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revision 1.44, Thu Oct 20 09:32:18 2005 UTC revision 1.118, Sat Sep 20 14:32:34 2008 UTC
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2    
3      use Data::Dumper;      use Data::Dumper;
4      use strict;      use strict;
     use Carp;  
5      use DBKernel;      use DBKernel;
6      use XML::Simple;      use XML::Simple;
7      use DBQuery;      use DBQuery;
8      use DBObject;      use ERDBObject;
     use ERDB;  
9      use Tracer;      use Tracer;
10      use FIGRules;      use FIGRules;
11        use FidCheck;
12      use Stats;      use Stats;
13      use POSIX qw(strftime);      use POSIX qw(strftime);
14        use BasicLocation;
15        use CustomAttributes;
16        use RemoteCustomAttributes;
17        use CGI;
18        use WikiTools;
19        use BioWords;
20        use base qw(ERDB);
21    
22  =head1 Sprout Database Manipulation Object  =head1 Sprout Database Manipulation Object
23    
# Line 25  Line 30 
30  on the constructor. For example, the following invocation specifies a PostgreSQL database named I<GenDB>  on the constructor. For example, the following invocation specifies a PostgreSQL database named I<GenDB>
31  whose definition and data files are in a co-directory named F<Data>.  whose definition and data files are in a co-directory named F<Data>.
32    
33  C<< my $sprout = Sprout->new('GenDB', { dbType => 'pg', dataDir => '../Data', xmlFileName => '../Data/SproutDBD.xml' }); >>      my $sprout = Sprout->new('GenDB', { dbType => 'pg', dataDir => '../Data', xmlFileName => '../Data/SproutDBD.xml' });
34    
35  Once you have a sprout object, you may use it to re-create the database, load the tables from  Once you have a sprout object, you may use it to re-create the database, load the tables from
36  tab-delimited flat files and perform queries. Several special methods are provided for common  tab-delimited flat files and perform queries. Several special methods are provided for common
37  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
38  L</dna_seq> returns the DNA sequence for a specified genome location.  L</DNASeq> returns the DNA sequence for a specified genome location.
39    
40    The Sprout object is a subclass of the ERDB object and inherits all its properties and methods.
41    
42  =cut  =cut
43    
# Line 40  Line 47 
47    
48  =head3 new  =head3 new
49    
50  C<< my $sprout = Sprout->new($dbName, \%options); >>      my $sprout = Sprout->new($dbName, \%options);
51    
52  This is the constructor for a sprout object. It connects to the database and loads the  This is the constructor for a sprout object. It connects to the database and loads the
53  database definition into memory. The positional first parameter specifies the name of the  database definition into memory. The positional first parameter specifies the name of the
# Line 62  Line 69 
69    
70  * 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>)
71    
72  * 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)
73    
74  * B<port> connection port (default C<0>)  * B<port> connection port (default C<0>)
75    
76    * B<sock> connection socket (default same as SEED)
77    
78  * B<maxSegmentLength> maximum number of residues per feature segment, (default C<4500>)  * B<maxSegmentLength> maximum number of residues per feature segment, (default C<4500>)
79    
80  * B<maxSequenceLength> maximum number of residues per sequence, (default C<8000>)  * B<maxSequenceLength> maximum number of residues per sequence, (default C<8000>)
81    
82  * B<noDBOpen> suppresses the connection to the database if TRUE, else FALSE  * B<noDBOpen> suppresses the connection to the database if TRUE, else FALSE
83    
84    * B<host> name of the database host
85    
86  =back  =back
87    
88  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
89  I<fig> with a password of I<admin>. The database load files are in the directory  I<fig> with a password of I<admin>. The database load files are in the directory
90  F</usr/fig/SproutData>.  F</usr/fig/SproutData>.
91    
92  C<< my $sprout = Sprout->new('Sprout', { userData =>; 'fig/admin', dataDir => '/usr/fig/SproutData' }); >>      my $sprout = Sprout->new('Sprout', { userData => 'fig/admin', dataDir => '/usr/fig/SproutData' });
93    
94  =cut  =cut
95    
96  sub new {  sub new {
97      # Get the parameters.      # Get the parameters.
98      my ($class, $dbName, $options) = @_;      my ($class, $dbName, $options) = @_;
99        # Compute the DBD directory.
100        my $dbd_dir = (defined($FIG_Config::dbd_dir) ? $FIG_Config::dbd_dir :
101                                                      $FIG_Config::fig );
102      # 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
103      # the incoming data.      # the incoming data.
104      my $optionTable = Tracer::GetOptions({      my $optionTable = Tracer::GetOptions({
# Line 92  Line 106 
106                                                          # database type                                                          # database type
107                         dataDir      => $FIG_Config::sproutData,                         dataDir      => $FIG_Config::sproutData,
108                                                          # data file directory                                                          # data file directory
109                         xmlFileName  => "$FIG_Config::sproutData/SproutDBD.xml",                         xmlFileName  => "$dbd_dir/SproutDBD.xml",
110                                                          # database definition file name                                                          # database definition file name
111                         userData     => "$FIG_Config::dbuser/$FIG_Config::dbpass",                         userData     => "$FIG_Config::sproutUser/$FIG_Config::sproutPass",
112                                                          # user name and password                                                          # user name and password
113                         port         => $FIG_Config::dbport,                         port         => $FIG_Config::sproutPort,
114                                                          # database connection port                                                          # database connection port
115                           sock         => $FIG_Config::sproutSock,
116                           host         => $FIG_Config::sprout_host,
117                         maxSegmentLength => 4500,        # maximum feature segment length                         maxSegmentLength => 4500,        # maximum feature segment length
118                         maxSequenceLength => 8000,       # maximum contig sequence length                         maxSequenceLength => 8000,       # maximum contig sequence length
119                         noDBOpen     => 0,               # 1 to suppress the database open                         noDBOpen     => 0,               # 1 to suppress the database open
# Line 110  Line 126 
126      # Connect to the database.      # Connect to the database.
127      my $dbh;      my $dbh;
128      if (! $optionTable->{noDBOpen}) {      if (! $optionTable->{noDBOpen}) {
129            Trace("Connect data: host = $optionTable->{host}, port = $optionTable->{port}.") if T(3);
130          $dbh = DBKernel->new($optionTable->{dbType}, $dbName, $userName,          $dbh = DBKernel->new($optionTable->{dbType}, $dbName, $userName,
131                                  $password, $optionTable->{port});                                  $password, $optionTable->{port}, $optionTable->{host}, $optionTable->{sock});
132      }      }
133      # Create the ERDB object.      # Create the ERDB object.
134      my $xmlFileName = "$optionTable->{xmlFileName}";      my $xmlFileName = "$optionTable->{xmlFileName}";
135      my $erdb = ERDB->new($dbh, $xmlFileName);      my $retVal = ERDB::new($class, $dbh, $xmlFileName);
136      # Create this object.      # Add the option table and XML file name.
137      my $self = { _erdb => $erdb, _options => $optionTable, _xmlName => $xmlFileName };      $retVal->{_options} = $optionTable;
138      # Bless and return it.      $retVal->{_xmlName} = $xmlFileName;
139      bless $self;      # Set up space for the group file data.
140      return $self;      $retVal->{groupHash} = undef;
141  }      # Set up space for the genome hash. We use this to identify NMPDR genomes.
142        $retVal->{genomeHash} = undef;
143  =head3 MaxSegment      # Connect to the attributes.
144        if ($FIG_Config::attrURL) {
145  C<< my $length = $sprout->MaxSegment(); >>          Trace("Remote attribute server $FIG_Config::attrURL chosen.") if T(3);
146            $retVal->{_ca} = RemoteCustomAttributes->new($FIG_Config::attrURL);
147  This method returns the maximum permissible length of a feature segment. The length is important      } elsif ($FIG_Config::attrDbName) {
148  because it enables us to make reasonable guesses at how to find features inside a particular          Trace("Local attribute database $FIG_Config::attrDbName chosen.") if T(3);
149  contig region. For example, if the maximum length is 4000 and we're looking for a feature that          my $user = ($FIG_Config::arch eq 'win' ? 'self' : scalar(getpwent()));
150  overlaps the region from 6000 to 7000 we know that the starting position must be between 2001          $retVal->{_ca} = CustomAttributes->new(user => $user);
 and 10999.  
   
 =cut  
 #: Return Type $;  
 sub MaxSegment {  
     my ($self) = @_;  
     return $self->{_options}->{maxSegmentLength};  
151  }  }
152        # Return it.
153  =head3 MaxSequence      return $retVal;
   
 C<< my $length = $sprout->MaxSequence(); >>  
   
 This method returns the maximum permissible length of a contig sequence. A contig is broken  
 into sequences in order to save memory resources. In particular, when manipulating features,  
 we generally only need a few sequences in memory rather than the entire contig.  
   
 =cut  
 #: Return Type $;  
 sub MaxSequence {  
     my ($self) = @_;  
     return $self->{_options}->{maxSequenceLength};  
154  }  }
155    
156  =head3 Get  =head3 CoreGenomes
   
 C<< my $query = $sprout->Get(\@objectNames, $filterClause, \@parameterList); >>  
   
 This method allows a general query against the Sprout data using a specified filter clause.  
   
 The filter is a standard WHERE/ORDER BY clause with question marks as parameter markers and each  
 field name represented in the form B<I<objectName>(I<fieldName>)>. For example, the  
 following call requests all B<Genome> objects for the genus specified in the variable  
 $genus.  
   
 C<< $query = $sprout->Get(['Genome'], "Genome(genus) = ?", [$genus]); >>  
   
 The WHERE clause contains a single question mark, so there is a single additional  
 parameter representing the parameter value. It would also be possible to code  
   
 C<< $query = $sprout->Get(['Genome'], "Genome(genus) = \'$genus\'"); >>  
   
 however, this version of the call would generate a syntax error if there were any quote  
 characters inside the variable C<$genus>.  
   
 The use of the strange parenthesized notation for field names enables us to distinguish  
 hyphens contained within field names from minus signs that participate in the computation  
 of the WHERE clause. All of the methods that manipulate fields will use this same notation.  
   
 It is possible to specify multiple entity and relationship names in order to retrieve more than  
 one object's data at the same time, which allows highly complex joined queries. For example,  
   
 C<< $query = $sprout->Get(['Genome', 'ComesFrom', 'Source'], "Genome(genus) = ?", [$genus]); >>  
   
 This query returns all the genomes for a particular genus and allows access to the  
 sources from which they came. The join clauses to go from Genome to Source are generated  
 automatically.  
   
 Finally, the filter clause can contain sort information. To do this, simply put an C<ORDER BY>  
 clause at the end of the filter. Field references in the ORDER BY section follow the same rules  
 as they do in the filter itself; in other words, each one must be of the form B<I<objectName>(I<fieldName>)>.  
 For example, the following filter string gets all genomes for a particular genus and sorts  
 them by species name.  
   
 C<< $query = $sprout->Get(['Genome'], "Genome(genus) = ? ORDER BY Genome(species)", [$genus]); >>  
   
 It is also permissible to specify I<only> an ORDER BY clause. For example, the following invocation gets  
 all genomes ordered by genus and species.  
157    
158  C<< $query = $sprout->Get(['Genome'], "ORDER BY Genome(genus), Genome(species)"); >>      my @genomes = $sprout->CoreGenomes($scope);
159    
160  Odd things may happen if one of the ORDER BY fields is in a secondary relation. So, for example, an  Return the IDs of NMPDR genomes in the specified scope.
 attempt to order B<Feature>s by alias may (depending on the underlying database engine used) cause  
 a single feature to appear more than once.  
   
