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revision 1.47, Thu Oct 20 12:02:43 2005 UTC revision 1.59, Wed Jun 7 01:53:03 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, $params, ['Genome(id)',
377                                                                         'Genome(genus)',
378                                                                         'Genome(species)']);
379        # Sort them by name.
380        my @sorted = sort { lc("$a->[1] $a->[2]") cmp lc("$b->[1] $b->[2]") } @genomes;
381        # Loop through the genomes, creating the option tags.
382        for my $genomeData (@sorted) {
383            # Get the data for this genome.
384            my ($genomeID, $genus, $species) = @{$genomeData};
385            # Get the contig count.
386            my $count = $self->ContigCount($genomeID);
387            my $counting = ($count == 1 ? "contig" : "contigs");
388            # Build the option tag.
389            $retVal .= "<option value=\"$genomeID\">$genus $species ($genomeID) [$count $counting]</option>\n";
390        }
391        # Close the SELECT tag.
392        $retVal .= "</select>\n";
393        # Return the result.
394        return $retVal;
395    }
396  =head3 Build  =head3 Build
397    
398  C<< $sprout->Build(); >>  C<< $sprout->Build(); >>
# Line 460  Line 407 
407      # Get the parameters.      # Get the parameters.
408      my ($self) = @_;      my ($self) = @_;
409      # Create the tables.      # Create the tables.
410      $self->{_erdb}->CreateTables;      $self->CreateTables();
411  }  }
412    
413  =head3 Genomes  =head3 Genomes
# Line 740  Line 687 
687  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,
688  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>.
689    
690    For example, the following would return the DNA sequence for contig C<83333.1:NC_000913>
691    between positions 1401 and 1532, inclusive.
692    
693        my $sequence = $sprout->DNASeq('83333.1:NC_000913_1401_1532');
694    
695  =over 4  =over 4
696    
697  =item locationList  =item locationList
698    
699  List of location specifiers, each in the form I<contigID>C<_>I<begin>I<dir>I<end> (see  List of location specifiers, each in the form I<contigID>C<_>I<begin>I<dir>I<len> or
700  L</FeatureLocation> for more about this format).  I<contigID>C<_>I<begin>C<_>I<end> (see L</FeatureLocation> for more about this format).
701    
702  =item RETURN  =item RETURN
703    
# Line 1176  Line 1128 
1128          # Get the annotation fields.          # Get the annotation fields.
1129          my ($timeStamp, $text, $user) = @{$annotation};          my ($timeStamp, $text, $user) = @{$annotation};
1130          # Check to see if this is a functional assignment.          # Check to see if this is a functional assignment.
1131          my ($type, $function) = _ParseAssignment($text);          my ($actualUser, $function) = _ParseAssignment($user, $text);
1132          if ($type && ! exists $retVal{$user}) {          if ($actualUser && ! exists $retVal{$actualUser}) {
1133              # Here it is a functional assignment and there has been no              # Here it is a functional assignment and there has been no
1134              # previous assignment for this user, so we stuff it in the              # previous assignment for this user, so we stuff it in the
1135              # return hash.              # return hash.
1136              $retVal{$user} = $function;              $retVal{$actualUser} = $function;
1137          }          }
1138      }      }
1139      # Return the hash of assignments found.      # Return the hash of assignments found.
# Line 1259  Line 1211 
1211              }              }
1212          }          }
1213          # Build a query for all of the feature's annotations, sorted by date.          # Build a query for all of the feature's annotations, sorted by date.
1214          my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation'],          my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1215                                 "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",                                 "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1216                                 [$featureID]);                                 [$featureID]);
1217          my $timeSelected = 0;          my $timeSelected = 0;
1218          # Loop until we run out of annotations.          # Loop until we run out of annotations.
1219          while (my $annotation = $query->Fetch()) {          while (my $annotation = $query->Fetch()) {
1220              # Get the annotation text.              # Get the annotation text.
