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revision 1.25, Sun Sep 11 17:29:52 2005 UTC revision 1.61, Wed Jun 14 20:15:48 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  }  }
204    
205  =head3 LoadUpdate  =head3 LoadUpdate
206    
207  C<< my %stats = $sprout->LoadUpdate($truncateFlag, \@tableList); >>  C<< my $stats = $sprout->LoadUpdate($truncateFlag, \@tableList); >>
208    
209  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
210  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 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;      $self->CreateTables();
411  }  }
412    
413  =head3 Genomes  =head3 Genomes
# Line 610  Line 557 
557          if ($prevContig eq $contigID && $dir eq $prevDir) {          if ($prevContig eq $contigID && $dir eq $prevDir) {
558              # Here the new segment is in the same direction on the same contig. Insure the              # Here the new segment is in the same direction on the same contig. Insure the
559              # new segment's beginning is next to the old segment's end.              # new segment's beginning is next to the old segment's end.
560              if (($dir eq "-" && $beg == $prevBeg - $prevLen) ||              if ($dir eq "-" && $beg + $len == $prevBeg) {
561                  ($dir eq "+" && $beg == $prevBeg + $prevLen)) {                  # Here we're merging two backward blocks, so we keep the new begin point
562                  # Here we need to merge two segments. Adjust the beginning and length values                  # and adjust the length.
563                  # to include both segments.                  $len += $prevLen;
564                    # Pop the old segment off. The new one will replace it later.
565                    pop @retVal;
566                } elsif ($dir eq "+" && $beg == $prevBeg + $prevLen) {
567                    # Here we need to merge two forward blocks. Adjust the beginning and
568                    # length values to include both segments.
569                  $beg = $prevBeg;                  $beg = $prevBeg;
570                  $len += $prevLen;                  $len += $prevLen;
571                  # Pop the old segment off. The new one will replace it later.                  # Pop the old segment off. The new one will replace it later.
# Line 622  Line 574 
574          }          }
575          # Remember this specifier for the adjacent-segment test the next time through.          # Remember this specifier for the adjacent-segment test the next time through.
576          ($prevContig, $prevBeg, $prevDir, $prevLen) = ($contigID, $beg, $dir, $len);          ($prevContig, $prevBeg, $prevDir, $prevLen) = ($contigID, $beg, $dir, $len);
577            # Compute the initial base pair.
578            my $start = ($dir eq "+" ? $beg : $beg + $len - 1);
579          # Add the specifier to the list.          # Add the specifier to the list.
580          push @retVal, "${contigID}_$beg$dir$len";          push @retVal, "${contigID}_$start$dir$len";
581      }      }
582      # Return the list in the format indicated by the context.      # Return the list in the format indicated by the context.
583      return (wantarray ? @retVal : join(',', @retVal));      return (wantarray ? @retVal : join(',', @retVal));
# Line 657  Line 611 
611      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
612      my ($location) = @_;      my ($location) = @_;
613      # Parse it into segments.      # Parse it into segments.
614      $location =~ /^(.*)_(\d*)([+-_])(\d*)$/;      $location =~ /^(.+)_(\d+)([+\-_])(\d+)$/;
615      my ($contigID, $start, $dir, $len) = ($1, $2, $3, $4);      my ($contigID, $start, $dir, $len) = ($1, $2, $3, $4);
616      # If the direction is an underscore, convert it to a + or -.      # If the direction is an underscore, convert it to a + or -.
617      if ($dir eq "_") {      if ($dir eq "_") {
# Line 733  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 = $sprout->DNASeq('83333.1:NC_000913_1401_1532');
694    
695  =over 4  =over 4
696    
697  =item locationList  =item locationList
698    
699  List of location specifiers, each in the form I<contigID>C<_>I<begin>I<dir>I<end> (see  List of location specifiers, each in the form I<contigID>C<_>I<begin>I<dir>I<len> or
700  L</FeatureLocation> for more about this format).  I<contigID>C<_>I<begin>C<_>I<end> (see L</FeatureLocation> for more about this format).