 If multiple names are specified, then the query processor will automatically determine a  
 join path between the entities and relationships. The algorithm used is very simplistic.  
 In particular, you can't specify any entity or relationship more than once, and if a  
 relationship is recursive, the path is determined by the order in which the entity  
 and the relationship appear. For example, consider a recursive relationship B<IsParentOf>  
 which relates B<People> objects to other B<People> objects. If the join path is  
 coded as C<['People', 'IsParentOf']>, then the people returned will be parents. If, however,  
 the join path is C<['IsParentOf', 'People']>, then the people returned will be children.  
161    
162  =over 4  =over 4
163    
164  =item objectNames  =item scope
   
 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.  
165    
166  =item parameterList  Scope of the desired genomes. C<core> covers the original core genomes,
167    C<nmpdr> covers all genomes in NMPDR groups, and C<all> covers all
168  List of the parameters to be substituted in for the parameters marks in the filter clause.  genomes in the system.
169    
170  =item RETURN  =item RETURN
171    
172  Returns a B<DBQuery> that can be used to iterate through all of the results.  Returns a list of the IDs for the genomes in the specified scope.
173    
174  =back  =back
175    
176  =cut  =cut
177    
178  sub Get {  sub CoreGenomes {
179      # Get the parameters.      # Get the parameters.
180      my ($self, $objectNames, $filterClause, $parameterList) = @_;      my ($self, $scope) = @_;
181      # We differ from the ERDB Get method in that the parameter list is passed in as a list reference      # Declare the return variable.
182      # rather than a list of parameters. The next step is to convert the parameters from a reference      my @retVal = ();
183      # to a real list. We can only do this if the parameters have been specified.      # If we want all genomes, then this is easy.
184      my @parameters;      if ($scope eq 'all') {
185      if ($parameterList) { @parameters = @{$parameterList}; }          @retVal = $self->Genomes();
186      return $self->{_erdb}->Get($objectNames, $filterClause, @parameters);      } else {
187            # Here we're dealing with groups. Get the hash of all the
188            # genome groups.
189            my %groups = $self->GetGroups();
190            # Loop through the groups, keeping the ones that we want.
191            for my $group (keys %groups) {
192                # Decide if we want to keep this group.
193                my $keepGroup = 0;
194                if ($scope eq 'nmpdr') {
195                    # NMPDR mode: keep all groups.
196                    $keepGroup = 1;
197                } elsif ($scope eq 'core') {
198                    # CORE mode. Only keep real core groups.
199                    if (grep { $group =~ /$_/ } @{$FIG_Config::realCoreGroups}) {
200                        $keepGroup = 1;
201                    }
202                }
203                # Add this group if we're keeping it.
204                if ($keepGroup) {
205                    push @retVal, @{$groups{$group}};
206                }
207            }
208        }
209        # Return the result.
210        return @retVal;
211  }  }
212    
213  =head3 GetEntity  =head3 SuperGroup
214    
215  C<< my $entityObject = $sprout->GetEntity($entityType, $ID); >>      my $superGroup = $sprout->SuperGroup($groupName);
216    
217  Return an object describing the entity instance with a specified ID.  Return the name of the super-group containing the specified NMPDR genome
218    group. If no appropriate super-group can be found, an error will be
219    thrown.
220    
221  =over 4  =over 4
222    
223  =item entityType  =item groupName
   
 Entity type name.  
224    
225  =item ID  Name of the group whose super-group is desired.
   
 ID of the desired entity.  
226    
227  =item RETURN  =item RETURN
228    
229  Returns a B<DBObject> representing the desired entity instance, or an undefined value if no  Returns the name of the super-group containing the incoming group.
 instance is found with the specified key.  
230    
231  =back  =back
232    
233  =cut  =cut
234    
235  sub GetEntity {  sub SuperGroup {
236      # Get the parameters.      # Get the parameters.
237      my ($self, $entityType, $ID) = @_;      my ($self, $groupName) = @_;
238      # Call the ERDB method.      # Declare the return variable.
239      return $self->{_erdb}->GetEntity($entityType, $ID);      my $retVal;
240        # Get the group hash.
241        my %groupHash = $self->CheckGroupFile();
242        # Find the super-group genus.
243        $groupName =~ /([A-Z]\w+)/;
244        my $nameThing = $1;
245        # See if it's directly in the group hash.
246        if (exists $groupHash{$nameThing}) {
247            # Yes, then it's our result.
248            $retVal = $nameThing;
249        } else {
250            # No, so we have to search.
251            for my $superGroup (keys %groupHash) {
252                # Get this super-group's item list.
253                my $list = $groupHash{$superGroup}->{contents};
254                # Search it.
255                if (grep { $_->[0] eq $nameThing } @{$list}) {
256                    $retVal = $superGroup;
257                }
258            }
259            # Make sure we found something.
260            if (! $retVal) {
261                Confess("No super-group found for \"$groupName\".");
262            }
263        }
264        # Return the result.
265        return $retVal;
266  }  }
267    
268  =head3 GetEntityValues  =head3 MaxSegment
   
 C<< my @values = GetEntityValues($entityType, $ID, \@fields); >>  
   
 Return a list of values from a specified entity instance.  
   
 =over 4  
   
 =item entityType  
   
 Entity type name.  
   
 =item ID  
   
 ID of the desired entity.  
   
 =item fields  
   
 List of field names, each of the form I<objectName>C<(>I<fieldName>C<)>.  
   
 =item RETURN  
269    
270  Returns a flattened list of the values of the specified fields for the specified entity.      my $length = $sprout->MaxSegment();
271    
272  =back  This method returns the maximum permissible length of a feature segment. The length is important
273    because it enables us to make reasonable guesses at how to find features inside a particular
274    contig region. For example, if the maximum length is 4000 and we're looking for a feature that
275    overlaps the region from 6000 to 7000 we know that the starting position must be between 2001
276    and 10999.
277    
278  =cut  =cut
279  #: Return Type @;  #: Return Type $;
280  sub GetEntityValues {  sub MaxSegment {
281      # Get the parameters.      my ($self) = @_;
282      my ($self, $entityType, $ID, $fields) = @_;      return $self->{_options}->{maxSegmentLength};
     # Call the ERDB method.  
     return $self->{_erdb}->GetEntityValues($entityType, $ID, $fields);  
283  }  }
284    
285  =head3 ShowMetaData  =head3 MaxSequence
   
 C<< $sprout->ShowMetaData($fileName); >>  
   
 This method outputs a description of the database to an HTML file in the data directory.  
   