1221              my ($text, $time) = $annotation->Values(['Annotation(annotation)','Annotation(time)']);              my ($text, $time, $user) = $annotation->Values(['Annotation(annotation)',
1222                                                         'Annotation(time)', 'MadeAnnotation(from-link)']);
1223              # Check to see if this is a functional assignment for a trusted user.              # Check to see if this is a functional assignment for a trusted user.
1224              my ($user, $function) = _ParseAssignment($text);              my ($actualUser, $function) = _ParseAssignment($user, $text);
1225              if ($user) {              Trace("Assignment user is $actualUser, text is $function.") if T(4);
1226                if ($actualUser) {
1227                  # Here it is a functional assignment. Check the time and the user                  # Here it is a functional assignment. Check the time and the user
1228                  # name. The time must be recent and the user must be trusted.                  # name. The time must be recent and the user must be trusted.
1229                  if ((exists $trusteeTable{$user}) && ($time > $timeSelected)) {                  if ((exists $trusteeTable{$actualUser}) && ($time > $timeSelected)) {
1230                      $retVal = $function;                      $retVal = $function;
1231                      $timeSelected = $time;                      $timeSelected = $time;
1232                  }                  }
# Line 1331  Line 1285 
1285          # users.          # users.
1286          my %trusteeTable = ();          my %trusteeTable = ();
1287          # Build a query for all of the feature's annotations, sorted by date.          # Build a query for all of the feature's annotations, sorted by date.
1288          my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation'],          my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1289                                 "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",                                 "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1290                                 [$featureID]);                                 [$featureID]);
1291          my $timeSelected = 0;          my $timeSelected = 0;
1292          # Loop until we run out of annotations.          # Loop until we run out of annotations.
1293          while (my $annotation = $query->Fetch()) {          while (my $annotation = $query->Fetch()) {
1294              # Get the annotation text.              # Get the annotation text.
1295              my ($text, $time) = $annotation->Values(['Annotation(annotation)','Annotation(time)']);              my ($text, $time, $user) = $annotation->Values(['Annotation(annotation)',
1296                                                                'Annotation(time)',
1297                                                                'MadeAnnotation(user)']);
1298              # Check to see if this is a functional assignment for a trusted user.              # Check to see if this is a functional assignment for a trusted user.
1299              my ($user, $function) = _ParseAssignment($text);              my ($actualUser, $function) = _ParseAssignment($user, $text);
1300              if ($user) {              if ($actualUser) {
1301                  # Here it is a functional assignment.                  # Here it is a functional assignment.
1302                  push @retVal, [$user, $function];                  push @retVal, [$actualUser, $function];
1303              }              }
1304          }          }
1305      } else {      } else {
1306          # Here we have a non-FIG feature ID. In this case the user ID does not          # Here we have a non-FIG feature ID. In this case the user ID does not
1307          # matter. We simply get the information from the External Alias Function          # matter. We simply get the information from the External Alias Function
1308          # table.          # table.
1309          push @retVal, $self->GetEntityValues('ExternalAliasFunc', $featureID, ['ExternalAliasFunc(func)']);          my @assignments = $self->GetEntityValues('ExternalAliasFunc', $featureID,
1310                                                     ['ExternalAliasFunc(func)']);
1311            push @retVal, map { ['master', $_] } @assignments;
1312      }      }
1313      # Return the assignments found.      # Return the assignments found.
1314      return @retVal;      return @retVal;
# Line 1476  Line 1434 
1434      my $genomeData = $self->GetEntity('Genome', $genomeID);      my $genomeData = $self->GetEntity('Genome', $genomeID);
1435      if ($genomeData) {      if ($genomeData) {
1436          # The genome exists, so get the completeness flag.          # The genome exists, so get the completeness flag.
1437          ($retVal) = $genomeData->Value('complete');          ($retVal) = $genomeData->Value('Genome(complete)');
1438      }      }
1439      # Return the result.      # Return the result.
1440      return $retVal;      return $retVal;
# Line 1516  Line 1474 
1474    
1475  C<< my $genomeID = $sprout->GenomeOf($featureID); >>  C<< my $genomeID = $sprout->GenomeOf($featureID); >>
1476    
1477  Return the genome that contains a specified feature.  Return the genome that contains a specified feature or contig.
