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revision 1.1, Sun Jan 23 16:12:29 2005 UTC revision 1.81, Thu Aug 24 17:32:09 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 FidCheck;
16          use Stats;          use Stats;
17        use POSIX qw(strftime);
18        use BasicLocation;
19    
20  =head1 Sprout Database Manipulation Object  =head1 Sprout Database Manipulation Object
21    
# Line 31  Line 35 
35  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
36  L</dna_seq> returns the DNA sequence for a specified genome location.  L</dna_seq> returns the DNA sequence for a specified genome location.
37    
38    The Sprout object is a subclass of the ERDB object and inherits all its properties and methods.
39    
40  =cut  =cut
41    
42  #  #: Constructor SFXlate->new_sprout_only();
43    
44  =head2 Public Methods  =head2 Public Methods
45    
# Line 61  Line 67 
67    
68  * 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>)
69    
70  * 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)
71    
72  * B<port> connection port (default C<0>)  * B<port> connection port (default C<0>)
73    
74    * B<sock> connection socket (default same as SEED)
75    
76  * B<maxSegmentLength> maximum number of residues per feature segment, (default C<4500>)  * B<maxSegmentLength> maximum number of residues per feature segment, (default C<4500>)
77    
78  * B<maxSequenceLength> maximum number of residues per sequence, (default C<8000>)  * B<maxSequenceLength> maximum number of residues per sequence, (default C<8000>)
79    
80    * B<noDBOpen> suppresses the connection to the database if TRUE, else FALSE
81    
82  =back  =back
83    
84  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 82  Line 92 
92  sub new {  sub new {
93          # Get the parameters.          # Get the parameters.
94          my ($class, $dbName, $options) = @_;          my ($class, $dbName, $options) = @_;
95        # Compute the DBD directory.
96        my $dbd_dir = (defined($FIG_Config::dbd_dir) ? $FIG_Config::dbd_dir :
97                                                      $FIG_Config::fig );
98          # Compute the options. We do this by starting with a table of defaults and overwriting with          # Compute the options. We do this by starting with a table of defaults and overwriting with
99          # the incoming data.          # the incoming data.
100          my $optionTable = Tracer::GetOptions({          my $optionTable = Tracer::GetOptions({
101                                             dbType               => 'mysql',                     # database type                         dbType       => $FIG_Config::dbms,
102                                             dataDir              => 'Data',                      # data file directory                                                          # database type
103                                             xmlFileName  => 'SproutDBD.xml', # database definition file name                         dataDir      => $FIG_Config::sproutData,
104                                             userData             => 'root/',                     # user name and password                                                          # data file directory
105                                             port                 => 0,                           # database connection port                         xmlFileName  => "$dbd_dir/SproutDBD.xml",
106                                                            # database definition file name
107                           userData     => "$FIG_Config::dbuser/$FIG_Config::dbpass",
108                                                            # user name and password
109                           port         => $FIG_Config::dbport,
110                                                            # database connection port
111                           sock         => $FIG_Config::dbsock,
112                           host         => $FIG_Config::dbhost,
113                                             maxSegmentLength => 4500,            # maximum feature segment length                                             maxSegmentLength => 4500,            # maximum feature segment length
114                                             maxSequenceLength => 8000,           # maximum contig sequence length                                             maxSequenceLength => 8000,           # maximum contig sequence length
115                           noDBOpen     => 0,               # 1 to suppress the database open
116                                            }, $options);                                            }, $options);
117          # Get the data directory.          # Get the data directory.
118          my $dataDir = $optionTable->{dataDir};          my $dataDir = $optionTable->{dataDir};
# Line 99  Line 120 
120          $optionTable->{userData} =~ m!([^/]*)/(.*)$!;          $optionTable->{userData} =~ m!([^/]*)/(.*)$!;
121          my ($userName, $password) = ($1, $2);          my ($userName, $password) = ($1, $2);
122          # Connect to the database.          # Connect to the database.
123          my $dbh = DBKernel->new($optionTable->{dbType}, $dbName, $userName, $password, $optionTable->{port});      my $dbh;
124        if (! $optionTable->{noDBOpen}) {
125            $dbh = DBKernel->new($optionTable->{dbType}, $dbName, $userName,
126                                    $password, $optionTable->{port}, $optionTable->{host}, $optionTable->{sock});
127        }
128          # Create the ERDB object.          # Create the ERDB object.
129          my $xmlFileName = "$optionTable->{xmlFileName}";          my $xmlFileName = "$optionTable->{xmlFileName}";
130          my $erdb = ERDB->new($dbh, $xmlFileName);      my $retVal = ERDB::new($class, $dbh, $xmlFileName);
131          # Create this object.      # Add the option table and XML file name.
132          my $self = { _erdb => $erdb, _options => $optionTable, _xmlName => $xmlFileName };      $retVal->{_options} = $optionTable;
133          # Bless and return it.      $retVal->{_xmlName} = $xmlFileName;
134          bless $self;      # Return it.
135          return $self;      return $retVal;
136  }  }
137    
138  =head3 MaxSegment  =head3 MaxSegment
# Line 121  Line 146 
146  and 10999.  and 10999.
147    
148  =cut  =cut
149    #: Return Type $;
150  sub MaxSegment {  sub MaxSegment {
151          my $self = shift @_;      my ($self) = @_;
152          return $self->{_options}->{maxSegmentLength};          return $self->{_options}->{maxSegmentLength};
153  }  }
154    
# Line 136  Line 161 
161  we generally only need a few sequences in memory rather than the entire contig.  we generally only need a few sequences in memory rather than the entire contig.
162    
163  =cut  =cut
164    #: Return Type $;
165  sub MaxSequence {  sub MaxSequence {
166          my $self = shift @_;      my ($self) = @_;
167          return $self->{_options}->{maxSequenceLength};          return $self->{_options}->{maxSequenceLength};
168  }  }
169    
170  =head3 Get  =head3 Load
   
 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]); >>  
171    
172  It is also permissible to specify I<only> an ORDER BY clause. For example, the following invocation gets  C<< $sprout->Load($rebuild); >>;
 all genomes ordered by genus and species.  
173    
174  C<< $query = $sprout->Get(['Genome'], "ORDER BY Genome(genus), Genome(species)"); >>  Load the database from files in the data directory, optionally re-creating the tables.
175    
176  Odd things may happen if one of the ORDER BY fields is in a secondary relation. So, for example, an  This method always deletes the data from the database before loading, even if the tables are not
177  attempt to order B<Feature>s by alias may (depending on the underlying database engine used) cause  re-created. The data is loaded into the relations from files in the data directory either having the
178  a single feature to appear more than once.  same name as the target relation with no extension or with an extension of C<.dtx>. Files without an
179    extension are used in preference to the files with an extension.
180    
181  If multiple names are specified, then the query processor will automatically determine a  The files are loaded based on the presumption that each line of the file is a record in the
182  join path between the entities and relationships. The algorithm used is very simplistic.  relation, and the individual fields are delimited by tabs. Tab and new-line characters inside
183  In particular, you can't specify any entity or relationship more than once, and if a  fields must be represented by the escape sequences C<\t> and C<\n>, respectively. The fields must
184  relationship is recursive, the path is determined by the order in which the entity  be presented in the order given in the relation tables produced by the L</ShowMetaData> method.
 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.  
185    
186  =over 4  =over 4
187    
188  =item objectNames  =item rebuild
   
 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  
189    
190  List of the parameters to be substituted in for the parameters marks in the filter clause.  TRUE if the data tables need to be created or re-created, else FALSE
191    
192  =item RETURN  =item RETURN
193    
194  Returns a B<DBQuery> that can be used to iterate through all of the results.  Returns a statistical object containing the number of records read, the number of duplicates found,
195    the number of errors, and a list of the error messages.
196    
197  =back  =back
198    
199  =cut  =cut
200    #: Return Type %;
201  sub Get {  sub Load {
202          # Get the parameters.          # Get the parameters.
203          my $self = shift @_;      my ($self, $rebuild) = @_;
204          my ($objectNames, $filterClause, $parameterList) = @_;      # Load the tables from the data directory.
205          # We differ from the ERDB Get method in that the parameter list is passed in as a list reference      my $retVal = $self->LoadTables($self->{_options}->{dataDir}, $rebuild);
206          # rather than a list of parameters. The next step is to convert the parameters from a reference      # Return the statistics.
207          # to a real list. We can only do this if the parameters have been specified.      return $retVal;
         my @parameters;  
         if ($parameterList) { @parameters = @{$parameterList}; }  
         return $self->{_erdb}->Get($objectNames, $filterClause, @parameters);  
208  }  }
209    
210  =head3 GetEntity  =head3 LoadUpdate
211    
212  C<< my $entityObject = $sprout->GetEntity($entityType, $ID); >>  C<< my $stats = $sprout->LoadUpdate($truncateFlag, \@tableList); >>
213    
214  Return an object describing the entity instance with a specified ID.  Load updates to one or more database tables. This method enables the client to make changes to one
215    or two tables without reloading the whole database. For each table, there must be a corresponding
216    file in the data directory, either with the same name as the table, or with a C<.dtx> suffix. So,
217    for example, to make updates to the B<FeatureTranslation> relation, there must be a
218    C<FeatureTranslation.dtx> file in the data directory. Unlike a full load, files without an extension
219    are not examined. This allows update files to co-exist with files from an original load.
220    
221  =over 4  =over 4
222    
223  =item entityType  =item truncateFlag
224    
225  Entity type name.  TRUE if the tables should be rebuilt before loading, else FALSE. A value of TRUE therefore causes
226    current data and schema of the tables to be replaced, while a value of FALSE means the new data
227    is added to the existing data in the various relations.
228    
229  =item ID  =item tableList
230    
231  ID of the desired entity.  List of the tables to be updated.
232    
233  =item RETURN  =item RETURN
234    
235  Returns a B<DBObject> representing the desired entity instance, or an undefined value if no  Returns a statistical object containing the number of records read, the number of duplicates found,
236  instance is found with the specified key.  the number of errors encountered, and a list of error messages.
237    
238  =back  =back
239    
240  =cut  =cut
241    #: Return Type $%;
242  sub GetEntity {  sub LoadUpdate {
243          # Get the parameters.          # Get the parameters.
244          my $self = shift @_;      my ($self, $truncateFlag, $tableList) = @_;
245          my ($entityType, $ID) = @_;      # Declare the return value.
246          # Create a query.      my $retVal = Stats->new();
247          my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);      # Get the data directory.
248          # Get the first (and only) object.      my $optionTable = $self->{_options};
249          my $retVal = $query->Fetch();      my $dataDir = $optionTable->{dataDir};
250          # Return the result.      # Loop through the incoming table names.
251        for my $tableName (@{$tableList}) {
252            # Find the table's file.
253            my $fileName = LoadFileName($dataDir, $tableName);
254            if (! $fileName) {
255                Trace("No load file found for $tableName in $dataDir.") if T(0);
256            } else {
257                # Attempt to load this table.
258                my $result = $self->LoadTable($fileName, $tableName, $truncateFlag);
259                # Accumulate the resulting statistics.
260                $retVal->Accumulate($result);
261            }
262        }
263        # Return the statistics.
264          return $retVal;          return $retVal;
265  }  }
266    
267  =head3 GetEntityValues  =head3 GenomeCounts
268    
269  C<< my @values = GetEntityValues($entityType, $ID, \@fields); >>  C<< my ($arch, $bact, $euk, $vir, $env, $unk) = $sprout->GenomeCounts($complete); >>
270    
271  Return a list of values from a specified entity instance.  Count the number of genomes in each domain. If I<$complete> is TRUE, only complete
272    genomes will be included in the counts.
273    
274  =over 4  =over 4
275    
276  =item entityType  =item complete
277    
278  Entity type name.  TRUE if only complete genomes are to be counted, FALSE if all genomes are to be
279    counted
 =item ID  
   
 ID of the desired entity.  
   
 =item fields  
   
 List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.  
280    
281  =item RETURN  =item RETURN
282    
283  Returns a flattened list of the values of the specified fields for the specified entity.  A six-element list containing the number of genomes in each of six categories--
284    Archaea, Bacteria, Eukaryota, Viral, Environmental, and Unknown, respectively.
285    
286  =back  =back
287    
288  =cut  =cut
289    
290  sub GetEntityValues {  sub GenomeCounts {
291          # Get the parameters.          # Get the parameters.
292          my $self = shift @_;      my ($self, $complete) = @_;
293          my ($entityType, $ID, $fields) = @_;      # Set the filter based on the completeness flag.
294          # Get the specified entity.      my $filter = ($complete ? "Genome(complete) = 1" : "");
295          my $entity = $self->GetEntity($entityType, $ID);      # Get all the genomes and the related taxonomy information.
296          # Declare the return list.      my @genomes = $self->GetAll(['Genome'], $filter, [], ['Genome(id)', 'Genome(taxonomy)']);
297          my @retVal = ();      # Clear the counters.
298          # If we found the entity, push the values into the return list.      my ($arch, $bact, $euk, $vir, $env, $unk) = (0, 0, 0, 0, 0, 0);
299          if ($entity) {      # Loop through, counting the domains.
300                  push @retVal, $entity->Values($fields);      for my $genome (@genomes) {
301          }          if    ($genome->[1] =~ /^archaea/i)  { ++$arch }
302          # Return the result.          elsif ($genome->[1] =~ /^bacter/i)   { ++$bact }
303          return @retVal;          elsif ($genome->[1] =~ /^eukar/i)    { ++$euk }
304            elsif ($genome->[1] =~ /^vir/i)      { ++$vir }
305            elsif ($genome->[1] =~ /^env/i)      { ++$env }
306            else  { ++$unk }
307  }  }
308        # Return the counts.
309  =head3 ShowMetaData      return ($arch, $bact, $euk, $vir, $env, $unk);
   
 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 $self = shift @_;  
         my ($fileName) = @_;  
         # Compute the file name.  
         my $options = $self->{_options};  
         # Call the show method on the underlying ERDB object.  
         $self->{_erdb}->ShowMetaData($fileName);  
310  }  }
311    
312  =head3 Load  =head3 ContigCount
   
 C<< $sprout->Load($rebuild); >>;  
   