 =over 4  
   
 =item fileName  
286    
287  Fully-qualified name to give to the output file.      my $length = $sprout->MaxSequence();
288    
289  =back  This method returns the maximum permissible length of a contig sequence. A contig is broken
290    into sequences in order to save memory resources. In particular, when manipulating features,
291    we generally only need a few sequences in memory rather than the entire contig.
292    
293  =cut  =cut
294    #: Return Type $;
295  sub ShowMetaData {  sub MaxSequence {
296      # Get the parameters.      my ($self) = @_;
297      my ($self, $fileName) = @_;      return $self->{_options}->{maxSequenceLength};
     # Compute the file name.  
     my $options = $self->{_options};  
     # Call the show method on the underlying ERDB object.  
     $self->{_erdb}->ShowMetaData($fileName);  
298  }  }
299    
300  =head3 Load  =head3 Load
301    
302  C<< $sprout->Load($rebuild); >>;      $sprout->Load($rebuild);;
303    
304  Load the database from files in the data directory, optionally re-creating the tables.  Load the database from files in the data directory, optionally re-creating the tables.
305    
# Line 379  Line 331 
331  sub Load {  sub Load {
332      # Get the parameters.      # Get the parameters.
333      my ($self, $rebuild) = @_;      my ($self, $rebuild) = @_;
     # Get the database object.  
     my $erdb = $self->{_erdb};  
334      # Load the tables from the data directory.      # Load the tables from the data directory.
335      my $retVal = $erdb->LoadTables($self->{_options}->{dataDir}, $rebuild);      my $retVal = $self->LoadTables($self->{_options}->{dataDir}, $rebuild);
336      # Return the statistics.      # Return the statistics.
337      return $retVal;      return $retVal;
338  }  }
339    
340  =head3 LoadUpdate  =head3 LoadUpdate
341    
342  C<< my $stats = $sprout->LoadUpdate($truncateFlag, \@tableList); >>      my $stats = $sprout->LoadUpdate($truncateFlag, \@tableList);
343    
344  Load updates to one or more database tables. This method enables the client to make changes to one  Load updates to one or more database tables. This method enables the client to make changes to one
345  or two tables without reloading the whole database. For each table, there must be a corresponding  or two tables without reloading the whole database. For each table, there must be a corresponding
# Line 422  Line 372 
372  sub LoadUpdate {  sub LoadUpdate {
373      # Get the parameters.      # Get the parameters.
374      my ($self, $truncateFlag, $tableList) = @_;      my ($self, $truncateFlag, $tableList) = @_;
     # Get the database object.  
     my $erdb = $self->{_erdb};  
375      # Declare the return value.      # Declare the return value.
376      my $retVal = Stats->new();      my $retVal = Stats->new();
377      # Get the data directory.      # Get the data directory.
# Line 437  Line 385 
385              Trace("No load file found for $tableName in $dataDir.") if T(0);              Trace("No load file found for $tableName in $dataDir.") if T(0);
386          } else {          } else {
387              # Attempt to load this table.              # Attempt to load this table.
388              my $result = $erdb->LoadTable($fileName, $tableName, $truncateFlag);              my $result = $self->LoadTable($fileName, $tableName, truncate => $truncateFlag);
389              # Accumulate the resulting statistics.              # Accumulate the resulting statistics.
390              $retVal->Accumulate($result);              $retVal->Accumulate($result);
391          }          }
# Line 446  Line 394 
394      return $retVal;      return $retVal;
395  }  }
396    
397    =head3 GenomeCounts
398    
399        my ($arch, $bact, $euk, $vir, $env, $unk) = $sprout->GenomeCounts($complete);
400    
401    Count the number of genomes in each domain. If I<$complete> is TRUE, only complete
402    genomes will be included in the counts.
403    
404    =over 4
405    
406    =item complete
407    
408    TRUE if only complete genomes are to be counted, FALSE if all genomes are to be
409    counted
410    
411    =item RETURN
412    
413    A six-element list containing the number of genomes in each of six categories--
414    Archaea, Bacteria, Eukaryota, Viral, Environmental, and Unknown, respectively.
415    
416    =back
417    
418    =cut
419    
420    sub GenomeCounts {
421        # Get the parameters.
422        my ($self, $complete) = @_;
423        # Set the filter based on the completeness flag.
424        my $filter = ($complete ? "Genome(complete) = 1" : "");
425        # Get all the genomes and the related taxonomy information.
426        my @genomes = $self->GetAll(['Genome'], $filter, [], ['Genome(id)', 'Genome(taxonomy)']);
427        # Clear the counters.
428        my ($arch, $bact, $euk, $vir, $env, $unk) = (0, 0, 0, 0, 0, 0);
429        # Loop through, counting the domains.
430        for my $genome (@genomes) {
431            if    ($genome->[1] =~ /^archaea/i)  { ++$arch }
432            elsif ($genome->[1] =~ /^bacter/i)   { ++$bact }
433            elsif ($genome->[1] =~ /^eukar/i)    { ++$euk }
434            elsif ($genome->[1] =~ /^vir/i)      { ++$vir }
435            elsif ($genome->[1] =~ /^env/i)      { ++$env }
436            else  { ++$unk }
437        }
438        # Return the counts.
439        return ($arch, $bact, $euk, $vir, $env, $unk);
440    }
441    
442    =head3 ContigCount
443    
444        my $count = $sprout->ContigCount($genomeID);
445    
446    Return the number of contigs for the specified genome ID.
447    
448    =over 4
449    
450    =item genomeID
451    
452    ID of the genome whose contig count is desired.
453    
454    =item RETURN
455    
456    Returns the number of contigs for the specified genome.
457    
458    =back
459    
460    =cut
461    
462    sub ContigCount {
463        # Get the parameters.
464        my ($self, $genomeID) = @_;
465        # Get the contig count.
466        my $retVal = $self->GetCount(['Contig', 'HasContig'], "HasContig(from-link) = ?", [$genomeID]);
467        # Return the result.
468        return $retVal;
469    }
470    
471    =head3 GenomeMenu
472    
473        my $html = $sprout->GenomeMenu(%options);
474    
475    Generate a genome selection control with the specified name and options.
476    This control is almost but not quite the same as the genome control in the
477    B<SearchHelper> class. Eventually, the two will be combined.
478    
479    =over 4
480    
481    =item options
482    
483    Optional parameters for the control (see below).
484    
485    =item RETURN
486    
487    Returns the HTML for a genome selection control on a form (sometimes called a popup menu).
488    
489    =back
490    
491    The valid options are as follows.
492    
493    =over 4
494    
495    =item name
496    
497    Name to give this control for use in passing it to the form. The default is C<myGenomeControl>.
498    Terrible things will happen if you have two controls with the same name on the same page.
499    
500    =item filter
501    
502    If specified, a filter for the list of genomes to display. The filter should be in the form of a
503    list reference. The first element of the list should be the filter string, and the remaining elements
504    the filter parameters.
505    
506    =item multiSelect
507    
508    If TRUE, then the user can select multiple genomes. If FALSE, the user can only select one genome.
509    
510    =item size
511    
512    Number of rows to display in the control. The default is C<10>
513    
514    =item id
515    
516    ID to give this control. The default is the value of the C<name> option. Nothing will work correctly
517    unless this ID is unique.
518    
519    =item selected
520    
521    A comma-delimited list of selected genomes, or a reference to a list of selected genomes. The
522    default is none.
523    
524    =item class
525    
526    If specified, a style class to assign to the genome control.
527    
528    =back
529    
530    =cut
531    
532    sub GenomeMenu {
533        # Get the parameters.
534        my ($self, %options) = @_;
535        # Get the control's name and ID.
536        my $menuName = $options{name} || $options{id} || 'myGenomeControl';
537        my $menuID = $options{id} || $menuName;
538        Trace("Genome menu name = $menuName with ID $menuID.") if T(3);
539        # Compute the IDs for the status display.
540        my $divID = "${menuID}_status";
541        my $urlID = "${menuID}_url";
542        # Compute the code to show selected genomes in the status area.
543        my $showSelect = "showSelected('$menuID', '$divID', '$urlID', 1000)";
544        # Check for single-select or multi-select.
545        my $multiSelect = $options{multiSelect} || 0;
546        # Get the style data.
547        my $class = $options{class} || '';
548        # Get the list of pre-selected items.
549        my $selections = $options{selected} || [];
550        if (ref $selections ne 'ARRAY') {
551            $selections = [ split /\s*,\s*/, $selections ];
552        }
553        my %selected = map { $_ => 1 } @{$selections};
554        # Extract the filter information. The default is no filtering. It can be passed as a tab-delimited
555        # string or a list reference.
556        my $filterParms = $options{filter} || "";
557        if (! ref $filterParms) {
558            $filterParms = [split /\t|\\t/, $filterParms];
559        }
560        my $filterString = shift @{$filterParms};
561        # Get a list of all the genomes in group order. In fact, we only need them ordered
562        # by name (genus,species,strain), but putting primary-group in front enables us to
563        # take advantage of an existing index.
564        my @genomeList = $self->GetAll(['Genome'], "$filterString ORDER BY Genome(primary-group), Genome(genus), Genome(species), Genome(unique-characterization)",
565                                       $filterParms,
566                                       [qw(Genome(primary-group) Genome(id) Genome(genus) Genome(species) Genome(unique-characterization) Genome(taxonomy) Genome(contigs))]);
567        # Create a hash to organize the genomes by group. Each group will contain a list of
568        # 2-tuples, the first element being the genome ID and the second being the genome
569        # name.
570        my %gHash = ();
571        for my $genome (@genomeList) {
572            # Get the genome data.
573            my ($group, $genomeID, $genus, $species, $strain, $taxonomy, $contigs) = @{$genome};
574            # Compute its name. This is the genus, species, strain (if any), and the contig count.
575            my $name = "$genus $species ";
576            $name .= "$strain " if $strain;
577            my $contigCount = ($contigs == 1 ? "" : ", $contigs contigs");
578            # Now we get the domain. The domain tells us the display style of the organism.
579            my ($domain) = split /\s*;\s*/, $taxonomy, 2;
580            # Now compute the display group. This is normally the primary group, but if the
581            # organism is supporting, we blank it out.
582            my $displayGroup = ($group eq $FIG_Config::otherGroup ? "" : $group);
583            # Push the genome into the group's list. Note that we use the real group
584            # name for the hash key here, not the display group name.
585            push @{$gHash{$group}}, [$genomeID, $name, $contigCount, $domain];
586        }
587        # We are almost ready to unroll the menu out of the group hash. The final step is to separate
588        # the supporting genomes by domain. First, we extract the NMPDR groups and sort them. They
589        # are sorted by the first capitalized word. Groups with "other" are sorted after groups
590        # that aren't "other". At some point, we will want to make this less complicated.
591        my %sortGroups = map { $_ =~ /(other)?(.*)([A-Z].+)/; "$3$1$2" => $_ }
592                             grep { $_ ne $FIG_Config::otherGroup } keys %gHash;
593        my @groups = map { $sortGroups{$_} } sort keys %sortGroups;
594        # Remember the number of NMPDR groups.
595        my $nmpdrGroupCount = scalar @groups;
596        # Loop through the supporting genomes, classifying them by domain. We'll also keep a list
597        # of the domains found.
598        my @otherGenomes = @{$gHash{$FIG_Config::otherGroup}};
599        my @domains = ();
600        for my $genomeData (@otherGenomes) {
601            my ($genomeID, $name, $contigCount, $domain) = @{$genomeData};
602            if (exists $gHash{$domain}) {
603                push @{$gHash{$domain}}, $genomeData;
604            } else {
605                $gHash{$domain} = [$genomeData];
606                push @domains, $domain;
607            }
608        }
609        # Add the domain groups at the end of the main group list. The main group list will now
610        # contain all the categories we need to display the genomes.
611        push @groups, sort @domains;
612        # Delete the supporting group.
613        delete $gHash{$FIG_Config::otherGroup};
614        # Now it gets complicated. We need a way to mark all the NMPDR genomes. We take advantage
615        # of the fact they come first in the list. We'll accumulate a count of the NMPDR genomes
616        # and use that to make the selections.
617        my $nmpdrCount = 0;
618        # Create the type counters.
619        my $groupCount = 1;
620        # Get the number of rows to display.
621        my $rows = $options{size} || 10;
622        # If we're multi-row, create an onChange event.
623        my $onChangeTag = ( $rows > 1 ? " onChange=\"$showSelect;\" onFocus=\"$showSelect;\"" : "" );
624        # Set up the multiple-select flag.
625        my $multipleTag = ($multiSelect ? " multiple" : "" );
626        # Set up the style class.
627        my $classTag = ($class ? " class=\"$class\"" : "" );
628        # Create the SELECT tag and stuff it into the output array.
629        my @lines = ("<SELECT name=\"$menuName\" id=\"$menuID\" $onChangeTag$multipleTag$classTag size=\"$rows\">");
630        # Loop through the groups.
631        for my $group (@groups) {
632            # Get the genomes in the group.
633            for my $genome (@{$gHash{$group}}) {
634                # If this is an NMPDR organism, we add an extra style and count it.
635                my $nmpdrStyle = "";
636                if ($nmpdrGroupCount > 0) {
637                    $nmpdrCount++;
638                    $nmpdrStyle = " Core";
639                }
640                # Get the organism ID, name, contig count, and domain.
641                my ($genomeID, $name, $contigCount, $domain) = @{$genome};
642                # See if we're pre-selected.
643                my $selectTag = ($selected{$genomeID} ? " SELECTED" : "");
644                # Compute the display name.
645                my $nameString = "$name ($genomeID$contigCount)";
646                # Generate the option tag.
647                my $optionTag = "<OPTION class=\"$domain$nmpdrStyle\" title=\"$group\" value=\"$genomeID\"$selectTag>$nameString</OPTION>";
648                push @lines, "    $optionTag";
649            }
650            # Record this group in the nmpdrGroup count. When that gets to 0, we've finished the NMPDR
651            # groups.
652            $nmpdrGroupCount--;
653        }
