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revision 1.48, Thu Oct 20 12:33:00 2005 UTC revision 1.69, Fri Jun 23 01:34:42 2006 UTC
# Line 1  Line 1 
1  package Sprout;  package Sprout;
2    
3        require Exporter;
4        use ERDB;
5        @ISA = qw(Exporter ERDB);
6      use Data::Dumper;      use Data::Dumper;
7      use strict;      use strict;
8      use Carp;      use Carp;
# Line 7  Line 10 
10      use XML::Simple;      use XML::Simple;
11      use DBQuery;      use DBQuery;
12      use DBObject;      use DBObject;
     use ERDB;  
13      use Tracer;      use Tracer;
14      use FIGRules;      use FIGRules;
15      use Stats;      use Stats;
# Line 32  Line 34 
34  query tasks. For example, L</genomes> lists the IDs of all the genomes in the database and  query tasks. For example, L</genomes> lists the IDs of all the genomes in the database and
35  L</dna_seq> returns the DNA sequence for a specified genome location.  L</dna_seq> returns the DNA sequence for a specified genome location.
36    
37    The Sprout object is a subclass of the ERDB object and inherits all its properties and methods.
38    
39  =cut  =cut
40    
41  #: Constructor SFXlate->new_sprout_only();  #: Constructor SFXlate->new_sprout_only();
# Line 62  Line 66 
66    
67  * B<xmlFileName> name of the XML file containing the database definition (default C<SproutDBD.xml>)  * B<xmlFileName> name of the XML file containing the database definition (default C<SproutDBD.xml>)
68    
69  * B<userData> user name and password, delimited by a slash (default C<root/>)  * B<userData> user name and password, delimited by a slash (default same as SEED)
70    
71  * B<port> connection port (default C<0>)  * B<port> connection port (default C<0>)
72    
73    * B<sock> connection socket (default same as SEED)
74    
75  * B<maxSegmentLength> maximum number of residues per feature segment, (default C<4500>)  * B<maxSegmentLength> maximum number of residues per feature segment, (default C<4500>)
76    
77  * B<maxSequenceLength> maximum number of residues per sequence, (default C<8000>)  * B<maxSequenceLength> maximum number of residues per sequence, (default C<8000>)
# Line 92  Line 98 
98                                                          # database type                                                          # database type
99                         dataDir      => $FIG_Config::sproutData,                         dataDir      => $FIG_Config::sproutData,
100                                                          # data file directory                                                          # data file directory
101                         xmlFileName  => "$FIG_Config::sproutData/SproutDBD.xml",                         xmlFileName  => "$FIG_Config::fig/SproutDBD.xml",
102                                                          # database definition file name                                                          # database definition file name
103                         userData     => "$FIG_Config::dbuser/$FIG_Config::dbpass",                         userData     => "$FIG_Config::dbuser/$FIG_Config::dbpass",
104                                                          # user name and password                                                          # user name and password
105                         port         => $FIG_Config::dbport,                         port         => $FIG_Config::dbport,
106                                                          # database connection port                                                          # database connection port
107                           sock         => $FIG_Config::dbsock,
108                         maxSegmentLength => 4500,        # maximum feature segment length                         maxSegmentLength => 4500,        # maximum feature segment length
109                         maxSequenceLength => 8000,       # maximum contig sequence length                         maxSequenceLength => 8000,       # maximum contig sequence length
110                         noDBOpen     => 0,               # 1 to suppress the database open                         noDBOpen     => 0,               # 1 to suppress the database open
# Line 111  Line 118 
118      my $dbh;      my $dbh;
119      if (! $optionTable->{noDBOpen}) {      if (! $optionTable->{noDBOpen}) {
120          $dbh = DBKernel->new($optionTable->{dbType}, $dbName, $userName,          $dbh = DBKernel->new($optionTable->{dbType}, $dbName, $userName,
121                                  $password, $optionTable->{port});                                  $password, $optionTable->{port}, undef, $optionTable->{sock});
122      }      }
123      # Create the ERDB object.      # Create the ERDB object.
124      my $xmlFileName = "$optionTable->{xmlFileName}";      my $xmlFileName = "$optionTable->{xmlFileName}";
125      my $erdb = ERDB->new($dbh, $xmlFileName);      my $retVal = ERDB::new($class, $dbh, $xmlFileName);
126      # Create this object.      # Add the option table and XML file name.
127      my $self = { _erdb => $erdb, _options => $optionTable, _xmlName => $xmlFileName };      $retVal->{_options} = $optionTable;
128      # Bless and return it.      $retVal->{_xmlName} = $xmlFileName;
129      bless $self;      # Return it.
130      return $self;      return $retVal;
131  }  }
132    
133  =head3 MaxSegment  =head3 MaxSegment
# Line 155  Line 162 
162      return $self->{_options}->{maxSequenceLength};      return $self->{_options}->{maxSequenceLength};
163  }  }
164    
 =head3 Get  
   
 C<< my $query = $sprout->Get(\@objectNames, $filterClause, \@parameterList); >>  
   
 This method allows a general query against the Sprout data using a specified filter clause.  
   