 Load the database from files in the data directory, optionally re-creating the tables.  
313    
314  This method always deletes the data from the database before loading, even if the tables are not  C<< my $count = $sprout->ContigCount($genomeID); >>
 re-created. The data is loaded into the relations from files in the data directory either having the  
 same name as the target relation with no extension or with an extension of C<.dtx>. Files without an  
 extension are used in preference to the files with an extension.  
315    
316  The files are loaded based on the presumption that each line of the file is a record in the  Return the number of contigs for the specified genome ID.
 relation, and the individual fields are delimited by tabs. Tab and new-line characters inside  
 fields must be represented by the escape sequences C<\t> and C<\n>, respectively. The fields must  
 be presented in the order given in the relation tables produced by the L</ShowMetaData> method.  
317    
318  =over 4  =over 4
319    
320  =item rebuild  =item genomeID
321    
322  TRUE if the data tables need to be created or re-created, else FALSE  ID of the genome whose contig count is desired.
323    
324  =item RETURN  =item RETURN
325    
326  Returns a statistical object containing the number of records read, the number of duplicates found,  Returns the number of contigs for the specified genome.
 the number of errors, and a list of the error messages.  
327    
328  =back  =back
329    
330  =cut  =cut
331    
332  sub Load {  sub ContigCount {
333          # Get the parameters.          # Get the parameters.
334          my $self = shift @_;      my ($self, $genomeID) = @_;
335          my ($rebuild) = @_;      # Get the contig count.
336          # Get the database object.      my $retVal = $self->GetCount(['Contig', 'HasContig'], "HasContig(from-link) = ?", [$genomeID]);
337          my $erdb = $self->{_erdb};      # Return the result.
         # Load the tables from the data directory.  
         my $retVal = $erdb->LoadTables($self->{_options}->{dataDir}, $rebuild);  
         # Return the statistics.  
338          return $retVal;          return $retVal;
339  }  }
340    
341  =head3 LoadUpdate  =head3 GeneMenu
342    
343  C<< my %stats = $sprout->LoadUpdate($truncateFlag, \@tableList); >>  C<< my $selectHtml = $sprout->GeneMenu(\%attributes, $filterString, \@params); >>
344    
345  Load updates to one or more database tables. This method enables the client to make changes to one  Return an HTML select menu of genomes. Each genome will be an option in the menu,
346  or two tables without reloading the whole database. For each table, there must be a corresponding  and will be displayed by name with the ID and a contig count attached. The selection
347  file in the data directory, either with the same name as the table, or with a C<.dtx> suffix. So,  value will be the genome ID. The genomes will be sorted by genus/species name.
 for example, to make updates to the B<FeatureTranslation> relation, there must be a  
 C<FeatureTranslation.dtx> file in the data directory. Unlike a full load, files without an extension  
 are not examined. This allows update files to co-exist with files from an original load.  
348    
349  =over 4  =over 4
350    
351  =item truncateFlag  =item attributes
352    
353  TRUE if the tables should be rebuilt before loading, else FALSE. A value of TRUE therefore causes  Reference to a hash mapping attributes to values for the SELECT tag generated.
 current data and schema of the tables to be replaced, while a value of FALSE means the new data  
 is added to the existing data in the various relations.  
354    
355  =item tableList  =item filterString
356    
357  List of the tables to be updated.  A filter string for use in selecting the genomes. The filter string must conform
358    to the rules for the C<< ERDB->Get >> method.
359    
360    =item params
361    
362    Reference to a list of values to be substituted in for the parameter marks in
363    the filter string.
364    
365  =item RETURN  =item RETURN
366    
367  Returns a statistical object containing the number of records read, the number of duplicates found,  Returns an HTML select menu with the specified genomes as selectable options.
 the number of errors encountered, and a list of error messages.  
368    
369  =back  =back
370    
371  =cut  =cut
372    
373  sub LoadUpdate {  sub GeneMenu {
374          # Get the parameters.          # Get the parameters.
375          my $self = shift @_;      my ($self, $attributes, $filterString, $params) = @_;
376          my ($truncateFlag, $tableList) = @_;      # Start the menu.
377          # Get the database object.      my $retVal = "<select " .
378          my $erdb = $self->{_erdb};          join(" ", map { "$_=\"$attributes->{$_}\"" } keys %{$attributes}) .
379          # Declare the return value.          ">\n";
380          my $retVal = Stats->new();      # Get the genomes.
381          # Get the data directory.      my @genomes = $self->GetAll(['Genome'], $filterString, $params, ['Genome(id)',
382          my $optionTable = $self->{_options};                                                                       'Genome(genus)',
383          my $dataDir = $optionTable->{dataDir};                                                                       'Genome(species)',
384          # Loop through the incoming table names.                                                                       'Genome(unique-characterization)']);
385          for my $tableName (@{$tableList}) {      # Sort them by name.
386                  # Find the table's file.      my @sorted = sort { lc("$a->[1] $a->[2]") cmp lc("$b->[1] $b->[2]") } @genomes;
387                  my $fileName = "$dataDir/$tableName";      # Loop through the genomes, creating the option tags.
388                  if (! -e $fileName) {      for my $genomeData (@sorted) {
389                          $fileName = "$fileName.dtx";          # Get the data for this genome.
390                  }          my ($genomeID, $genus, $species, $strain) = @{$genomeData};
391                  # Attempt to load this table.          # Get the contig count.
392                  my $result = $erdb->LoadTable($fileName, $tableName, $truncateFlag);          my $count = $self->ContigCount($genomeID);
393                  # Accumulate the resulting statistics.          my $counting = ($count == 1 ? "contig" : "contigs");
394                  $retVal->Accumulate($result);          # Build the option tag.
395            $retVal .= "<option value=\"$genomeID\">$genus $species $strain ($genomeID) [$count $counting]</option>\n";
396            Trace("Option tag built for $genomeID: $genus $species $strain.") if T(3);
397          }          }
398          # Return the statistics.      # Close the SELECT tag.
399        $retVal .= "</select>\n";
400        # Return the result.
401          return $retVal;          return $retVal;
402  }  }
   