654        # Close the SELECT tag.
655        push @lines, "</SELECT>";
656        if ($rows > 1) {
657            # We're in a non-compact mode, so we need to add some selection helpers. First is
658            # the search box. This allows the user to type text and change which genomes are
659            # displayed. For multiple-select mode, we include a button that selects the displayed
660            # genes. For single-select mode, we use a plain label instead.
661            my $searchThingName = "${menuID}_SearchThing";
662            my $searchThingLabel = ($multiSelect ? "<INPUT type=\"button\" name=\"MacroSearch\" class=\"button\" value=\"Select genomes containing\" onClick=\"selectShowing('$menuID', '$searchThingName'); $showSelect;\" />"
663                                                 : "Show genomes containing");
664            push @lines, "<br />$searchThingLabel&nbsp;" .
665                         "<INPUT type=\"text\" id=\"$searchThingName\" name=\"$searchThingName\" size=\"30\" onKeyup=\"showTyped('$menuID', '$searchThingName');\" />" .
666                         Hint("GenomeControl", "Type here to filter the genomes displayed.") . "<br />";
667            # For multi-select mode, we also have buttons to set and clear selections.
668            if ($multiSelect) {
669                push @lines, "<INPUT type=\"button\" name=\"ClearAll\" class=\"bigButton\"  value=\"Clear All\" onClick=\"clearAll('$menuID'); $showSelect\" />";
670                push @lines, "<INPUT type=\"button\" name=\"SelectAll\" class=\"bigButton\" value=\"Select All\" onClick=\"selectAll('$menuID'); $showSelect\" />";
671                push @lines, "<INPUT type=\"button\" name=\"NMPDROnly\" class=\"bigButton\"  value=\"Select NMPDR\" onClick=\"selectSome('$menuID', $nmpdrCount, true); $showSelect;\" />";
672            }
673            # Add a hidden field we can use to generate organism page hyperlinks.
674            push @lines, "<INPUT type=\"hidden\" id=\"$urlID\" value=\"$FIG_Config::cgi_url/wiki/rest.cgi/NmpdrPlugin/SeedViewer?page=Organism;organism=\" />";
675            # Add the status display. This tells the user what's selected no matter where the list is scrolled.
676            push @lines, "<DIV id=\"$divID\" class=\"Panel\"></DIV>";
677        }
678        # Assemble all the lines into a string.
679        my $retVal = join("\n", @lines, "");
680        # Return the result.
681        return $retVal;
682    }
683    
684    
685    =head3 Stem
686    
687        my $stem = $sprout->Stem($word);
688    
689    Return the stem of the specified word, or C<undef> if the word is not
690    stemmable. Note that even if the word is stemmable, the stem may be
691    the same as the original word.
692    
693    =over 4
694    
695    =item word
696    
697    Word to convert into a stem.
698    
699    =item RETURN
700    
701    Returns a stem of the word (which may be the word itself), or C<undef> if
702    the word is not stemmable.
703    
704    =back
705    
706    =cut
707    
708    sub Stem {
709        # Get the parameters.
710        my ($self, $word) = @_;
711        # Get the stemmer object.
712        my $stemmer = $self->{stemmer};
713        if (! defined $stemmer) {
714            # We don't have one pre-built, so we build and save it now.
715            $stemmer = BioWords->new(exceptions => "$FIG_Config::sproutData/Exceptions.txt",
716                                     stops => "$FIG_Config::sproutData/StopWords.txt",
717                                     cache => 1);
718            $self->{stemmer} = $stemmer;
719        }
720        # Try to stem the word.
721        my $retVal = $stemmer->Process($word);
722        # Return the result.
723        return $retVal;
724    }
725    
726    
727  =head3 Build  =head3 Build
728    
729  C<< $sprout->Build(); >>      $sprout->Build();
730    
731  Build the database. The database will be cleared and the tables re-created from the metadata.  Build the database. The database will be cleared and the tables re-created from the metadata.
732  This method is useful when a database is brand new or when the database definition has  This method is useful when a database is brand new or when the database definition has
# Line 460  Line 738 
738      # Get the parameters.      # Get the parameters.
739      my ($self) = @_;      my ($self) = @_;
740      # Create the tables.      # Create the tables.
741      $self->{_erdb}->CreateTables;      $self->CreateTables();
742  }  }
743    
744  =head3 Genomes  =head3 Genomes
745    
746  C<< my @genomes = $sprout->Genomes(); >>      my @genomes = $sprout->Genomes();
747    
748  Return a list of all the genome IDs.  Return a list of all the genome IDs.
749    
# Line 482  Line 760 
760    
761  =head3 GenusSpecies  =head3 GenusSpecies
762    
763  C<< my $infoString = $sprout->GenusSpecies($genomeID); >>      my $infoString = $sprout->GenusSpecies($genomeID);
764    
765  Return the genus, species, and unique characterization for a genome.  Return the genus, species, and unique characterization for a genome.
766    
# Line 514  Line 792 
792    
793  =head3 FeaturesOf  =head3 FeaturesOf
794    
795  C<< my @features = $sprout->FeaturesOf($genomeID, $ftype); >>      my @features = $sprout->FeaturesOf($genomeID, $ftype);
796    
797  Return a list of the features relevant to a specified genome.  Return a list of the features relevant to a specified genome.
798    
# Line 559  Line 837 
837    
838  =head3 FeatureLocation  =head3 FeatureLocation
839    
840  C<< my @locations = $sprout->FeatureLocation($featureID); >>      my @locations = $sprout->FeatureLocation($featureID);
841    
842  Return the location of a feature in its genome's contig segments. In a list context, this method  Return the location of a feature in its genome's contig segments. In a list context, this method
843  will return a list of the locations. In a scalar context, it will return the locations as a space-  will return a list of the locations. In a scalar context, it will return the locations as a space-
# Line 583  Line 861 
861  =item RETURN  =item RETURN
862    
863  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
864  context and as a comma-delimited string in a scalar context.  context and as a comma-delimited string in a scalar context. An empty list means the feature
865    wasn't found.
866    
867  =back  =back
868    
869  =cut  =cut
870  #: Return Type @;  
 #: Return Type $;  
871  sub FeatureLocation {  sub FeatureLocation {
872      # Get the parameters.      # Get the parameters.
873      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
874      # Create a query for the feature locations.      # Declare the return variable.
     my $query = $self->Get(['IsLocatedIn'], "IsLocatedIn(from-link) = ? ORDER BY IsLocatedIn(locN)",  
                            [$featureID]);  
     # Create the return list.  
875      my @retVal = ();      my @retVal = ();
876      # Set up the variables used to determine if we have adjacent segments. This initial setup will      # Get the feature record.
877      # not match anything.      my $object = $self->GetEntity('Feature', $featureID);
878      my ($prevContig, $prevBeg, $prevDir, $prevLen) = ("", 0, "0", 0);      # Only proceed if we found it.
879      # Loop through the query results, creating location specifiers.      if (defined $object) {
880      while (my $location = $query->Fetch()) {          # Get the location string.
881          # Get the location parameters.          my $locString = $object->PrimaryValue('Feature(location-string)');
882          my ($contigID, $beg, $dir, $len) = $location->Values(['IsLocatedIn(to-link)',          # Create the return list.
883              'IsLocatedIn(beg)', 'IsLocatedIn(dir)', 'IsLocatedIn(len)']);          @retVal = split /\s*,\s*/, $locString;
         # Check to see if we are adjacent to the previous segment.  
         if ($prevContig eq $contigID && $dir eq $prevDir) {  
             # Here the new segment is in the same direction on the same contig. Insure the  
             # new segment's beginning is next to the old segment's end.  
             if ($dir eq "-" && $beg + $len == $prevBeg) {  
                 # Here we're merging two backward blocks, so we keep the new begin point  
                 # and adjust the length.  
                 $len += $prevLen;  
                 # Pop the old segment off. The new one will replace it later.  
                 pop @retVal;  
             } elsif ($dir eq "+" && $beg == $prevBeg + $prevLen) {  
                 # Here we need to merge two forward blocks. Adjust the beginning and  
                 # length values to include both segments.  
                 $beg = $prevBeg;  
                 $len += $prevLen;  
                 # Pop the old segment off. The new one will replace it later.  
                 pop @retVal;  
             }  
         }  
         # Remember this specifier for the adjacent-segment test the next time through.  
         ($prevContig, $prevBeg, $prevDir, $prevLen) = ($contigID, $beg, $dir, $len);  
         # Compute the initial base pair.  
         my $start = ($dir eq "+" ? $beg : $beg + $len - 1);  
         # Add the specifier to the list.  
         push @retVal, "${contigID}_$start$dir$len";  
884      }      }
885      # Return the list in the format indicated by the context.      # Return the list in the format indicated by the context.
886      return (wantarray ? @retVal : join(',', @retVal));      return (wantarray ? @retVal : join(',', @retVal));
# Line 638  Line 888 
888    
889  =head3 ParseLocation  =head3 ParseLocation
890    
891  C<< my ($contigID, $start, $dir, $len) = Sprout::ParseLocation($location); >>      my ($contigID, $start, $dir, $len) = Sprout::ParseLocation($location);
892    
893  Split a location specifier into the contig ID, the starting point, the direction, and the  Split a location specifier into the contig ID, the starting point, the direction, and the
894  length.  length.
# Line 657  Line 907 
907  =back  =back
908    
909  =cut  =cut
910  #: Return Type @;  
911  sub ParseLocation {  sub ParseLocation {
912      # Get the parameter. Note that if we're called as an instance method, we ignore      # Get the parameter. Note that if we're called as an instance method, we ignore
913      # the first parameter.      # the first parameter.
# Line 680  Line 930 
930      return ($contigID, $start, $dir, $len);      return ($contigID, $start, $dir, $len);
931  }  }
932    
933    
934    
935  =head3 PointLocation  =head3 PointLocation
936    
937  C<< my $found = Sprout::PointLocation($location, $point); >>      my $found = Sprout::PointLocation($location, $point);
938    
939  Return the offset into the specified location of the specified point on the contig. If  Return the offset into the specified location of the specified point on the contig. If
940  the specified point is before the location, a negative value will be returned. If it is  the specified point is before the location, a negative value will be returned. If it is
# Line 711  Line 963 
963  =back  =back
964    
965  =cut  =cut
966  #: Return Type $;  
967  sub PointLocation {  sub PointLocation {
968      # Get the parameter. Note that if we're called as an instance method, we ignore      # Get the parameter. Note that if we're called as an instance method, we ignore
969      # the first parameter.      # the first parameter.
# Line 734  Line 986 
986    
987  =head3 DNASeq  =head3 DNASeq
988    
989  C<< my $sequence = $sprout->DNASeq(\@locationList); >>      my $sequence = $sprout->DNASeq(\@locationList);
990    
991  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
992  should be of the form returned by L</featureLocation> when in a list context. In other words,  should be of the form returned by L</featureLocation> when in a list context. In other words,
993  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>.
994    
995    For example, the following would return the DNA sequence for contig C<83333.1:NC_000913>
996    between positions 1401 and 1532, inclusive.
997    
998        my $sequence = $sprout->DNASeq('83333.1:NC_000913_1401_1532');
999    
1000  =over 4  =over 4
1001    
1002  =item locationList  =item locationList
1003    
1004  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
1005  L</FeatureLocation> for more about this format).  I<contigID>C<_>I<begin>C<_>I<end> (see L</FeatureLocation> for more about this format).
1006    
1007  =item RETURN  =item RETURN
1008    
# Line 813  Line 1070 
1070    
1071  =head3 AllContigs  =head3 AllContigs
1072    
1073  C<< my @idList = $sprout->AllContigs($genomeID); >>      my @idList = $sprout->AllContigs($genomeID);
1074    
1075  Return a list of all the contigs for a genome.  Return a list of all the contigs for a genome.
1076    
# Line 841  Line 1098 
1098      return @retVal;      return @retVal;
1099  }  }
1100    
1101  =head3 ContigLength  =head3 GenomeLength
1102    
1103  C<< my $length = $sprout->ContigLength($contigID); >>      my $length = $sprout->GenomeLength($genomeID);
1104    
1105  Compute the length of a contig.  Return the length of the specified genome in base pairs.
1106    
1107  =over 4  =over 4
1108    
1109  =item contigID  =item genomeID
1110    
1111  ID of the contig whose length is desired.  ID of the genome whose base pair count is desired.
1112    
1113  =item RETURN  =item RETURN
1114    
1115  Returns the number of positions in the contig.  Returns the number of base pairs in all the contigs of the specified
1116    genome.
1117    
1118  =back  =back
1119    
1120  =cut  =cut
1121  #: Return Type $;  
1122  sub ContigLength {  sub GenomeLength {
1123      # Get the parameters.      # Get the parameters.
1124      my ($self, $contigID) = @_;      my ($self, $genomeID) = @_;
1125      # Get the contig's last sequence.      # Declare the return variable.
1126      my $query = $self->Get(['IsMadeUpOf'],      my $retVal = 0;
1127          "IsMadeUpOf(from-link) = ? ORDER BY IsMadeUpOf(start-position) DESC",      # Get the genome's contig sequence lengths.
1128          [$contigID]);      my @lens = $self->GetFlat(['HasContig', 'IsMadeUpOf'], 'HasContig(from-link) = ?',
1129      my $sequence = $query->Fetch();                         [$genomeID], 'IsMadeUpOf(len)');
1130      # Declare the return value.      # Sum the lengths.
1131        map { $retVal += $_ } @lens;
1132        # Return the result.
1133        return $retVal;
1134    }
1135    
1136    =head3 FeatureCount
1137    
1138        my $count = $sprout->FeatureCount($genomeID, $type);
1139    
1140    Return the number of features of the specified type in the specified genome.
1141    
1142    =over 4
1143    
1144    =item genomeID
1145    
1146    ID of the genome whose feature count is desired.
1147    
1148    =item type
1149    
1150    Type of feature to count (eg. C<peg>, C<rna>, etc.).
1151    
1152    =item RETURN
1153    
1154    Returns the number of features of the specified type for the specified genome.
1155    
1156    =back
1157    
1158    =cut
1159    
1160    sub FeatureCount {
1161        # Get the parameters.
1162        my ($self, $genomeID, $type) = @_;
1163        # Compute the count.
1164        my $retVal = $self->GetCount(['HasFeature', 'Feature'],
1165                                    "HasFeature(from-link) = ? AND Feature(feature-type) = ?",