 The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each  
 field name represented in the form B<I<objectName>(I<fieldName>)>. For example, the  
 following call requests all B<Genome> objects for the genus specified in the variable  
 $genus.  
   
 C<< $query = $sprout->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>  
   
 The WHERE clause contains a single question mark, so there is a single additional  
 parameter representing the parameter value. It would also be possible to code  
   
 C<< $query = $sprout->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>  
   
 however, this version of the call would generate a syntax error if there were any quote  
 characters inside the variable C<$genus>.  
   
 The use of the strange parenthesized notation for field names enables us to distinguish  
 hyphens contained within field names from minus signs that participate in the computation  
 of the WHERE clause. All of the methods that manipulate fields will use this same notation.  
   
 It is possible to specify multiple entity and relationship names in order to retrieve more than  
 one object's data at the same time, which allows highly complex joined queries. For example,  
   
 C<< $query = $sprout->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>  
   
 This query returns all the genomes for a particular genus and allows access to the  
 sources from which they came. The join clauses to go from Genome to Source are generated  
 automatically.  
   
 Finally, the filter clause can contain sort information. To do this, simply put an C<ORDER BY>  
 clause at the end of the filter. Field references in the ORDER BY section follow the same rules  
 as they do in the filter itself; in other words, each one must be of the form B<I<objectName>(I<fieldName>)>.  
 For example, the following filter string gets all genomes for a particular genus and sorts  
 them by species name.  
   
 C<< $query = $sprout->Get(['Genome'], "Genome(genus) = ? ORDER BY Genome(species)", [$genus]); >>  
   
 It is also permissible to specify I<only> an ORDER BY clause. For example, the following invocation gets  
 all genomes ordered by genus and species.  
   
 C<< $query = $sprout->Get(['Genome'], "ORDER BY Genome(genus), Genome(species)"); >>  
   
 Odd things may happen if one of the ORDER BY fields is in a secondary relation. So, for example, an  
 attempt to order B<Feature>s by alias may (depending on the underlying database engine used) cause  
 a single feature to appear more than once.  
   
 If multiple names are specified, then the query processor will automatically determine a  
 join path between the entities and relationships. The algorithm used is very simplistic.  
 In particular, you can't specify any entity or relationship more than once, and if a  
 relationship is recursive, the path is determined by the order in which the entity  
 and the relationship appear. For example, consider a recursive relationship B<IsParentOf>  
 which relates B<People> objects to other B<People> objects. If the join path is  
 coded as C<['People', 'IsParentOf']>, then the people returned will be parents. If, however,  
 the join path is C<['IsParentOf', 'People']>, then the people returned will be children.  
   
 =over 4  
   
 =item objectNames  
   
 List containing the names of the entity and relationship objects to be retrieved.  
   
 =item filterClause  
   
 WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  
 be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form  
 B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the  
 parameter list as additional parameters. The fields in a filter clause can come from primary  
 entity relations, relationship relations, or secondary entity relations; however, all of the  
 entities and relationships involved must be included in the list of object names.  
   
 =item parameterList  
   
 List of the parameters to be substituted in for the parameters marks in the filter clause.  
   
 =item RETURN  
   
 Returns a B<DBQuery> that can be used to iterate through all of the results.  
   
 =back  
   
 =cut  
   
 sub Get {  
     # Get the parameters.  
     my ($self, $objectNames, $filterClause, $parameterList) = @_;  
     # We differ from the ERDB Get method in that the parameter list is passed in as a list reference  
     # rather than a list of parameters. The next step is to convert the parameters from a reference  
     # to a real list. We can only do this if the parameters have been specified.  
     my @parameters;  
     if ($parameterList) { @parameters = @{$parameterList}; }  
     return $self->{_erdb}->Get($objectNames, $filterClause, @parameters);  
 }  
   
 =head3 GetEntity  
   
 C<< my $entityObject = $sprout->GetEntity($entityType, $ID); >>  
   
 Return an object describing the entity instance with a specified ID.  
   
 =over 4  
   
 =item entityType  
   
 Entity type name.  
   
 =item ID  
   
 ID of the desired entity.  
   
 =item RETURN  
   
 Returns a B<DBObject> representing the desired entity instance, or an undefined value if no  
 instance is found with the specified key.  
   