403  =head3 Build  =head3 Build
404    
405  C<< $sprout->Build(); >>  C<< $sprout->Build(); >>
# Line 459  Line 409 
409  changed.  changed.
410    
411  =cut  =cut
412    #: Return Type ;
413  sub Build {  sub Build {
414          # Get the parameters.          # Get the parameters.
415          my $self = shift @_;      my ($self) = @_;
416          # Create the tables.          # Create the tables.
417          $self->{_erdb}->CreateTables;      $self->CreateTables();
418  }  }
419    
420  =head3 Genomes  =head3 Genomes
# Line 474  Line 424 
424  Return a list of all the genome IDs.  Return a list of all the genome IDs.
425    
426  =cut  =cut
427    #: Return Type @;
428  sub Genomes {  sub Genomes {
429          # Get the parameters.          # Get the parameters.
430          my $self = shift @_;      my ($self) = @_;
431          # Get all the genomes.          # Get all the genomes.
432          my @retVal = $self->GetFlat(['Genome'], "", [], 'Genome(id)');          my @retVal = $self->GetFlat(['Genome'], "", [], 'Genome(id)');
433          # Return the list of IDs.          # Return the list of IDs.
# Line 504  Line 454 
454  =back  =back
455    
456  =cut  =cut
457    #: Return Type $;
458  sub GenusSpecies {  sub GenusSpecies {
459          # Get the parameters.          # Get the parameters.
460          my $self = shift @_;      my ($self, $genomeID) = @_;
         my ($genomeID) = @_;  
461          # Get the data for the specified genome.          # Get the data for the specified genome.
462          my @values = $self->GetEntityValues('Genome', $genomeID, ['Genome(genus)', 'Genome(species)',          my @values = $self->GetEntityValues('Genome', $genomeID, ['Genome(genus)', 'Genome(species)',
463                                                                                                                            'Genome(unique-characterization)']);                                                                                                                            'Genome(unique-characterization)']);
# Line 541  Line 490 
490  =back  =back
491    
492  =cut  =cut
493    #: Return Type @;
494  sub FeaturesOf {  sub FeaturesOf {
495          # Get the parameters.          # Get the parameters.
496          my $self = shift @_;      my ($self, $genomeID,$ftype) = @_;
         my ($genomeID,$ftype) = @_;  
497          # Get the features we want.          # Get the features we want.
498          my @features;          my @features;
499          if (!$ftype) {          if (!$ftype) {
# Line 589  Line 537 
537  =item RETURN  =item RETURN
538    
539  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
540  context and as a space-delimited string in a scalar context.  context and as a comma-delimited string in a scalar context.
541    
542  =back  =back
543    
544  =cut  =cut
545    #: Return Type @;
546    #: Return Type $;
547  sub FeatureLocation {  sub FeatureLocation {
548          # Get the parameters.          # Get the parameters.
549          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
550          # Create a query for the feature locations.          # Create a query for the feature locations.
551          my $query = $self->Get(['IsLocatedIn'], "IsLocatedIn(from-link) = ? ORDER BY IsLocatedIn(locN)",          my $query = $self->Get(['IsLocatedIn'], "IsLocatedIn(from-link) = ? ORDER BY IsLocatedIn(locN)",
552                                                     [$featureID]);                                                     [$featureID]);
# Line 616  Line 564 
564                  if ($prevContig eq $contigID && $dir eq $prevDir) {                  if ($prevContig eq $contigID && $dir eq $prevDir) {
565                          # Here the new segment is in the same direction on the same contig. Insure the                          # Here the new segment is in the same direction on the same contig. Insure the
566                          # new segment's beginning is next to the old segment's end.                          # new segment's beginning is next to the old segment's end.
567                          if (($dir eq "-" && $beg == $prevBeg - $prevLen) ||              if ($dir eq "-" && $beg + $len == $prevBeg) {
568                                  ($dir eq "+" && $beg == $prevBeg + $prevLen)) {                  # Here we're merging two backward blocks, so we keep the new begin point
569                                  # Here we need to merge two segments. Adjust the beginning and length values                  # and adjust the length.
570                                  # to include both segments.                  $len += $prevLen;
571                    # Pop the old segment off. The new one will replace it later.
572                    pop @retVal;
573                } elsif ($dir eq "+" && $beg == $prevBeg + $prevLen) {
574                    # Here we need to merge two forward blocks. Adjust the beginning and
575                    # length values to include both segments.
576                                  $beg = $prevBeg;                                  $beg = $prevBeg;
577                                  $len += $prevLen;                                  $len += $prevLen;
578                                  # Pop the old segment off. The new one will replace it later.                                  # Pop the old segment off. The new one will replace it later.
# Line 628  Line 581 
581                  }                  }
582                  # Remember this specifier for the adjacent-segment test the next time through.                  # Remember this specifier for the adjacent-segment test the next time through.
583                  ($prevContig, $prevBeg, $prevDir, $prevLen) = ($contigID, $beg, $dir, $len);                  ($prevContig, $prevBeg, $prevDir, $prevLen) = ($contigID, $beg, $dir, $len);
584            # Compute the initial base pair.
585            my $start = ($dir eq "+" ? $beg : $beg + $len - 1);
586                  # Add the specifier to the list.                  # Add the specifier to the list.
587                  push @retVal, "${contigID}_$beg$dir$len";          push @retVal, "${contigID}_$start$dir$len";
588          }          }
589          # Return the list in the format indicated by the context.          # Return the list in the format indicated by the context.
590          return (wantarray ? @retVal : join(' ', @retVal));      return (wantarray ? @retVal : join(',', @retVal));
591  }  }
592    
593  =head3 ParseLocation  =head3 ParseLocation
# Line 656  Line 611 
611  =back  =back
612    
613  =cut  =cut
614    #: Return Type @;
615  sub ParseLocation {  sub ParseLocation {
616          # Get the parameter.      # Get the parameter. Note that if we're called as an instance method, we ignore
617        # the first parameter.
618        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
619          my ($location) = @_;          my ($location) = @_;
620          # Parse it into segments.          # Parse it into segments.
621          $location =~ /^(.*)_(\d*)([+-_])(\d*)$/;      $location =~ /^(.+)_(\d+)([+\-_])(\d+)$/;
622          my ($contigID, $start, $dir, $len) = ($1, $2, $3, $4);          my ($contigID, $start, $dir, $len) = ($1, $2, $3, $4);
623          # If the direction is an underscore, convert it to a + or -.          # If the direction is an underscore, convert it to a + or -.
624          if ($dir eq "_") {          if ($dir eq "_") {
# Line 677  Line 634 
634          return ($contigID, $start, $dir, $len);          return ($contigID, $start, $dir, $len);
635  }  }
636    
637    =head3 PointLocation
638    
639    C<< my $found = Sprout::PointLocation($location, $point); >>
640    
641    Return the offset into the specified location of the specified point on the contig. If
642    the specified point is before the location, a negative value will be returned. If it is
643    beyond the location, an undefined value will be returned. It is assumed that the offset
644    is for the location's contig. The location can either be new-style (using a C<+> or C<->
645    and a length) or old-style (using C<_> and start and end positions.
646    
647    =over 4
648    
649    =item location
650    
651    A location specifier (see L</FeatureLocation> for a description).
652    
653    =item point
654    
655    The offset into the contig of the point in which we're interested.
656    
657    =item RETURN
658    
659    Returns the offset inside the specified location of the specified point, a negative
660    number if the point is before the location, or an undefined value if the point is past
661    the location. If the length of the location is 0, this method will B<always> denote
662    that it is outside the location. The offset will always be relative to the left-most
663    position in the location.
664    
665    =back
666    
667    =cut
668    #: Return Type $;
669    sub PointLocation {
670        # Get the parameter. Note that if we're called as an instance method, we ignore
671        # the first parameter.
672        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
673        my ($location, $point) = @_;
674        # Parse out the location elements. Note that this works on both old-style and new-style
675        # locations.
676        my ($contigID, $start, $dir, $len) = ParseLocation($location);
677        # Declare the return variable.
678        my $retVal;
679        # Compute the offset. The computation is dependent on the direction of the location.
680        my $offset = (($dir == '+') ? $point - $start : $point - ($start - $len + 1));
681        # Return the offset if it's valid.
682        if ($offset < $len) {
683            $retVal = $offset;
684        }
685        # Return the offset found.
686        return $retVal;
687    }
688    
689  =head3 DNASeq  =head3 DNASeq
690    
691  C<< my $sequence = $sprout->DNASeq(\@locationList); >>  C<< my $sequence = $sprout->DNASeq(\@locationList); >>
692    
693  This method returns the DNA sequence represented by a list of locations. The list of locations  This method returns the DNA sequence represented by a list of locations. The list of locations
694  should be of the form returned by L</feature_location> 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,
695  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>.
696    
697    For example, the following would return the DNA sequence for contig C<83333.1:NC_000913>
698    between positions 1401 and 1532, inclusive.
699    
700        my $sequence = $sprout->DNASeq('83333.1:NC_000913_1401_1532');
701    
702  =over 4  =over 4
703    
704  =item locationList  =item locationList
705    
706  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
707  L</FeatureLocation> for more about this format).  I<contigID>C<_>I<begin>C<_>I<end> (see L</FeatureLocation> for more about this format).
708    
709  =item RETURN  =item RETURN
710    
# Line 699  Line 713 
713  =back  =back
714    
715  =cut  =cut
716    #: Return Type $;
717  sub DNASeq {  sub DNASeq {
718          # Get the parameters.          # Get the parameters.
719          my $self = shift @_;      my ($self, $locationList) = @_;
         my ($locationList) = @_;  
720          # Create the return string.          # Create the return string.
721          my $retVal = "";          my $retVal = "";
722          # Loop through the locations.          # Loop through the locations.
# Line 718  Line 731 
731                  # the start point is the ending. Note that in the latter case we must reverse the DNA string                  # the start point is the ending. Note that in the latter case we must reverse the DNA string
732                  # before putting it in the return value.                  # before putting it in the return value.
733                  my ($start, $stop);                  my ($start, $stop);
734            Trace("Parse of \"$location\" is $beg$dir$len.") if T(SDNA => 4);
735                  if ($dir eq "+") {                  if ($dir eq "+") {
736                          $start = $beg;                          $start = $beg;
737                          $stop = $beg + $len - 1;                          $stop = $beg + $len - 1;
738                  } else {                  } else {
739                          $start = $beg + $len + 1;              $start = $beg - $len + 1;
740                          $stop = $beg;                          $stop = $beg;
741                  }                  }
742            Trace("Looking for sequences containing $start through $stop.") if T(SDNA => 4);
743                  my $query = $self->Get(['IsMadeUpOf','Sequence'],                  my $query = $self->Get(['IsMadeUpOf','Sequence'],
744                          "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .                          "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .
745                          " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",                          " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",
# Line 736  Line 751 
751                                  $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)',                                  $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)',
752                                                                     'IsMadeUpOf(len)']);                                                                     'IsMadeUpOf(len)']);
753                          my $stopPosition = $startPosition + $sequenceLength;                          my $stopPosition = $startPosition + $sequenceLength;
754                Trace("Sequence is from $startPosition to $stopPosition.") if T(SDNA => 4);
755                          # Figure out the start point and length of the relevant section.                          # Figure out the start point and length of the relevant section.
756                          my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);                          my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);
757                          my $len = ($stopPosition <= $stop ? $stopPosition : $stop) - $startPosition - $pos1;              my $len1 = ($stopPosition < $stop ? $stopPosition : $stop) + 1 - $startPosition - $pos1;
758                Trace("Position is $pos1 for length $len1.") if T(SDNA => 4);
759                          # Add the relevant data to the location data.                          # Add the relevant data to the location data.
760                          $locationDNA .= substr($sequenceData, $pos1, $len);              $locationDNA .= substr($sequenceData, $pos1, $len1);
761                  }                  }
762                  # Add this location's data to the return string. Note that we may need to reverse it.                  # Add this location's data to the return string. Note that we may need to reverse it.
763                  if ($dir eq '+') {                  if ($dir eq '+') {
764                          $retVal .= $locationDNA;                          $retVal .= $locationDNA;
765                  } else {                  } else {
766                          $locationDNA = join('', reverse split //, $locationDNA);              $retVal .= FIG::reverse_comp($locationDNA);
                         $retVal .= $locationDNA;  
767                  }                  }
768          }          }
769          # Return the result.          # Return the result.
# Line 773  Line 789 
789  =back  =back
790    
791  =cut  =cut
792    #: Return Type @;
793  sub AllContigs {  sub AllContigs {
794          # Get the parameters.          # Get the parameters.
795          my $self = shift @_;      my ($self, $genomeID) = @_;
         my ($genomeID) = @_;  
796          # Ask for the genome's Contigs.          # Ask for the genome's Contigs.
797          my @retVal = $self->GetFlat(['HasContig'], "HasContig(from-link) = ?", [$genomeID],          my @retVal = $self->GetFlat(['HasContig'], "HasContig(from-link) = ?", [$genomeID],
798                                                                  'HasContig(to-link)');                                                                  'HasContig(to-link)');
# Line 785  Line 800 
800          return @retVal;          return @retVal;
801  }  }
802    
803  =head3 ContigLength  =head3 GenomeLength
804    
805  C<< my $length = $sprout->ContigLength($contigID); >>  C<< my $length = $sprout->GenomeLength($genomeID); >>
806    
807  Compute the length of a contig.  Return the length of the specified genome in base pairs.
808    
809  =over 4  =over 4
810    
811  =item contigID  =item genomeID
812    
813  ID of the contig whose length is desired.  ID of the genome whose base pair count is desired.
814    
815    =item RETURN
816    
817    Returns the number of base pairs in all the contigs of the specified
818    genome.
819    
820  =back  =back
821    
822  =cut  =cut
823    
824  sub ContigLength {  sub GenomeLength {
825          # Get the parameters.          # Get the parameters.
826          my $self = shift @_;      my ($self, $genomeID) = @_;
827          my ($contigID) = @_;      # Declare the return variable.
         # Get the contig's last sequence.  
         my $query = $self->Get(['IsMadeUpOf'],  
                 "IsMadeUpOf(from-link) = ? ORDER BY IsMadeUpOf(start-position) DESC",  
                 [$contigID]);  
         my $sequence = $query->Fetch();  
         # Declare the return value.  
828          my $retVal = 0;          my $retVal = 0;
829          # Set it from the sequence data, if any.      # Get the genome's contig sequence lengths.
830          if ($sequence) {      my @lens = $self->GetFlat(['HasContig', 'IsMadeUpOf'], 'HasContig(from-link) = ?',
831                  my ($start, $len) = $sequence->Values(['IsMadeUpOf(start-position)', 'IsMadeUpOf(len)']);                         [$genomeID], 'IsMadeUpOf(len)');
832                  $retVal = $start + $len;      # Sum the lengths.
833          }      map { $retVal += $_ } @lens;
834          # Return the result.          # Return the result.
835          return $retVal;          return $retVal;
836  }  }
837    
838  =head3 GenesInRegion  =head3 FeatureCount
839    
840  C<< my (\@featureIDList, $beg, $end) = $sprout->GenesInRegion($contigID, $start, $stop); >>  C<< my $count = $sprout->FeatureCount($genomeID, $type); >>
841    
842  List the features which overlap a specified region in a contig.  Return the number of features of the specified type in the specified genome.
843    
844  =over 4  =over 4
845    
846  =item contigID  =item genomeID
847    
848  ID of the contig containing the region of interest.  ID of the genome whose feature count is desired.
849    
850  =item start  =item type
851    
852  Offset of the first residue in the region of interest.  Type of feature to count (eg. C<peg>, C<rna>, etc.).
853    
854  =item stop  =item RETURN
855    
856  Offset of the last residue in the region of interest.  Returns the number of features of the specified type for the specified genome.
857    
858    =back
859    
860    =cut
861    
862    sub FeatureCount {
863        # Get the parameters.
864        my ($self, $genomeID, $type) = @_;
865        # Compute the count.
866        my $retVal = $self->GetCount(['HasFeature', 'Feature'],
867                                    "HasFeature(from-link) = ? AND Feature(feature-type) = ?",
868                                    [$genomeID, $type]);
869        # Return the result.
870        return $retVal;
871    }
872    
873    =head3 GenomeAssignments
874    
875    C<< my $fidHash = $sprout->GenomeAssignments($genomeID); >>
876    
877    Return a list of a genome's assigned features. The return hash will contain each
878    assigned feature of the genome mapped to the text of its most recent functional
879    assignment.
880    
881    =over 4
882    
883    =item genomeID
884    
885    ID of the genome whose functional assignments are desired.
886    
887  =item RETURN  =item RETURN
888    
889  Returns a three-element list. The first element is a list of feature IDs for the features that  Returns a reference to a hash which maps each feature to its most recent
890  overlap the region of interest. The second and third elements are the minimum and maximum  functional assignment.
 locations of the features provided on the specified contig. These may extend outside  
 the start and stop values.  
891    
892  =back  =back
893    
894  =cut  =cut
895    
896  sub GenesInRegion {  sub GenomeAssignments {
897          # Get the parameters.          # Get the parameters.
898          my $self = shift @_;      my ($self, $genomeID) = @_;
899          my ($contigID, $start, $stop) = @_;      # Declare the return variable.
900          # Get the maximum segment length.      my $retVal = {};
901          my $maximumSegmentLength = $self->MaxSegment;      # Query the genome's features and annotations. We'll put the oldest annotations
902          # Create a hash to receive the feature list. We use a hash so that we can eliminate      # first so that the last assignment to go into the hash will be the correct one.