1166                                    [$genomeID, $type]);
1167        # Return the result.
1168        return $retVal;
1169    }
1170    
1171    =head3 GenomeAssignments
1172    
1173        my $fidHash = $sprout->GenomeAssignments($genomeID);
1174    
1175    Return a list of a genome's assigned features. The return hash will contain each
1176    assigned feature of the genome mapped to the text of its most recent functional
1177    assignment.
1178    
1179    =over 4
1180    
1181    =item genomeID
1182    
1183    ID of the genome whose functional assignments are desired.
1184    
1185    =item RETURN
1186    
1187    Returns a reference to a hash which maps each feature to its most recent
1188    functional assignment.
1189    
1190    =back
1191    
1192    =cut
1193    
1194    sub GenomeAssignments {
1195        # Get the parameters.
1196        my ($self, $genomeID) = @_;
1197        # Declare the return variable.
1198        my $retVal = {};
1199        # Query the genome's features.
1200        my $query = $self->Get(['HasFeature', 'Feature'], "HasFeature(from-link) = ?",
1201                               [$genomeID]);
1202        # Loop through the features.
1203        while (my $data = $query->Fetch) {
1204            # Get the feature ID and assignment.
1205            my ($fid, $assignment) = $data->Values(['Feature(id)', 'Feature(assignment)']);
1206            if ($assignment) {
1207                $retVal->{$fid} = $assignment;
1208            }
1209        }
1210        # Return the result.
1211        return $retVal;
1212    }
1213    
1214    =head3 ContigLength
1215    
1216        my $length = $sprout->ContigLength($contigID);
1217    
1218    Compute the length of a contig.
1219    
1220    =over 4
1221    
1222    =item contigID
1223    
1224    ID of the contig whose length is desired.
1225    
1226    =item RETURN
1227    
1228    Returns the number of positions in the contig.
1229    
1230    =back
1231    
1232    =cut
1233    #: Return Type $;
1234    sub ContigLength {
1235        # Get the parameters.
1236        my ($self, $contigID) = @_;
1237        # Get the contig's last sequence.
1238        my $query = $self->Get(['IsMadeUpOf'],
1239            "IsMadeUpOf(from-link) = ? ORDER BY IsMadeUpOf(start-position) DESC",
1240            [$contigID]);
1241        my $sequence = $query->Fetch();
1242        # Declare the return value.
1243      my $retVal = 0;      my $retVal = 0;
1244      # Set it from the sequence data, if any.      # Set it from the sequence data, if any.
1245      if ($sequence) {      if ($sequence) {
# Line 882  Line 1252 
1252    
1253  =head3 ClusterPEGs  =head3 ClusterPEGs
1254    
1255  C<< my $clusteredList = $sprout->ClusterPEGs($sub, \@pegs); >>      my $clusteredList = $sprout->ClusterPEGs($sub, \@pegs);
1256    
1257  Cluster the PEGs in a list according to the cluster coding scheme of the specified  Cluster the PEGs in a list according to the cluster coding scheme of the specified
1258  subsystem. In order for this to work properly, the subsystem object must have  subsystem. In order for this to work properly, the subsystem object must have
1259  been used recently to retrieve the PEGs using the B<get_pegs_from_cell> method.  been used recently to retrieve the PEGs using the B<get_pegs_from_cell> or
1260  This causes the cluster numbers to be pulled into the subsystem's color hash.  B<get_row> methods. This causes the cluster numbers to be pulled into the
1261  If a PEG is not found in the color hash, it will not appear in the output  subsystem's color hash. If a PEG is not found in the color hash, it will not
1262  sequence.  appear in the output sequence.
1263    
1264  =over 4  =over 4
1265    
# Line 930  Line 1300 
1300    
1301  =head3 GenesInRegion  =head3 GenesInRegion
1302    
1303  C<< my (\@featureIDList, $beg, $end) = $sprout->GenesInRegion($contigID, $start, $stop); >>      my (\@featureIDList, $beg, $end) = $sprout->GenesInRegion($contigID, $start, $stop);
1304    
1305  List the features which overlap a specified region in a contig.  List the features which overlap a specified region in a contig.
1306    
# Line 959  Line 1329 
1329  =back  =back
1330    
1331  =cut  =cut
1332  #: Return Type @@;  
1333  sub GenesInRegion {  sub GenesInRegion {
1334      # Get the parameters.      # Get the parameters.
1335      my ($self, $contigID, $start, $stop) = @_;      my ($self, $contigID, $start, $stop) = @_;
1336      # Get the maximum segment length.      # Get the maximum segment length.
1337      my $maximumSegmentLength = $self->MaxSegment;      my $maximumSegmentLength = $self->MaxSegment;
     # Create a hash to receive the feature list. We use a hash so that we can eliminate  
     # duplicates easily. The hash key will be the feature ID. The value will be a two-element  
     # containing the minimum and maximum offsets. We will use the offsets to sort the results  
     # when we're building the result set.  
     my %featuresFound = ();  
1338      # Prime the values we'll use for the returned beginning and end.      # Prime the values we'll use for the returned beginning and end.
1339      my @initialMinMax = ($self->ContigLength($contigID), 0);      my @initialMinMax = ($self->ContigLength($contigID), 0);
1340      my ($min, $max) = @initialMinMax;      my ($min, $max) = @initialMinMax;
1341      # Create a table of parameters for each query. Each query looks for features travelling in      # Get the overlapping features.
1342        my @featureObjects = $self->GeneDataInRegion($contigID, $start, $stop);
1343        # We'l use this hash to help us track the feature IDs and sort them. The key is the
1344        # feature ID and the value is a [$left,$right] pair indicating the maximum extent
1345        # of the feature's locations.
1346        my %featureMap = ();
1347        # Loop through them to do the begin/end analysis.
1348        for my $featureObject (@featureObjects) {
1349            # Get the feature's location string. This may contain multiple actual locations.
1350            my ($locations, $fid) = $featureObject->Values([qw(Feature(location-string) Feature(id))]);
1351            my @locationSegments = split /\s*,\s*/, $locations;
1352            # Loop through the locations.
1353            for my $locationSegment (@locationSegments) {
1354                # Construct an object for the location.
1355                my $locationObject = BasicLocation->new($locationSegment);
1356                # Merge the current segment's begin and end into the min and max.
1357                my ($left, $right) = ($locationObject->Left, $locationObject->Right);
1358                my ($beg, $end);
1359                if (exists $featureMap{$fid}) {
1360                    ($beg, $end) = @{$featureMap{$fid}};
1361                    $beg = $left if $left < $beg;
1362                    $end = $right if $right > $end;
1363                } else {
1364                    ($beg, $end) = ($left, $right);
1365                }
1366                $min = $beg if $beg < $min;
1367                $max = $end if $end > $max;
1368                # Store the feature's new extent back into the hash table.
1369                $featureMap{$fid} = [$beg, $end];
1370            }
1371        }
1372        # Now we must compute the list of the IDs for the features found. We start with a list
1373        # of midpoints / feature ID pairs. (It's not really a midpoint, it's twice the midpoint,
1374        # but the result of the sort will be the same.)
1375        my @list = map { [$featureMap{$_}->[0] + $featureMap{$_}->[1], $_] } keys %featureMap;
1376        # Now we sort by midpoint and yank out the feature IDs.
1377        my @retVal = map { $_->[1] } sort { $a->[0] <=> $b->[0] } @list;
1378        # Return it along with the min and max.
1379        return (\@retVal, $min, $max);
1380    }
1381    
1382    =head3 GeneDataInRegion
1383    
1384        my @featureList = $sprout->GenesInRegion($contigID, $start, $stop);
1385    
1386    List the features which overlap a specified region in a contig.
1387    
1388    =over 4
1389    
1390    =item contigID
1391    
1392    ID of the contig containing the region of interest.
1393    
1394    =item start
1395    
1396    Offset of the first residue in the region of interest.
1397    
1398    =item stop
1399    
1400    Offset of the last residue in the region of interest.
1401    
1402    =item RETURN
1403    
1404    Returns a list of B<ERDBObjects> for the desired features. Each object will
1405    contain a B<Feature> record.
1406    
1407    =back
1408    
1409    =cut
1410    
1411    sub GeneDataInRegion {
1412        # Get the parameters.
1413        my ($self, $contigID, $start, $stop) = @_;
1414        # Get the maximum segment length.
1415        my $maximumSegmentLength = $self->MaxSegment;
1416        # Create a hash to receive the feature list. We use a hash so that we can eliminate
1417        # duplicates easily. The hash key will be the feature ID. The value will be the feature's
1418        # ERDBObject from the query.
1419        my %featuresFound = ();
1420        # Create a table of parameters for the queries. Each query looks for features travelling in
1421      # a particular direction. The query parameters include the contig ID, the feature direction,      # a particular direction. The query parameters include the contig ID, the feature direction,
1422      # the lowest possible start position, and the highest possible start position. This works      # the lowest possible start position, and the highest possible start position. This works
1423      # 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.
# Line 982  Line 1426 
1426      # Loop through the query parameters.      # Loop through the query parameters.
1427      for my $parms (values %queryParms) {      for my $parms (values %queryParms) {
1428          # Create the query.          # Create the query.
1429          my $query = $self->Get(['IsLocatedIn'],          my $query = $self->Get([qw(Feature IsLocatedIn)],
1430              "IsLocatedIn(to-link)= ? AND IsLocatedIn(dir) = ? AND IsLocatedIn(beg) >= ? AND IsLocatedIn(beg) <= ?",              "IsLocatedIn(to-link)= ? AND IsLocatedIn(dir) = ? AND IsLocatedIn(beg) >= ? AND IsLocatedIn(beg) <= ?",
1431              $parms);              $parms);
1432          # Loop through the feature segments found.          # Loop through the feature segments found.
1433          while (my $segment = $query->Fetch) {          while (my $segment = $query->Fetch) {
1434              # Get the data about this segment.              # Get the data about this segment.
1435              my ($featureID, $dir, $beg, $len) = $segment->Values(['IsLocatedIn(from-link)',              my ($featureID, $contig, $dir, $beg, $len) = $segment->Values([qw(IsLocatedIn(from-link)
1436                  'IsLocatedIn(dir)', 'IsLocatedIn(beg)', 'IsLocatedIn(len)']);                  IsLocatedIn(to-link) IsLocatedIn(dir) IsLocatedIn(beg) IsLocatedIn(len))]);
1437              # Determine if this feature actually overlaps the region. The query insures that              # Determine if this feature segment actually overlaps the region. The query insures that
1438              # this will be the case if the segment is the maximum length, so to fine-tune              # this will be the case if the segment is the maximum length, so to fine-tune
1439              # the results we insure that the inequality from the query holds using the actual              # the results we insure that the inequality from the query holds using the actual
1440              # length.              # length.
1441              my ($found, $end) = (0, 0);              my $loc = BasicLocation->new($contig, $beg, $dir, $len);
1442              if ($dir eq '+') {              my $found = $loc->Overlap($start, $stop);
                 $end = $beg + $len;  
                 if ($end >= $start) {  
                     # Denote we found a useful feature.  
                     $found = 1;  
                 }  
             } elsif ($dir eq '-') {  
                 # Note we switch things around so that the beginning is to the left of the  
                 # ending.  
                 ($beg, $end) = ($beg - $len, $beg);  
                 if ($beg <= $stop) {  
                     # Denote we found a useful feature.  
                     $found = 1;  
                 }  
             }  
1443              if ($found) {              if ($found) {
1444                  # Here we need to record the feature and update the minima and maxima. First,                  # Save this feature in the result list.
1445                  # get the current entry for the specified feature.                  $featuresFound{$featureID} = $segment;
                 my ($loc1, $loc2) = (exists $featuresFound{$featureID} ? @{$featuresFound{$featureID}} :  
                                      @initialMinMax);  
                 # Merge the current segment's begin and end into the feature begin and end and the  
                 # global min and max.  
                 if ($beg < $loc1) {  
                     $loc1 = $beg;  
                     $min = $beg if $beg < $min;  
                 }  
                 if ($end > $loc2) {  
                     $loc2 = $end;  
                     $max = $end if $end > $max;  
                 }  
                 # Store the entry back into the hash table.  
                 $featuresFound{$featureID} = [$loc1, $loc2];  
1446              }              }
1447          }          }
1448      }      }
1449      # Now we must compute the list of the IDs for the features found. We start with a list      # Return the ERDB objects for the features found.
1450      # of midpoints / feature ID pairs. (It's not really a midpoint, it's twice the midpoint,      return values %featuresFound;
     # but the result of the sort will be the same.)  
     my @list = map { [$featuresFound{$_}->[0] + $featuresFound{$_}->[1], $_] } keys %featuresFound;  
     # Now we sort by midpoint and yank out the feature IDs.  
     my @retVal = map { $_->[1] } sort { $a->[0] <=> $b->[0] } @list;  
     # Return it along with the min and max.  
     return (\@retVal, $min, $max);  
1451  }  }
1452    
1453  =head3 FType  =head3 FType
1454    
1455  C<< my $ftype = $sprout->FType($featureID); >>      my $ftype = $sprout->FType($featureID);
1456    
1457  Return the type of a feature.  Return the type of a feature.
1458    
# Line 1072  Line 1482 
1482    
1483  =head3 FeatureAnnotations  =head3 FeatureAnnotations
1484    
1485  C<< my @descriptors = $sprout->FeatureAnnotations($featureID, $rawFlag); >>      my @descriptors = $sprout->FeatureAnnotations($featureID, $rawFlag);
1486    
1487  Return the annotations of a feature.  Return the annotations of a feature.
1488    
# Line 1135  Line 1545 
1545    
1546  =head3 AllFunctionsOf  =head3 AllFunctionsOf
1547    
1548  C<< my %functions = $sprout->AllFunctionsOf($featureID); >>      my %functions = $sprout->AllFunctionsOf($featureID);
1549    
1550  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
1551  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,
# Line 1153  Line 1563 
1563    
1564  =item RETURN  =item RETURN
1565    
1566  Returns a hash mapping the functional assignment IDs to user IDs.  Returns a hash mapping the user IDs to functional assignment IDs.
1567    
1568  =back  =back
