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revision 1.19, Sun Aug 14 23:32:08 2005 UTC revision 1.69, Fri Jun 23 01:34:42 2006 UTC
# Line 1  Line 1 
1  package Sprout;  package Sprout;
2    
3        require Exporter;
4        use ERDB;
5        @ISA = qw(Exporter ERDB);
6      use Data::Dumper;      use Data::Dumper;
7      use strict;      use strict;
8      use Carp;      use Carp;
# Line 7  Line 10 
10      use XML::Simple;      use XML::Simple;
11      use DBQuery;      use DBQuery;
12      use DBObject;      use DBObject;
     use ERDB;  
13      use Tracer;      use Tracer;
14      use FIGRules;      use FIGRules;
15      use Stats;      use Stats;
# Line 32  Line 34 
34  query tasks. For example, L</genomes> lists the IDs of all the genomes in the database and  query tasks. For example, L</genomes> lists the IDs of all the genomes in the database and
35  L</dna_seq> returns the DNA sequence for a specified genome location.  L</dna_seq> returns the DNA sequence for a specified genome location.
36    
37    The Sprout object is a subclass of the ERDB object and inherits all its properties and methods.
38    
39  =cut  =cut
40    
41  #: Constructor SFXlate->new_sprout_only();  #: Constructor SFXlate->new_sprout_only();
# Line 62  Line 66 
66    
67  * B<xmlFileName> name of the XML file containing the database definition (default C<SproutDBD.xml>)  * B<xmlFileName> name of the XML file containing the database definition (default C<SproutDBD.xml>)
68    
69  * B<userData> user name and password, delimited by a slash (default C<root/>)  * B<userData> user name and password, delimited by a slash (default same as SEED)
70    
71  * B<port> connection port (default C<0>)  * B<port> connection port (default C<0>)
72    
73    * B<sock> connection socket (default same as SEED)
74    
75  * B<maxSegmentLength> maximum number of residues per feature segment, (default C<4500>)  * B<maxSegmentLength> maximum number of residues per feature segment, (default C<4500>)
76    
77  * B<maxSequenceLength> maximum number of residues per sequence, (default C<8000>)  * B<maxSequenceLength> maximum number of residues per sequence, (default C<8000>)
78    
79    * B<noDBOpen> suppresses the connection to the database if TRUE, else FALSE
80    
81  =back  =back
82    
83  For example, the following constructor call specifies a database named I<Sprout> and a user name of  For example, the following constructor call specifies a database named I<Sprout> and a user name of
# Line 90  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
111                        }, $options);                        }, $options);
112      # Get the data directory.      # Get the data directory.
113      my $dataDir = $optionTable->{dataDir};      my $dataDir = $optionTable->{dataDir};
# Line 105  Line 115 
115      $optionTable->{userData} =~ m!([^/]*)/(.*)$!;      $optionTable->{userData} =~ m!([^/]*)/(.*)$!;
116      my ($userName, $password) = ($1, $2);      my ($userName, $password) = ($1, $2);
117      # Connect to the database.      # Connect to the database.
118      my $dbh = DBKernel->new($optionTable->{dbType}, $dbName, $userName, $password, $optionTable->{port});      my $dbh;
119        if (! $optionTable->{noDBOpen}) {
120            $dbh = DBKernel->new($optionTable->{dbType}, $dbName, $userName,
121                                    $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 148  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 372  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 415  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 430  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 439  Line 259 
259      return $retVal;      return $retVal;
260  }  }
261    
262    =head3 GenomeCounts
263    
264    C<< my ($arch, $bact, $euk, $vir, $env, $unk) = $sprout->GenomeCounts($complete); >>
265    
266    Count the number of genomes in each domain. If I<$complete> is TRUE, only complete
267    genomes will be included in the counts.
268    
269    =over 4
270    
271    =item complete
272    
273    TRUE if only complete genomes are to be counted, FALSE if all genomes are to be
274    counted
275    
276    =item RETURN
277    
278    A six-element list containing the number of genomes in each of six categories--
279    Archaea, Bacteria, Eukaryota, Viral, Environmental, and Unknown, respectively.
280    
281    =back
282    
283    =cut
284    
285    sub GenomeCounts {
286        # Get the parameters.
287        my ($self, $complete) = @_;
288        # Set the filter based on the completeness flag.
289        my $filter = ($complete ? "Genome(complete) = 1" : "");
290        # Get all the genomes and the related taxonomy information.
291        my @genomes = $self->GetAll(['Genome'], $filter, [], ['Genome(id)', 'Genome(taxonomy)']);
292        # Clear the counters.
293        my ($arch, $bact, $euk, $vir, $env, $unk) = (0, 0, 0, 0, 0, 0);
294        # Loop through, counting the domains.
295        for my $genome (@genomes) {
296            if    ($genome->[1] =~ /^archaea/i)  { ++$arch }
297            elsif ($genome->[1] =~ /^bacter/i)   { ++$bact }
298            elsif ($genome->[1] =~ /^eukar/i)    { ++$euk }
299            elsif ($genome->[1] =~ /^vir/i)      { ++$vir }
300            elsif ($genome->[1] =~ /^env/i)      { ++$env }
301            else  { ++$unk }
302        }
303        # Return the counts.
304        return ($arch, $bact, $euk, $vir, $env, $unk);
305    }
306    
307    =head3 ContigCount
308    
309    C<< my $count = $sprout->ContigCount($genomeID); >>
310    
311    Return the number of contigs for the specified genome ID.
312    
313    =over 4
314    
315    =item genomeID
316    
317    ID of the genome whose contig count is desired.
318    
319    =item RETURN
320    
321    Returns the number of contigs for the specified genome.
322    
323    =back
324    
325    =cut
326    
327    sub ContigCount {
328        # Get the parameters.
329        my ($self, $genomeID) = @_;
330        # Get the contig count.
331        my $retVal = $self->GetCount(['Contig', 'HasContig'], "HasContig(from-link) = ?", [$genomeID]);
332        # Return the result.
333        return $retVal;
334    }
335    
336    =head3 GeneMenu
337    
338    C<< my $selectHtml = $sprout->GeneMenu(\%attributes, $filterString, \@params); >>
339    
340    Return an HTML select menu of genomes. Each genome will be an option in the menu,
341    and will be displayed by name with the ID and a contig count attached. The selection
342    value will be the genome ID. The genomes will be sorted by genus/species name.
343    
344    =over 4
345    
346    =item attributes
347    
348    Reference to a hash mapping attributes to values for the SELECT tag generated.
349    
350    =item filterString
351    
352    A filter string for use in selecting the genomes. The filter string must conform
353    to the rules for the C<< ERDB->Get >> method.
354    
355    =item params
356    
357    Reference to a list of values to be substituted in for the parameter marks in
358    the filter string.
359    
360    =item RETURN
361    
362    Returns an HTML select menu with the specified genomes as selectable options.
363    
364    =back
365    
366    =cut
367    
368    sub GeneMenu {
369        # Get the parameters.
370        my ($self, $attributes, $filterString, $params) = @_;
371        # Start the menu.