903          # duplicates easily.      my $query = $self->Get(['HasFeature', 'IsTargetOfAnnotation', 'Annotation'],
904          my %featuresFound = ();                             "HasFeature(from-link) = ? ORDER BY Annotation(time)",
905          # Prime the values we'll use for the returned beginning and end.                             [$genomeID]);
906          my ($min, $max) = ($self->ContigLength($contigID), 0);      # Loop through the annotations.
907          # Create a table of parameters for each query. Each query looks for features travelling in      while (my $data = $query->Fetch) {
908          # a particular direction. The query parameters include the contig ID, the feature direction,          # Get the feature ID and annotation text.
909          # the lowest possible start position, and the highest possible start position. This works          my ($fid, $annotation) = $data->Values(['HasFeature(to-link)',
910                                                    'Annotation(annotation)']);
911            # Check to see if this is an assignment. Note that the user really
912            # doesn't matter to us, other than we use it to determine whether or
913            # not this is an assignment.
914            my ($user, $assignment) = _ParseAssignment('fig', $annotation);
915            if ($user) {
916                # Here it's an assignment. We put it in the return hash, overwriting
917                # any older assignment that might be present.
918                $retVal->{$fid} = $assignment;
919            }
920        }
921        # Return the result.
922        return $retVal;
923    }
924    
925    =head3 ContigLength
926    
927    C<< my $length = $sprout->ContigLength($contigID); >>
928    
929    Compute the length of a contig.
930    
931    =over 4
932    
933    =item contigID
934    
935    ID of the contig whose length is desired.
936    
937    =item RETURN
938    
939    Returns the number of positions in the contig.
940    
941    =back
942    
943    =cut
944    #: Return Type $;
945    sub ContigLength {
946        # Get the parameters.
947        my ($self, $contigID) = @_;
948        # Get the contig's last sequence.
949        my $query = $self->Get(['IsMadeUpOf'],
950            "IsMadeUpOf(from-link) = ? ORDER BY IsMadeUpOf(start-position) DESC",
951            [$contigID]);
952        my $sequence = $query->Fetch();
953        # Declare the return value.
954        my $retVal = 0;
955        # Set it from the sequence data, if any.
956        if ($sequence) {
957            my ($start, $len) = $sequence->Values(['IsMadeUpOf(start-position)', 'IsMadeUpOf(len)']);
958            $retVal = $start + $len - 1;
959        }
960        # Return the result.
961        return $retVal;
962    }
963    
964    =head3 ClusterPEGs
965    
966    C<< my $clusteredList = $sprout->ClusterPEGs($sub, \@pegs); >>
967    
968    Cluster the PEGs in a list according to the cluster coding scheme of the specified
969    subsystem. In order for this to work properly, the subsystem object must have
970    been used recently to retrieve the PEGs using the B<get_pegs_from_cell> method.
971    This causes the cluster numbers to be pulled into the subsystem's color hash.
972    If a PEG is not found in the color hash, it will not appear in the output
973    sequence.
974    
975    =over 4
976    
977    =item sub
978    
979    Sprout subsystem object for the relevant subsystem, from the L</get_subsystem>
980    method.
981    
982    =item pegs
983    
984    Reference to the list of PEGs to be clustered.
985    
986    =item RETURN
987    
988    Returns a list of the PEGs, grouped into smaller lists by cluster number.
989    
990    =back
991    
992    =cut
993    #: Return Type $@@;
994    sub ClusterPEGs {
995        # Get the parameters.
996        my ($self, $sub, $pegs) = @_;
997        # Declare the return variable.
998        my $retVal = [];
999        # Loop through the PEGs, creating arrays for each cluster.
1000        for my $pegID (@{$pegs}) {
1001            my $clusterNumber = $sub->get_cluster_number($pegID);
1002            # Only proceed if the PEG is in a cluster.
1003            if ($clusterNumber >= 0) {
1004                # Push this PEG onto the sub-list for the specified cluster number.
1005                push @{$retVal->[$clusterNumber]}, $pegID;
1006            }
1007        }
1008        # Return the result.
1009        return $retVal;
1010    }
1011    
1012    =head3 GenesInRegion
1013    
1014    C<< my (\@featureIDList, $beg, $end) = $sprout->GenesInRegion($contigID, $start, $stop); >>
1015    
1016    List the features which overlap a specified region in a contig.
1017    
1018    =over 4
1019    
1020    =item contigID
1021    
1022    ID of the contig containing the region of interest.
1023    
1024    =item start
1025    
1026    Offset of the first residue in the region of interest.
1027    
1028    =item stop
1029    
1030    Offset of the last residue in the region of interest.
1031    
1032    =item RETURN
1033    
1034    Returns a three-element list. The first element is a list of feature IDs for the features that
1035    overlap the region of interest. The second and third elements are the minimum and maximum
1036    locations of the features provided on the specified contig. These may extend outside
1037    the start and stop values. The first element (that is, the list of features) is sorted
1038    roughly by location.
1039    
1040    =back
1041    
1042    =cut
1043    #: Return Type @@;
1044    sub GenesInRegion {
1045        # Get the parameters.
1046        my ($self, $contigID, $start, $stop) = @_;
1047        # Get the maximum segment length.
1048        my $maximumSegmentLength = $self->MaxSegment;
1049        # Create a hash to receive the feature list. We use a hash so that we can eliminate
1050        # duplicates easily. The hash key will be the feature ID. The value will be a two-element
1051        # containing the minimum and maximum offsets. We will use the offsets to sort the results
1052        # when we're building the result set.
1053        my %featuresFound = ();
1054        # Prime the values we'll use for the returned beginning and end.
1055        my @initialMinMax = ($self->ContigLength($contigID), 0);
1056        my ($min, $max) = @initialMinMax;
1057        # Create a table of parameters for each query. Each query looks for features travelling in
1058        # a particular direction. The query parameters include the contig ID, the feature direction,
1059        # the lowest possible start position, and the highest possible start position. This works
1060          # because each feature segment length must be no greater than the maximum segment length.          # because each feature segment length must be no greater than the maximum segment length.
1061          my %queryParms = (forward => [$contigID, '+', $start - $maximumSegmentLength + 1, $stop],          my %queryParms = (forward => [$contigID, '+', $start - $maximumSegmentLength + 1, $stop],
1062                                            reverse => [$contigID, '-', $start, $stop + $maximumSegmentLength - 1]);                                            reverse => [$contigID, '-', $start, $stop + $maximumSegmentLength - 1]);
# Line 892  Line 1083 
1083                                          $found = 1;                                          $found = 1;
1084                                  }                                  }
1085                          } elsif ($dir eq '-') {                          } elsif ($dir eq '-') {
1086                                  $end = $beg - $len;                  # Note we switch things around so that the beginning is to the left of the
1087                                  if ($end <= $stop) {                  # ending.
1088                    ($beg, $end) = ($beg - $len, $beg);
1089                    if ($beg <= $stop) {
1090                                          # Denote we found a useful feature.                                          # Denote we found a useful feature.
1091                                          $found = 1;                                          $found = 1;
1092                                  }                                  }
1093                          }                          }
1094                          if ($found) {                          if ($found) {
1095                                  # Here we need to record the feature and update the minimum and maximum.                  # Here we need to record the feature and update the minima and maxima. First,
1096                                  $featuresFound{$featureID} = 1;                  # get the current entry for the specified feature.
1097                                  if ($beg < $min) { $min = $beg; }                  my ($loc1, $loc2) = (exists $featuresFound{$featureID} ? @{$featuresFound{$featureID}} :
1098                                  if ($end < $min) { $min = $end; }                                       @initialMinMax);
1099                                  if ($beg > $max) { $max = $beg; }                  # Merge the current segment's begin and end into the feature begin and end and the
1100                                  if ($end > $max) { $max = $end; }                  # global min and max.
1101                    if ($beg < $loc1) {
1102                        $loc1 = $beg;
1103                        $min = $beg if $beg < $min;
1104                    }
1105                    if ($end > $loc2) {
1106                        $loc2 = $end;
1107                        $max = $end if $end > $max;
1108                    }
1109                    # Store the entry back into the hash table.
1110                    $featuresFound{$featureID} = [$loc1, $loc2];
1111                          }                          }
1112                  }                  }
1113          }          }
1114          # Compute a list of the IDs for the features found.      # Now we must compute the list of the IDs for the features found. We start with a list
1115          my @list = (sort (keys %featuresFound));      # of midpoints / feature ID pairs. (It's not really a midpoint, it's twice the midpoint,
1116        # but the result of the sort will be the same.)
1117        my @list = map { [$featuresFound{$_}->[0] + $featuresFound{$_}->[1], $_] } keys %featuresFound;
1118        # Now we sort by midpoint and yank out the feature IDs.
1119        my @retVal = map { $_->[1] } sort { $a->[0] <=> $b->[0] } @list;
1120          # Return it along with the min and max.          # Return it along with the min and max.
1121          return (\@list, $min, $max);      return (\@retVal, $min, $max);
1122  }  }
1123    
1124  =head3 FType  =head3 FType
# Line 934  Line 1141 
1141  =back  =back
1142    
1143  =cut  =cut
1144    #: Return Type $;
1145  sub FType {  sub FType {
1146          # Get the parameters.          # Get the parameters.
1147          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
1148          # Get the specified feature's type.          # Get the specified feature's type.
1149          my ($retVal) = $self->GetEntityValues('Feature', $featureID, ['Feature(feature-type)']);          my ($retVal) = $self->GetEntityValues('Feature', $featureID, ['Feature(feature-type)']);
1150          # Return the result.          # Return the result.
# Line 947  Line 1153 
1153    
1154  =head3 FeatureAnnotations  =head3 FeatureAnnotations
1155    
1156  C<< my @descriptors = $sprout->FeatureAnnotations($featureID); >>  C<< my @descriptors = $sprout->FeatureAnnotations($featureID, $rawFlag); >>
1157    
1158  Return the annotations of a feature.  Return the annotations of a feature.
1159    
# Line 957  Line 1163 
1163    
1164  ID of the feature whose annotations are desired.  ID of the feature whose annotations are desired.
1165    
1166    =item rawFlag
1167    
1168    If TRUE, the annotation timestamps will be returned in raw form; otherwise, they
1169    will be returned in human-readable form.
1170    
1171  =item RETURN  =item RETURN
1172    
1173  Returns a list of annotation descriptors. Each descriptor is a hash with the following fields.  Returns a list of annotation descriptors. Each descriptor is a hash with the following fields.
# Line 972  Line 1183 
1183  =back  =back
1184    
1185  =cut  =cut
1186    #: Return Type @%;
1187  sub FeatureAnnotations {  sub FeatureAnnotations {
1188          # Get the parameters.          # Get the parameters.
1189          my $self = shift @_;      my ($self, $featureID, $rawFlag) = @_;
         my ($featureID) = @_;  
1190          # 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.
1191          my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],          my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1192                                                     "IsTargetOfAnnotation(from-link) = ?", [$featureID]);                                                     "IsTargetOfAnnotation(from-link) = ?", [$featureID]);
# Line 989  Line 1199 
1199                          $annotation->Values(['IsTargetOfAnnotation(from-link)',                          $annotation->Values(['IsTargetOfAnnotation(from-link)',
1200                                                                   'Annotation(time)', 'MadeAnnotation(from-link)',                                                                   'Annotation(time)', 'MadeAnnotation(from-link)',
1201                                                                   'Annotation(annotation)']);                                                                   'Annotation(annotation)']);
1202            # Convert the time, if necessary.
1203            if (! $rawFlag) {
1204                $timeStamp = FriendlyTimestamp($timeStamp);
1205            }
1206                  # Assemble them into a hash.                  # Assemble them into a hash.
1207                  my $annotationHash = { featureID => $featureID, timeStamp => $timeStamp,          my $annotationHash = { featureID => $featureID,
1208                                   timeStamp => $timeStamp,
1209                                                             user => $user, text => $text };                                                             user => $user, text => $text };
1210                  # Add it to the return list.                  # Add it to the return list.
1211                  push @retVal, $annotationHash;                  push @retVal, $annotationHash;
# Line 1004  Line 1219 
1219  C<< my %functions = $sprout->AllFunctionsOf($featureID); >>  C<< my %functions = $sprout->AllFunctionsOf($featureID); >>
1220    
1221  Return all of the functional assignments for a particular feature. The data is returned as a  Return all of the functional assignments for a particular feature. The data is returned as a
1222  hash of functional assignments to user IDs. A functional assignment is a type of annotation.  hash of functional assignments to user IDs. A functional assignment is a type of annotation,
1223  It has the format "XXXX\nset XXXX function to\nYYYYY". In this instance, XXXX is the user ID  Functional assignments are described in the L</ParseAssignment> function. Its worth noting that
1224  and YYYYY is the functional assignment text. Its worth noting that we cannot filter on the content  we cannot filter on the content of the annotation itself because it's a text field; however,
1225  of the annotation itself because it's a text field; however, this is not a big problem because most  this is not a big problem because most features only have a small number of annotations.
1226  features only have a small number of annotations.  Finally, if a single user has multiple functional assignments, we will only keep the most
1227    recent one.
1228    
1229  =over 4  =over 4
1230    
# Line 1016  Line 1232 
1232    
1233  ID of the feature whose functional assignments are desired.  ID of the feature whose functional assignments are desired.
1234    
1235    =item RETURN
1236    
1237    Returns a hash mapping the user IDs to functional assignment IDs.
1238    
1239  =back  =back
1240    
1241  =cut  =cut
1242    #: Return Type %;
1243  sub AllFunctionsOf {  sub AllFunctionsOf {
1244          # Get the parameters.          # Get the parameters.
1245          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
1246          # Get all of the feature's annotations.          # Get all of the feature's annotations.
1247          my @query = $self->GetFlat(['IsTargetOfAnnotation', 'Annotation'],      my @query = $self->GetAll(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1248                                                      "IsTargetOfAnnotation(from-link) = ?",                                                      "IsTargetOfAnnotation(from-link) = ?",
1249                                                          [$featureID], 'Annotation(annotation)');                              [$featureID], ['Annotation(time)', 'Annotation(annotation)',
1250                                               'MadeAnnotation(from-link)']);
1251          # Declare the return hash.          # Declare the return hash.
1252          my %retVal;          my %retVal;
1253        # Now we sort the assignments by timestamp in reverse.
1254        my @sortedQuery = sort { -($a->[0] <=> $b->[0]) } @query;
1255          # Loop until we run out of annotations.          # Loop until we run out of annotations.
1256          for my $text (@query) {      for my $annotation (@sortedQuery) {
1257            # Get the annotation fields.
1258            my ($timeStamp, $text, $user) = @{$annotation};
1259                  # Check to see if this is a functional assignment.                  # Check to see if this is a functional assignment.
1260                  my ($user, $function) = ParseAssignment($text);          my ($actualUser, $function) = _ParseAssignment($user, $text);
1261                  if ($user) {          if ($actualUser && ! exists $retVal{$actualUser}) {
1262                          # Here it is, so stuff it in the return hash.              # Here it is a functional assignment and there has been no
1263                          $retVal{$function} = $user;              # previous assignment for this user, so we stuff it in the
1264                # return hash.
1265                $retVal{$actualUser} = $function;
1266                  }                  }
1267          }          }
1268          # Return the hash of assignments found.          # Return the hash of assignments found.
# Line 1047  Line 1273 
1273    
1274  C<< my $functionText = $sprout->FunctionOf($featureID, $userID); >>  C<< my $functionText = $sprout->FunctionOf($featureID, $userID); >>
1275    
1276  Return the most recently-determined functional assignment of a particular feature. A functional  Return the most recently-determined functional assignment of a particular feature.
1277  assignment is a type of annotation. It has the format "XXXX\nset XXXX function to\nYYYYY". In this  
1278  instance, XXXX is the user ID and YYYYY is the functional assignment text. Its worth noting that  The functional assignment is handled differently depending on the type of feature. If
1279  we cannot filter on the content of the annotation itself because it's a text field; however, this  the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional
1280  is not a big problem because most features only have a small number of annotations.  assignment is a type of annotation. The format of an assignment is described in
1281    L</ParseAssignment>. Its worth noting that we cannot filter on the content of the
1282    annotation itself because it's a text field; however, this is not a big problem because
1283    most features only have a small number of annotations.
1284    
1285    Each user has an associated list of trusted users. The assignment returned will be the most
1286    recent one by at least one of the trusted users. If no trusted user list is available, then
1287    the specified user and FIG are considered trusted. If the user ID is omitted, only FIG
1288    is trusted.
1289    
1290    If the feature is B<not> identified by a FIG ID, then the functional assignment
1291    information is taken from the B<ExternalAliasFunc> table. If the table does
1292    not contain an entry for the feature, an undefined value is returned.
1293    
1294  =over 4  =over 4
1295    
# Line 1061  Line 1299 
1299    
1300  =item userID (optional)  =item userID (optional)
1301    
1302  ID of the user whose function determination is desired. If omitted, C<FIG> is assumed.  ID of the user whose function determination is desired. If omitted, only the latest
1303    C<FIG> assignment will be returned.
1304    
1305  =item RETURN  =item RETURN
1306    
# Line 1070  Line 1309 
1309  =back  =back
1310    
1311  =cut  =cut
1312    #: Return Type $;
1313  sub FunctionOf {  sub FunctionOf {
1314          # Get the parameters.          # Get the parameters.