1569    
# Line 1163  Line 1573 
1573      # Get the parameters.      # Get the parameters.
1574      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
1575      # Get all of the feature's annotations.      # Get all of the feature's annotations.
1576      my @query = $self->GetAll(['IsTargetOfAnnotation', 'Annotation'],      my @query = $self->GetAll(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1577                              "IsTargetOfAnnotation(from-link) = ?",                              "IsTargetOfAnnotation(from-link) = ?",
1578                              [$featureID], ['Annotation(time)', 'Annotation(annotation)']);                              [$featureID], ['Annotation(time)', 'Annotation(annotation)',
1579                                               'MadeAnnotation(from-link)']);
1580      # Declare the return hash.      # Declare the return hash.
1581      my %retVal;      my %retVal;
     # Declare a hash for insuring we only make one assignment per user.  
     my %timeHash = ();  
1582      # Now we sort the assignments by timestamp in reverse.      # Now we sort the assignments by timestamp in reverse.
1583      my @sortedQuery = sort { -($a->[0] <=> $b->[0]) } @query;      my @sortedQuery = sort { -($a->[0] <=> $b->[0]) } @query;
1584      # Loop until we run out of annotations.      # Loop until we run out of annotations.
1585      for my $annotation (@sortedQuery) {      for my $annotation (@sortedQuery) {
1586          # Get the annotation fields.          # Get the annotation fields.
1587          my ($timeStamp, $text) = @{$annotation};          my ($timeStamp, $text, $user) = @{$annotation};
1588          # Check to see if this is a functional assignment.          # Check to see if this is a functional assignment.
1589          my ($user, $function) = _ParseAssignment($text);          my ($actualUser, $function) = _ParseAssignment($user, $text);
1590          if ($user && ! exists $timeHash{$user}) {          if ($actualUser && ! exists $retVal{$actualUser}) {
1591              # Here it is a functional assignment and there has been no              # Here it is a functional assignment and there has been no
1592              # previous assignment for this user, so we stuff it in the              # previous assignment for this user, so we stuff it in the
1593              # return hash.              # return hash.
1594              $retVal{$function} = $user;              $retVal{$actualUser} = $function;
             # Insure we don't assign to this user again.  
             $timeHash{$user} = 1;  
1595          }          }
1596      }      }
1597      # Return the hash of assignments found.      # Return the hash of assignments found.
# Line 1193  Line 1600 
1600    
1601  =head3 FunctionOf  =head3 FunctionOf
1602    
1603  C<< my $functionText = $sprout->FunctionOf($featureID, $userID); >>      my $functionText = $sprout->FunctionOf($featureID, $userID);
1604    
1605  Return the most recently-determined functional assignment of a particular feature.  Return the most recently-determined functional assignment of a particular feature.
1606    
1607  The functional assignment is handled differently depending on the type of feature. If  The functional assignment is handled differently depending on the type of feature. If
1608  the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional  the feature is identified by a FIG ID (begins with the string C<fig|>), then the functional
1609  assignment is a type of annotation. The format of an assignment is described in  assignment is taken from the B<Feature> or C<Annotation> table, depending.
 L</ParseLocation>. Its worth noting that we cannot filter on the content of the  
 annotation itself because it's a text field; however, this is not a big problem because  
 most features only have a small number of annotations.  
1610    
1611  Each user has an associated list of trusted users. The assignment returned will be the most  Each user has an associated list of trusted users. The assignment returned will be the most
1612  recent one by at least one of the trusted users. If no trusted user list is available, then  recent one by at least one of the trusted users. If no trusted user list is available, then
1613  the specified user and FIG are considered trusted. If the user ID is omitted, only FIG  the specified user and FIG are considered trusted. If the user ID is omitted, only FIG
1614  is trusted.  is trusted.
1615    
1616  If the feature is B<not> identified by a FIG ID, then the functional assignment  If the feature is B<not> identified by a FIG ID, then we search the aliases for it.
1617  information is taken from the B<ExternalAliasFunc> table. If the table does  If no matching alias is found, we return an undefined value.
 not contain an entry for the feature, an undefined value is returned.  
1618    
1619  =over 4  =over 4
1620    
# Line 1221  Line 1624 
1624    
1625  =item userID (optional)  =item userID (optional)
1626    
1627  ID of the user whose function determination is desired. If omitted, only the latest  ID of the user whose function determination is desired. If omitted, the primary
1628  C<FIG> assignment will be returned.  functional assignment in the B<Feature> table will be returned.
1629    
1630  =item RETURN  =item RETURN
1631    
# Line 1237  Line 1640 
1640      my ($self, $featureID, $userID) = @_;      my ($self, $featureID, $userID) = @_;
1641      # Declare the return value.      # Declare the return value.
1642      my $retVal;      my $retVal;
1643      # Determine the ID type.      # Find a FIG ID for this feature.
1644      if ($featureID =~ m/^fig\|/) {      my ($fid) = $self->FeaturesByAlias($featureID);
1645          # Here we have a FIG feature ID. We must build the list of trusted      # Only proceed if we have an ID.
1646          # users.      if ($fid) {
1647            # Here we have a FIG feature ID.
1648            if (!$userID) {
1649                # Use the primary assignment.
1650                ($retVal) = $self->GetEntityValues('Feature', $fid, ['Feature(assignment)']);
1651            } else {
1652                # We must build the list of trusted users.
1653          my %trusteeTable = ();          my %trusteeTable = ();
1654          # Check the user ID.          # Check the user ID.
1655          if (!$userID) {          if (!$userID) {
# Line 1262  Line 1671 
1671              }              }
1672          }          }
1673          # Build a query for all of the feature's annotations, sorted by date.          # Build a query for all of the feature's annotations, sorted by date.
1674          my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation'],              my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1675                                 "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",                                 "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1676                                 [$featureID]);                                     [$fid]);
1677          my $timeSelected = 0;          my $timeSelected = 0;
1678          # Loop until we run out of annotations.          # Loop until we run out of annotations.
1679          while (my $annotation = $query->Fetch()) {          while (my $annotation = $query->Fetch()) {
1680              # Get the annotation text.              # Get the annotation text.
1681              my ($text, $time) = $annotation->Values(['Annotation(annotation)','Annotation(time)']);                  my ($text, $time, $user) = $annotation->Values(['Annotation(annotation)',
1682                                                             'Annotation(time)', 'MadeAnnotation(from-link)']);
1683              # Check to see if this is a functional assignment for a trusted user.              # Check to see if this is a functional assignment for a trusted user.
1684              my ($user, $function) = _ParseAssignment($text);                  my ($actualUser, $function) = _ParseAssignment($user, $text);
1685              if ($user) {                  Trace("Assignment user is $actualUser, text is $function.") if T(4);
1686                    if ($actualUser) {
1687                  # Here it is a functional assignment. Check the time and the user                  # Here it is a functional assignment. Check the time and the user
1688                  # name. The time must be recent and the user must be trusted.                  # name. The time must be recent and the user must be trusted.
1689                  if ((exists $trusteeTable{$user}) && ($time > $timeSelected)) {                      if ((exists $trusteeTable{$actualUser}) && ($time > $timeSelected)) {
1690                      $retVal = $function;                      $retVal = $function;
1691                      $timeSelected = $time;                      $timeSelected = $time;
1692                  }                  }
1693              }              }
1694          }          }
1695      } else {          }
         # Here we have a non-FIG feature ID. In this case the user ID does not  
         # matter. We simply get the information from the External Alias Function  
         # table.  
         ($retVal) = $self->GetEntityValues('ExternalAliasFunc', $featureID, ['ExternalAliasFunc(func)']);  
1696      }      }
1697      # Return the assignment found.      # Return the assignment found.
1698      return $retVal;      return $retVal;
1699  }  }
1700    
1701    =head3 FunctionsOf
1702    
1703        my @functionList = $sprout->FunctionOf($featureID, $userID);
1704    
1705    Return the functional assignments of a particular feature.
1706    
1707    The functional assignment is handled differently depending on the type of feature. If
1708    the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional
1709    assignment is a type of annotation. The format of an assignment is described in
1710    L</ParseAssignment>. Its worth noting that we cannot filter on the content of the
1711    annotation itself because it's a text field; however, this is not a big problem because
1712    most features only have a small number of annotations.
1713    
1714    =over 4
1715    
1716    =item featureID
1717    
1718    ID of the feature whose functional assignments are desired.
1719    
1720    =item RETURN
1721    
1722    Returns a list of 2-tuples, each consisting of a user ID and the text of an assignment by
1723    that user.
1724    
1725    =back
1726    
1727    =cut
1728    #: Return Type @@;
1729    sub FunctionsOf {
1730        # Get the parameters.
1731        my ($self, $featureID) = @_;
1732        # Declare the return value.
1733        my @retVal = ();
1734        # Convert to a FIG ID.
1735        my ($fid) = $self->FeaturesByAlias($featureID);
1736        # Only proceed if we found one.
1737        if ($fid) {
1738            # Here we have a FIG feature ID. We must build the list of trusted
1739            # users.
1740            my %trusteeTable = ();
1741            # Build a query for all of the feature's annotations, sorted by date.
1742            my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1743                                   "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1744                                   [$fid]);
1745            my $timeSelected = 0;
1746            # Loop until we run out of annotations.
1747            while (my $annotation = $query->Fetch()) {
1748                # Get the annotation text.
1749                my ($text, $time, $user) = $annotation->Values(['Annotation(annotation)',
1750                                                                'Annotation(time)',
1751                                                                'MadeAnnotation(user)']);
1752                # Check to see if this is a functional assignment for a trusted user.
1753                my ($actualUser, $function) = _ParseAssignment($user, $text);
1754                if ($actualUser) {
1755                    # Here it is a functional assignment.
1756                    push @retVal, [$actualUser, $function];
1757                }
1758            }
1759        }
1760        # Return the assignments found.
1761        return @retVal;
1762    }
1763    
1764  =head3 BBHList  =head3 BBHList
1765    
1766  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>      my $bbhHash = $sprout->BBHList($genomeID, \@featureList);
1767    
1768  Return a hash mapping the features in a specified list to their bidirectional best hits  Return a hash mapping the features in a specified list to their bidirectional best hits
1769  on a specified target genome.  on a specified target genome.
# Line 1324  Line 1794 
1794      my %retVal = ();      my %retVal = ();
1795      # Loop through the incoming features.      # Loop through the incoming features.
1796      for my $featureID (@{$featureList}) {      for my $featureID (@{$featureList}) {
1797          # Create a query to get the feature's best hit.          # Ask the server for the feature's best hit.
1798          my $query = $self->Get(['IsBidirectionalBestHitOf'],          my @bbhData = FIGRules::BBHData($featureID);
                                "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",  
                                [$featureID, $genomeID]);  
1799          # Peel off the BBHs found.          # Peel off the BBHs found.
1800          my @found = ();          my @found = ();
1801          while (my $bbh = $query->Fetch) {          for my $bbh (@bbhData) {
1802              push @found, $bbh->Value('IsBidirectionalBestHitOf(to-link)');              my $fid = $bbh->[0];
1803                my $bbGenome = $self->GenomeOf($fid);
1804                if ($bbGenome eq $genomeID) {
1805                    push @found, $fid;
1806                }
1807          }          }
1808          $retVal{$featureID} = \@found;          $retVal{$featureID} = \@found;
1809      }      }
# Line 1341  Line 1813 
1813    
1814  =head3 SimList  =head3 SimList
1815    
1816  C<< my %similarities = $sprout->SimList($featureID, $count); >>      my %similarities = $sprout->SimList($featureID, $count);
1817    
1818  Return a list of the similarities to the specified feature.  Return a list of the similarities to the specified feature.
1819    
1820  Sprout does not support real similarities, so this method just returns the bidirectional  This method just returns the bidirectional best hits for performance reasons.
 best hits.  
1821    
1822  =over 4  =over 4
1823    
# Line 1366  Line 1837 
1837      # Get the parameters.      # Get the parameters.
1838      my ($self, $featureID, $count) = @_;      my ($self, $featureID, $count) = @_;
1839      # Ask for the best hits.      # Ask for the best hits.
1840      my @lists = $self->GetAll(['IsBidirectionalBestHitOf'],      my @lists = FIGRules::BBHData($featureID);
                               "IsBidirectionalBestHitOf(from-link) = ? ORDER BY IsBidirectionalBestHitOf(score) DESC",  
                               [$featureID], ['IsBidirectionalBestHitOf(to-link)', 'IsBidirectionalBestHitOf(score)'],  
                               $count);  
1841      # Create the return value.      # Create the return value.
1842      my %retVal = ();      my %retVal = ();
1843      for my $tuple (@lists) {      for my $tuple (@lists) {
# Line 1379  Line 1847 
1847      return %retVal;      return %retVal;
1848  }  }
1849    
   