 =back  
   
 =cut  
   
 sub GetEntity {  
     # Get the parameters.  
     my ($self, $entityType, $ID) = @_;  
     # Call the ERDB method.  
     return $self->{_erdb}->GetEntity($entityType, $ID);  
 }  
   
 =head3 GetEntityValues  
   
 C<< my @values = GetEntityValues($entityType, $ID, \@fields); >>  
   
 Return a list of values from a specified entity instance.  
   
 =over 4  
   
 =item entityType  
   
 Entity type name.  
   
 =item ID  
   
 ID of the desired entity.  
   
 =item fields  
   
 List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.  
   
 =item RETURN  
   
 Returns a flattened list of the values of the specified fields for the specified entity.  
   
 =back  
   
 =cut  
 #: Return Type @;  
 sub GetEntityValues {  
     # Get the parameters.  
     my ($self, $entityType, $ID, $fields) = @_;  
     # Call the ERDB method.  
     return $self->{_erdb}->GetEntityValues($entityType, $ID, $fields);  
 }  
   
 =head3 ShowMetaData  
   
 C<< $sprout->ShowMetaData($fileName); >>  
   
 This method outputs a description of the database to an HTML file in the data directory.  
   
 =over 4  
   
 =item fileName  
   
 Fully-qualified name to give to the output file.  
   
 =back  
   
 =cut  
   
 sub ShowMetaData {  
     # Get the parameters.  
     my ($self, $fileName) = @_;  
     # Compute the file name.  
     my $options = $self->{_options};  
     # Call the show method on the underlying ERDB object.  
     $self->{_erdb}->ShowMetaData($fileName);  
 }  
   