1315          my $self = shift @_;      my ($self, $featureID, $userID) = @_;
1316          my ($featureID, $userID) = @_;      # Declare the return value.
         if (!$userID) { $userID = 'FIG'; }  
         # Build a query for all of the feature's annotation, sorted by date.  
         my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation'],  
                                                     "IsTargetOfAnnotation(from-link) = ?", [$featureID]);  
         # Declare the return value. We'll set this to the most recent annotation for the  
         # specified user.  
1317          my $retVal;          my $retVal;
1318        # Determine the ID type.
1319        if ($featureID =~ m/^fig\|/) {
1320            # Here we have a FIG feature ID. We must build the list of trusted
1321            # users.
1322            my %trusteeTable = ();
1323            # Check the user ID.
1324            if (!$userID) {
1325                # No user ID, so only FIG is trusted.
1326                $trusteeTable{FIG} = 1;
1327            } else {
1328                # Add this user's ID.
1329                $trusteeTable{$userID} = 1;
1330                # Look for the trusted users in the database.
1331                my @trustees = $self->GetFlat(['IsTrustedBy'], 'IsTrustedBy(from-link) = ?', [$userID], 'IsTrustedBy(to-link)');
1332                if (! @trustees) {
1333                    # None were found, so build a default list.
1334                    $trusteeTable{FIG} = 1;
1335                } else {
1336                    # Otherwise, put all the trustees in.
1337                    for my $trustee (@trustees) {
1338                        $trusteeTable{$trustee} = 1;
1339                    }
1340                }
1341            }
1342            # Build a query for all of the feature's annotations, sorted by date.
1343            my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1344                                   "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1345                                   [$featureID]);
1346          my $timeSelected = 0;          my $timeSelected = 0;
1347          # Loop until we run out of annotations.          # Loop until we run out of annotations.
1348          while (my $annotation = $query->Fetch()) {          while (my $annotation = $query->Fetch()) {
1349                  # Get the annotation text.                  # Get the annotation text.
1350                  my ($text, $time) = $annotation->Values(['Annotation(annotation)','Annotation(time)']);              my ($text, $time, $user) = $annotation->Values(['Annotation(annotation)',
1351                  # Check to see if this is a functional assignment for the desired user.                                                       'Annotation(time)', 'MadeAnnotation(from-link)']);
1352                  my ($user, $type, $function) = split(/\n/, $text);              # Check to see if this is a functional assignment for a trusted user.
1353                  if ($type =~ m/^set $userID function to$/i) {              my ($actualUser, $function) = _ParseAssignment($user, $text);
1354                          # Here it is, so we check the time and save the assignment value.              Trace("Assignment user is $actualUser, text is $function.") if T(4);
1355                          if ($time > $timeSelected) {              if ($actualUser) {
1356                    # Here it is a functional assignment. Check the time and the user
1357                    # name. The time must be recent and the user must be trusted.
1358                    if ((exists $trusteeTable{$actualUser}) && ($time > $timeSelected)) {
1359                                  $retVal = $function;                                  $retVal = $function;
1360                                  $timeSelected = $time;                                  $timeSelected = $time;
1361                          }                          }
1362                  }                  }
1363          }          }
1364        } else {
1365            # Here we have a non-FIG feature ID. In this case the user ID does not
1366            # matter. We simply get the information from the External Alias Function
1367            # table.
1368            ($retVal) = $self->GetEntityValues('ExternalAliasFunc', $featureID, ['ExternalAliasFunc(func)']);
1369        }
1370          # Return the assignment found.          # Return the assignment found.
1371          return $retVal;          return $retVal;
1372  }  }
1373    
1374    =head3 FunctionsOf
1375    
1376    C<< my @functionList = $sprout->FunctionOf($featureID, $userID); >>
1377    
1378    Return the functional assignments of a particular feature.
1379    
1380    The functional assignment is handled differently depending on the type of feature. If
1381    the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional
1382    assignment is a type of annotation. The format of an assignment is described in
1383    L</ParseAssignment>. Its worth noting that we cannot filter on the content of the
1384    annotation itself because it's a text field; however, this is not a big problem because
1385    most features only have a small number of annotations.
1386    
1387    If the feature is B<not> identified by a FIG ID, then the functional assignment
1388    information is taken from the B<ExternalAliasFunc> table. If the table does
1389    not contain an entry for the feature, an empty list is returned.
1390    
1391    =over 4
1392    
1393    =item featureID
1394    
1395    ID of the feature whose functional assignments are desired.
1396    
1397    =item RETURN
1398    
1399    Returns a list of 2-tuples, each consisting of a user ID and the text of an assignment by
1400    that user.
1401    
1402    =back
1403    
1404    =cut
1405    #: Return Type @@;
1406    sub FunctionsOf {
1407        # Get the parameters.
1408        my ($self, $featureID) = @_;
1409        # Declare the return value.
1410        my @retVal = ();
1411        # Determine the ID type.
1412        if ($featureID =~ m/^fig\|/) {
1413            # Here we have a FIG feature ID. We must build the list of trusted
1414            # users.
1415            my %trusteeTable = ();
1416            # Build a query for all of the feature's annotations, sorted by date.
1417            my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1418                                   "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1419                                   [$featureID]);
1420            my $timeSelected = 0;
1421            # Loop until we run out of annotations.
1422            while (my $annotation = $query->Fetch()) {
1423                # Get the annotation text.
1424                my ($text, $time, $user) = $annotation->Values(['Annotation(annotation)',
1425                                                                'Annotation(time)',
1426                                                                'MadeAnnotation(user)']);
1427                # Check to see if this is a functional assignment for a trusted user.
1428                my ($actualUser, $function) = _ParseAssignment($user, $text);
1429                if ($actualUser) {
1430                    # Here it is a functional assignment.
1431                    push @retVal, [$actualUser, $function];
1432                }
1433            }
1434        } else {
1435            # Here we have a non-FIG feature ID. In this case the user ID does not
1436            # matter. We simply get the information from the External Alias Function
1437            # table.
1438            my @assignments = $self->GetEntityValues('ExternalAliasFunc', $featureID,
1439                                                     ['ExternalAliasFunc(func)']);
1440            push @retVal, map { ['master', $_] } @assignments;
1441        }
1442        # Return the assignments found.
1443        return @retVal;
1444    }
1445    
1446  =head3 BBHList  =head3 BBHList
1447    
1448  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>
# Line 1120  Line 1462 
1462    
1463  =item RETURN  =item RETURN
1464    
1465  Returns a reference to a hash that maps the IDs of the incoming features to the IDs of  Returns a reference to a hash that maps the IDs of the incoming features to the best hits
1466  their best hits.  on the target genome.
1467    
1468  =back  =back
1469    
1470  =cut  =cut
1471    #: Return Type %;
1472  sub BBHList {  sub BBHList {
1473          # Get the parameters.          # Get the parameters.
1474          my $self = shift @_;      my ($self, $genomeID, $featureList) = @_;
         my ($genomeID, $featureList) = @_;  
1475          # Create the return structure.          # Create the return structure.
1476          my %retVal = ();          my %retVal = ();
1477          # Loop through the incoming features.          # Loop through the incoming features.
# Line 1139  Line 1480 
1480                  my $query = $self->Get(['IsBidirectionalBestHitOf'],                  my $query = $self->Get(['IsBidirectionalBestHitOf'],
1481                                                             "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",                                                             "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",
1482                                                             [$featureID, $genomeID]);                                                             [$featureID, $genomeID]);
1483                  # Look for the best hit.          # Peel off the BBHs found.
1484                  my $bbh = $query->Fetch;          my @found = ();
1485                  if ($bbh) {          while (my $bbh = $query->Fetch) {
1486                          my ($targetFeature) = $bbh->Value('IsBidirectionalBestHitOf(to-link)');              push @found, $bbh->Value('IsBidirectionalBestHitOf(to-link)');
                         $retVal{$featureID} = $targetFeature;  
1487                  }                  }
1488            $retVal{$featureID} = \@found;
1489          }          }
1490          # Return the mapping.          # Return the mapping.
1491          return \%retVal;          return \%retVal;
1492  }  }
1493    
1494    =head3 SimList
1495    
1496    C<< my %similarities = $sprout->SimList($featureID, $count); >>
1497    
1498    Return a list of the similarities to the specified feature.
1499    
1500    Sprout does not support real similarities, so this method just returns the bidirectional
1501    best hits.
1502    
1503    =over 4
1504    
1505    =item featureID
1506    
1507    ID of the feature whose similarities are desired.
1508    
1509    =item count
1510    
1511    Maximum number of similar features to be returned, or C<0> to return them all.
1512    
1513    =back
1514    
1515    =cut
1516    #: Return Type %;
1517    sub SimList {
1518        # Get the parameters.
1519        my ($self, $featureID, $count) = @_;
1520        # Ask for the best hits.
1521        my @lists = $self->GetAll(['IsBidirectionalBestHitOf'],
1522                                  "IsBidirectionalBestHitOf(from-link) = ? ORDER BY IsBidirectionalBestHitOf(score) DESC",
1523                                  [$featureID], ['IsBidirectionalBestHitOf(to-link)', 'IsBidirectionalBestHitOf(score)'],
1524                                  $count);
1525        # Create the return value.
1526        my %retVal = ();
1527        for my $tuple (@lists) {
1528            $retVal{$tuple->[0]} = $tuple->[1];
1529        }
1530        # Return the result.
1531        return %retVal;
1532    }
1533    
1534    
1535    
1536    =head3 IsComplete
1537    
1538    C<< my $flag = $sprout->IsComplete($genomeID); >>
1539    
1540    Return TRUE if the specified genome is complete, else FALSE.
1541    
1542    =over 4
1543    
1544    =item genomeID
1545    
1546    ID of the genome whose completeness status is desired.
1547    
1548    =item RETURN
1549    
1550    Returns TRUE if the genome is complete, FALSE if it is incomplete, and C<undef> if it is
1551    not found.
1552    
1553    =back
1554    
1555    =cut
1556    #: Return Type $;
1557    sub IsComplete {
1558        # Get the parameters.
1559        my ($self, $genomeID) = @_;
1560        # Declare the return variable.
1561        my $retVal;
1562        # Get the genome's data.
1563        my $genomeData = $self->GetEntity('Genome', $genomeID);
1564        if ($genomeData) {
1565            # The genome exists, so get the completeness flag.
1566            ($retVal) = $genomeData->Value('Genome(complete)');
1567        }
1568        # Return the result.
1569        return $retVal;
1570    }
1571    
1572  =head3 FeatureAliases  =head3 FeatureAliases
1573    
1574  C<< my @aliasList = $sprout->FeatureAliases($featureID); >>  C<< my @aliasList = $sprout->FeatureAliases($featureID); >>
# Line 1170  Line 1589 
1589  =back  =back
1590    
1591  =cut  =cut
1592    #: Return Type @;
1593  sub FeatureAliases {  sub FeatureAliases {
1594          # Get the parameters.          # Get the parameters.
1595          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
1596          # Get the desired feature's aliases          # Get the desired feature's aliases
1597          my @retVal = $self->GetEntityValues('Feature', $featureID, ['Feature(alias)']);          my @retVal = $self->GetEntityValues('Feature', $featureID, ['Feature(alias)']);
1598          # Return the result.          # Return the result.
# Line 1185  Line 1603 
1603    
1604  C<< my $genomeID = $sprout->GenomeOf($featureID); >>  C<< my $genomeID = $sprout->GenomeOf($featureID); >>
1605    
1606  Return the genome that contains a specified feature.  Return the genome that contains a specified feature or contig.
1607    
1608  =over 4  =over 4
1609    
1610  =item featureID  =item featureID
1611    
1612  ID of the feature whose genome is desired.  ID of the feature or contig whose genome is desired.
1613    
1614  =item RETURN  =item RETURN
1615    
1616  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
1617  an undefined value.  found, returns an undefined value.
1618    
1619  =back  =back
1620    
1621  =cut  =cut
1622    #: Return Type $;
1623  sub GenomeOf {  sub GenomeOf {
1624          # Get the parameters.          # Get the parameters.
1625          my $self = shift @_;      my ($self, $featureID) = @_;
1626          my ($featureID) = @_;      # Create a query to find the genome associated with the incoming ID.
1627          # Create a query to find the genome associated with the feature.      my $query = $self->Get(['IsLocatedIn', 'HasContig'], "IsLocatedIn(from-link) = ? OR HasContig(to-link) = ?",
1628          my $query = $self->Get(['IsLocatedIn', 'HasContig'], "IsLocatedIn(from-link) = ?", [$featureID]);                             [$featureID, $featureID]);
1629          # Declare the return value.          # Declare the return value.
1630          my $retVal;          my $retVal;
1631          # Get the genome ID.          # Get the genome ID.
# Line 1238  Line 1656 
1656  =back  =back
1657    
1658  =cut  =cut
1659    #: Return Type %;
1660  sub CoupledFeatures {  sub CoupledFeatures {
1661          # Get the parameters.          # Get the parameters.
1662          my $self = shift @_;      my ($self, $featureID) = @_;
1663          my ($featureID) = @_;      Trace("Looking for features coupled to $featureID.") if T(coupling => 3);
1664          # Create a query to retrieve the functionally-coupled features. Note that we depend on the      # Create a query to retrieve the functionally-coupled features.
1665          # fact that the functional coupling is physically paired. If (A,B) is in the database, then      my $query = $self->Get(['ParticipatesInCoupling', 'Coupling'],
1666          # (B,A) will also be found.                             "ParticipatesInCoupling(from-link) = ?", [$featureID]);
         my $query = $self->Get(['IsClusteredOnChromosomeWith'],  
                                                    "IsClusteredOnChromosomeWith(from-link) = ?", [$featureID]);  
1667          # This value will be set to TRUE if we find at least one coupled feature.          # This value will be set to TRUE if we find at least one coupled feature.
1668          my $found = 0;          my $found = 0;
1669          # Create the return hash.          # Create the return hash.
1670          my %retVal = ();          my %retVal = ();
1671          # Retrieve the relationship records and store them in the hash.          # Retrieve the relationship records and store them in the hash.
1672          while (my $clustering = $query->Fetch()) {          while (my $clustering = $query->Fetch()) {
1673                  my ($otherFeatureID, $score) = $clustering->Values(['IsClusteredOnChromosomeWith(to-link)',          # Get the ID and score of the coupling.
1674                                                                      'IsClusteredOnChromosomeWith(score)']);          my ($couplingID, $score) = $clustering->Values(['Coupling(id)',
1675                                                            'Coupling(score)']);
1676            Trace("$featureID coupled with score $score to ID $couplingID.") if T(coupling => 4);
1677            # Get the other feature that participates in the coupling.
1678            my ($otherFeatureID) = $self->GetFlat(['ParticipatesInCoupling'],
1679                                               "ParticipatesInCoupling(to-link) = ? AND ParticipatesInCoupling(from-link) <> ?",
1680                                               [$couplingID, $featureID], 'ParticipatesInCoupling(from-link)');
1681            Trace("$couplingID target feature is $otherFeatureID.") if T(coupling => 4);
1682            # Attach the other feature's score to its ID.
1683                  $retVal{$otherFeatureID} = $score;                  $retVal{$otherFeatureID} = $score;
1684                  $found = 1;                  $found = 1;
1685          }          }
# Line 1268  Line 1692 
1692          return %retVal;          return %retVal;
1693  }  }
1694    
1695  =head3 GetEntityTypes  =head3 CouplingEvidence
1696    
1697  C<< my @entityList = $sprout->GetEntityTypes(); >>  C<< my @evidence = $sprout->CouplingEvidence($peg1, $peg2); >>
1698    
1699  Return the list of supported entity types.  Return the evidence for a functional coupling.
1700    
1701  =cut  A pair of features is considered evidence of a coupling between two other
1702    features if they occur close together on a contig and both are similar to
1703    the coupled features. So, if B<A1> and B<A2> are close together on a contig,
1704    B<B1> and B<B2> are considered evidence for the coupling if (1) B<B1> and
1705    B<B2> are close together, (2) B<B1> is similar to B<A1>, and (3) B<B2> is
1706    similar to B<A2>.
1707    
1708    The score of a coupling is determined by the number of pieces of evidence
1709    that are considered I<representative>. If several evidence items belong to
1710    a group of genomes that are close to each other, only one of those items
1711    is considered representative. The other evidence items are presumed to be
1712    there because of the relationship between the genomes rather than because
1713    the two proteins generated by the features have a related functionality.
1714    
1715    Each evidence item is returned as a three-tuple in the form C<[>I<$peg1a>C<,>
1716    I<$peg2a>C<,> I<$rep>C<]>, where I<$peg1a> is similar to I<$peg1>, I<$peg2a>
1717    is similar to I<$peg2>, and I<$rep> is TRUE if the evidence is representative
1718    and FALSE otherwise.
1719    
1720    =over 4
1721    
1722    =item peg1
1723    
1724    ID of the feature of interest.
1725    
1726    =item peg2
1727    
1728    ID of a feature functionally coupled to the feature of interest.
1729    
1730    =item RETURN
1731    
1732  sub GetEntityTypes {  Returns a list of 3-tuples. Each tuple consists of a feature similar to the feature
1733    of interest, a feature similar to the functionally coupled feature, and a flag
1734    that is TRUE for a representative piece of evidence and FALSE otherwise.
1735    
1736    =back
1737    
1738    =cut
1739    #: Return Type @@;
1740    sub CouplingEvidence {
1741          # Get the parameters.          # Get the parameters.
1742          my $self = shift @_;      my ($self, $peg1, $peg2) = @_;
1743          # Get the underlying database object.      # Declare the return variable.
1744          my $erdb = $self->{_erdb};      my @retVal = ();
1745          # Get its entity type list.      # Our first task is to find out the nature of the coupling: whether or not
1746          my @retVal = $erdb->GetEntityTypes();      # it exists, its score, and whether the features are stored in the same
1747        # order as the ones coming in.
1748        my ($couplingID, $inverted, $score) = $self->GetCoupling($peg1, $peg2);
1749        # Only proceed if a coupling exists.
1750        if ($couplingID) {
1751            # Determine the ordering to place on the evidence items. If we're