   
1850  =head3 IsComplete  =head3 IsComplete
1851    
1852  C<< my $flag = $sprout->IsComplete($genomeID); >>      my $flag = $sprout->IsComplete($genomeID);
1853    
1854  Return TRUE if the specified genome is complete, else FALSE.  Return TRUE if the specified genome is complete, else FALSE.
1855    
# Line 1411  Line 1877 
1877      my $genomeData = $self->GetEntity('Genome', $genomeID);      my $genomeData = $self->GetEntity('Genome', $genomeID);
1878      if ($genomeData) {      if ($genomeData) {
1879          # The genome exists, so get the completeness flag.          # The genome exists, so get the completeness flag.
1880          ($retVal) = $genomeData->Value('complete');          $retVal = $genomeData->PrimaryValue('Genome(complete)');
1881      }      }
1882      # Return the result.      # Return the result.
1883      return $retVal;      return $retVal;
# Line 1419  Line 1885 
1885    
1886  =head3 FeatureAliases  =head3 FeatureAliases
1887    
1888  C<< my @aliasList = $sprout->FeatureAliases($featureID); >>      my @aliasList = $sprout->FeatureAliases($featureID);
1889    
1890  Return a list of the aliases for a specified feature.  Return a list of the aliases for a specified feature.
1891    
# Line 1442  Line 1908 
1908      # Get the parameters.      # Get the parameters.
1909      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
1910      # Get the desired feature's aliases      # Get the desired feature's aliases
1911      my @retVal = $self->GetEntityValues('Feature', $featureID, ['Feature(alias)']);      my @retVal = $self->GetFlat(['IsAliasOf'], "IsAliasOf(to-link) = ?", [$featureID], 'IsAliasOf(from-link)');
1912      # Return the result.      # Return the result.
1913      return @retVal;      return @retVal;
1914  }  }
1915    
1916  =head3 GenomeOf  =head3 GenomeOf
1917    
1918  C<< my $genomeID = $sprout->GenomeOf($featureID); >>      my $genomeID = $sprout->GenomeOf($featureID);
1919    
1920  Return the genome that contains a specified feature.  Return the genome that contains a specified feature or contig.
1921    
1922  =over 4  =over 4
1923    
1924  =item featureID  =item featureID
1925    
1926  ID of the feature whose genome is desired.  ID of the feature or contig whose genome is desired.
1927    
1928  =item RETURN  =item RETURN
1929    
1930  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
1931  an undefined value.  found, returns an undefined value.
1932    
1933  =back  =back
1934    
# Line 1471  Line 1937 
1937  sub GenomeOf {  sub GenomeOf {
1938      # Get the parameters.      # Get the parameters.
1939      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
     # Create a query to find the genome associated with the feature.  
     my $query = $self->Get(['IsLocatedIn', 'HasContig'], "IsLocatedIn(from-link) = ?", [$featureID]);  
1940      # Declare the return value.      # Declare the return value.
1941      my $retVal;      my $retVal;
1942      # Get the genome ID.      # Parse the genome ID from the feature ID.
1943      if (my $relationship = $query->Fetch()) {      if ($featureID =~ /^fig\|(\d+\.\d+)/) {
1944          ($retVal) = $relationship->Value('HasContig(from-link)');          $retVal = $1;
1945        } else {
1946            # Find the feature by alias.
1947            my ($realFeatureID) = $self->FeaturesByAlias($featureID);
1948            if ($realFeatureID && $realFeatureID =~ /^fig\|(\d+\.\d+)/) {
1949                $retVal = $1;
1950            }
1951      }      }
1952      # Return the value found.      # Return the value found.
1953      return $retVal;      return $retVal;
# Line 1485  Line 1955 
1955    
1956  =head3 CoupledFeatures  =head3 CoupledFeatures
1957    
1958  C<< my %coupleHash = $sprout->CoupledFeatures($featureID); >>      my %coupleHash = $sprout->CoupledFeatures($featureID);
1959    
1960  Return the features functionally coupled with a specified feature. Features are considered  Return the features functionally coupled with a specified feature. Features are considered
1961  functionally coupled if they tend to be clustered on the same chromosome.  functionally coupled if they tend to be clustered on the same chromosome.
# Line 1507  Line 1977 
1977  sub CoupledFeatures {  sub CoupledFeatures {
1978      # Get the parameters.      # Get the parameters.
1979      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
1980      # Create a query to retrieve the functionally-coupled features.      # Ask the coupling server for the data.
1981      my $query = $self->Get(['ParticipatesInCoupling', 'Coupling'],      Trace("Looking for features coupled to $featureID.") if T(coupling => 3);
1982                             "ParticipatesInCoupling(from-link) = ?", [$featureID]);      my @rawPairs = FIGRules::NetCouplingData('coupled_to', id1 => $featureID);
1983      # This value will be set to TRUE if we find at least one coupled feature.      Trace(scalar(@rawPairs) . " couplings returned.") if T(coupling => 3);
1984      my $found = 0;      # Form them into a hash.
     # Create the return hash.  
1985      my %retVal = ();      my %retVal = ();
1986      # Retrieve the relationship records and store them in the hash.      for my $pair (@rawPairs) {
1987      while (my $clustering = $query->Fetch()) {          # Get the feature ID and score.
1988          # Get the ID and score of the coupling.          my ($featureID2, $score) = @{$pair};
1989          my ($couplingID, $score) = $clustering->Values(['Coupling(id)',          # Only proceed if the feature is in NMPDR.
1990                                                          'Coupling(score)']);          if ($self->_CheckFeature($featureID2)) {
1991          # The coupling ID contains the two feature IDs separated by a space. We use              $retVal{$featureID2} = $score;
1992          # this information to find the ID of the other feature.          }
         my ($fid1, $fid2) = split / /, $couplingID;  
         my $otherFeatureID = ($featureID eq $fid1 ? $fid2 : $fid1);  
         # Attach the other feature's score to its ID.  
         $retVal{$otherFeatureID} = $score;  
         $found = 1;  
1993      }      }
1994      # Functional coupling is reflexive. If we found at least one coupled feature, we must add      # Functional coupling is reflexive. If we found at least one coupled feature, we must add
1995      # the incoming feature as well.      # the incoming feature as well.
1996      if ($found) {      if (keys %retVal) {
1997          $retVal{$featureID} = 9999;          $retVal{$featureID} = 9999;
1998      }      }
1999      # Return the hash.      # Return the hash.
# Line 1538  Line 2002 
2002    
2003  =head3 CouplingEvidence  =head3 CouplingEvidence
2004    
2005  C<< my @evidence = $sprout->CouplingEvidence($peg1, $peg2); >>      my @evidence = $sprout->CouplingEvidence($peg1, $peg2);
2006    
2007  Return the evidence for a functional coupling.  Return the evidence for a functional coupling.
2008    
# Line 1586  Line 2050 
2050      my ($self, $peg1, $peg2) = @_;      my ($self, $peg1, $peg2) = @_;
2051      # Declare the return variable.      # Declare the return variable.
2052      my @retVal = ();      my @retVal = ();
2053      # Our first task is to find out the nature of the coupling: whether or not      # Get the coupling and evidence data.
2054      # it exists, its score, and whether the features are stored in the same      my @rawData = FIGRules::NetCouplingData('coupling_evidence', id1 => $peg1, id2 => $peg2);
2055      # order as the ones coming in.      # Loop through the raw data, saving the ones that are in NMPDR genomes.
2056      my ($couplingID, $inverted, $score) = $self->GetCoupling($peg1, $peg2);      for my $rawTuple (@rawData) {
2057      # Only proceed if a coupling exists.          if ($self->_CheckFeature($rawTuple->[0]) && $self->_CheckFeature($rawTuple->[1])) {
2058      if ($couplingID) {              push @retVal, $rawTuple;
2059          # Determine the ordering to place on the evidence items. If we're          }
         # inverted, we want to see feature 2 before feature 1 (descending); otherwise,  
         # we want feature 1 before feature 2 (normal).  
         Trace("Coupling evidence for ($peg1, $peg2) with inversion flag $inverted.") if T(Coupling => 4);  
         my $ordering = ($inverted ? "DESC" : "");  
         # Get the coupling evidence.  
         my @evidenceList = $self->GetAll(['IsEvidencedBy', 'PCH', 'UsesAsEvidence'],  
                                           "IsEvidencedBy(from-link) = ? ORDER BY PCH(id), UsesAsEvidence(pos) $ordering",  
                                           [$couplingID],  
                                           ['PCH(used)', 'UsesAsEvidence(to-link)']);  
         # Loop through the evidence items. Each piece of evidence is represented by two  
         # positions in the evidence list, one for each feature on the other side of the  
         # evidence link. If at some point we want to generalize to couplings with  
         # more than two positions, this section of code will need to be re-done.  
         while (@evidenceList > 0) {  
             my $peg1Data = shift @evidenceList;  
             my $peg2Data = shift @evidenceList;  
             Trace("Peg 1 is " . $peg1Data->[1] . " and Peg 2 is " . $peg2Data->[1] . ".") if T(Coupling => 4);  
             push @retVal, [$peg1Data->[1], $peg2Data->[1], $peg1Data->[0]];  
         }  
         Trace("Last index in evidence result is is $#retVal.") if T(Coupling => 4);  
2060      }      }
2061      # Return the result.      # Return the result.
2062      return @retVal;      return @retVal;
2063  }  }
2064    
2065  =head3 GetCoupling  =head3 GetSynonymGroup
   