165  =head3 Load  =head3 Load
166    
167  C<< $sprout->Load($rebuild); >>;  C<< $sprout->Load($rebuild); >>;
# Line 379  Line 196 
196  sub Load {  sub Load {
197      # Get the parameters.      # Get the parameters.
198      my ($self, $rebuild) = @_;      my ($self, $rebuild) = @_;
     # Get the database object.  
     my $erdb = $self->{_erdb};  
199      # Load the tables from the data directory.      # Load the tables from the data directory.
200      my $retVal = $erdb->LoadTables($self->{_options}->{dataDir}, $rebuild);      my $retVal = $self->LoadTables($self->{_options}->{dataDir}, $rebuild);
201      # Return the statistics.      # Return the statistics.
202      return $retVal;      return $retVal;
203  }  }
# Line 422  Line 237 
237  sub LoadUpdate {  sub LoadUpdate {
238      # Get the parameters.      # Get the parameters.
239      my ($self, $truncateFlag, $tableList) = @_;      my ($self, $truncateFlag, $tableList) = @_;
     # Get the database object.  
     my $erdb = $self->{_erdb};  
240      # Declare the return value.      # Declare the return value.
241      my $retVal = Stats->new();      my $retVal = Stats->new();
242      # Get the data directory.      # Get the data directory.
# Line 437  Line 250 
250              Trace("No load file found for $tableName in $dataDir.") if T(0);              Trace("No load file found for $tableName in $dataDir.") if T(0);
251          } else {          } else {
252              # Attempt to load this table.              # Attempt to load this table.
253              my $result = $erdb->LoadTable($fileName, $tableName, $truncateFlag);              my $result = $self->LoadTable($fileName, $tableName, $truncateFlag);
254              # Accumulate the resulting statistics.              # Accumulate the resulting statistics.
255              $retVal->Accumulate($result);              $retVal->Accumulate($result);
256          }          }
# Line 446  Line 259 
259      return $retVal;      return $retVal;
260  }  }
261    
262    =head3 GenomeCounts
263    
264    C<< my ($arch, $bact, $euk, $vir, $env, $unk) = $sprout->GenomeCounts($complete); >>
265    
266    Count the number of genomes in each domain. If I<$complete> is TRUE, only complete
267    genomes will be included in the counts.
268    
269    =over 4
270    
271    =item complete
272    
273    TRUE if only complete genomes are to be counted, FALSE if all genomes are to be
274    counted
275    
276    =item RETURN
277    
278    A six-element list containing the number of genomes in each of six categories--
279    Archaea, Bacteria, Eukaryota, Viral, Environmental, and Unknown, respectively.
280    
281    =back
282    
283    =cut
284    
285    sub GenomeCounts {
286        # Get the parameters.
287        my ($self, $complete) = @_;
288        # Set the filter based on the completeness flag.
289        my $filter = ($complete ? "Genome(complete) = 1" : "");
290        # Get all the genomes and the related taxonomy information.
291        my @genomes = $self->GetAll(['Genome'], $filter, [], ['Genome(id)', 'Genome(taxonomy)']);
292        # Clear the counters.
293        my ($arch, $bact, $euk, $vir, $env, $unk) = (0, 0, 0, 0, 0, 0);
294        # Loop through, counting the domains.
295        for my $genome (@genomes) {
296            if    ($genome->[1] =~ /^archaea/i)  { ++$arch }
297            elsif ($genome->[1] =~ /^bacter/i)   { ++$bact }
298            elsif ($genome->[1] =~ /^eukar/i)    { ++$euk }
299            elsif ($genome->[1] =~ /^vir/i)      { ++$vir }
300            elsif ($genome->[1] =~ /^env/i)      { ++$env }
301            else  { ++$unk }
302        }
303        # Return the counts.
304        return ($arch, $bact, $euk, $vir, $env, $unk);
305    }
306    
307    =head3 ContigCount
308    
309    C<< my $count = $sprout->ContigCount($genomeID); >>
310    
311    Return the number of contigs for the specified genome ID.
312    
313    =over 4
314    
315    =item genomeID
316    
317    ID of the genome whose contig count is desired.
318    
319    =item RETURN
320    
321    Returns the number of contigs for the specified genome.
322    
323    =back
324    
325    =cut
326    
327    sub ContigCount {
328        # Get the parameters.
329        my ($self, $genomeID) = @_;
330        # Get the contig count.
331        my $retVal = $self->GetCount(['Contig', 'HasContig'], "HasContig(from-link) = ?", [$genomeID]);
332        # Return the result.
333        return $retVal;
334    }
335    
336    =head3 GeneMenu
337    
338    C<< my $selectHtml = $sprout->GeneMenu(\%attributes, $filterString, \@params); >>
339    
340    Return an HTML select menu of genomes. Each genome will be an option in the menu,
341    and will be displayed by name with the ID and a contig count attached. The selection
342    value will be the genome ID. The genomes will be sorted by genus/species name.
343    
344    =over 4
345    
346    =item attributes
347    
348    Reference to a hash mapping attributes to values for the SELECT tag generated.
349    
350    =item filterString
351    
352    A filter string for use in selecting the genomes. The filter string must conform
353    to the rules for the C<< ERDB->Get >> method.
354    
355    =item params
356    
357    Reference to a list of values to be substituted in for the parameter marks in
358    the filter string.
359    
360    =item RETURN
361    
362    Returns an HTML select menu with the specified genomes as selectable options.
363    
364    =back
365    
366    =cut
367    
368    sub GeneMenu {
369        # Get the parameters.
370        my ($self, $attributes, $filterString, $params) = @_;
371        # Start the menu.
372        my $retVal = "<select " .
373            join(" ", map { "$_=\"$attributes->{$_}\"" } keys %{$attributes}) .
374            ">\n";
375        # Get the genomes.
376        my @genomes = $self->GetAll(['Genome'], $filterString, $params, ['Genome(id)',
377                                                                         'Genome(genus)',