1752            # inverted, we want to see feature 2 before feature 1 (descending); otherwise,
1753            # we want feature 1 before feature 2 (normal).
1754            Trace("Coupling evidence for ($peg1, $peg2) with inversion flag $inverted.") if T(Coupling => 4);
1755            my $ordering = ($inverted ? "DESC" : "");
1756            # Get the coupling evidence.
1757            my @evidenceList = $self->GetAll(['IsEvidencedBy', 'PCH', 'UsesAsEvidence'],
1758                                              "IsEvidencedBy(from-link) = ? ORDER BY PCH(id), UsesAsEvidence(pos) $ordering",
1759                                              [$couplingID],
1760                                              ['PCH(used)', 'UsesAsEvidence(to-link)']);
1761            # Loop through the evidence items. Each piece of evidence is represented by two
1762            # positions in the evidence list, one for each feature on the other side of the
1763            # evidence link. If at some point we want to generalize to couplings with
1764            # more than two positions, this section of code will need to be re-done.
1765            while (@evidenceList > 0) {
1766                my $peg1Data = shift @evidenceList;
1767                my $peg2Data = shift @evidenceList;
1768                Trace("Peg 1 is " . $peg1Data->[1] . " and Peg 2 is " . $peg2Data->[1] . ".") if T(Coupling => 4);
1769                push @retVal, [$peg1Data->[1], $peg2Data->[1], $peg1Data->[0]];
1770            }
1771            Trace("Last index in evidence result is is $#retVal.") if T(Coupling => 4);
1772        }
1773        # Return the result.
1774        return @retVal;
1775  }  }
1776    
1777  =head3 ReadFasta  =head3 GetCoupling
1778    
1779  C<< my %sequenceData = Sprout::ReadFasta($fileName, $prefix); >>  C<< my ($couplingID, $inverted, $score) = $sprout->GetCoupling($peg1, $peg2); >>
1780    
1781  Read sequence data from a FASTA-format file. Each sequence in a FASTA file is represented by  Return the coupling (if any) for the specified pair of PEGs. If a coupling
1782  one or more lines of data. The first line begins with a > character and contains an ID.  exists, we return the coupling ID along with an indicator of whether the
1783  The remaining lines contain the sequence data in order.  coupling is stored as C<(>I<$peg1>C<, >I<$peg2>C<)> or C<(>I<$peg2>C<, >I<$peg1>C<)>.
1784    In the second case, we say the coupling is I<inverted>. The importance of an
1785    inverted coupling is that the PEGs in the evidence will appear in reverse order.
1786    
1787  =over 4  =over 4
1788    
1789  =item fileName  =item peg1
1790    
1791  Name of the FASTA file.  ID of the feature of interest.
1792    
1793  =item prefix (optional)  =item peg2
1794    
1795  Prefix to be put in front of each ID found.  ID of the potentially coupled feature.
1796    
1797  =item RETURN  =item RETURN
1798    
1799  Returns a hash that maps each ID to its sequence.  Returns a three-element list. The first element contains the database ID of
1800    the coupling. The second element is FALSE if the coupling is stored in the
1801    database in the caller specified order and TRUE if it is stored in the
1802    inverted order. The third element is the coupling's score. If the coupling
1803    does not exist, all three list elements will be C<undef>.
1804    
1805  =back  =back
1806    
1807  =cut  =cut
1808    #: Return Type $%@;
1809  sub ReadFasta {  sub GetCoupling {
1810          # Get the parameters.          # Get the parameters.
1811          my ($fileName, $prefix) = @_;      my ($self, $peg1, $peg2) = @_;
1812          # Create the return hash.      # Declare the return values. We'll start with the coupling ID and undefine the
1813          my %retVal = ();      # flag and score until we have more information.
1814          # Open the file for input.      my ($retVal, $inverted, $score) = ($self->CouplingID($peg1, $peg2), undef, undef);
1815          open FASTAFILE, '<', $fileName;      # Find the coupling data.
1816          # Declare the ID variable and clear the sequence accumulator.      my @pegs = $self->GetAll(['Coupling', 'ParticipatesInCoupling'],
1817          my $sequence = "";                                   "Coupling(id) = ? ORDER BY ParticipatesInCoupling(pos)",
1818          my $id = "";                                   [$retVal], ["ParticipatesInCoupling(from-link)", "Coupling(score)"]);
1819          # Loop through the file.      # Check to see if we found anything.
1820          while (<FASTAFILE>) {      if (!@pegs) {
1821            Trace("No coupling found.") if T(Coupling => 4);
1822            # No coupling, so undefine the return value.
1823            $retVal = undef;
1824        } else {
1825            # We have a coupling! Get the score and check for inversion.
1826            $score = $pegs[0]->[1];
1827            my $firstFound = $pegs[0]->[0];
1828            $inverted = ($firstFound ne $peg1);
1829            Trace("Coupling score is $score. First peg is $firstFound, peg 1 is $peg1.") if T(Coupling => 4);
1830        }
1831        # Return the result.
1832        return ($retVal, $inverted, $score);
1833    }
1834    
1835    =head3 GetSynonymGroup
1836    
1837    C<< my $id = $sprout->GetSynonymGroup($fid); >>
1838    
1839    Return the synonym group name for the specified feature.
1840    
1841    =over 4
1842    
1843    =item fid
1844    
1845    ID of the feature whose synonym group is desired.
1846    
1847    =item RETURN
1848    
1849    The name of the synonym group to which the feature belongs. If the feature does
1850    not belong to a synonym group, the feature ID itself is returned.
1851    
1852    =back
1853    
1854    =cut
1855    
1856    sub GetSynonymGroup {
1857        # Get the parameters.
1858        my ($self, $fid) = @_;
1859        # Declare the return variable.
1860        my $retVal;
1861        # Find the synonym group.
1862        my @groups = $self->GetFlat(['IsSynonymGroupFor'], "IsSynonymGroupFor(to-link) = ?",
1863                                       [$fid], 'IsSynonymGroupFor(from-link)');
1864        # Check to see if we found anything.
1865        if (@groups) {
1866            $retVal = $groups[0];
1867        } else {
1868            $retVal = $fid;
1869        }
1870        # Return the result.
1871        return $retVal;
1872    }
1873    
1874    =head3 GetBoundaries
1875    
1876    C<< my ($contig, $beg, $end) = $sprout->GetBoundaries(@locList); >>
1877    
1878    Determine the begin and end boundaries for the locations in a list. All of the
1879    locations must belong to the same contig and have mostly the same direction in
1880    order for this method to produce a meaningful result. The resulting
1881    begin/end pair will contain all of the bases in any of the locations.
1882    
1883    =over 4
1884    
1885    =item locList
1886    
1887    List of locations to process.
1888    
1889    =item RETURN
1890    
1891    Returns a 3-tuple consisting of the contig ID, the beginning boundary,
1892    and the ending boundary. The beginning boundary will be left of the
1893    end for mostly-forward locations and right of the end for mostly-backward
1894    locations.
1895    
1896    =back
1897    
1898    =cut
1899    
1900    sub GetBoundaries {
1901        # Get the parameters.
1902        my ($self, @locList) = @_;
1903        # Set up the counters used to determine the most popular direction.
1904        my %counts = ( '+' => 0, '-' => 0 );
1905        # Get the last location and parse it.
1906        my $locObject = BasicLocation->new(pop @locList);
1907        # Prime the loop with its data.
1908        my ($contig, $beg, $end) = ($locObject->Contig, $locObject->Left, $locObject->Right);
1909        # Count its direction.
1910        $counts{$locObject->Dir}++;
1911        # Loop through the remaining locations. Note that in most situations, this loop
1912        # will not iterate at all, because most of the time we will be dealing with a
1913        # singleton list.
1914        for my $loc (@locList) {
1915            # Create a location object.
1916            my $locObject = BasicLocation->new($loc);
1917            # Count the direction.
1918            $counts{$locObject->Dir}++;
1919            # Get the left end and the right end.
1920            my $left = $locObject->Left;
1921            my $right = $locObject->Right;
1922            # Merge them into the return variables.
1923            if ($left < $beg) {
1924                $beg = $left;
1925            }
1926            if ($right > $end) {
1927                $end = $right;
1928            }
1929        }
1930        # If the most common direction is reverse, flip the begin and end markers.
1931        if ($counts{'-'} > $counts{'+'}) {
1932            ($beg, $end) = ($end, $beg);
1933        }
1934        # Return the result.
1935        return ($contig, $beg, $end);
1936    }
1937    
1938    =head3 CouplingID
1939    
1940    C<< my $couplingID = $sprout->CouplingID($peg1, $peg2); >>
1941    
1942    Return the coupling ID for a pair of feature IDs.
1943    
1944    The coupling ID is currently computed by joining the feature IDs in
1945    sorted order with a space. Client modules (that is, modules which
1946    use Sprout) should not, however, count on this always being the
1947    case. This method provides a way for abstracting the concept of a
1948    coupling ID. All that we know for sure about it is that it can be
1949    generated easily from the feature IDs and the order of the IDs
1950    in the parameter list does not matter (i.e. C<CouplingID("a1", "b1")>
1951    will have the same value as C<CouplingID("b1", "a1")>.
1952    
1953    =over 4
1954    
1955    =item peg1
1956    
1957    First feature of interest.
1958    
1959    =item peg2
1960    
1961    Second feature of interest.
1962    
1963    =item RETURN
1964    
1965    Returns the ID that would be used to represent a functional coupling of
1966    the two specified PEGs.
1967    
1968    =back
1969    
1970    =cut
1971    #: Return Type $;
1972    sub CouplingID {
1973        my ($self, @pegs) = @_;
1974        return $self->DigestKey(join " ", sort @pegs);
1975    }
1976    
1977    =head3 ReadFasta
1978    
1979    C<< my %sequenceData = Sprout::ReadFasta($fileName, $prefix); >>
1980    
1981    Read sequence data from a FASTA-format file. Each sequence in a FASTA file is represented by
1982    one or more lines of data. The first line begins with a > character and contains an ID.
1983    The remaining lines contain the sequence data in order.
1984    
1985    =over 4
1986    
1987    =item fileName
1988    
1989    Name of the FASTA file.
1990    
1991    =item prefix (optional)
1992    
1993    Prefix to be put in front of each ID found.
1994    
1995    =item RETURN
1996    
1997    Returns a hash that maps each ID to its sequence.
1998    
1999    =back
2000    
2001    =cut
2002    #: Return Type %;
2003    sub ReadFasta {
2004        # Get the parameters.
2005        my ($fileName, $prefix) = @_;
2006        # Create the return hash.
2007        my %retVal = ();
2008        # Open the file for input.
2009        open FASTAFILE, '<', $fileName;
2010        # Declare the ID variable and clear the sequence accumulator.
2011        my $sequence = "";
2012        my $id = "";
2013        # Loop through the file.
2014        while (<FASTAFILE>) {
2015                  # Get the current line.                  # Get the current line.
2016                  my $line = $_;                  my $line = $_;
2017                  # Check for a header line.                  # Check for a header line.
2018                  if ($line =~ m/^>\s*(.+?)(\s|\n)/) {                  if ($line =~ m/^>\s*(.+?)(\s|\n)/) {
2019                          # Here we have a new header. Store the current sequence if we have one.                          # Here we have a new header. Store the current sequence if we have one.
2020                          if ($id) {                          if ($id) {
2021                                  $retVal{$id} = $sequence;                  $retVal{$id} = lc $sequence;
2022                          }                          }
2023                          # Clear the sequence accumulator and save the new ID.                          # Clear the sequence accumulator and save the new ID.
2024                          ($id, $sequence) = ("$prefix$1", "");                          ($id, $sequence) = ("$prefix$1", "");
2025                  } else {                  } else {
2026                          # 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.
2027                          # First, we get the actual data out.              # First, we get the actual data out. Note that we normalize to lower
2028                # case.
2029                          $line =~ /^\s*(.*?)(\s|\n)/;                          $line =~ /^\s*(.*?)(\s|\n)/;
2030                          $sequence .= $1;                          $sequence .= $1;
2031                  }                  }
2032          }          }
2033          # Flush out the last sequence (if any).          # Flush out the last sequence (if any).
2034          if ($sequence) {          if ($sequence) {
2035                  $retVal {$id} = $sequence;          $retVal{$id} = lc $sequence;
2036          }          }
2037        # Close the file.
2038        close FASTAFILE;
2039          # Return the hash constructed from the file.          # Return the hash constructed from the file.
2040          return %retVal;          return %retVal;
2041  }  }
# Line 1354  Line 2046 
2046    
2047  Insure that a list of feature locations is in the Sprout format. The Sprout feature location  Insure that a list of feature locations is in the Sprout format. The Sprout feature location
2048  format is I<contig>_I<beg*len> where I<*> is C<+> for a forward gene and C<-> for a backward  format is I<contig>_I<beg*len> where I<*> is C<+> for a forward gene and C<-> for a backward
2049  gene. The old format is I<contig>_I<beg>_I<end>.  gene. The old format is I<contig>_I<beg>_I<end>. If a feature is in the new format already,
2050    it will not be changed; otherwise, it will be converted. This method can also be used to
2051    perform the reverse task-- insuring that all the locations are in the old format.
2052    
2053  =over 4  =over 4
2054    
# Line 1378  Line 2072 
2072  =back  =back
2073    
2074  =cut  =cut
2075    #: Return Type @;
2076  sub FormatLocations {  sub FormatLocations {
2077          # Get the parameters.          # Get the parameters.
2078          my $self = shift @_;      my ($self, $prefix, $locations, $oldFormat) = @_;
         my ($prefix, $locations, $oldFormat) = @_;  
2079          # Create the return list.          # Create the return list.
2080          my @retVal = ();          my @retVal = ();
2081          # Check to see if any locations were passed in.          # Check to see if any locations were passed in.
2082          if ($locations eq '') {          if ($locations eq '') {
2083              confess "No locations specified.";          Confess("No locations specified.");
2084          } else {          } else {
2085                  # Loop through the locations, converting them to the new format.                  # Loop through the locations, converting them to the new format.
2086                  for my $location (@{$locations}) {                  for my $location (@{$locations}) {
# Line 1422  Line 2115 
2115    
2116  sub DumpData {  sub DumpData {
2117          # Get the parameters.          # Get the parameters.
2118          my $self = shift @_;      my ($self) = @_;
2119          # Get the data directory name.          # Get the data directory name.
2120          my $outputDirectory = $self->{_options}->{dataDir};          my $outputDirectory = $self->{_options}->{dataDir};
2121          # Dump the relations.          # Dump the relations.
2122          $self->{_erdb}->DumpRelations($outputDirectory);      $self->DumpRelations($outputDirectory);
2123  }  }
2124    
2125  =head3 XMLFileName  =head3 XMLFileName
# Line 1436  Line 2129 
2129  Return the name of this database's XML definition file.  Return the name of this database's XML definition file.
2130    
2131  =cut  =cut
2132    #: Return Type $;
2133  sub XMLFileName {  sub XMLFileName {
2134          my $self = shift @_;      my ($self) = @_;
2135          return $self->{_xmlName};          return $self->{_xmlName};
2136  }  }
2137    
# Line 1458  Line 2151 
2151  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
2152  property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.  property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
2153    
2154  C<< $sprout->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence = 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>  C<< $sprout->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>
2155    
2156  =over 4  =over 4
2157    
# Line 1473  Line 2166 
2166  =back  =back
2167    
2168  =cut  =cut
2169    #: Return Type ;
2170  sub Insert {  sub Insert {
2171          # Get the parameters.          # Get the parameters.
2172          my $self = shift @_;      my ($self, $objectType, $fieldHash) = @_;
         my ($objectType, $fieldHash) = @_;  
2173          # Call the underlying method.          # Call the underlying method.
2174          $self->{_erdb}->InsertObject($objectType, $fieldHash);      $self->InsertObject($objectType, $fieldHash);
2175  }  }
2176    
2177  =head3 Annotate  =head3 Annotate
# Line 1515  Line 2207 
2207  =back  =back
2208    
2209  =cut  =cut
2210    #: Return Type $;
2211  sub Annotate {  sub Annotate {
2212          # Get the parameters.          # Get the parameters.
2213          my $self = shift @_;      my ($self, $fid, $timestamp, $user, $text) = @_;
         my ($fid, $timestamp, $user, $text) = @_;  
2214          # Create the annotation ID.          # Create the annotation ID.
2215          my $aid = "$fid:$timestamp";          my $aid = "$fid:$timestamp";
2216          # Insert the Annotation object.          # Insert the Annotation object.
# Line 1539  Line 2230 
2230    
2231  =head3 AssignFunction  =head3 AssignFunction
2232    
2233  C<< my $ok = $sprout->AssignFunction($featureID, $user, $function); >>  C<< my $ok = $sprout->AssignFunction($featureID, $user, $function, $assigningUser); >>
2234    
2235  This method assigns a function to a feature. Functions are a special type of annotation. The general  This method assigns a function to a feature. Functions are a special type of annotation. The general
2236  format is "XXXX\nset XXXX function to\nYYYYY" where XXXX is the feature type and YYYY is the functional  format is described in L</ParseAssignment>.
 assignment text.  
2237    
2238  =over 4  =over 4
2239    
# Line 1553  Line 2243 
2243    
2244  =item user  =item user
2245    
2246  Name of the user making the assignment. This is frequently a group name, like C<kegg> or C<fig>.  Name of the user group making the assignment, such as C<kegg> or C<fig>.
2247    
2248  =item function  =item function
2249    
2250  Text of the function being assigned.  Text of the function being assigned.
2251    
2252    =item assigningUser (optional)
2253    
2254    Name of the individual user making the assignment. If omitted, defaults to the user group.
2255    
2256  =item RETURN  =item RETURN
2257    
2258  Returns 1 if successful, 0 if an error occurred.  Returns 1 if successful, 0 if an error occurred.
# Line 1566  Line 2260 
2260  =back  =back
2261    
2262  =cut  =cut
2263    #: Return Type $;
2264  sub AssignFunction {  sub AssignFunction {
2265          # Get the parameters.          # Get the parameters.
2266          my $self = shift @_;      my ($self, $featureID, $user, $function, $assigningUser) = @_;
2267          my ($featureID, $user, $function) = @_;      # Default the assigning user.
2268        if (! $assigningUser) {
2269            $assigningUser = $user;
2270        }
2271          # Create an annotation string from the parameters.          # Create an annotation string from the parameters.
2272          my $annotationText = "$user\nset $user function to\n$function";      my $annotationText = "$assigningUser\nset $user function to\n$function";
2273          # Get the current time.          # Get the current time.
2274          my $now = time;          my $now = time;
2275          # Declare the return variable.          # Declare the return variable.
# Line 1614  Line 2311 
2311  =back  =back
2312    
2313  =cut  =cut
2314    #: Return Type @;
2315  sub FeaturesByAlias {  sub FeaturesByAlias {
2316          # Get the parameters.          # Get the parameters.
2317          my $self = shift @_;      my ($self, $alias) = @_;
         my ($alias) = @_;  
2318          # Declare the return variable.          # Declare the return variable.
2319          my @retVal = ();          my @retVal = ();
2320          # Parse the alias.          # Parse the alias.
# Line 1634  Line 2330 
2330          return @retVal;          return @retVal;
2331  }  }
2332    
 =head3 Exists  
   