701    
702  =item RETURN  =item RETURN
703    
# Line 765  Line 724 
724          # the start point is the ending. Note that in the latter case we must reverse the DNA string          # the start point is the ending. Note that in the latter case we must reverse the DNA string
725          # before putting it in the return value.          # before putting it in the return value.
726          my ($start, $stop);          my ($start, $stop);
727            Trace("Parse of \"$location\" is $beg$dir$len.") if T(SDNA => 4);
728          if ($dir eq "+") {          if ($dir eq "+") {
729              $start = $beg;              $start = $beg;
730              $stop = $beg + $len - 1;              $stop = $beg + $len - 1;
731          } else {          } else {
732              $start = $beg + $len + 1;              $start = $beg - $len + 1;
733              $stop = $beg;              $stop = $beg;
734          }          }
735            Trace("Looking for sequences containing $start through $stop.") if T(SDNA => 4);
736          my $query = $self->Get(['IsMadeUpOf','Sequence'],          my $query = $self->Get(['IsMadeUpOf','Sequence'],
737              "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .              "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .
738              " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",              " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",
# Line 783  Line 744 
744                  $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)',                  $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)',
745                                     'IsMadeUpOf(len)']);                                     'IsMadeUpOf(len)']);
746              my $stopPosition = $startPosition + $sequenceLength;              my $stopPosition = $startPosition + $sequenceLength;
747                Trace("Sequence is from $startPosition to $stopPosition.") if T(SDNA => 4);
748              # Figure out the start point and length of the relevant section.              # Figure out the start point and length of the relevant section.
749              my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);              my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);
750              my $len = ($stopPosition <= $stop ? $stopPosition : $stop) - $startPosition - $pos1;              my $len1 = ($stopPosition < $stop ? $stopPosition : $stop) + 1 - $startPosition - $pos1;
751                Trace("Position is $pos1 for length $len1.") if T(SDNA => 4);
752              # Add the relevant data to the location data.              # Add the relevant data to the location data.
753              $locationDNA .= substr($sequenceData, $pos1, $len);              $locationDNA .= substr($sequenceData, $pos1, $len1);
754          }          }
755          # Add this location's data to the return string. Note that we may need to reverse it.          # Add this location's data to the return string. Note that we may need to reverse it.
756          if ($dir eq '+') {          if ($dir eq '+') {
757              $retVal .= $locationDNA;              $retVal .= $locationDNA;
758          } else {          } else {
759              $locationDNA = join('', reverse split //, $locationDNA);              $retVal .= FIG::reverse_comp($locationDNA);
             $retVal .= $locationDNA;  
760          }          }
761      }      }
762      # Return the result.      # Return the result.
# Line 864  Line 826 
826      # Set it from the sequence data, if any.      # Set it from the sequence data, if any.
827      if ($sequence) {      if ($sequence) {
828          my ($start, $len) = $sequence->Values(['IsMadeUpOf(start-position)', 'IsMadeUpOf(len)']);          my ($start, $len) = $sequence->Values(['IsMadeUpOf(start-position)', 'IsMadeUpOf(len)']);
829          $retVal = $start + $len;          $retVal = $start + $len - 1;
830        }
831        # Return the result.
832        return $retVal;
833    }
834    
835    =head3 ClusterPEGs
836    
837    C<< my $clusteredList = $sprout->ClusterPEGs($sub, \@pegs); >>
838    
839    Cluster the PEGs in a list according to the cluster coding scheme of the specified
840    subsystem. In order for this to work properly, the subsystem object must have
841    been used recently to retrieve the PEGs using the B<get_pegs_from_cell> method.
842    This causes the cluster numbers to be pulled into the subsystem's color hash.
843    If a PEG is not found in the color hash, it will not appear in the output
844    sequence.
845    
846    =over 4
847    
848    =item sub
849    
850    Sprout subsystem object for the relevant subsystem, from the L</get_subsystem>
851    method.