378                                                                         'Genome(species)',
379                                                                         'Genome(unique-characterization)']);
380        # Sort them by name.
381        my @sorted = sort { lc("$a->[1] $a->[2]") cmp lc("$b->[1] $b->[2]") } @genomes;
382        # Loop through the genomes, creating the option tags.
383        for my $genomeData (@sorted) {
384            # Get the data for this genome.
385            my ($genomeID, $genus, $species, $strain) = @{$genomeData};
386            # Get the contig count.
387            my $count = $self->ContigCount($genomeID);
388            my $counting = ($count == 1 ? "contig" : "contigs");
389            # Build the option tag.
390            $retVal .= "<option value=\"$genomeID\">$genus $species $strain ($genomeID) [$count $counting]</option>\n";
391        }
392        # Close the SELECT tag.
393        $retVal .= "</select>\n";
394        # Return the result.
395        return $retVal;
396    }
397  =head3 Build  =head3 Build
398    
399  C<< $sprout->Build(); >>  C<< $sprout->Build(); >>
# Line 460  Line 408 
408      # Get the parameters.      # Get the parameters.
409      my ($self) = @_;      my ($self) = @_;
410      # Create the tables.      # Create the tables.
411      $self->{_erdb}->CreateTables;      $self->CreateTables();
412  }  }
413    
414  =head3 Genomes  =head3 Genomes
# Line 740  Line 688 
688  should be of the form returned by L</featureLocation> when in a list context. In other words,  should be of the form returned by L</featureLocation> when in a list context. In other words,
689  each location is of the form I<contigID>C<_>I<begin>I<dir>I<end>.  each location is of the form I<contigID>C<_>I<begin>I<dir>I<end>.
690    
691    For example, the following would return the DNA sequence for contig C<83333.1:NC_000913>
692    between positions 1401 and 1532, inclusive.
693    
694        my $sequence = $sprout->DNASeq('83333.1:NC_000913_1401_1532');
695    
696  =over 4  =over 4
697    
698  =item locationList  =item locationList
699    
700  List of location specifiers, each in the form I<contigID>C<_>I<begin>I<dir>I<end> (see  List of location specifiers, each in the form I<contigID>C<_>I<begin>I<dir>I<len> or
701  L</FeatureLocation> for more about this format).  I<contigID>C<_>I<begin>C<_>I<end> (see L</FeatureLocation> for more about this format).
702    
703  =item RETURN  =item RETURN
704    
# Line 841  Line 794 
794      return @retVal;      return @retVal;
795  }  }
796    
797    =head3 GenomeLength
798    
799    C<< my $length = $sprout->GenomeLength($genomeID); >>
800    
801    Return the length of the specified genome in base pairs.
802    
803    =over 4
804    
805    =item genomeID
806    
807    ID of the genome whose base pair count is desired.
808    
809    =item RETURN
810    
811    Returns the number of base pairs in all the contigs of the specified
812    genome.
813    
814    =back
815    
816    =cut
817    
818    sub GenomeLength {
819        # Get the parameters.
820        my ($self, $genomeID) = @_;
821        # Declare the return variable.
822        my $retVal = 0;
823        # Get the genome's contig sequence lengths.
824        my @lens = $self->GetFlat(['HasContig', 'IsMadeUpOf'], 'HasContig(from-link) = ?',
825                           [$genomeID], 'IsMadeUpOf(len)');
826        # Sum the lengths.
827        map { $retVal += $_ } @lens;
828        # Return the result.
829        return $retVal;
830    }
831    
832    =head3 FeatureCount
833    
834    C<< my $count = $sprout->FeatureCount($genomeID, $type); >>
835    
836    Return the number of features of the specified type in the specified genome.
837    
838    =over 4
839    
840    =item genomeID
841    
842    ID of the genome whose feature count is desired.
843    
844    =item type
845    
846    Type of feature to count (eg. C<peg>, C<rna>, etc.).
847    
848    =item RETURN
849    
850    Returns the number of features of the specified type for the specified genome.
851    
852    =back
853    
854    =cut
855    
856    sub FeatureCount {
857        # Get the parameters.
858        my ($self, $genomeID, $type) = @_;
859        # Compute the count.
860        my $retVal = $self->GetCount(['HasFeature', 'Feature'],
861                                    "HasFeature(from-link) = ? AND Feature(feature-type) = ?",
862                                    [$genomeID, $type]);
863        # Return the result.
864        return $retVal;
865    }
866    
867    =head3 GenomeAssignments
868    
869    C<< my $fidHash = $sprout->GenomeAssignments($genomeID); >>
870    
871    Return a list of a genome's assigned features. The return hash will contain each
872    assigned feature of the genome mapped to the text of its most recent functional
873    assignment.
874    
875    =over 4
876    
877    =item genomeID
878    
879    ID of the genome whose functional assignments are desired.
880    
881    =item RETURN
882    
883    Returns a reference to a hash which maps each feature to its most recent
884    functional assignment.
885    
886    =back
887    
888    =cut
889    
890    sub GenomeAssignments {
891        # Get the parameters.
892        my ($self, $genomeID) = @_;
893        # Declare the return variable.
894        my $retVal = {};
895        # Query the genome's features and annotations. We'll put the oldest annotations
896        # first so that the last assignment to go into the hash will be the correct one.
897        my $query = $self->Get(['HasFeature', 'IsTargetOfAnnotation', 'Annotation'],
898                               "HasFeature(from-link) = ? ORDER BY Annotation(time)",
899                               [$genomeID]);
900        # Loop through the annotations.
901        while (my $data = $query->Fetch) {
902            # Get the feature ID and annotation text.
903            my ($fid, $annotation) = $data->Values(['HasFeature(to-link)',