 C<< my $found = $sprout->Exists($entityName, $entityID); >>  
   
 Return TRUE if an entity exists, else FALSE.  
   
 =over 4  
   
 =item entityName  
   
 Name of the entity type (e.g. C<Feature>) relevant to the existence check.  
   
 =item entityID  
   
 ID of the entity instance whose existence is to be checked.  
   
 =item RETURN  
   
 Returns TRUE if the entity instance exists, else FALSE.  
   
 =back  
   
 =cut  
   
 sub Exists {  
         # Get the parameters.  
         my $self = shift @_;  
         my ($entityName, $entityID) = @_;  
         # Check for the entity instance.  
         my $testInstance = $self->GetEntity($entityName, $entityID);  
         # Return an existence indicator.  
         my $retVal = ($testInstance ? 1 : 0);  
         return $retVal;  
 }  
   
2333  =head3 FeatureTranslation  =head3 FeatureTranslation
2334    
2335  C<< my $translation = $sprout->FeatureTranslation($featureID); >>  C<< my $translation = $sprout->FeatureTranslation($featureID); >>
# Line 1688  Line 2349 
2349  =back  =back
2350    
2351  =cut  =cut
2352    #: Return Type $;
2353  sub FeatureTranslation {  sub FeatureTranslation {
2354          # Get the parameters.          # Get the parameters.
2355          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
2356          # Get the specified feature's translation.          # Get the specified feature's translation.
2357          my ($retVal) = $self->GetEntityValues("Feature", $featureID, ['Feature(translation)']);          my ($retVal) = $self->GetEntityValues("Feature", $featureID, ['Feature(translation)']);
2358          return $retVal;          return $retVal;
# Line 1721  Line 2381 
2381  =back  =back
2382    
2383  =cut  =cut
2384    #: Return Type @;
2385  sub Taxonomy {  sub Taxonomy {
2386          # Get the parameters.          # Get the parameters.
2387          my $self = shift @_;      my ($self, $genome) = @_;
         my ($genome) = @_;  
2388          # Find the specified genome's taxonomy string.          # Find the specified genome's taxonomy string.
2389          my ($list) = $self->GetEntityValues('Genome', $genome, ['Genome(taxonomy)']);          my ($list) = $self->GetEntityValues('Genome', $genome, ['Genome(taxonomy)']);
2390          # Declare the return variable.          # Declare the return variable.
# Line 1765  Line 2424 
2424  =back  =back
2425    
2426  =cut  =cut
2427    #: Return Type $;
2428  sub CrudeDistance {  sub CrudeDistance {
2429          # Get the parameters.          # Get the parameters.
2430          my $self = shift @_;      my ($self, $genome1, $genome2) = @_;
         my ($genome1, $genome2) = @_;  
2431          # Insure that the distance is commutative by sorting the genome IDs.          # Insure that the distance is commutative by sorting the genome IDs.
2432          my ($genomeA, $genomeB);          my ($genomeA, $genomeB);
2433          if ($genome2 < $genome2) {          if ($genome2 < $genome2) {
# Line 1813  Line 2471 
2471  =back  =back
2472    
2473  =cut  =cut
2474    #: Return Type $;
2475  sub RoleName {  sub RoleName {
2476          # Get the parameters.          # Get the parameters.
2477          my $self = shift @_;      my ($self, $roleID) = @_;
         my ($roleID) = @_;  
2478          # Get the specified role's name.          # Get the specified role's name.
2479          my ($retVal) = $self->GetEntityValues('Role', $roleID, ['Role(name)']);          my ($retVal) = $self->GetEntityValues('Role', $roleID, ['Role(name)']);
2480          # Use the ID if the role has no name.          # Use the ID if the role has no name.
# Line 1847  Line 2504 
2504  =back  =back
2505    
2506  =cut  =cut
2507    #: Return Type @;
2508  sub RoleDiagrams {  sub RoleDiagrams {
2509          # Get the parameters.          # Get the parameters.
2510          my $self = shift @_;      my ($self, $roleID) = @_;
         my ($roleID) = @_;  
2511          # Query for the diagrams.          # Query for the diagrams.
2512          my @retVal = $self->GetFlat(['RoleOccursIn'], "RoleOccursIn(from-link) = ?", [$roleID],          my @retVal = $self->GetFlat(['RoleOccursIn'], "RoleOccursIn(from-link) = ?", [$roleID],
2513                                                                  'RoleOccursIn(to-link)');                                                                  'RoleOccursIn(to-link)');
# Line 1859  Line 2515 
2515          return @retVal;          return @retVal;
2516  }  }
2517    
2518    =head3 GetProperties
2519    
2520    C<< my @list = $sprout->GetProperties($fid, $key, $value, $url); >>
2521    
2522    Return a list of the properties with the specified characteristics.
2523    
2524    Properties are arbitrary key-value pairs associated with a feature. (At some point they
2525    will also be associated with genomes.) A property value is represented by a 4-tuple of
2526    the form B<($fid, $key, $value, $url)>. These exactly correspond to the parameter
2527    
2528    =over 4
2529    
2530    =item fid
2531    
2532    ID of the feature possessing the property.
2533    
2534    =item key
2535    
2536    Name or key of the property.
2537    
2538    =item value
2539    
2540    Value of the property.
2541    
2542    =item url
2543    
2544    URL of the document that indicated the property should have this particular value, or an
2545    empty string if no such document exists.
2546    
2547    =back
2548    
2549    The parameters act as a filter for the desired data. Any non-null parameter will
2550    automatically match all the tuples returned. So, specifying just the I<$fid> will
2551    return all the properties of the specified feature; similarly, specifying the I<$key>
2552    and I<$value> parameters will return all the features having the specified property
2553    value.
2554    
2555    A single property key can have many values, representing different ideas about the
2556    feature in question. For example, one paper may declare that a feature C<fig|83333.1.peg.10> is
2557    virulent, and another may declare that it is not virulent. A query about the virulence of
2558    C<fig|83333.1.peg.10> would be coded as
2559    
2560        my @list = $sprout->GetProperties('fig|83333.1.peg.10', 'virulence', '', '');
2561    
2562    Here the I<$value> and I<$url> fields are left blank, indicating that those fields are
2563    not to be filtered. The tuples returned would be
2564    
2565        ('fig|83333.1.peg.10', 'virulence', 'yes', 'http://www.somewhere.edu/first.paper.pdf')
2566        ('fig|83333.1.peg.10', 'virulence', 'no', 'http://www.somewhere.edu/second.paper.pdf')
2567    
2568    =cut
2569    #: Return Type @@;
2570    sub GetProperties {
2571        # Get the parameters.
2572        my ($self, @parms) = @_;
2573        # Declare the return variable.
2574        my @retVal = ();
2575        # Now we need to create a WHERE clause that will get us the data we want. First,
2576        # we create a list of the columns containing the data for each parameter.
2577        my @colNames = ('HasProperty(from-link)', 'Property(property-name)',
2578                        'Property(property-value)', 'HasProperty(evidence)');
2579        # Now we build the WHERE clause and the list of parameter values.
2580        my @where = ();
2581        my @values = ();
2582        for (my $i = 0; $i <= $#colNames; $i++) {
2583            my $parm = $parms[$i];
2584            if (defined $parm && ($parm ne '')) {
2585                push @where, "$colNames[$i] = ?";
2586                push @values, $parm;
2587            }
2588        }
2589        # Format the WHERE clause.
2590        my $filter = (@values > 0 ? (join " AND ", @where) : undef);
2591        # Ask for all the propertie values with the desired characteristics.
2592        my $query = $self->Get(['HasProperty', 'Property'], $filter, \@values);
2593        while (my $valueObject = $query->Fetch()) {
2594            my @tuple = $valueObject->Values(\@colNames);
2595            push @retVal, \@tuple;
2596        }
2597        # Return the result.
2598        return @retVal;
2599    }
2600    
2601  =head3 FeatureProperties  =head3 FeatureProperties
2602    
2603  C<< my @properties = $sprout->FeatureProperties($featureID); >>  C<< my @properties = $sprout->FeatureProperties($featureID); >>
# Line 1885  Line 2624 
2624  =back  =back
2625    
2626  =cut  =cut
2627    #: Return Type @@;
2628  sub FeatureProperties {  sub FeatureProperties {
2629          # Get the parameters.          # Get the parameters.
2630          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
2631          # Get the properties.          # Get the properties.
2632          my @retVal = $self->GetAll(['HasProperty', 'Property'], "HasProperty(from-link) = ?", [$featureID],          my @retVal = $self->GetAll(['HasProperty', 'Property'], "HasProperty(from-link) = ?", [$featureID],
2633                                                          ['Property(property-name)', 'Property(property-value)',                                                          ['Property(property-name)', 'Property(property-value)',
# Line 1917  Line 2655 
2655  =back  =back
2656    
2657  =cut  =cut
2658    #: Return Type $;
2659  sub DiagramName {  sub DiagramName {
2660          # Get the parameters.          # Get the parameters.
2661          my $self = shift @_;      my ($self, $diagramID) = @_;
         my ($diagramID) = @_;  
2662          # Get the specified diagram's name and return it.          # Get the specified diagram's name and return it.
2663          my ($retVal) = $self->GetEntityValues('Diagram', $diagramID, ['Diagram(name)']);          my ($retVal) = $self->GetEntityValues('Diagram', $diagramID, ['Diagram(name)']);
2664          return $retVal;          return $retVal;
# Line 1950  Line 2687 
2687  =back  =back
2688    
2689  =cut  =cut
2690    #: Return Type @;
2691  sub MergedAnnotations {  sub MergedAnnotations {
2692          # Get the parameters.          # Get the parameters.
2693          my $self = shift @_;      my ($self, $list) = @_;
         my ($list) = @_;  
2694          # Create a list to hold the annotation tuples found.          # Create a list to hold the annotation tuples found.
2695          my @tuples = ();          my @tuples = ();
2696          # Loop through the features in the input list.          # Loop through the features in the input list.
# Line 1969  Line 2705 
2705          }          }
2706          # Sort the result list by timestamp.          # Sort the result list by timestamp.
2707          my @retVal = sort { $a->[1] <=> $b->[1] } @tuples;          my @retVal = sort { $a->[1] <=> $b->[1] } @tuples;
2708        # Loop through and make the time stamps friendly.
2709        for my $tuple (@retVal) {
2710            $tuple->[1] = FriendlyTimestamp($tuple->[1]);
2711        }
2712          # Return the sorted list.          # Return the sorted list.
2713          return @retVal;          return @retVal;
2714  }  }
# Line 1995  Line 2735 
2735  =back  =back
2736    
2737  =cut  =cut
2738    #: Return Type @;
2739  sub RoleNeighbors {  sub RoleNeighbors {
2740          # Get the parameters.          # Get the parameters.
2741          my $self = shift @_;      my ($self, $roleID) = @_;
         my ($roleID) = @_;  
2742          # Get all the diagrams containing this role.          # Get all the diagrams containing this role.
2743          my @diagrams = $self->GetFlat(['RoleOccursIn'], "RoleOccursIn(from-link) = ?", [$roleID],          my @diagrams = $self->GetFlat(['RoleOccursIn'], "RoleOccursIn(from-link) = ?", [$roleID],
2744                                                                    'RoleOccursIn(to-link)');                                                                    'RoleOccursIn(to-link)');
# Line 2038  Line 2777 
2777  =back  =back
2778    
2779  =cut  =cut
2780    #: Return Type @;
2781  sub FeatureLinks {  sub FeatureLinks {
2782          # Get the parameters.          # Get the parameters.
2783          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
2784          # Get the feature's links.          # Get the feature's links.
2785          my @retVal = $self->GetEntityValues('Feature', $featureID, ['Feature(link)']);          my @retVal = $self->GetEntityValues('Feature', $featureID, ['Feature(link)']);
2786          # Return the feature's links.          # Return the feature's links.
# Line 2054  Line 2792 
2792  C<< my %subsystems = $sprout->SubsystemsOf($featureID); >>  C<< my %subsystems = $sprout->SubsystemsOf($featureID); >>
2793    
2794  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
2795  to the role the feature performs.  to the roles the feature performs.
2796    
2797  =over 4  =over 4
2798    
# Line 2064  Line 2802 
2802    
2803  =item RETURN  =item RETURN
2804    
2805  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.
2806    
2807  =back  =back
2808    
2809  =cut  =cut
2810    #: Return Type %@;
2811  sub SubsystemsOf {  sub SubsystemsOf {
2812          # Get the parameters.          # Get the parameters.
2813          my $self = shift @_;      my ($self, $featureID) = @_;
2814          my ($featureID) = @_;      # Get the subsystem list.
         # Use the SSCell to connect features to subsystems.  
2815          my @subsystems = $self->GetAll(['ContainsFeature', 'HasSSCell', 'IsRoleOf'],          my @subsystems = $self->GetAll(['ContainsFeature', 'HasSSCell', 'IsRoleOf'],
2816                                                                          "ContainsFeature(to-link) = ?", [$featureID],                                                                          "ContainsFeature(to-link) = ?", [$featureID],
2817                                                                          ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);                                                                          ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);
2818          # Create the return value.          # Create the return value.
2819          my %retVal = ();          my %retVal = ();
2820        # Build a hash to weed out duplicates. Sometimes the same PEG and role appears
2821        # in two spreadsheet cells.
2822        my %dupHash = ();
2823          # Loop through the results, adding them to the hash.          # Loop through the results, adding them to the hash.
2824          for my $record (@subsystems) {          for my $record (@subsystems) {
2825                  $retVal{$record->[0]} = $record->[1];          # Get this subsystem and role.
2826            my ($subsys, $role) = @{$record};
2827            # Insure it's the first time for both.
2828            my $dupKey = "$subsys\n$role";
2829            if (! exists $dupHash{"$subsys\n$role"}) {
2830                $dupHash{$dupKey} = 1;
2831                push @{$retVal{$subsys}}, $role;
2832            }
2833          }          }
2834          # Return the hash.          # Return the hash.
2835          return %retVal;          return %retVal;
2836  }  }
2837    
2838    =head3 SubsystemList
2839    
2840    C<< my @subsystems = $sprout->SubsystemList($featureID); >>
2841    
2842    Return a list containing the names of the subsystems in which the specified
2843    feature participates. Unlike L</SubsystemsOf>, this method only returns the
2844    subsystem names, not the roles.
2845    
2846    =over 4
2847    
2848    =item featureID
2849    
2850    ID of the feature whose subsystem names are desired.
2851    
2852    =item RETURN
2853    
2854    Returns a list of the names of the subsystems in which the feature participates.
2855    
2856    =back
2857    
2858    =cut
2859    #: Return Type @;
2860    sub SubsystemList {
2861        # Get the parameters.
2862        my ($self, $featureID) = @_;
2863        # Get the list of names.
2864        my @retVal = $self->GetFlat(['ContainsFeature', 'HasSSCell'], "ContainsFeature(to-link) = ?",
2865                                    [$featureID], 'HasSSCell(from-link)');
2866        # Return the result.
2867        return @retVal;
2868    }
2869    
2870    =head3 GenomeSubsystemData
2871    
2872    C<< my %featureData = $sprout->GenomeSubsystemData($genomeID); >>
2873    
2874    Return a hash mapping genome features to their subsystem roles.
2875    
2876    =over 4
2877    
2878    =item genomeID
2879    
2880    ID of the genome whose subsystem feature map is desired.
2881    
2882    =item RETURN
2883    
2884    Returns a hash mapping each feature of the genome to a list of 2-tuples. Eacb
2885    2-tuple contains a subsystem name followed by a role ID.
2886    
2887    =back
2888    
2889    =cut
2890    
2891    sub GenomeSubsystemData {
2892        # Get the parameters.
2893        my ($self, $genomeID) = @_;
2894        # Declare the return variable.
2895        my %retVal = ();
2896        # Get a list of the genome features that participate in subsystems. For each
2897        # feature we get its spreadsheet cells and the corresponding roles.
2898        my @roleData = $self->GetAll(['HasFeature', 'ContainsFeature', 'IsRoleOf'],
2899                                 "HasFeature(from-link) = ?", [$genomeID],
2900                                 ['HasFeature(to-link)', 'IsRoleOf(to-link)', 'IsRoleOf(from-link)']);
2901        # Now we get a list of the spreadsheet cells and their associated subsystems. Subsystems
2902        # with an unknown variant code (-1) are skipped. Note the genome ID is at both ends of the
2903        # list. We use it at the beginning to get all the spreadsheet cells for the genome and
2904        # again at the end to filter out participation in subsystems with a negative variant code.
2905        my @cellData = $self->GetAll(['IsGenomeOf', 'HasSSCell', 'ParticipatesIn'],
2906                                     "IsGenomeOf(from-link) = ? AND ParticipatesIn(variant-code) >= 0 AND ParticipatesIn(from-link) = ?",
2907                                     [$genomeID, $genomeID], ['HasSSCell(to-link)', 'HasSSCell(from-link)']);
2908        # Now "@roleData" lists the spreadsheet cell and role for each of the genome's features.
2909        # "@cellData" lists the subsystem name for each of the genome's spreadsheet cells. We
2910        # link these two lists together to create the result. First, we want a hash mapping
2911        # spreadsheet cells to subsystem names.
2912        my %subHash = map { $_->[0] => $_->[1] } @cellData;
2913        # We loop through @cellData to build the hash.
2914        for my $roleEntry (@roleData) {
2915            # Get the data for this feature and cell.
2916            my ($fid, $cellID, $role) = @{$roleEntry};
2917            # Check for a subsystem name.
2918            my $subsys = $subHash{$cellID};
2919            if ($subsys) {
2920                # Insure this feature has an entry in the return hash.
2921                if (! exists $retVal{$fid}) { $retVal{$fid} = []; }
2922                # Merge in this new data.
2923                push @{$retVal{$fid}}, [$subsys, $role];
2924            }
2925        }
2926        # Return the result.
2927        return %retVal;
2928    }
2929    
2930  =head3 RelatedFeatures  =head3 RelatedFeatures
2931    
2932  C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>  C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>
# Line 2118  Line 2957 
2957  =back  =back
2958    
2959  =cut  =cut
2960    #: Return Type @;
2961  sub RelatedFeatures {  sub RelatedFeatures {
2962          # Get the parameters.          # Get the parameters.
2963          my $self = shift @_;      my ($self, $featureID, $function, $userID) = @_;
         my ($featureID, $function, $userID) = @_;  
2964          # Get a list of the features that are BBHs of the incoming feature.          # Get a list of the features that are BBHs of the incoming feature.
2965          my @bbhFeatures = $self->GetFlat(['IsBidirectionalBestHitOf'],          my @bbhFeatures = $self->GetFlat(['IsBidirectionalBestHitOf'],
2966                                                                           "IsBidirectionalBestHitOf(from-link) = ?", [$featureID],                                                                           "IsBidirectionalBestHitOf(from-link) = ?", [$featureID],
# Line 2167  Line 3005 
3005  =back  =back
3006    
3007  =cut  =cut
3008    #: Return Type @;
3009  sub TaxonomySort {  sub TaxonomySort {
3010          # Get the parameters.          # Get the parameters.
3011          my $self = shift @_;      my ($self, $featureIDs) = @_;
         my ($featureIDs) = @_;  
3012          # Create the working hash table.          # Create the working hash table.
3013          my %hashBuffer = ();          my %hashBuffer = ();
3014          # Loop through the features.          # Loop through the features.
# Line 2180  Line 3017 
3017                  my ($taxonomy) = $self->GetFlat(['IsLocatedIn', 'HasContig', 'Genome'], "IsLocatedIn(from-link) = ?",                  my ($taxonomy) = $self->GetFlat(['IsLocatedIn', 'HasContig', 'Genome'], "IsLocatedIn(from-link) = ?",
3018                                                                                  [$fid], 'Genome(taxonomy)');                                                                                  [$fid], 'Genome(taxonomy)');
3019                  # Add this feature to the hash buffer.                  # Add this feature to the hash buffer.
3020                  if (exists $hashBuffer{$taxonomy}) {          Tracer::AddToListMap(\%hashBuffer, $taxonomy, $fid);
                         push @{$hashBuffer{$taxonomy}}, $fid;  
                 } else {  
                         $hashBuffer{$taxonomy} = [$fid];  
                 }  
3021          }          }
3022          # Sort the keys and get the elements.          # Sort the keys and get the elements.
3023          my @retVal = ();          my @retVal = ();
# Line 2195  Line 3028 
3028          return @retVal;          return @retVal;
3029  }  }
3030    
 =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  
   
 sub GetAll {  
         # Get the parameters.  
         my $self = shift @_;  
         my ($objectNames, $filterClause, $parameterList, $fields, $count) = @_;  
         # Create the query.  
         my $query = $self->Get($objectNames, $filterClause, $parameterList);  
         # Set up a counter of the number of records read.  
         my $fetched = 0;  
         # Insure the counter has a value.  
         if (!defined $count) {  
                 $count = 0;  
         }  
         # Loop through the records returned, extracting the fields. Note that if the  
         # counter is non-zero, we stop when the number of records read hits the count.  
         my @retVal = ();  
         while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {  
                 my @rowData = $row->Values($fields);  
                 push @retVal, \@rowData;  
                 $fetched++;  
         }  
         # 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  
   
 sub GetFlat {  
         # Get the parameters.  
         my $self = shift @_;  
         my ($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;  
 }  
   