372        my $retVal = "<select " .
373            join(" ", map { "$_=\"$attributes->{$_}\"" } keys %{$attributes}) .
374            ">\n";
375        # Get the genomes.
376        my @genomes = $self->GetAll(['Genome'], $filterString, $params, ['Genome(id)',
377                                                                         'Genome(genus)',
378                                                                         'Genome(species)',
379                                                                         'Genome(unique-characterization)']);
380        # Sort them by name.
381        my @sorted = sort { lc("$a->[1] $a->[2]") cmp lc("$b->[1] $b->[2]") } @genomes;
382        # Loop through the genomes, creating the option tags.
383        for my $genomeData (@sorted) {
384            # Get the data for this genome.
385            my ($genomeID, $genus, $species, $strain) = @{$genomeData};
386            # Get the contig count.
387            my $count = $self->ContigCount($genomeID);
388            my $counting = ($count == 1 ? "contig" : "contigs");
389            # Build the option tag.
390            $retVal .= "<option value=\"$genomeID\">$genus $species $strain ($genomeID) [$count $counting]</option>\n";
391        }
392        # Close the SELECT tag.
393        $retVal .= "</select>\n";
394        # Return the result.
395        return $retVal;
396    }
397  =head3 Build  =head3 Build
398    
399  C<< $sprout->Build(); >>  C<< $sprout->Build(); >>
# Line 453  Line 408 
408      # Get the parameters.      # Get the parameters.
409      my ($self) = @_;      my ($self) = @_;
410      # Create the tables.      # Create the tables.
411      $self->{_erdb}->CreateTables;      $self->CreateTables();
412  }  }
413    
414  =head3 Genomes  =head3 Genomes
# Line 576  Line 531 
531  =item RETURN  =item RETURN
532    
533  Returns a list of the feature's contig segments. The locations are returned as a list in a list  Returns a list of the feature's contig segments. The locations are returned as a list in a list
534  context and as a space-delimited string in a scalar context.  context and as a comma-delimited string in a scalar context.
535    
536  =back  =back
537    
# Line 603  Line 558 
558          if ($prevContig eq $contigID && $dir eq $prevDir) {          if ($prevContig eq $contigID && $dir eq $prevDir) {
559              # Here the new segment is in the same direction on the same contig. Insure the              # Here the new segment is in the same direction on the same contig. Insure the
560              # new segment's beginning is next to the old segment's end.              # new segment's beginning is next to the old segment's end.
561              if (($dir eq "-" && $beg == $prevBeg - $prevLen) ||              if ($dir eq "-" && $beg + $len == $prevBeg) {
562                  ($dir eq "+" && $beg == $prevBeg + $prevLen)) {                  # Here we're merging two backward blocks, so we keep the new begin point
563                  # Here we need to merge two segments. Adjust the beginning and length values                  # and adjust the length.
564                  # to include both segments.                  $len += $prevLen;
565                    # Pop the old segment off. The new one will replace it later.
566                    pop @retVal;
567                } elsif ($dir eq "+" && $beg == $prevBeg + $prevLen) {
568                    # Here we need to merge two forward blocks. Adjust the beginning and
569                    # length values to include both segments.
570                  $beg = $prevBeg;                  $beg = $prevBeg;
571                  $len += $prevLen;                  $len += $prevLen;
572                  # Pop the old segment off. The new one will replace it later.                  # Pop the old segment off. The new one will replace it later.
# Line 615  Line 575 
575          }          }
576          # Remember this specifier for the adjacent-segment test the next time through.          # Remember this specifier for the adjacent-segment test the next time through.
577          ($prevContig, $prevBeg, $prevDir, $prevLen) = ($contigID, $beg, $dir, $len);          ($prevContig, $prevBeg, $prevDir, $prevLen) = ($contigID, $beg, $dir, $len);
578            # Compute the initial base pair.
579            my $start = ($dir eq "+" ? $beg : $beg + $len - 1);
580          # Add the specifier to the list.          # Add the specifier to the list.
581          push @retVal, "${contigID}_$beg$dir$len";          push @retVal, "${contigID}_$start$dir$len";
582      }      }
583      # Return the list in the format indicated by the context.      # Return the list in the format indicated by the context.
584      return (wantarray ? @retVal : join(' ', @retVal));      return (wantarray ? @retVal : join(',', @retVal));
585  }  }
586    
587  =head3 ParseLocation  =head3 ParseLocation
# Line 650  Line 612 
612      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
613      my ($location) = @_;      my ($location) = @_;
614      # Parse it into segments.      # Parse it into segments.
615      $location =~ /^(.*)_(\d*)([+-_])(\d*)$/;      $location =~ /^(.+)_(\d+)([+\-_])(\d+)$/;
616      my ($contigID, $start, $dir, $len) = ($1, $2, $3, $4);      my ($contigID, $start, $dir, $len) = ($1, $2, $3, $4);
617      # If the direction is an underscore, convert it to a + or -.      # If the direction is an underscore, convert it to a + or -.
618      if ($dir eq "_") {      if ($dir eq "_") {
# Line 726  Line 688 
688  should be of the form returned by L</featureLocation> when in a list context. In other words,  should be of the form returned by L</featureLocation> when in a list context. In other words,
689  each location is of the form I<contigID>C<_>I<begin>I<dir>I<end>.  each location is of the form I<contigID>C<_>I<begin>I<dir>I<end>.
690    
691    For example, the following would return the DNA sequence for contig C<83333.1:NC_000913>
692    between positions 1401 and 1532, inclusive.
693    
694        my $sequence = $sprout->DNASeq('83333.1:NC_000913_1401_1532');
695    
696  =over 4  =over 4
697    
698  =item locationList  =item locationList
699    
700  List of location specifiers, each in the form I<contigID>C<_>I<begin>I<dir>I<end> (see  List of location specifiers, each in the form I<contigID>C<_>I<begin>I<dir>I<len> or
701  L</FeatureLocation> for more about this format).  I<contigID>C<_>I<begin>C<_>I<end> (see L</FeatureLocation> for more about this format).
702    
703  =item RETURN  =item RETURN
704    
# Line 758  Line 725 
725          # the start point is the ending. Note that in the latter case we must reverse the DNA string          # the start point is the ending. Note that in the latter case we must reverse the DNA string
726          # before putting it in the return value.          # before putting it in the return value.
727          my ($start, $stop);          my ($start, $stop);
728            Trace("Parse of \"$location\" is $beg$dir$len.") if T(SDNA => 4);
729          if ($dir eq "+") {          if ($dir eq "+") {
730              $start = $beg;              $start = $beg;
731              $stop = $beg + $len - 1;              $stop = $beg + $len - 1;
732          } else {          } else {
733              $start = $beg + $len + 1;              $start = $beg - $len + 1;
734              $stop = $beg;              $stop = $beg;