852    
853    =item pegs
854    
855    Reference to the list of PEGs to be clustered.
856    
857    =item RETURN
858    
859    Returns a list of the PEGs, grouped into smaller lists by cluster number.
860    
861    =back
862    
863    =cut
864    #: Return Type $@@;
865    sub ClusterPEGs {
866        # Get the parameters.
867        my ($self, $sub, $pegs) = @_;
868        # Declare the return variable.
869        my $retVal = [];
870        # Loop through the PEGs, creating arrays for each cluster.
871        for my $pegID (@{$pegs}) {
872            my $clusterNumber = $sub->get_cluster_number($pegID);
873            # Only proceed if the PEG is in a cluster.
874            if ($clusterNumber >= 0) {
875                # Push this PEG onto the sub-list for the specified cluster number.
876                push @{$retVal->[$clusterNumber]}, $pegID;
877            }
878      }      }
879      # Return the result.      # Return the result.
880      return $retVal;      return $retVal;
# Line 1014  Line 1024 
1024    
1025  =head3 FeatureAnnotations  =head3 FeatureAnnotations
1026    
1027  C<< my @descriptors = $sprout->FeatureAnnotations($featureID); >>  C<< my @descriptors = $sprout->FeatureAnnotations($featureID, $rawFlag); >>
1028    
1029  Return the annotations of a feature.  Return the annotations of a feature.
1030    
# Line 1024  Line 1034 
1034    
1035  ID of the feature whose annotations are desired.  ID of the feature whose annotations are desired.
1036    
1037    =item rawFlag
1038    
1039    If TRUE, the annotation timestamps will be returned in raw form; otherwise, they
1040    will be returned in human-readable form.
1041    
1042  =item RETURN  =item RETURN
1043    
1044  Returns a list of annotation descriptors. Each descriptor is a hash with the following fields.  Returns a list of annotation descriptors. Each descriptor is a hash with the following fields.
1045    
1046  * B<featureID> ID of the relevant feature.  * B<featureID> ID of the relevant feature.
1047    
1048  * B<timeStamp> time the annotation was made, in user-friendly format.  * B<timeStamp> time the annotation was made.
1049    
1050  * B<user> ID of the user who made the annotation  * B<user> ID of the user who made the annotation
1051    
# Line 1042  Line 1057 
1057  #: Return Type @%;  #: Return Type @%;
1058  sub FeatureAnnotations {  sub FeatureAnnotations {
1059      # Get the parameters.      # Get the parameters.
1060      my ($self, $featureID) = @_;      my ($self, $featureID, $rawFlag) = @_;
1061      # 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.
1062      my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],      my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1063                             "IsTargetOfAnnotation(from-link) = ?", [$featureID]);                             "IsTargetOfAnnotation(from-link) = ?", [$featureID]);
# Line 1055  Line 1070 
1070              $annotation->Values(['IsTargetOfAnnotation(from-link)',              $annotation->Values(['IsTargetOfAnnotation(from-link)',
1071                                   'Annotation(time)', 'MadeAnnotation(from-link)',                                   'Annotation(time)', 'MadeAnnotation(from-link)',
1072                                   'Annotation(annotation)']);                                   'Annotation(annotation)']);
1073            # Convert the time, if necessary.
1074            if (! $rawFlag) {
1075                $timeStamp = FriendlyTimestamp($timeStamp);
1076            }
1077          # Assemble them into a hash.          # Assemble them into a hash.
1078          my $annotationHash = { featureID => $featureID,          my $annotationHash = { featureID => $featureID,
1079                                 timeStamp => FriendlyTimestamp($timeStamp),                                 timeStamp => $timeStamp,
1080                                 user => $user, text => $text };                                 user => $user, text => $text };
1081          # Add it to the return list.          # Add it to the return list.
1082          push @retVal, $annotationHash;          push @retVal, $annotationHash;
# Line 1086  Line 1105 
1105    
1106  =item RETURN  =item RETURN
1107    
1108  Returns a hash mapping the functional assignment IDs to user IDs.  Returns a hash mapping the user IDs to functional assignment IDs.