1478    
1479  =over 4  =over 4
1480    
1481  =item featureID  =item featureID
1482    
1483  ID of the feature whose genome is desired.  ID of the feature or contig whose genome is desired.
1484    
1485  =item RETURN  =item RETURN
1486    
1487  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
1488  an undefined value.  found, returns an undefined value.
1489    
1490  =back  =back
1491    
# Line 1536  Line 1494 
1494  sub GenomeOf {  sub GenomeOf {
1495      # Get the parameters.      # Get the parameters.
1496      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
1497      # Create a query to find the genome associated with the feature.      # Create a query to find the genome associated with the incoming ID.
1498      my $query = $self->Get(['IsLocatedIn', 'HasContig'], "IsLocatedIn(from-link) = ?", [$featureID]);      my $query = $self->Get(['IsLocatedIn', 'HasContig'], "IsLocatedIn(from-link) = ? OR HasContig(to-link) = ?",
1499                               [$featureID, $featureID]);
1500      # Declare the return value.      # Declare the return value.
1501      my $retVal;      my $retVal;
1502      # Get the genome ID.      # Get the genome ID.
# Line 1779  Line 1738 
1738      return join " ", sort @_;      return join " ", sort @_;
1739  }  }
1740    
 =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();  
 }  
   
1741  =head3 ReadFasta  =head3 ReadFasta
1742    
1743  C<< my %sequenceData = Sprout::ReadFasta($fileName, $prefix); >>  C<< my %sequenceData = Sprout::ReadFasta($fileName, $prefix); >>
# Line 1941  Line 1883 
1883      # Get the data directory name.      # Get the data directory name.
1884      my $outputDirectory = $self->{_options}->{dataDir};      my $outputDirectory = $self->{_options}->{dataDir};
1885      # Dump the relations.      # Dump the relations.
1886      $self->{_erdb}->DumpRelations($outputDirectory);      $self->DumpRelations($outputDirectory);
1887  }  }
1888    
1889  =head3 XMLFileName  =head3 XMLFileName
# Line 1993  Line 1935 
1935      # Get the parameters.      # Get the parameters.
1936      my ($self, $objectType, $fieldHash) = @_;      my ($self, $objectType, $fieldHash) = @_;
1937      # Call the underlying method.      # Call the underlying method.
1938      $self->{_erdb}->InsertObject($objectType, $fieldHash);      $self->InsertObject($objectType, $fieldHash);
1939  }  }
1940    
1941  =head3 Annotate  =head3 Annotate
# Line 2724  Line 2666 
2666      return @retVal;      return @retVal;
2667  }  }
2668    
2669    
2670    
2671  =head3 RelatedFeatures  =head3 RelatedFeatures
2672    
2673  C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>  C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>
# Line 2825  Line 2769 
2769      return @retVal;      return @retVal;
2770  }  }
2771    
 =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;  
 }  
   
2772  =head3 Protein  =head3 Protein
2773    
2774  C<< my $protein = Sprout::Protein($sequence, $table); >>  C<< my $protein = Sprout::Protein($sequence, $table); >>
# Line 3045  Line 2870 
2870      # Create the return list, priming it with the name of the data directory.      # Create the return list, priming it with the name of the data directory.
2871      my @retVal = ($self->{_options}->{dataDir});      my @retVal = ($self->{_options}->{dataDir});
2872      # Concatenate the table names.      # Concatenate the table names.
2873      push @retVal, $self->{_erdb}->GetTableNames();      push @retVal, $self->GetTableNames();
2874      # Return the result.      # Return the result.