735          }          }
736            Trace("Looking for sequences containing $start through $stop.") if T(SDNA => 4);
737          my $query = $self->Get(['IsMadeUpOf','Sequence'],          my $query = $self->Get(['IsMadeUpOf','Sequence'],
738              "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .              "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .
739              " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",              " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",
# Line 776  Line 745 
745                  $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)',                  $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)',
746                                     'IsMadeUpOf(len)']);                                     'IsMadeUpOf(len)']);
747              my $stopPosition = $startPosition + $sequenceLength;              my $stopPosition = $startPosition + $sequenceLength;
748                Trace("Sequence is from $startPosition to $stopPosition.") if T(SDNA => 4);
749              # Figure out the start point and length of the relevant section.              # Figure out the start point and length of the relevant section.
750              my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);              my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);
751              my $len = ($stopPosition <= $stop ? $stopPosition : $stop) - $startPosition - $pos1;              my $len1 = ($stopPosition < $stop ? $stopPosition : $stop) + 1 - $startPosition - $pos1;
752                Trace("Position is $pos1 for length $len1.") if T(SDNA => 4);
753              # Add the relevant data to the location data.              # Add the relevant data to the location data.
754              $locationDNA .= substr($sequenceData, $pos1, $len);              $locationDNA .= substr($sequenceData, $pos1, $len1);
755          }          }
756          # Add this location's data to the return string. Note that we may need to reverse it.          # Add this location's data to the return string. Note that we may need to reverse it.
757          if ($dir eq '+') {          if ($dir eq '+') {
758              $retVal .= $locationDNA;              $retVal .= $locationDNA;
759          } else {          } else {
760              $locationDNA = join('', reverse split //, $locationDNA);              $retVal .= FIG::reverse_comp($locationDNA);
             $retVal .= $locationDNA;  
761          }          }
762      }      }
763      # Return the result.      # Return the result.
# Line 824  Line 794 
794      return @retVal;      return @retVal;
795  }  }
796    
797    =head3 GenomeLength
798    
799    C<< my $length = $sprout->GenomeLength($genomeID); >>
800    
801    Return the length of the specified genome in base pairs.
802    
803    =over 4
804    
805    =item genomeID
806    
807    ID of the genome whose base pair count is desired.
808    
809    =item RETURN
810    
811    Returns the number of base pairs in all the contigs of the specified
812    genome.
813    
814    =back
815    
816    =cut
817    
818    sub GenomeLength {
819        # Get the parameters.
820        my ($self, $genomeID) = @_;
821        # Declare the return variable.
822        my $retVal = 0;
823        # Get the genome's contig sequence lengths.
824        my @lens = $self->GetFlat(['HasContig', 'IsMadeUpOf'], 'HasContig(from-link) = ?',
825                           [$genomeID], 'IsMadeUpOf(len)');
826        # Sum the lengths.
827        map { $retVal += $_ } @lens;
828        # Return the result.
829        return $retVal;
830    }
831    
832    =head3 FeatureCount
833    
834    C<< my $count = $sprout->FeatureCount($genomeID, $type); >>
835    
836    Return the number of features of the specified type in the specified genome.
837    
838    =over 4
839    
840    =item genomeID
841    
842    ID of the genome whose feature count is desired.
843    
844    =item type
845    
846    Type of feature to count (eg. C<peg>, C<rna>, etc.).
847    
848    =item RETURN
849    
850    Returns the number of features of the specified type for the specified genome.
851    
852    =back
853    
854    =cut
855    
856    sub FeatureCount {
857        # Get the parameters.
858        my ($self, $genomeID, $type) = @_;
859        # Compute the count.
860        my $retVal = $self->GetCount(['HasFeature', 'Feature'],
861                                    "HasFeature(from-link) = ? AND Feature(feature-type) = ?",
862                                    [$genomeID, $type]);
863        # Return the result.
864        return $retVal;
865    }
866    
867    =head3 GenomeAssignments
868    
869    C<< my $fidHash = $sprout->GenomeAssignments($genomeID); >>
870    
871    Return a list of a genome's assigned features. The return hash will contain each
872    assigned feature of the genome mapped to the text of its most recent functional
873    assignment.
874    
875    =over 4
876    
877    =item genomeID
878    
879    ID of the genome whose functional assignments are desired.
880    
881    =item RETURN
882    
883    Returns a reference to a hash which maps each feature to its most recent
884    functional assignment.
885    
886    =back
887    
888    =cut
889    
890    sub GenomeAssignments {
891        # Get the parameters.
892        my ($self, $genomeID) = @_;
893        # Declare the return variable.
894        my $retVal = {};
895        # Query the genome's features and annotations. We'll put the oldest annotations
896        # first so that the last assignment to go into the hash will be the correct one.
897        my $query = $self->Get(['HasFeature', 'IsTargetOfAnnotation', 'Annotation'],
898                               "HasFeature(from-link) = ? ORDER BY Annotation(time)",
899                               [$genomeID]);
900        # Loop through the annotations.
901        while (my $data = $query->Fetch) {
902            # Get the feature ID and annotation text.
903            my ($fid, $annotation) = $data->Values(['HasFeature(to-link)',
904                                                    'Annotation(annotation)']);
905            # Check to see if this is an assignment. Note that the user really
906            # doesn't matter to us, other than we use it to determine whether or
907            # not this is an assignment.
908            my ($user, $assignment) = _ParseAssignment('fig', $annotation);
909            if ($user) {
910                # Here it's an assignment. We put it in the return hash, overwriting
911                # any older assignment that might be present.
912                $retVal->{$fid} = $assignment;
913            }
914        }
915        # Return the result.
916        return $retVal;
917    }
918    
919  =head3 ContigLength  =head3 ContigLength
920    
921  C<< my $length = $sprout->ContigLength($contigID); >>  C<< my $length = $sprout->ContigLength($contigID); >>
# Line 857  Line 949 
949      # Set it from the sequence data, if any.      # Set it from the sequence data, if any.
950      if ($sequence) {      if ($sequence) {
951          my ($start, $len) = $sequence->Values(['IsMadeUpOf(start-position)', 'IsMadeUpOf(len)']);          my ($start, $len) = $sequence->Values(['IsMadeUpOf(start-position)', 'IsMadeUpOf(len)']);
952          $retVal = $start + $len;          $retVal = $start + $len - 1;