1109    
1110  =back  =back
1111    
# Line 1096  Line 1115 
1115      # Get the parameters.      # Get the parameters.
1116      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
1117      # Get all of the feature's annotations.      # Get all of the feature's annotations.
1118      my @query = $self->GetAll(['IsTargetOfAnnotation', 'Annotation'],      my @query = $self->GetAll(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1119                              "IsTargetOfAnnotation(from-link) = ?",                              "IsTargetOfAnnotation(from-link) = ?",
1120                              [$featureID], ['Annotation(time)', 'Annotation(annotation)']);                              [$featureID], ['Annotation(time)', 'Annotation(annotation)',
1121                                               'MadeAnnotation(from-link)']);
1122      # Declare the return hash.      # Declare the return hash.
1123      my %retVal;      my %retVal;
     # Declare a hash for insuring we only make one assignment per user.  
     my %timeHash = ();  
1124      # Now we sort the assignments by timestamp in reverse.      # Now we sort the assignments by timestamp in reverse.
1125      my @sortedQuery = sort { -($a->[0] <=> $b->[0]) } @query;      my @sortedQuery = sort { -($a->[0] <=> $b->[0]) } @query;
1126      # Loop until we run out of annotations.      # Loop until we run out of annotations.
1127      for my $annotation (@sortedQuery) {      for my $annotation (@sortedQuery) {
1128          # Get the annotation fields.          # Get the annotation fields.
1129          my ($timeStamp, $text) = @{$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 ($user, $function) = _ParseAssignment($text);          my ($actualUser, $function) = _ParseAssignment($user, $text);
1132          if ($user && ! exists $timeHash{$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              $retVal{$function} = $user;              $retVal{$actualUser} = $function;
             # Insure we don't assign to this user again.  
             $timeHash{$user} = 1;  
1137          }          }
1138      }      }
1139      # Return the hash of assignments found.      # Return the hash of assignments found.
# Line 1133  Line 1149 
1149  The functional assignment is handled differently depending on the type of feature. If  The functional assignment is handled differently depending on the type of feature. If
1150  the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional  the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional
1151  assignment is a type of annotation. The format of an assignment is described in  assignment is a type of annotation. The format of an assignment is described in
1152  L</ParseLocation>. Its worth noting that we cannot filter on the content of the  L</ParseAssignment>. Its worth noting that we cannot filter on the content of the
1153  annotation itself because it's a text field; however, this is not a big problem because  annotation itself because it's a text field; however, this is not a big problem because
1154  most features only have a small number of annotations.  most features only have a small number of annotations.
1155    
# Line 1195  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 1224  Line 1242 
1242      return $retVal;      return $retVal;
1243  }  }
1244    
1245    =head3 FunctionsOf
1246    
1247    C<< my @functionList = $sprout->FunctionOf($featureID, $userID); >>
1248    
1249    Return the functional assignments of a particular feature.
1250    
1251    The functional assignment is handled differently depending on the type of feature. If
1252    the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional
1253    assignment is a type of annotation. The format of an assignment is described in
1254    L</ParseAssignment>. Its worth noting that we cannot filter on the content of the
1255    annotation itself because it's a text field; however, this is not a big problem because
1256    most features only have a small number of annotations.
1257    
1258    If the feature is B<not> identified by a FIG ID, then the functional assignment
1259    information is taken from the B<ExternalAliasFunc> table. If the table does
1260    not contain an entry for the feature, an empty list is returned.
1261    
1262    =over 4
1263    
1264    =item featureID
1265    
1266    ID of the feature whose functional assignments are desired.
1267    
1268    =item RETURN
1269    
1270    Returns a list of 2-tuples, each consisting of a user ID and the text of an assignment by
1271    that user.
1272    
1273    =back
1274    
1275    =cut
1276    #: Return Type @@;
1277    sub FunctionsOf {
1278        # Get the parameters.
1279        my ($self, $featureID) = @_;
1280        # Declare the return value.
1281        my @retVal = ();
1282        # Determine the ID type.
1283        if ($featureID =~ m/^fig\|/) {
1284            # Here we have a FIG feature ID. We must build the list of trusted
1285            # users.
