3178        # Return the result.
3179        return @retVal;
3180    }
3181    
3182    =head3 LoadFileName
3183    
3184    C<< my $fileName = Sprout::LoadFileName($dataDir, $tableName); >>
3185    
3186    Return the name of the load file for the specified table in the specified data
3187    directory.
3188    
3189    =over 4
3190    
3191    =item dataDir
3192    
3193    Directory containing the Sprout load files.
3194    
3195    =item tableName
3196    
3197    Name of the table whose load file is desired.
3198    
3199    =item RETURN
3200    
3201    Returns the name of the file containing the load data for the specified table, or
3202    C<undef> if no load file is present.
3203    
3204    =back
3205    
3206    =cut
3207    #: Return Type $;
3208    sub LoadFileName {
3209        # Get the parameters.
3210        my ($dataDir, $tableName) = @_;
3211        # Declare the return variable.
3212        my $retVal;
3213        # Check for the various file names.
3214        if (-e "$dataDir/$tableName") {
3215            $retVal = "$dataDir/$tableName";
3216        } elsif (-e "$dataDir/$tableName.dtx") {
3217            $retVal = "$dataDir/$tableName.dtx";
3218        }
3219        # Return the result.
3220        return $retVal;
3221    }
3222    
3223  =head2 Internal Utility Methods  =head2 Internal Utility Methods
3224    
3225  =head3 ParseAssignment  =head3 ParseAssignment
3226    
3227  Parse annotation text to determine whether or not it is a functional assignment. If it is,  Parse annotation text to determine whether or not it is a functional assignment. If it is,
3228  the user and function text will be returned as a 2-element list. If it isn't, an empty list  the user, function text, and assigning user will be returned as a 3-element list. If it
3229  will be returned.  isn't, an empty list will be returned.
3230    
3231    A functional assignment is always of the form
3232    
3233        C<set >I<YYYY>C< function to\n>I<ZZZZZ>
3234    
3235    where I<YYYY> is the B<user>, and I<ZZZZ> is the actual functional role. In most cases,
3236    the user and the assigning user (from MadeAnnotation) will be the same, but that is
3237    not always the case.
3238    
3239  This is a static method.  This is a static method.
3240    
3241  =over 4  =over 4
3242    
3243    =item user
3244    
3245    Name of the assigning user.
3246    
3247  =item text  =item text
3248    
3249  Text of the annotation.  Text of the annotation.
# Line 2505  Line 3257 
3257    
3258  =cut  =cut
3259    
3260  sub ParseAssignment {  sub _ParseAssignment {
3261          # Get the parameters.          # Get the parameters.
3262          my ($text) = @_;      my ($user, $text) = @_;
3263          # Declare the return value.          # Declare the return value.
3264          my @retVal = ();          my @retVal = ();
3265          # Check to see if this is a functional assignment.          # Check to see if this is a functional assignment.
3266          my ($user, $type, $function) = split(/\n/, $text);      my ($type, $function) = split(/\n/, $text);
3267          if ($type =~ m/^set $user function to$/i) {      if ($type =~ m/^set function to$/i) {
3268                  # Here it is, so we return the user name and function text.          # Here we have an assignment without a user, so we use the incoming user ID.
3269                  @retVal = ($user, $function);                  @retVal = ($user, $function);
3270        } elsif ($type =~ m/^set (\S+) function to$/i) {
3271            # Here we have an assignment with a user, that is passed back to the caller.
3272            @retVal = ($1, $function);
3273          }          }
3274          # Return the result list.          # Return the result list.
3275          return @retVal;          return @retVal;
3276  }  }
3277    
3278    =head3 FriendlyTimestamp
3279    
3280    Convert a time number to a user-friendly time stamp for display.
3281    
3282    This is a static method.
3283    
3284    =over 4
3285    
3286    =item timeValue
3287    
3288    Numeric time value.
3289    
3290    =item RETURN
3291    
3292    Returns a string containing the same time in user-readable format.
3293    
3294    =back
3295    
3296    =cut
3297    
3298    sub FriendlyTimestamp {
3299        my ($timeValue) = @_;
3300        my $retVal = localtime($timeValue);
3301        return $retVal;
3302    }
3303    
3304    =head3 AddProperty
3305    
3306    C<< my  = $sprout->AddProperty($featureID, $key, $value, $url); >>
3307    
3308    Add a new attribute value (Property) to a feature. In the SEED system, attributes can
3309    be added to almost any object. In Sprout, they can only be added to features. In
3310    Sprout, attributes are implemented using I<properties>. A property represents a key/value
3311    pair. If the particular key/value pair coming in is not already in the database, a new
3312    B<Property> record is created to hold it.
3313    
3314    =over 4
3315    
3316    =item peg
3317    
3318    ID of the feature to which the attribute is to be replied.
3319    
3320    =item key
3321    
3322    Name of the attribute (key).
3323    
3324    =item value
3325    
3326    Value of the attribute.
3327    
3328    =item url
3329    
3330    URL or text citation from which the property was obtained.
3331    
3332    =back
3333    
3334    =cut
3335    #: Return Type ;
3336    sub AddProperty {
3337        # Get the parameters.
3338        my ($self, $featureID, $key, $value, $url) = @_;
3339        # Declare the variable to hold the desired property ID.
3340        my $propID;
3341        # Attempt to find a property record for this key/value pair.
3342        my @properties = $self->GetFlat(['Property'],
3343                                       "Property(property-name) = ? AND Property(property-value) = ?",
3344                                       [$key, $value], 'Property(id)');
3345        if (@properties) {
3346            # Here the property is already in the database. We save its ID.
3347            $propID = $properties[0];
3348            # Here the property value does not exist. We need to generate an ID. It will be set
3349            # to a number one greater than the maximum value in the database. This call to
3350            # GetAll will stop after one record.
3351            my @maxProperty = $self->GetAll(['Property'], "ORDER BY Property(id) DESC", [], ['Property(id)'],
3352                                            1);
3353            $propID = $maxProperty[0]->[0] + 1;
3354            # Insert the new property value.
3355            $self->Insert('Property', { 'property-name' => $key, 'property-value' => $value, id => $propID });
3356        }
3357        # Now we connect the incoming feature to the property.
3358        $self->Insert('HasProperty', { 'from-link' => $featureID, 'to-link' => $propID, evidence => $url });
3359    }
3360    
3361  1;  1;

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