953        }
954        # Return the result.
955        return $retVal;
956    }
957    
958    =head3 ClusterPEGs
959    
960    C<< my $clusteredList = $sprout->ClusterPEGs($sub, \@pegs); >>
961    
962    Cluster the PEGs in a list according to the cluster coding scheme of the specified
963    subsystem. In order for this to work properly, the subsystem object must have
964    been used recently to retrieve the PEGs using the B<get_pegs_from_cell> method.
965    This causes the cluster numbers to be pulled into the subsystem's color hash.
966    If a PEG is not found in the color hash, it will not appear in the output
967    sequence.
968    
969    =over 4
970    
971    =item sub
972    
973    Sprout subsystem object for the relevant subsystem, from the L</get_subsystem>
974    method.
975    
976    =item pegs
977    
978    Reference to the list of PEGs to be clustered.
979    
980    =item RETURN
981    
982    Returns a list of the PEGs, grouped into smaller lists by cluster number.
983    
984    =back
985    
986    =cut
987    #: Return Type $@@;
988    sub ClusterPEGs {
989        # Get the parameters.
990        my ($self, $sub, $pegs) = @_;
991        # Declare the return variable.
992        my $retVal = [];
993        # Loop through the PEGs, creating arrays for each cluster.
994        for my $pegID (@{$pegs}) {
995            my $clusterNumber = $sub->get_cluster_number($pegID);
996            # Only proceed if the PEG is in a cluster.
997            if ($clusterNumber >= 0) {
998                # Push this PEG onto the sub-list for the specified cluster number.
999                push @{$retVal->[$clusterNumber]}, $pegID;
1000            }
1001      }      }
1002      # Return the result.      # Return the result.
1003      return $retVal;      return $retVal;
# Line 1007  Line 1147 
1147    
1148  =head3 FeatureAnnotations  =head3 FeatureAnnotations
1149    
1150  C<< my @descriptors = $sprout->FeatureAnnotations($featureID); >>  C<< my @descriptors = $sprout->FeatureAnnotations($featureID, $rawFlag); >>
1151    
1152  Return the annotations of a feature.  Return the annotations of a feature.
1153    
# Line 1017  Line 1157 
1157    
1158  ID of the feature whose annotations are desired.  ID of the feature whose annotations are desired.
1159    
1160    =item rawFlag
1161    
1162    If TRUE, the annotation timestamps will be returned in raw form; otherwise, they
1163    will be returned in human-readable form.
1164    
1165  =item RETURN  =item RETURN
1166    
1167  Returns a list of annotation descriptors. Each descriptor is a hash with the following fields.  Returns a list of annotation descriptors. Each descriptor is a hash with the following fields.
1168    
1169  * B<featureID> ID of the relevant feature.  * B<featureID> ID of the relevant feature.
1170    
1171  * B<timeStamp> time the annotation was made, in user-friendly format.  * B<timeStamp> time the annotation was made.
1172    
1173  * B<user> ID of the user who made the annotation  * B<user> ID of the user who made the annotation
1174    
# Line 1035  Line 1180 
1180  #: Return Type @%;  #: Return Type @%;
1181  sub FeatureAnnotations {  sub FeatureAnnotations {
1182      # Get the parameters.      # Get the parameters.
1183      my ($self, $featureID) = @_;      my ($self, $featureID, $rawFlag) = @_;
1184      # 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.
1185      my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],      my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1186                             "IsTargetOfAnnotation(from-link) = ?", [$featureID]);                             "IsTargetOfAnnotation(from-link) = ?", [$featureID]);
# Line 1048  Line 1193 
1193              $annotation->Values(['IsTargetOfAnnotation(from-link)',              $annotation->Values(['IsTargetOfAnnotation(from-link)',
1194                                   'Annotation(time)', 'MadeAnnotation(from-link)',                                   'Annotation(time)', 'MadeAnnotation(from-link)',
1195                                   'Annotation(annotation)']);                                   'Annotation(annotation)']);
1196            # Convert the time, if necessary.
1197            if (! $rawFlag) {
1198                $timeStamp = FriendlyTimestamp($timeStamp);
1199            }
1200          # Assemble them into a hash.          # Assemble them into a hash.
1201          my $annotationHash = { featureID => $featureID,          my $annotationHash = { featureID => $featureID,
1202                                 timeStamp => FriendlyTimestamp($timeStamp),                                 timeStamp => $timeStamp,
1203                                 user => $user, text => $text };                                 user => $user, text => $text };
1204          # Add it to the return list.          # Add it to the return list.
1205          push @retVal, $annotationHash;          push @retVal, $annotationHash;
# Line 1079  Line 1228 
1228    
1229  =item RETURN  =item RETURN
1230    
1231  Returns a hash mapping the functional assignment IDs to user IDs.  Returns a hash mapping the user IDs to functional assignment IDs.
1232    
1233  =back  =back
1234    
# Line 1089  Line 1238 
1238      # Get the parameters.      # Get the parameters.
1239      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
1240      # Get all of the feature's annotations.      # Get all of the feature's annotations.
1241      my @query = $self->GetAll(['IsTargetOfAnnotation', 'Annotation'],      my @query = $self->GetAll(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1242                              "IsTargetOfAnnotation(from-link) = ?",                              "IsTargetOfAnnotation(from-link) = ?",
1243                              [$featureID], ['Annotation(time)', 'Annotation(annotation)']);                              [$featureID], ['Annotation(time)', 'Annotation(annotation)',
1244                                               'MadeAnnotation(from-link)']);
1245      # Declare the return hash.      # Declare the return hash.
1246      my %retVal;      my %retVal;
     # Declare a hash for insuring we only make one assignment per user.  
     my %timeHash = ();  
1247      # Now we sort the assignments by timestamp in reverse.      # Now we sort the assignments by timestamp in reverse.
1248      my @sortedQuery = sort { -($a->[0] <=> $b->[0]) } @query;      my @sortedQuery = sort { -($a->[0] <=> $b->[0]) } @query;
1249      # Loop until we run out of annotations.      # Loop until we run out of annotations.
1250      for my $annotation (@sortedQuery) {      for my $annotation (@sortedQuery) {
1251          # Get the annotation fields.          # Get the annotation fields.
1252          my ($timeStamp, $text) = @{$annotation};          my ($timeStamp, $text, $user) = @{$annotation};
1253          # Check to see if this is a functional assignment.          # Check to see if this is a functional assignment.
1254          my ($user, $function) = _ParseAssignment($text);          my ($actualUser, $function) = _ParseAssignment($user, $text);
1255          if ($user && ! exists $timeHash{$user}) {          if ($actualUser && ! exists $retVal{$actualUser}) {
1256              # Here it is a functional assignment and there has been no              # Here it is a functional assignment and there has been no