904                                                    'Annotation(annotation)']);
905            # Check to see if this is an assignment. Note that the user really
906            # doesn't matter to us, other than we use it to determine whether or
907            # not this is an assignment.
908            my ($user, $assignment) = _ParseAssignment('fig', $annotation);
909            if ($user) {
910                # Here it's an assignment. We put it in the return hash, overwriting
911                # any older assignment that might be present.
912                $retVal->{$fid} = $assignment;
913            }
914        }
915        # Return the result.
916        return $retVal;
917    }
918    
919  =head3 ContigLength  =head3 ContigLength
920    
921  C<< my $length = $sprout->ContigLength($contigID); >>  C<< my $length = $sprout->ContigLength($contigID); >>
# Line 1270  Line 1345 
1345                                                       'Annotation(time)', 'MadeAnnotation(from-link)']);                                                       'Annotation(time)', 'MadeAnnotation(from-link)']);
1346              # Check to see if this is a functional assignment for a trusted user.              # Check to see if this is a functional assignment for a trusted user.
1347              my ($actualUser, $function) = _ParseAssignment($user, $text);              my ($actualUser, $function) = _ParseAssignment($user, $text);
1348                Trace("Assignment user is $actualUser, text is $function.") if T(4);
1349              if ($actualUser) {              if ($actualUser) {
1350                  # Here it is a functional assignment. Check the time and the user                  # Here it is a functional assignment. Check the time and the user
1351                  # name. The time must be recent and the user must be trusted.                  # name. The time must be recent and the user must be trusted.
1352                  if ((exists $trusteeTable{$user}) && ($time > $timeSelected)) {                  if ((exists $trusteeTable{$actualUser}) && ($time > $timeSelected)) {
1353                      $retVal = $function;                      $retVal = $function;
1354                      $timeSelected = $time;                      $timeSelected = $time;
1355                  }                  }
# Line 1481  Line 1557 
1557      my $genomeData = $self->GetEntity('Genome', $genomeID);      my $genomeData = $self->GetEntity('Genome', $genomeID);
1558      if ($genomeData) {      if ($genomeData) {
1559          # The genome exists, so get the completeness flag.          # The genome exists, so get the completeness flag.
1560          ($retVal) = $genomeData->Value('complete');          ($retVal) = $genomeData->Value('Genome(complete)');
1561      }      }
1562      # Return the result.      # Return the result.
1563      return $retVal;      return $retVal;
# Line 1521  Line 1597 
1597    
1598  C<< my $genomeID = $sprout->GenomeOf($featureID); >>  C<< my $genomeID = $sprout->GenomeOf($featureID); >>
1599    
1600  Return the genome that contains a specified feature.  Return the genome that contains a specified feature or contig.
1601    
1602  =over 4  =over 4
1603    
1604  =item featureID  =item featureID
1605    
1606  ID of the feature whose genome is desired.  ID of the feature or contig whose genome is desired.
1607    
1608  =item RETURN  =item RETURN
1609    
1610  Returns the ID of the genome for the specified feature. If the feature is not found, returns  Returns the ID of the genome for the specified feature or contig. If the feature or contig is not
1611  an undefined value.  found, returns an undefined value.
1612    
1613  =back  =back
1614    
# Line 1541  Line 1617 
1617  sub GenomeOf {  sub GenomeOf {
1618      # Get the parameters.      # Get the parameters.
1619      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
1620      # Create a query to find the genome associated with the feature.      # Create a query to find the genome associated with the incoming ID.
1621      my $query = $self->Get(['IsLocatedIn', 'HasContig'], "IsLocatedIn(from-link) = ?", [$featureID]);      my $query = $self->Get(['IsLocatedIn', 'HasContig'], "IsLocatedIn(from-link) = ? OR HasContig(to-link) = ?",
1622                               [$featureID, $featureID]);
1623      # Declare the return value.      # Declare the return value.
1624      my $retVal;      my $retVal;
1625      # Get the genome ID.      # Get the genome ID.
# Line 1589  Line 1666 
1666          # Get the ID and score of the coupling.          # Get the ID and score of the coupling.
1667          my ($couplingID, $score) = $clustering->Values(['Coupling(id)',          my ($couplingID, $score) = $clustering->Values(['Coupling(id)',
1668                                                          'Coupling(score)']);                                                          'Coupling(score)']);
1669          # The coupling ID contains the two feature IDs separated by a space. We use          # Get the other feature that participates in the coupling.
1670          # this information to find the ID of the other feature.          my ($otherFeatureID) = $self->GetFlat(['ParticipatesInCoupling'],
1671          my ($fid1, $fid2) = split / /, $couplingID;                                             "ParticipatesInCoupling(to-link) = ? AND ParticipatesInCoupling(from-link) <> ?",
1672          my $otherFeatureID = ($featureID eq $fid1 ? $fid2 : $fid1);                                             [$couplingID, $featureID], 'ParticipatesInCoupling(from-link)');
1673          # Attach the other feature's score to its ID.          # Attach the other feature's score to its ID.
1674          $retVal{$otherFeatureID} = $score;          $retVal{$otherFeatureID} = $score;
1675          $found = 1;          $found = 1;
# Line 1784  Line 1861 
1861      return join " ", sort @_;      return join " ", sort @_;
1862  }  }
1863    
 =head3 GetEntityTypes  
   