3031  =head3 Protein  =head3 Protein
3032    
3033  C<< my $protein = Sprout::Protein($sequence, $table); >>  C<< my $protein = Sprout::Protein($sequence, $table); >>
# Line 2423  Line 3122 
3122  to load the entire database.  to load the entire database.
3123    
3124  =cut  =cut
3125    #: Return Type @;
3126  sub LoadInfo {  sub LoadInfo {
3127          # Get the parameters.          # Get the parameters.
3128          my $self = shift @_;      my ($self) = @_;
3129          # 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.
3130          my @retVal = ($self->{_options}->{dataDir});          my @retVal = ($self->{_options}->{dataDir});
3131          # Concatenate the table names.          # Concatenate the table names.
3132          push @retVal, $self->{_erdb}->GetTableNames();      push @retVal, $self->GetTableNames();
3133          # Return the result.          # Return the result.
3134          return @retVal;          return @retVal;
3135  }  }
3136    
3137  =head3 LowBBHs  =head3 LowBBHs
3138    
3139  C<< my %bbhMap = $sprout->GoodBBHs($featureID, $cutoff); >>  C<< my %bbhMap = $sprout->LowBBHs($featureID, $cutoff); >>
3140    
3141  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
3142  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 2460  Line 3159 
3159  =back  =back
3160    
3161  =cut  =cut
3162    #: Return Type %;
3163  sub LowBBHs {  sub LowBBHs {
3164          # Get the parsameters.          # Get the parsameters.
3165          my $self = shift @_;      my ($self, $featureID, $cutoff) = @_;
         my ($featureID, $cutoff) = @_;  
3166          # Create the return hash.          # Create the return hash.
3167          my %retVal = ();          my %retVal = ();
3168          # Create a query to get the desired BBHs.          # Create a query to get the desired BBHs.
# Line 2480  Line 3178 
3178          return %retVal;          return %retVal;
3179  }  }
3180    
3181    =head3 Sims
3182    
3183    C<< my $simList = $sprout->Sims($fid, $maxN, $maxP, $select, $max_expand, $filters); >>
3184    
3185    Get a list of similarities for a specified feature. Similarity information is not kept in the
3186    Sprout database; rather, they are retrieved from a network server. The similarities are
3187    returned as B<Sim> objects. A Sim object is actually a list reference that has been blessed
3188    so that its elements can be accessed by name.
3189    
3190    Similarities can be either raw or expanded. The raw similarities are basic
3191    hits between features with similar DNA. Expanding a raw similarity drags in any
3192    features considered substantially identical. So, for example, if features B<A1>,
3193    B<A2>, and B<A3> are all substatially identical to B<A>, then a raw similarity
3194    B<[C,A]> would be expanded to B<[C,A] [C,A1] [C,A2] [C,A3]>.
3195    
3196    =over 4
3197    
3198    =item fid
3199    
3200    ID of the feature whose similarities are desired.
3201    
3202    =item maxN
3203    
3204    Maximum number of similarities to return.
3205    
3206    =item maxP
3207    
3208    Minumum allowable similarity score.
3209    
3210    =item select
3211    
3212    Selection criterion: C<raw> means only raw similarities are returned; C<fig>
3213    means only similarities to FIG features are returned; C<all> means all expanded
3214    similarities are returned; and C<figx> means similarities are expanded until the
3215    number of FIG features equals the maximum.
3216    
3217    =item max_expand
3218    
3219    The maximum number of features to expand.
3220    
3221    =item filters
3222    
3223    Reference to a hash containing filter information, or a subroutine that can be
3224    used to filter the sims.
3225    
3226    =item RETURN
3227    
3228    Returns a reference to a list of similarity objects, or C<undef> if an error
3229    occurred.
3230    
3231    =back
3232    
3233    =cut
3234    
3235    sub Sims {
3236        # Get the parameters.
3237        my ($self, $fid, $maxN, $maxP, $select, $max_expand, $filters) = @_;
3238        # Create the shim object to test for deleted FIDs.
3239        my $shim = FidCheck->new($self);
3240        # Ask the network for sims.
3241        my $retVal = FIGRules::GetNetworkSims($shim, $fid, {}, $maxN, $maxP, $select, $max_expand, $filters);
3242        # Return the result.
3243        return $retVal;
3244    }
3245    
3246    =head3 GetGroups
3247    
3248    C<< my %groups = $sprout->GetGroups(\@groupList); >>
3249    
3250    Return a hash mapping each group to the IDs of the genomes in the group.
3251    A list of groups may be specified, in which case only those groups will be
3252    shown. Alternatively, if no parameter is supplied, all groups will be
3253    included. Genomes that are not in any group are omitted.
3254    
3255    =cut
3256    #: Return Type %@;
3257    sub GetGroups {
3258        # Get the parameters.
3259        my ($self, $groupList) = @_;
3260        # Declare the return value.
3261        my %retVal = ();
3262        # Determine whether we are getting all the groups or just some.
3263        if (defined $groupList) {
3264            # Here we have a group list. Loop through them individually,
3265            # getting a list of the relevant genomes.
3266            for my $group (@{$groupList}) {
3267                my @genomeIDs = $self->GetFlat(['Genome'], "Genome(group-name) = ?",
3268                    [$group], "Genome(id)");
3269                $retVal{$group} = \@genomeIDs;
3270            }
3271        } else {
3272            # Here we need all of the groups. In this case, we run through all
3273            # of the genome records, putting each one found into the appropriate
3274            # group. Note that we use a filter clause to insure that only genomes
3275            # in groups are included in the return set.
3276            my @genomes = $self->GetAll(['Genome'], "Genome(group-name) > ' '", [],
3277                                        ['Genome(id)', 'Genome(group-name)']);
3278            # Loop through the genomes found.
3279            for my $genome (@genomes) {
3280                # Pop this genome's ID off the current list.
3281                my @groups = @{$genome};
3282                my $genomeID = shift @groups;
3283                # Loop through the groups, adding the genome ID to each group's
3284                # list.
3285                for my $group (@groups) {
3286                    Tracer::AddToListMap(\%retVal, $group, $genomeID);
3287                }
3288            }
3289        }
3290        # Return the hash we just built.
3291        return %retVal;
3292    }
3293    
3294    =head3 MyGenomes
3295    
3296    C<< my @genomes = Sprout::MyGenomes($dataDir); >>
3297    
3298    Return a list of the genomes to be included in the Sprout.
3299    
3300    This method is provided for use during the Sprout load. It presumes the Genome load file has
3301    already been created. (It will be in the Sprout data directory and called either C<Genome>
3302    or C<Genome.dtx>.) Essentially, it reads in the Genome load file and strips out the genome
3303    IDs.
3304    
3305    =over 4
3306    
3307    =item dataDir
3308    
3309    Directory containing the Sprout load files.
3310    
3311    =back
3312    
3313    =cut
3314    #: Return Type @;
3315    sub MyGenomes {
3316        # Get the parameters.
3317        my ($dataDir) = @_;
3318        # Compute the genome file name.
3319        my $genomeFileName = LoadFileName($dataDir, "Genome");
3320        # Extract the genome IDs from the files.
3321        my @retVal = map { $_ =~ /^(\S+)/; $1 } Tracer::GetFile($genomeFileName);
3322        # Return the result.
3323        return @retVal;
3324    }
3325    
3326    =head3 LoadFileName
3327    
3328    C<< my $fileName = Sprout::LoadFileName($dataDir, $tableName); >>
3329    
3330    Return the name of the load file for the specified table in the specified data
3331    directory.
3332    
3333    =over 4
3334    
3335    =item dataDir
3336    
3337    Directory containing the Sprout load files.
3338    
3339    =item tableName
3340    
3341    Name of the table whose load file is desired.
3342    
3343    =item RETURN
3344    
3345    Returns the name of the file containing the load data for the specified table, or
3346    C<undef> if no load file is present.
3347    
3348    =back
3349    
3350    =cut
3351    #: Return Type $;
3352    sub LoadFileName {
3353        # Get the parameters.
3354        my ($dataDir, $tableName) = @_;
3355        # Declare the return variable.
3356        my $retVal;
3357        # Check for the various file names.
3358        if (-e "$dataDir/$tableName") {
3359            $retVal = "$dataDir/$tableName";
3360        } elsif (-e "$dataDir/$tableName.dtx") {
3361            $retVal = "$dataDir/$tableName.dtx";
3362        }
3363        # Return the result.
3364        return $retVal;
3365    }
3366    
3367    =head3 DeleteGenome
3368    
3369    C<< my $stats = $sprout->DeleteGenome($genomeID, $testFlag); >>
3370    
3371    Delete a genome from the database.
3372    
3373    =over 4
3374    
3375    =item genomeID
3376    
3377    ID of the genome to delete
3378    
3379    =item testFlag
3380    
3381    If TRUE, then the DELETE statements will be traced, but no deletions will occur.
3382    
3383    =item RETURN
3384    
3385    Returns a statistics object describing the rows deleted.
3386    
3387    =back
3388    
3389    =cut
3390    #: Return Type $%;
3391    sub DeleteGenome {
3392        # Get the parameters.
3393        my ($self, $genomeID, $testFlag) = @_;
3394        # Perform the delete for the genome's features.
3395        my $retVal = $self->Delete('Feature', "fig|$genomeID.%", $testFlag);
3396        # Perform the delete for the primary genome data.
3397        my $stats = $self->Delete('Genome', $genomeID, $testFlag);
3398        $retVal->Accumulate($stats);
3399        # Return the result.
3400        return $retVal;
3401    }
3402    
3403  =head2 Internal Utility Methods  =head2 Internal Utility Methods
3404    
3405  =head3 ParseAssignment  =head3 ParseAssignment
3406    
3407  Parse annotation text to determine whether or not it is a functional assignment. If it is,  Parse annotation text to determine whether or not it is a functional assignment. If it is,
3408  the user and function text will be returned as a 2-element list. If it isn't, an empty list  the user, function text, and assigning user will be returned as a 3-element list. If it
3409  will be returned.  isn't, an empty list will be returned.
3410    
3411    A functional assignment is always of the form
3412    
3413        C<set >I<YYYY>C< function to\n>I<ZZZZZ>
3414    
3415    where I<YYYY> is the B<user>, and I<ZZZZ> is the actual functional role. In most cases,
3416    the user and the assigning user (from MadeAnnotation) will be the same, but that is
3417    not always the case.
3418    
3419    In addition, the functional role may contain extra data that is stripped, such as
3420    terminating spaces or a comment separated from the rest of the text by a tab.
3421    
3422  This is a static method.  This is a static method.
3423    
3424  =over 4  =over 4
3425    
3426    =item user
3427    
3428    Name of the assigning user.
3429    
3430  =item text  =item text
3431    
3432  Text of the annotation.  Text of the annotation.
# Line 2505  Line 3440 
3440    
3441  =cut  =cut
3442    
3443  sub ParseAssignment {  sub _ParseAssignment {
3444          # Get the parameters.          # Get the parameters.
3445          my ($text) = @_;      my ($user, $text) = @_;
3446          # Declare the return value.          # Declare the return value.
3447          my @retVal = ();          my @retVal = ();
3448          # Check to see if this is a functional assignment.          # Check to see if this is a functional assignment.
3449          my ($user, $type, $function) = split(/\n/, $text);      my ($type, $function) = split(/\n/, $text);
3450          if ($type =~ m/^set $user function to$/i) {      if ($type =~ m/^set function to$/i) {
3451                  # Here it is, so we return the user name and function text.          # Here we have an assignment without a user, so we use the incoming user ID.
3452                  @retVal = ($user, $function);                  @retVal = ($user, $function);
3453        } elsif ($type =~ m/^set (\S+) function to$/i) {
3454            # Here we have an assignment with a user that is passed back to the caller.
3455            @retVal = ($1, $function);
3456        }
3457        # If we have an assignment, we need to clean the function text. There may be
3458        # extra junk at the end added as a note from the user.
3459        if (defined( $retVal[1] )) {
3460            $retVal[1] =~ s/(\t\S)?\s*$//;
3461          }          }
3462          # Return the result list.          # Return the result list.
3463          return @retVal;          return @retVal;
3464  }  }
3465    
3466    =head3 FriendlyTimestamp
3467    
3468    Convert a time number to a user-friendly time stamp for display.
3469    
3470    This is a static method.
3471    
3472    =over 4
3473    
3474    =item timeValue
3475    
3476    Numeric time value.
3477    
3478    =item RETURN
3479    
3480    Returns a string containing the same time in user-readable format.
3481    
3482    =back
3483    
3484    =cut
3485    
3486    sub FriendlyTimestamp {
3487        my ($timeValue) = @_;
3488        my $retVal = localtime($timeValue);
3489        return $retVal;
3490    }
3491    
3492    =head3 AddProperty
3493    
3494    C<< my  = $sprout->AddProperty($featureID, $key, $value, $url); >>
3495    
3496    Add a new attribute value (Property) to a feature. In the SEED system, attributes can
3497    be added to almost any object. In Sprout, they can only be added to features. In
3498    Sprout, attributes are implemented using I<properties>. A property represents a key/value
3499    pair. If the particular key/value pair coming in is not already in the database, a new
3500    B<Property> record is created to hold it.
3501    
3502    =over 4
3503    
3504    =item peg
3505    
3506    ID of the feature to which the attribute is to be replied.
3507    
3508    =item key
3509    
3510    Name of the attribute (key).
3511    
3512    =item value
3513    
3514    Value of the attribute.
3515    
3516    =item url
3517    
3518    URL or text citation from which the property was obtained.
3519    
3520    =back
3521    
3522    =cut
3523    #: Return Type ;
3524    sub AddProperty {
3525        # Get the parameters.
3526        my ($self, $featureID, $key, $value, $url) = @_;
3527        # Declare the variable to hold the desired property ID.
3528        my $propID;
3529        # Attempt to find a property record for this key/value pair.
3530        my @properties = $self->GetFlat(['Property'],
3531                                       "Property(property-name) = ? AND Property(property-value) = ?",
3532                                       [$key, $value], 'Property(id)');
3533        if (@properties) {
3534            # Here the property is already in the database. We save its ID.
3535            $propID = $properties[0];
3536            # Here the property value does not exist. We need to generate an ID. It will be set
3537            # to a number one greater than the maximum value in the database. This call to
3538            # GetAll will stop after one record.
3539            my @maxProperty = $self->GetAll(['Property'], "ORDER BY Property(id) DESC", [], ['Property(id)'],
3540                                            1);
3541            $propID = $maxProperty[0]->[0] + 1;
3542            # Insert the new property value.
3543            $self->Insert('Property', { 'property-name' => $key, 'property-value' => $value, id => $propID });
3544        }
3545        # Now we connect the incoming feature to the property.
3546        $self->Insert('HasProperty', { 'from-link' => $featureID, 'to-link' => $propID, evidence => $url });
3547    }
3548    
3549    
3550  1;  1;

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