1257              # previous assignment for this user, so we stuff it in the              # previous assignment for this user, so we stuff it in the
1258              # return hash.              # return hash.
1259              $retVal{$function} = $user;              $retVal{$actualUser} = $function;
             # Insure we don't assign to this user again.  
             $timeHash{$user} = 1;  
1260          }          }
1261      }      }
1262      # Return the hash of assignments found.      # Return the hash of assignments found.
# Line 1126  Line 1272 
1272  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
1273  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
1274  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
1275  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
1276  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
1277  most features only have a small number of annotations.  most features only have a small number of annotations.
1278    
# Line 1188  Line 1334 
1334              }              }
1335          }          }
1336          # 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.
1337          my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation'],          my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1338                                 "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",                                 "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1339                                 [$featureID]);                                 [$featureID]);
1340          my $timeSelected = 0;          my $timeSelected = 0;
1341          # Loop until we run out of annotations.          # Loop until we run out of annotations.
1342          while (my $annotation = $query->Fetch()) {          while (my $annotation = $query->Fetch()) {
1343              # Get the annotation text.              # Get the annotation text.
1344              my ($text, $time) = $annotation->Values(['Annotation(annotation)','Annotation(time)']);              my ($text, $time, $user) = $annotation->Values(['Annotation(annotation)',
1345                                                         'Annotation(time)', 'MadeAnnotation(from-link)']);
1346              # Check to see if this is a functional assignment for a trusted user.              # Check to see if this is a functional assignment for a trusted user.
1347              my ($user, $function) = _ParseAssignment($text);              my ($actualUser, $function) = _ParseAssignment($user, $text);
1348              if ($user) {              Trace("Assignment user is $actualUser, text is $function.") if T(4);
1349                if ($actualUser) {
1350                  # Here it is a functional assignment. Check the time and the user                  # Here it is a functional assignment. Check the time and the user
1351                  # name. The time must be recent and the user must be trusted.                  # name. The time must be recent and the user must be trusted.
1352                  if ((exists $trusteeTable{$user}) && ($time > $timeSelected)) {                  if ((exists $trusteeTable{$actualUser}) && ($time > $timeSelected)) {
1353                      $retVal = $function;                      $retVal = $function;
1354                      $timeSelected = $time;                      $timeSelected = $time;
1355                  }                  }
# Line 1217  Line 1365 
1365      return $retVal;      return $retVal;
1366  }  }
1367    
1368    =head3 FunctionsOf
1369    
1370    C<< my @functionList = $sprout->FunctionOf($featureID, $userID); >>
1371    
1372    Return the functional assignments of a particular feature.
1373    
1374    The functional assignment is handled differently depending on the type of feature. If
1375    the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional
1376    assignment is a type of annotation. The format of an assignment is described in
1377    L</ParseAssignment>. Its worth noting that we cannot filter on the content of the
1378    annotation itself because it's a text field; however, this is not a big problem because
1379    most features only have a small number of annotations.
1380    
1381    If the feature is B<not> identified by a FIG ID, then the functional assignment
1382    information is taken from the B<ExternalAliasFunc> table. If the table does
1383    not contain an entry for the feature, an empty list is returned.
1384    
1385    =over 4
1386    
1387    =item featureID
1388    
1389    ID of the feature whose functional assignments are desired.
1390    
1391    =item RETURN
1392    
1393    Returns a list of 2-tuples, each consisting of a user ID and the text of an assignment by
1394    that user.
1395    
1396    =back
1397    
1398    =cut
1399    #: Return Type @@;
1400    sub FunctionsOf {
1401        # Get the parameters.
1402        my ($self, $featureID) = @_;
1403        # Declare the return value.
1404        my @retVal = ();
1405        # Determine the ID type.
1406        if ($featureID =~ m/^fig\|/) {
1407            # Here we have a FIG feature ID. We must build the list of trusted
1408            # users.
1409            my %trusteeTable = ();
1410            # Build a query for all of the feature's annotations, sorted by date.
1411            my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1412                                   "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1413                                   [$featureID]);
1414            my $timeSelected = 0;
1415            # Loop until we run out of annotations.
1416            while (my $annotation = $query->Fetch()) {
1417                # Get the annotation text.
1418                my ($text, $time, $user) = $annotation->Values(['Annotation(annotation)',
1419                                                                'Annotation(time)',
1420                                                                'MadeAnnotation(user)']);
1421                # Check to see if this is a functional assignment for a trusted user.
1422                my ($actualUser, $function) = _ParseAssignment($user, $text);
1423                if ($actualUser) {
1424                    # Here it is a functional assignment.
1425                    push @retVal, [$actualUser, $function];
1426                }
1427            }
1428        } else {
1429            # Here we have a non-FIG feature ID. In this case the user ID does not
1430            # matter. We simply get the information from the External Alias Function
1431            # table.
1432            my @assignments = $self->GetEntityValues('ExternalAliasFunc', $featureID,
1433                                                     ['ExternalAliasFunc(func)']);
1434            push @retVal, map { ['master', $_] } @assignments;
1435        }
1436        # Return the assignments found.
1437        return @retVal;
1438    }
1439    
1440  =head3 BBHList  =head3 BBHList
1441    
1442  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>
# Line 1254  Line 1474 
1474          my $query = $self->Get(['IsBidirectionalBestHitOf'],          my $query = $self->Get(['IsBidirectionalBestHitOf'],
1475                                 "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",                                 "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",