2875      return @retVal;      return @retVal;
2876  }  }
2877    
2878  =head3 LowBBHs  =head3 LowBBHs
2879    
2880  C<< my %bbhMap = $sprout->GoodBBHs($featureID, $cutoff); >>  C<< my %bbhMap = $sprout->LowBBHs($featureID, $cutoff); >>
2881    
2882  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
2883  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 3215  Line 3040 
3040      return $retVal;      return $retVal;
3041  }  }
3042    
3043    =head3 DeleteGenome
3044    
3045    C<< my $stats = $sprout->DeleteGenome($genomeID, $testFlag); >>
3046    
3047    Delete a genome from the database.
3048    
3049    =over 4
3050    
3051    =item genomeID
3052    
3053    ID of the genome to delete
3054    
3055    =item testFlag
3056    
3057    If TRUE, then the DELETE statements will be traced, but no deletions will occur.
3058    
3059    =item RETURN
3060    
3061    Returns a statistics object describing the rows deleted.
3062    
3063    =back
3064    
3065    =cut
3066    #: Return Type $%;
3067    sub DeleteGenome {
3068        # Get the parameters.
3069        my ($self, $genomeID, $testFlag) = @_;
3070        # Perform the delete for the genome's features.
3071        my $retVal = $self->Delete('Feature', "fig|$genomeID.%", $testFlag);
3072        # Perform the delete for the primary genome data.
3073        my $stats = $self->Delete('Genome', $genomeID, $testFlag);
3074        $retVal->Accumulate($stats);
3075        # Return the result.
3076        return $retVal;
3077    }
3078    
3079  =head2 Internal Utility Methods  =head2 Internal Utility Methods
3080    
3081  =head3 ParseAssignment  =head3 ParseAssignment
# Line 3225  Line 3086 
3086    
3087  A functional assignment is always of the form  A functional assignment is always of the form
3088    
3089      I<XXXX>C<\nset >I<YYYY>C< function to\n>I<ZZZZZ>      C<set >I<YYYY>C< function to\n>I<ZZZZZ>
3090    
3091  where I<XXXX> is the B<assigning user>, I<YYYY> is the B<user>, and I<ZZZZ> is the  where I<YYYY> is the B<user>, and I<ZZZZ> is the actual functional role. In most cases,
3092  actual functional role. In most cases, the user and the assigning user will be the  the user and the assigning user (from MadeAnnotation) will be the same, but that is
3093  same, but that is not always the case.  not always the case.
3094    
3095    In addition, the functional role may contain extra data that is stripped, such as
3096    terminating spaces or a comment separated from the rest of the text by a tab.
3097    
3098  This is a static method.  This is a static method.
3099    
3100  =over 4  =over 4
3101    
3102    =item user
3103    
3104    Name of the assigning user.
3105    
3106  =item text  =item text
3107    
3108  Text of the annotation.  Text of the annotation.
# Line 3250  Line 3118 
3118    
3119  sub _ParseAssignment {  sub _ParseAssignment {
3120      # Get the parameters.      # Get the parameters.
3121      my ($text) = @_;      my ($user, $text) = @_;
3122      # Declare the return value.      # Declare the return value.
3123      my @retVal = ();      my @retVal = ();
3124      # Check to see if this is a functional assignment.      # Check to see if this is a functional assignment.
3125      my ($type, $function) = split(/\n/, $text);      my ($type, $function) = split(/\n/, $text);
3126      if ($type =~ m/^set ([^ ]+) function to$/i) {      if ($type =~ m/^set function to$/i) {
3127          # Here it is, so we return the user name (which is in $1), the functional role text,          # Here we have an assignment without a user, so we use the incoming user ID.
3128          # and the assigning user.          @retVal = ($user, $function);
3129        } elsif ($type =~ m/^set (\S+) function to$/i) {
3130            # Here we have an assignment with a user that is passed back to the caller.
3131          @retVal = ($1, $function);          @retVal = ($1, $function);
3132      }      }
3133        # If we have an assignment, we need to clean the function text. There may be
3134        # extra junk at the end added as a note from the user.
3135        if (@retVal) {
3136            $retVal[1] =~ s/(\t\S)?\s*$//;
3137        }
3138      # Return the result list.      # Return the result list.
3139      return @retVal;      return @retVal;
3140  }  }
# Line 3348  Line 3223 
3223  }  }
3224    
3225    
   
3226  1;  1;

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