1286            my %trusteeTable = ();
1287            # Build a query for all of the feature's annotations, sorted by date.
1288            my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1289                                   "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1290                                   [$featureID]);
1291            my $timeSelected = 0;
1292            # Loop until we run out of annotations.
1293            while (my $annotation = $query->Fetch()) {
1294                # Get the annotation text.
1295                my ($text, $time, $user) = $annotation->Values(['Annotation(annotation)',
1296                                                                'Annotation(time)',
1297                                                                'MadeAnnotation(user)']);
1298                # Check to see if this is a functional assignment for a trusted user.
1299                my ($actualUser, $function) = _ParseAssignment($user, $text);
1300                if ($actualUser) {
1301                    # Here it is a functional assignment.
1302                    push @retVal, [$actualUser, $function];
1303                }
1304            }
1305        } else {
1306            # 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
1308            # table.
1309            my @assignments = $self->GetEntityValues('ExternalAliasFunc', $featureID,
1310                                                     ['ExternalAliasFunc(func)']);
1311            push @retVal, map { ['master', $_] } @assignments;
1312        }
1313        # Return the assignments found.
1314        return @retVal;
1315    }
1316    
1317  =head3 BBHList  =head3 BBHList
1318    
1319  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>
# Line 1261  Line 1351 
1351          my $query = $self->Get(['IsBidirectionalBestHitOf'],          my $query = $self->Get(['IsBidirectionalBestHitOf'],
1352                                 "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",                                 "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",
1353                                 [$featureID, $genomeID]);                                 [$featureID, $genomeID]);
1354          # Look for the best hit.          # Peel off the BBHs found.
1355          my $bbh = $query->Fetch;          my @found = ();
1356          if ($bbh) {          while (my $bbh = $query->Fetch) {
1357              my ($targetFeature) = $bbh->Value('IsBidirectionalBestHitOf(to-link)');              push @found, $bbh->Value('IsBidirectionalBestHitOf(to-link)');
             $retVal{$featureID} = $targetFeature;  
1358          }          }
1359            $retVal{$featureID} = \@found;
1360      }      }
1361      # Return the mapping.      # Return the mapping.
1362      return \%retVal;      return \%retVal;
# Line 1344  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 1384  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 1404  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 $retVal;
1502      # Get the genome ID.      # Get the genome ID.
# Line 1452  Line 1543 
1543          # Get the ID and score of the coupling.          # Get the ID and score of the coupling.
1544          my ($couplingID, $score) = $clustering->Values(['Coupling(id)',          my ($couplingID, $score) = $clustering->Values(['Coupling(id)',
1545                                                          'Coupling(score)']);                                                          'Coupling(score)']);
1546          # The coupling ID contains the two feature IDs separated by a space. We use          # Get the other feature that participates in the coupling.
1547          # this information to find the ID of the other feature.          my ($otherFeatureID) = $self->GetFlat(['ParticipatesInCoupling'],
1548          my ($fid1, $fid2) = split / /, $couplingID;                                             "ParticipatesInCoupling(to-link) = ? AND ParticipatesInCoupling(from-link) <> ?",
1549          my $otherFeatureID = ($featureID eq $fid1 ? $fid2 : $fid1);                                             [$couplingID, $featureID], 'ParticipatesInCoupling(from-link)');
1550          # Attach the other feature's score to its ID.          # Attach the other feature's score to its ID.
1551          $retVal{$otherFeatureID} = $score;          $retVal{$otherFeatureID} = $score;
1552          $found = 1;          $found = 1;
# Line 1647  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 1809  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 1861  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, $fieldHash);
1939  }  }
1940    
1941  =head3 Annotate  =head3 Annotate
# Line 2048  Line 2122 
2122      # Get the parameters.      # Get the parameters.
2123      my ($self, $entityName, $entityID) = @_;      my ($self, $entityName, $entityID) = @_;
2124      # Check for the entity instance.      # Check for the entity instance.