1476                                 [$featureID, $genomeID]);                                 [$featureID, $genomeID]);
1477          # Look for the best hit.          # Peel off the BBHs found.
1478          my $bbh = $query->Fetch;          my @found = ();
1479          if ($bbh) {          while (my $bbh = $query->Fetch) {
1480              my ($targetFeature) = $bbh->Value('IsBidirectionalBestHitOf(to-link)');              push @found, $bbh->Value('IsBidirectionalBestHitOf(to-link)');
             $retVal{$featureID} = $targetFeature;  
1481          }          }
1482            $retVal{$featureID} = \@found;
1483      }      }
1484      # Return the mapping.      # Return the mapping.
1485      return \%retVal;      return \%retVal;
# Line 1337  Line 1557 
1557      my $genomeData = $self->GetEntity('Genome', $genomeID);      my $genomeData = $self->GetEntity('Genome', $genomeID);
1558      if ($genomeData) {      if ($genomeData) {
1559          # The genome exists, so get the completeness flag.          # The genome exists, so get the completeness flag.
1560          ($retVal) = $genomeData->Value('complete');          ($retVal) = $genomeData->Value('Genome(complete)');
1561      }      }
1562      # Return the result.      # Return the result.
1563      return $retVal;      return $retVal;
# Line 1377  Line 1597 
1597    
1598  C<< my $genomeID = $sprout->GenomeOf($featureID); >>  C<< my $genomeID = $sprout->GenomeOf($featureID); >>
1599    
1600  Return the genome that contains a specified feature.  Return the genome that contains a specified feature or contig.
1601    
1602  =over 4  =over 4
1603    
1604  =item featureID  =item featureID
1605    
1606  ID of the feature whose genome is desired.  ID of the feature or contig whose genome is desired.
1607    
1608  =item RETURN  =item RETURN
1609    
1610  Returns the ID of the genome for the specified feature. If the feature is not found, returns  Returns the ID of the genome for the specified feature or contig. If the feature or contig is not
1611  an undefined value.  found, returns an undefined value.
1612    
1613  =back  =back
1614    
# Line 1397  Line 1617 
1617  sub GenomeOf {  sub GenomeOf {
1618      # Get the parameters.      # Get the parameters.
1619      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
1620      # Create a query to find the genome associated with the feature.      # Create a query to find the genome associated with the incoming ID.
1621      my $query = $self->Get(['IsLocatedIn', 'HasContig'], "IsLocatedIn(from-link) = ?", [$featureID]);      my $query = $self->Get(['IsLocatedIn', 'HasContig'], "IsLocatedIn(from-link) = ? OR HasContig(to-link) = ?",
1622                               [$featureID, $featureID]);
1623      # Declare the return value.      # Declare the return value.
1624      my $retVal;      my $retVal;
1625      # Get the genome ID.      # Get the genome ID.
# Line 1445  Line 1666 
1666          # Get the ID and score of the coupling.          # Get the ID and score of the coupling.
1667          my ($couplingID, $score) = $clustering->Values(['Coupling(id)',          my ($couplingID, $score) = $clustering->Values(['Coupling(id)',
1668                                                          'Coupling(score)']);                                                          'Coupling(score)']);
1669          # The coupling ID contains the two feature IDs separated by a space. We use          # Get the other feature that participates in the coupling.
1670          # this information to find the ID of the other feature.          my ($otherFeatureID) = $self->GetFlat(['ParticipatesInCoupling'],
1671          my ($fid1, $fid2) = split / /, $couplingID;                                             "ParticipatesInCoupling(to-link) = ? AND ParticipatesInCoupling(from-link) <> ?",
1672          my $otherFeatureID = ($featureID eq $fid1 ? $fid2 : $fid1);                                             [$couplingID, $featureID], 'ParticipatesInCoupling(from-link)');
1673          # Attach the other feature's score to its ID.          # Attach the other feature's score to its ID.
1674          $retVal{$otherFeatureID} = $score;          $retVal{$otherFeatureID} = $score;
1675          $found = 1;          $found = 1;
# Line 1521  Line 1742 
1742          # Determine the ordering to place on the evidence items. If we're          # Determine the ordering to place on the evidence items. If we're
1743          # inverted, we want to see feature 2 before feature 1 (descending); otherwise,          # inverted, we want to see feature 2 before feature 1 (descending); otherwise,
1744          # we want feature 1 before feature 2 (normal).          # we want feature 1 before feature 2 (normal).
1745            Trace("Coupling evidence for ($peg1, $peg2) with inversion flag $inverted.") if T(Coupling => 4);
1746          my $ordering = ($inverted ? "DESC" : "");          my $ordering = ($inverted ? "DESC" : "");
1747          # Get the coupling evidence.          # Get the coupling evidence.
1748          my @evidenceList = $self->GetAll(['IsEvidencedBy', 'PCH', 'UsesAsEvidence'],          my @evidenceList = $self->GetAll(['IsEvidencedBy', 'PCH', 'UsesAsEvidence'],
# Line 1534  Line 1756 
1756          while (@evidenceList > 0) {          while (@evidenceList > 0) {
1757              my $peg1Data = shift @evidenceList;              my $peg1Data = shift @evidenceList;
1758              my $peg2Data = shift @evidenceList;              my $peg2Data = shift @evidenceList;
1759                Trace("Peg 1 is " . $peg1Data->[1] . " and Peg 2 is " . $peg2Data->[1] . ".") if T(Coupling => 4);
1760              push @retVal, [$peg1Data->[1], $peg2Data->[1], $peg1Data->[0]];              push @retVal, [$peg1Data->[1], $peg2Data->[1], $peg1Data->[0]];
1761          }          }
1762            Trace("Last index in evidence result is is $#retVal.") if T(Coupling => 4);
1763      }      }
1764      # Return the result.      # Return the result.
1765      return @retVal;      return @retVal;
# Line 1585  Line 1809 
1809                                   [$retVal], ["ParticipatesInCoupling(from-link)", "Coupling(score)"]);                                   [$retVal], ["ParticipatesInCoupling(from-link)", "Coupling(score)"]);
1810      # Check to see if we found anything.      # Check to see if we found anything.
1811      if (!@pegs) {      if (!@pegs) {
1812            Trace("No coupling found.") if T(Coupling => 4);
1813          # No coupling, so undefine the return value.          # No coupling, so undefine the return value.
1814          $retVal = undef;          $retVal = undef;
1815      } else {      } else {
1816          # We have a coupling! Get the score and check for inversion.          # We have a coupling! Get the score and check for inversion.
1817          $score = $pegs[0]->[1];          $score = $pegs[0]->[1];
1818          $inverted = ($pegs[0]->[0] eq $peg1);          my $firstFound = $pegs[0]->[0];
1819            $inverted = ($firstFound ne $peg1);
1820            Trace("Coupling score is $score. First peg is $firstFound, peg 1 is $peg1.") if T(Coupling => 4);
1821      }      }
1822      # Return the result.      # Return the result.
1823      return ($retVal, $inverted, $score);      return ($retVal, $inverted, $score);
# Line 1634  Line 1861 
1861      return join " ", sort @_;      return join " ", sort @_;
1862  }  }
1863    
 =head3 GetEntityTypes  
   