 C<< my @entityList = $sprout->GetEntityTypes(); >>  
   
 Return the list of supported entity types.  
   
 =cut  
 #: Return Type @;  
 sub GetEntityTypes {  
     # Get the parameters.  
     my ($self) = @_;  
     # Get the underlying database object.  
     my $erdb = $self->{_erdb};  
     # Get its entity type list.  
     my @retVal = $erdb->GetEntityTypes();  
 }  
   
1864  =head3 ReadFasta  =head3 ReadFasta
1865    
1866  C<< my %sequenceData = Sprout::ReadFasta($fileName, $prefix); >>  C<< my %sequenceData = Sprout::ReadFasta($fileName, $prefix); >>
# Line 1946  Line 2006 
2006      # Get the data directory name.      # Get the data directory name.
2007      my $outputDirectory = $self->{_options}->{dataDir};      my $outputDirectory = $self->{_options}->{dataDir};
2008      # Dump the relations.      # Dump the relations.
2009      $self->{_erdb}->DumpRelations($outputDirectory);      $self->DumpRelations($outputDirectory);
2010  }  }
2011    
2012  =head3 XMLFileName  =head3 XMLFileName
# Line 1998  Line 2058 
2058      # Get the parameters.      # Get the parameters.
2059      my ($self, $objectType, $fieldHash) = @_;      my ($self, $objectType, $fieldHash) = @_;
2060      # Call the underlying method.      # Call the underlying method.
2061      $self->{_erdb}->InsertObject($objectType, $fieldHash);      $self->InsertObject($objectType, $fieldHash);
2062  }  }
2063    
2064  =head3 Annotate  =head3 Annotate
# Line 2729  Line 2789 
2789      return @retVal;      return @retVal;
2790  }  }
2791    
2792    
2793    
2794  =head3 RelatedFeatures  =head3 RelatedFeatures
2795    
2796  C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>  C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>
# Line 2830  Line 2892 
2892      return @retVal;      return @retVal;
2893  }  }
2894    
 =head3 GetAll  
   
 C<< my @list = $sprout->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>  
   
 Return a list of values taken from the objects returned by a query. The first three  
 parameters correspond to the parameters of the L</Get> method. The final parameter is  
 a list of the fields desired from each record found by the query. The field name  
 syntax is the standard syntax used for fields in the B<ERDB> system--  
 B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity  
 or relationship and I<fieldName> is the name of the field.  
   
 The list returned will be a list of lists. Each element of the list will contain  
 the values returned for the fields specified in the fourth parameter. If one of the  
 fields specified returns multiple values, they are flattened in with the rest. For  
 example, the following call will return a list of the features in a particular  
 spreadsheet cell, and each feature will be represented by a list containing the  
 feature ID followed by all of its aliases.  
   
 C<< $query = $sprout->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>  
   
 =over 4  
   
 =item objectNames  
   
 List containing the names of the entity and relationship objects to be retrieved.  
   
 =item filterClause  
   
 WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  
 be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form  
 B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the  
 parameter list as additional parameters. The fields in a filter clause can come from primary  
 entity relations, relationship relations, or secondary entity relations; however, all of the  
 entities and relationships involved must be included in the list of object names.  
   
 =item parameterList  
   
 List of the parameters to be substituted in for the parameters marks in the filter clause.  
   
 =item fields  
   
 List of the fields to be returned in each element of the list returned.  
   
 =item count  
   
 Maximum number of records to return. If omitted or 0, all available records will be returned.  
   
 =item RETURN  
   
 Returns a list of list references. Each element of the return list contains the values for the  
 fields specified in the B<fields> parameter.  
   
 =back  
   
 =cut  
 #: Return Type @@;  
 sub GetAll {  
     # Get the parameters.  
     my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;  
     # Call the ERDB method.  
     my @retVal = $self->{_erdb}->GetAll($objectNames, $filterClause, $parameterList,  
                                         $fields, $count);  
     # Return the resulting list.  
     return @retVal;  
 }  
   
 =head3 GetFlat  
   
 C<< my @list = $sprout->GetFlat(\@objectNames, $filterClause, $parameterList, $field); >>  
   
 This is a variation of L</GetAll> that asks for only a single field per record and  
 returns a single flattened list.  
   
 =over 4  
   
 =item objectNames  
   
 List containing the names of the entity and relationship objects to be retrieved.  
   
 =item filterClause  
   
 WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  
 be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form  
 B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the  
 parameter list as additional parameters. The fields in a filter clause can come from primary  
 entity relations, relationship relations, or secondary entity relations; however, all of the  
 entities and relationships involved must be included in the list of object names.  
   
 =item parameterList  
   
 List of the parameters to be substituted in for the parameters marks in the filter clause.  
   
 =item field  
   
 Name of the field to be used to get the elements of the list returned.  
   
 =item RETURN  
   
 Returns a list of values.  
   