2125        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
2126      my $testInstance = $self->GetEntity($entityName, $entityID);      my $testInstance = $self->GetEntity($entityName, $entityID);
2127      # Return an existence indicator.      # Return an existence indicator.
2128      my $retVal = ($testInstance ? 1 : 0);      my $retVal = ($testInstance ? 1 : 0);
# Line 2541  Line 2616 
2616                                      ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);                                      ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);
2617      # Create the return value.      # Create the return value.
2618      my %retVal = ();      my %retVal = ();
2619        # Build a hash to weed out duplicates. Sometimes the same PEG and role appears
2620        # in two spreadsheet cells.
2621        my %dupHash = ();
2622      # Loop through the results, adding them to the hash.      # Loop through the results, adding them to the hash.
2623      for my $record (@subsystems) {      for my $record (@subsystems) {
2624            # Get this subsystem and role.
2625          my ($subsys, $role) = @{$record};          my ($subsys, $role) = @{$record};
2626          if (exists $retVal{$subsys}) {          # Insure it's the first time for both.
2627            my $dupKey = "$subsys\n$role";
2628            if (! exists $dupHash{"$subsys\n$role"}) {
2629                $dupHash{$dupKey} = 1;
2630              push @{$retVal{$subsys}}, $role;              push @{$retVal{$subsys}}, $role;
         } else {  
             $retVal{$subsys} = [$role];  
2631          }          }
2632      }      }
2633      # Return the hash.      # Return the hash.
# Line 2586  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 2687  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, $table); >>
# Line 2907  Line 2870 
2870      # Create the return list, priming it with the name of the data directory.      # Create the return list, priming it with the name of the data directory.
2871      my @retVal = ($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 3077  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 $retVal;
3077    }
3078    
3079  =head2 Internal Utility Methods  =head2 Internal Utility Methods
3080    
3081  =head3 ParseAssignment  =head3 ParseAssignment
# Line 3087  Line 3086 
3086    
3087  A functional assignment is always of the form  A functional assignment is always of the form
3088    
3089      I<XXXX>C<\nset >I<YYYY>C< function to\n>I<ZZZZZ>      C<set >I<YYYY>C< function to\n>I<ZZZZZ>
3090    
3091  where I<XXXX> is the B<assigning user>, I<YYYY> is the B<user>, and I<ZZZZ> is the  where I<YYYY> is the B<user>, and I<ZZZZ> is the actual functional role. In most cases,
3092  actual functional role. In most cases, the user and the assigning user will be the  the user and the assigning user (from MadeAnnotation) will be the same, but that is
3093  same, but that is not always the case.  not always the case.
3094    
3095    In addition, the functional role may contain extra data that is stripped, such as
3096    terminating spaces or a comment separated from the rest of the text by a tab.
3097    
3098  This is a static method.  This is a static method.
3099    
3100  =over 4  =over 4
3101    
3102    =item user
3103    
3104    Name of the assigning user.
3105    
3106  =item text  =item text
3107    
3108  Text of the annotation.  Text of the annotation.
# Line 3112  Line 3118 
3118    
3119  sub _ParseAssignment {  sub _ParseAssignment {
3120      # Get the parameters.      # Get the parameters.
3121      my ($text) = @_;      my ($user, $text) = @_;
3122      # Declare the return value.      # Declare the return value.
3123      my @retVal = ();      my @retVal = ();
3124      # Check to see if this is a functional assignment.      # Check to see if this is a functional assignment.
3125      my ($user, $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          @retVal = ($1, $function, $user);      } elsif ($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);
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;
# Line 3148  Line 3161 
3161    
3162  sub FriendlyTimestamp {  sub FriendlyTimestamp {
3163      my ($timeValue) = @_;      my ($timeValue) = @_;
3164      my $retVal = strftime("%a %b %e %H:%M:%S %Y", localtime($timeValue));      my $retVal = localtime($timeValue);
3165      return $retVal;      return $retVal;
3166  }  }
3167    
# Line 3210  Line 3223 
3223  }  }
3224    
3225    
   
3226  1;  1;

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