 C<< my @entityList = $sprout->GetEntityTypes(); >>  
   
 Return the list of supported entity types.  
   
 =cut  
 #: Return Type @;  
 sub GetEntityTypes {  
     # Get the parameters.  
     my ($self) = @_;  
     # Get the underlying database object.  
     my $erdb = $self->{_erdb};  
     # Get its entity type list.  
     my @retVal = $erdb->GetEntityTypes();  
 }  
   
1864  =head3 ReadFasta  =head3 ReadFasta
1865    
1866  C<< my %sequenceData = Sprout::ReadFasta($fileName, $prefix); >>  C<< my %sequenceData = Sprout::ReadFasta($fileName, $prefix); >>
# Line 1695  Line 1905 
1905          if ($line =~ m/^>\s*(.+?)(\s|\n)/) {          if ($line =~ m/^>\s*(.+?)(\s|\n)/) {
1906              # Here we have a new header. Store the current sequence if we have one.              # Here we have a new header. Store the current sequence if we have one.
1907              if ($id) {              if ($id) {
1908                  $retVal{$id} = uc $sequence;                  $retVal{$id} = lc $sequence;
1909              }              }
1910              # Clear the sequence accumulator and save the new ID.              # Clear the sequence accumulator and save the new ID.
1911              ($id, $sequence) = ("$prefix$1", "");              ($id, $sequence) = ("$prefix$1", "");
1912          } else {          } else {
1913              # Here we have a data line, so we add it to the sequence accumulator.              # Here we have a data line, so we add it to the sequence accumulator.
1914              # First, we get the actual data out. Note that we normalize to upper              # First, we get the actual data out. Note that we normalize to lower
1915              # case.              # case.
1916              $line =~ /^\s*(.*?)(\s|\n)/;              $line =~ /^\s*(.*?)(\s|\n)/;
1917              $sequence .= $1;              $sequence .= $1;
# Line 1709  Line 1919 
1919      }      }
1920      # Flush out the last sequence (if any).      # Flush out the last sequence (if any).
1921      if ($sequence) {      if ($sequence) {
1922          $retVal{$id} = uc $sequence;          $retVal{$id} = lc $sequence;
1923      }      }
1924      # Close the file.      # Close the file.
1925      close FASTAFILE;      close FASTAFILE;
# Line 1796  Line 2006 
2006      # Get the data directory name.      # Get the data directory name.
2007      my $outputDirectory = $self->{_options}->{dataDir};      my $outputDirectory = $self->{_options}->{dataDir};
2008      # Dump the relations.      # Dump the relations.
2009      $self->{_erdb}->DumpRelations($outputDirectory);      $self->DumpRelations($outputDirectory);
2010  }  }
2011    
2012  =head3 XMLFileName  =head3 XMLFileName
# Line 1848  Line 2058 
2058      # Get the parameters.      # Get the parameters.
2059      my ($self, $objectType, $fieldHash) = @_;      my ($self, $objectType, $fieldHash) = @_;
2060      # Call the underlying method.      # Call the underlying method.
2061      $self->{_erdb}->InsertObject($objectType, $fieldHash);      $self->InsertObject($objectType, $fieldHash);
2062  }  }
2063    
2064  =head3 Annotate  =head3 Annotate
# Line 2035  Line 2245 
2245      # Get the parameters.      # Get the parameters.
2246      my ($self, $entityName, $entityID) = @_;      my ($self, $entityName, $entityID) = @_;
2247      # Check for the entity instance.      # Check for the entity instance.
2248        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
2249      my $testInstance = $self->GetEntity($entityName, $entityID);      my $testInstance = $self->GetEntity($entityName, $entityID);
2250      # Return an existence indicator.      # Return an existence indicator.
2251      my $retVal = ($testInstance ? 1 : 0);      my $retVal = ($testInstance ? 1 : 0);
# Line 2503  Line 2714 
2714  C<< my %subsystems = $sprout->SubsystemsOf($featureID); >>  C<< my %subsystems = $sprout->SubsystemsOf($featureID); >>
2715    
2716  Return a hash describing all the subsystems in which a feature participates. Each subsystem is mapped  Return a hash describing all the subsystems in which a feature participates. Each subsystem is mapped
2717  to the role the feature performs.  to the roles the feature performs.
2718    
2719  =over 4  =over 4
2720    
# Line 2513  Line 2724 
2724    
2725  =item RETURN  =item RETURN
2726    
2727  Returns a hash mapping all the feature's subsystems to the feature's role.  Returns a hash mapping all the feature's subsystems to a list of the feature's roles.
2728    
2729  =back  =back
2730    
2731  =cut  =cut
2732  #: Return Type %;  #: Return Type %@;
2733  sub SubsystemsOf {  sub SubsystemsOf {
2734      # Get the parameters.      # Get the parameters.
2735      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
# Line 2528  Line 2739 
2739                                      ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);                                      ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);
2740      # Create the return value.      # Create the return value.
2741      my %retVal = ();      my %retVal = ();
2742        # Build a hash to weed out duplicates. Sometimes the same PEG and role appears
2743        # in two spreadsheet cells.
2744        my %dupHash = ();
2745      # Loop through the results, adding them to the hash.      # Loop through the results, adding them to the hash.
2746      for my $record (@subsystems) {      for my $record (@subsystems) {
2747          $retVal{$record->[0]} = $record->[1];          # Get this subsystem and role.
2748            my ($subsys, $role) = @{$record};
2749            # Insure it's the first time for both.
2750            my $dupKey = "$subsys\n$role";
2751            if (! exists $dupHash{"$subsys\n$role"}) {
2752                $dupHash{$dupKey} = 1;
2753                push @{$retVal{$subsys}}, $role;
2754            }
2755      }      }
2756      # Return the hash.      # Return the hash.
2757      return %retVal;      return %retVal;
# Line 2568  Line 2789 
2789      return @retVal;      return @retVal;
2790  }  }
2791    
2792    
2793    
2794  =head3 RelatedFeatures  =head3 RelatedFeatures
2795    
2796  C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>  C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>
# Line 2669  Line 2892 
2892      return @retVal;      return @retVal;
2893  }  }
2894    
 =head3 GetAll  
   
 C<< my @list = $sprout->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>  
   
 Return a list of values taken from the objects returned by a query. The first three  
 parameters correspond to the parameters of the L</Get> method. The final parameter is  
 a list of the fields desired from each record found by the query. The field name  
 syntax is the standard syntax used for fields in the B<ERDB> system--  
 B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity  
 or relationship and I<fieldName> is the name of the field.  
   
 The list returned will be a list of lists. Each element of the list will contain  
 the values returned for the fields specified in the fourth parameter. If one of the  
 fields specified returns multiple values, they are flattened in with the rest. For  
 example, the following call will return a list of the features in a particular  
 spreadsheet cell, and each feature will be represented by a list containing the  
 feature ID followed by all of its aliases.  
   
 C<< $query = $sprout->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>  
   
 =over 4  
   
 =item objectNames  
   
 List containing the names of the entity and relationship objects to be retrieved.  
   
 =item filterClause  
   
 WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  
 be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form  
 B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the  
 parameter list as additional parameters. The fields in a filter clause can come from primary  
 entity relations, relationship relations, or secondary entity relations; however, all of the  
 entities and relationships involved must be included in the list of object names.  
   
 =item parameterList  
   
 List of the parameters to be substituted in for the parameters marks in the filter clause.  
   
 =item fields  
   
 List of the fields to be returned in each element of the list returned.  
   
 =item count  
   
 Maximum number of records to return. If omitted or 0, all available records will be returned.  
   
 =item RETURN  
   
 Returns a list of list references. Each element of the return list contains the values for the  
 fields specified in the B<fields> parameter.  
   
 =back  
   
 =cut  
 #: Return Type @@;  
 sub GetAll {  
     # Get the parameters.  
     my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;  
     # Call the ERDB method.  
     my @retVal = $self->{_erdb}->GetAll($objectNames, $filterClause, $parameterList,  
                                         $fields, $count);  
     # Return the resulting list.  
     return @retVal;  
 }  
   
 =head3 GetFlat  
   
 C<< my @list = $sprout->GetFlat(\@objectNames, $filterClause, $parameterList, $field); >>  
   
 This is a variation of L</GetAll> that asks for only a single field per record and  
 returns a single flattened list.  
   