 =back  
   
 =cut  
 #: Return Type @;  
 sub GetFlat {  
     # Get the parameters.  
     my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;  
     # Construct the query.  
     my $query = $self->Get($objectNames, $filterClause, $parameterList);  
     # Create the result list.  
     my @retVal = ();  
     # Loop through the records, adding the field values found to the result list.  
     while (my $row = $query->Fetch()) {  
         push @retVal, $row->Value($field);  
     }  
     # Return the list created.  
     return @retVal;  
 }  
   
2895  =head3 Protein  =head3 Protein
2896    
2897  C<< my $protein = Sprout::Protein($sequence, $table); >>  C<< my $protein = Sprout::Protein($sequence, $table); >>
# Line 3050  Line 2993 
2993      # Create the return list, priming it with the name of the data directory.      # Create the return list, priming it with the name of the data directory.
2994      my @retVal = ($self->{_options}->{dataDir});      my @retVal = ($self->{_options}->{dataDir});
2995      # Concatenate the table names.      # Concatenate the table names.
2996      push @retVal, $self->{_erdb}->GetTableNames();      push @retVal, $self->GetTableNames();
2997      # Return the result.      # Return the result.
2998      return @retVal;      return @retVal;
2999  }  }
3000    
3001  =head3 LowBBHs  =head3 LowBBHs
3002    
3003  C<< my %bbhMap = $sprout->GoodBBHs($featureID, $cutoff); >>  C<< my %bbhMap = $sprout->LowBBHs($featureID, $cutoff); >>
3004    
3005  Return the bidirectional best hits of a feature whose score is no greater than a  Return the bidirectional best hits of a feature whose score is no greater than a
3006  specified cutoff value. A higher cutoff value will allow inclusion of hits with  specified cutoff value. A higher cutoff value will allow inclusion of hits with
# Line 3220  Line 3163 
3163      return $retVal;      return $retVal;
3164  }  }
3165    
3166    =head3 DeleteGenome
3167    
3168    C<< my $stats = $sprout->DeleteGenome($genomeID, $testFlag); >>
3169    
3170    Delete a genome from the database.
3171    
3172    =over 4
3173    
3174    =item genomeID
3175    
3176    ID of the genome to delete
3177    
3178    =item testFlag
3179    
3180    If TRUE, then the DELETE statements will be traced, but no deletions will occur.
3181    
3182    =item RETURN
3183    
3184    Returns a statistics object describing the rows deleted.
3185    
3186    =back
3187    
3188    =cut
3189    #: Return Type $%;
3190    sub DeleteGenome {
3191        # Get the parameters.
3192        my ($self, $genomeID, $testFlag) = @_;
3193        # Perform the delete for the genome's features.
3194        my $retVal = $self->Delete('Feature', "fig|$genomeID.%", $testFlag);
3195        # Perform the delete for the primary genome data.
3196        my $stats = $self->Delete('Genome', $genomeID, $testFlag);
3197        $retVal->Accumulate($stats);
3198        # Return the result.
3199        return $retVal;
3200    }
3201    
3202  =head2 Internal Utility Methods  =head2 Internal Utility Methods
3203    
3204  =head3 ParseAssignment  =head3 ParseAssignment
# Line 3236  Line 3215 
3215  the user and the assigning user (from MadeAnnotation) will be the same, but that is  the user and the assigning user (from MadeAnnotation) will be the same, but that is
3216  not always the case.  not always the case.
3217    
3218    In addition, the functional role may contain extra data that is stripped, such as
3219    terminating spaces or a comment separated from the rest of the text by a tab.
3220    
3221  This is a static method.  This is a static method.
3222    
3223  =over 4  =over 4
# Line 3268  Line 3250 
3250          # Here we have an assignment without a user, so we use the incoming user ID.          # Here we have an assignment without a user, so we use the incoming user ID.
3251          @retVal = ($user, $function);          @retVal = ($user, $function);
3252      } elsif ($type =~ m/^set (\S+) function to$/i) {      } elsif ($type =~ m/^set (\S+) function to$/i) {
3253          # Here we have an assignment with a user, that is passed back to the caller.          # Here we have an assignment with a user that is passed back to the caller.
3254          @retVal = ($1, $function);          @retVal = ($1, $function);
3255      }      }
3256        # If we have an assignment, we need to clean the function text. There may be
3257        # extra junk at the end added as a note from the user.
3258        if (@retVal) {
3259            $retVal[1] =~ s/(\t\S)?\s*$//;
3260        }
3261      # Return the result list.      # Return the result list.
3262      return @retVal;      return @retVal;
3263  }  }
# Line 3358  Line 3345 
3345      $self->Insert('HasProperty', { 'from-link' => $featureID, 'to-link' => $propID, evidence => $url });      $self->Insert('HasProperty', { 'from-link' => $featureID, 'to-link' => $propID, evidence => $url });
3346  }  }
3347    
3348    
3349  1;  1;

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