 =over 4  
   
 =item objectNames  
   
 List containing the names of the entity and relationship objects to be retrieved.  
   
 =item filterClause  
   
 WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  
 be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form  
 B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the  
 parameter list as additional parameters. The fields in a filter clause can come from primary  
 entity relations, relationship relations, or secondary entity relations; however, all of the  
 entities and relationships involved must be included in the list of object names.  
   
 =item parameterList  
   
 List of the parameters to be substituted in for the parameters marks in the filter clause.  
   
 =item field  
   
 Name of the field to be used to get the elements of the list returned.  
   
 =item RETURN  
   
 Returns a list of values.  
   
 =back  
   
 =cut  
 #: Return Type @;  
 sub GetFlat {  
     # Get the parameters.  
     my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;  
     # Construct the query.  
     my $query = $self->Get($objectNames, $filterClause, $parameterList);  
     # Create the result list.  
     my @retVal = ();  
     # Loop through the records, adding the field values found to the result list.  
     while (my $row = $query->Fetch()) {  
         push @retVal, $row->Value($field);  
     }  
     # Return the list created.  
     return @retVal;  
 }  
   
2895  =head3 Protein  =head3 Protein
2896    
2897  C<< my $protein = Sprout::Protein($sequence, $table); >>  C<< my $protein = Sprout::Protein($sequence, $table); >>
# Line 2889  Line 2993 
2993      # Create the return list, priming it with the name of the data directory.      # Create the return list, priming it with the name of the data directory.
2994      my @retVal = ($self->{_options}->{dataDir});      my @retVal = ($self->{_options}->{dataDir});
2995      # Concatenate the table names.      # Concatenate the table names.
2996      push @retVal, $self->{_erdb}->GetTableNames();      push @retVal, $self->GetTableNames();
2997      # Return the result.      # Return the result.
2998      return @retVal;      return @retVal;
2999  }  }
3000    
3001  =head3 LowBBHs  =head3 LowBBHs
3002    
3003  C<< my %bbhMap = $sprout->GoodBBHs($featureID, $cutoff); >>  C<< my %bbhMap = $sprout->LowBBHs($featureID, $cutoff); >>
3004    
3005  Return the bidirectional best hits of a feature whose score is no greater than a  Return the bidirectional best hits of a feature whose score is no greater than a
3006  specified cutoff value. A higher cutoff value will allow inclusion of hits with  specified cutoff value. A higher cutoff value will allow inclusion of hits with
# Line 3059  Line 3163 
3163      return $retVal;      return $retVal;
3164  }  }
3165    
3166    =head3 DeleteGenome
3167    
3168    C<< my $stats = $sprout->DeleteGenome($genomeID, $testFlag); >>
3169    
3170    Delete a genome from the database.
3171    
3172    =over 4
3173    
3174    =item genomeID
3175    
3176    ID of the genome to delete
3177    
3178    =item testFlag
3179    
3180    If TRUE, then the DELETE statements will be traced, but no deletions will occur.
3181    
3182    =item RETURN
3183    
3184    Returns a statistics object describing the rows deleted.
3185    
3186    =back
3187    
3188    =cut
3189    #: Return Type $%;
3190    sub DeleteGenome {
3191        # Get the parameters.
3192        my ($self, $genomeID, $testFlag) = @_;
3193        # Perform the delete for the genome's features.
3194        my $retVal = $self->Delete('Feature', "fig|$genomeID.%", $testFlag);
3195        # Perform the delete for the primary genome data.
3196        my $stats = $self->Delete('Genome', $genomeID, $testFlag);
3197        $retVal->Accumulate($stats);
3198        # Return the result.
3199        return $retVal;
3200    }
3201    
3202  =head2 Internal Utility Methods  =head2 Internal Utility Methods
3203    
3204  =head3 ParseAssignment  =head3 ParseAssignment
# Line 3069  Line 3209 
3209    
3210  A functional assignment is always of the form  A functional assignment is always of the form
3211    
3212      I<XXXX>C<\nset >I<YYYY>C< function to\n>I<ZZZZZ>      C<set >I<YYYY>C< function to\n>I<ZZZZZ>
3213    
3214    where I<YYYY> is the B<user>, and I<ZZZZ> is the actual functional role. In most cases,
3215    the user and the assigning user (from MadeAnnotation) will be the same, but that is
3216    not always the case.
3217    
3218  where I<XXXX> is the B<assigning user>, I<YYYY> is the B<user>, and I<ZZZZ> is the  In addition, the functional role may contain extra data that is stripped, such as
3219  actual functional role. In most cases, the user and the assigning user will be the  terminating spaces or a comment separated from the rest of the text by a tab.
 same, but that is not always the case.  
3220    
3221  This is a static method.  This is a static method.
3222    
3223  =over 4  =over 4
3224    
3225    =item user
3226    
3227    Name of the assigning user.
3228    
3229  =item text  =item text
3230    
3231  Text of the annotation.  Text of the annotation.
# Line 3094  Line 3241 
3241    
3242  sub _ParseAssignment {  sub _ParseAssignment {
3243      # Get the parameters.      # Get the parameters.
3244      my ($text) = @_;      my ($user, $text) = @_;
3245      # Declare the return value.      # Declare the return value.
3246      my @retVal = ();      my @retVal = ();
3247      # Check to see if this is a functional assignment.      # Check to see if this is a functional assignment.
3248      my ($user, $type, $function) = split(/\n/, $text);      my ($type, $function) = split(/\n/, $text);
3249      if ($type =~ m/^set ([^ ]+) function to$/i) {      if ($type =~ m/^set function to$/i) {
3250          # Here it is, so we return the user name (which is in $1), the functional role text,          # Here we have an assignment without a user, so we use the incoming user ID.
3251          # and the assigning user.          @retVal = ($user, $function);
3252          @retVal = ($1, $function, $user);      } elsif ($type =~ m/^set (\S+) function to$/i) {
3253            # Here we have an assignment with a user that is passed back to the caller.
3254            @retVal = ($1, $function);
3255        }
3256        # If we have an assignment, we need to clean the function text. There may be
3257        # extra junk at the end added as a note from the user.
3258        if (@retVal) {
3259            $retVal[1] =~ s/(\t\S)?\s*$//;
3260      }      }
3261      # Return the result list.      # Return the result list.
3262      return @retVal;      return @retVal;
# Line 3130  Line 3284 
3284    
3285  sub FriendlyTimestamp {  sub FriendlyTimestamp {
3286      my ($timeValue) = @_;      my ($timeValue) = @_;
3287      my $retVal = strftime("%a %b %e %H:%M:%S %Y", localtime($timeValue));      my $retVal = localtime($timeValue);
3288      return $retVal;      return $retVal;
3289  }  }
3290    
# Line 3192  Line 3346 
3346  }  }
3347    
3348    
   
3349  1;  1;

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