 C<< my ($couplingID, $inverted, $score) = $sprout->GetCoupling($peg1, $peg2); >>  
   
 Return the coupling (if any) for the specified pair of PEGs. If a coupling  
 exists, we return the coupling ID along with an indicator of whether the  
 coupling is stored as C<(>I<$peg1>C<, >I<$peg2>C<)> or C<(>I<$peg2>C<, >I<$peg1>C<)>.  
 In the second case, we say the coupling is I<inverted>. The importance of an  
 inverted coupling is that the PEGs in the evidence will appear in reverse order.  
2066    
2067  =over 4      my $id = $sprout->GetSynonymGroup($fid);
2068    
2069  =item peg1  Return the synonym group name for the specified feature.
2070    
2071  ID of the feature of interest.  =over 4
2072    
2073  =item peg2  =item fid
2074    
2075  ID of the potentially coupled feature.  ID of the feature whose synonym group is desired.
2076    
2077  =item RETURN  =item RETURN
2078    
2079  Returns a three-element list. The first element contains the database ID of  The name of the synonym group to which the feature belongs. If the feature does
2080  the coupling. The second element is FALSE if the coupling is stored in the  not belong to a synonym group, the feature ID itself is returned.
 database in the caller specified order and TRUE if it is stored in the  
 inverted order. The third element is the coupling's score. If the coupling  
 does not exist, all three list elements will be C<undef>.  
2081    
2082  =back  =back
2083    
2084  =cut  =cut
2085  #: Return Type $%@;  
2086  sub GetCoupling {  sub GetSynonymGroup {
2087      # Get the parameters.      # Get the parameters.
2088      my ($self, $peg1, $peg2) = @_;      my ($self, $fid) = @_;
2089      # Declare the return values. We'll start with the coupling ID and undefine the      # Declare the return variable.
2090      # flag and score until we have more information.      my $retVal;
2091      my ($retVal, $inverted, $score) = (CouplingID($peg1, $peg2), undef, undef);      # Find the synonym group.
2092      # Find the coupling data.      my @groups = $self->GetFlat(['IsSynonymGroupFor'], "IsSynonymGroupFor(to-link) = ?",
2093      my @pegs = $self->GetAll(['Coupling', 'ParticipatesInCoupling'],                                     [$fid], 'IsSynonymGroupFor(from-link)');
                                  "Coupling(id) = ? ORDER BY ParticipatesInCoupling(pos)",  
                                  [$retVal], ["ParticipatesInCoupling(from-link)", "Coupling(score)"]);  
2094      # Check to see if we found anything.      # Check to see if we found anything.
2095      if (!@pegs) {      if (@groups) {
2096          Trace("No coupling found.") if T(Coupling => 4);          $retVal = $groups[0];
         # No coupling, so undefine the return value.  
         $retVal = undef;  
2097      } else {      } else {
2098          # We have a coupling! Get the score and check for inversion.          $retVal = $fid;
         $score = $pegs[0]->[1];  
         my $firstFound = $pegs[0]->[0];  
         $inverted = ($firstFound ne $peg1);  
         Trace("Coupling score is $score. First peg is $firstFound, peg 1 is $peg1.") if T(Coupling => 4);  
2099      }      }
2100      # Return the result.      # Return the result.
2101      return ($retVal, $inverted, $score);      return $retVal;
2102  }  }
2103    
2104  =head3 CouplingID  =head3 GetBoundaries
   
 C<< my $couplingID = Sprout::CouplingID($peg1, $peg2); >>  
2105    
2106  Return the coupling ID for a pair of feature IDs.      my ($contig, $beg, $end) = $sprout->GetBoundaries(@locList);
2107    
2108  The coupling ID is currently computed by joining the feature IDs in  Determine the begin and end boundaries for the locations in a list. All of the
2109  sorted order with a space. Client modules (that is, modules which  locations must belong to the same contig and have mostly the same direction in
2110  use Sprout) should not, however, count on this always being the  order for this method to produce a meaningful result. The resulting
2111  case. This method provides a way for abstracting the concept of a  begin/end pair will contain all of the bases in any of the locations.
 coupling ID. All that we know for sure about it is that it can be  
 generated easily from the feature IDs and the order of the IDs  
 in the parameter list does not matter (i.e. C<CouplingID("a1", "b1")>  
 will have the same value as C<CouplingID("b1", "a1")>.  
2112    
2113  =over 4  =over 4
2114    
2115  =item peg1  =item locList
   
 First feature of interest.  
   
 =item peg2  
2116    
2117  Second feature of interest.  List of locations to process.
2118    
2119  =item RETURN  =item RETURN
2120    
2121  Returns the ID that would be used to represent a functional coupling of  Returns a 3-tuple consisting of the contig ID, the beginning boundary,
2122  the two specified PEGs.  and the ending boundary. The beginning boundary will be left of the
2123    end for mostly-forward locations and right of the end for mostly-backward
2124    locations.
2125    
2126  =back  =back
2127    
2128  =cut  =cut
 #: Return Type $;  
 sub CouplingID {  
     return join " ", sort @_;  
 }  
   
 =head3 GetEntityTypes  
   
 C<< my @entityList = $sprout->GetEntityTypes(); >>  
2129    
2130  Return the list of supported entity types.  sub GetBoundaries {
   
 =cut  
 #: Return Type @;  
 sub GetEntityTypes {  
2131      # Get the parameters.      # Get the parameters.
2132      my ($self) = @_;      my ($self, @locList) = @_;
2133      # Get the underlying database object.      # Set up the counters used to determine the most popular direction.
2134      my $erdb = $self->{_erdb};      my %counts = ( '+' => 0, '-' => 0 );
2135      # Get its entity type list.      # Get the last location and parse it.
2136      my @retVal = $erdb->GetEntityTypes();      my $locObject = BasicLocation->new(pop @locList);
2137        # Prime the loop with its data.
2138        my ($contig, $beg, $end) = ($locObject->Contig, $locObject->Left, $locObject->Right);
2139        # Count its direction.
2140        $counts{$locObject->Dir}++;
2141        # Loop through the remaining locations. Note that in most situations, this loop
2142        # will not iterate at all, because most of the time we will be dealing with a
2143        # singleton list.
2144        for my $loc (@locList) {
2145            # Create a location object.
2146            my $locObject = BasicLocation->new($loc);
2147            # Count the direction.
2148            $counts{$locObject->Dir}++;
2149            # Get the left end and the right end.
2150            my $left = $locObject->Left;
2151            my $right = $locObject->Right;
2152            # Merge them into the return variables.
2153            if ($left < $beg) {
2154                $beg = $left;
2155            }
2156            if ($right > $end) {
2157                $end = $right;
2158            }
2159        }
2160        # If the most common direction is reverse, flip the begin and end markers.
2161        if ($counts{'-'} > $counts{'+'}) {
2162            ($beg, $end) = ($end, $beg);
2163        }
2164        # Return the result.
2165        return ($contig, $beg, $end);
2166  }  }
2167    
2168  =head3 ReadFasta  =head3 ReadFasta
2169    
2170  C<< my %sequenceData = Sprout::ReadFasta($fileName, $prefix); >>      my %sequenceData = Sprout::ReadFasta($fileName, $prefix);
2171    
2172  Read sequence data from a FASTA-format file. Each sequence in a FASTA file is represented by  Read sequence data from a FASTA-format file. Each sequence in a FASTA file is represented by
2173  one or more lines of data. The first line begins with a > character and contains an ID.  one or more lines of data. The first line begins with a > character and contains an ID.
# Line 1799  Line 2233 
2233    
2234  =head3 FormatLocations  =head3 FormatLocations
2235    
2236  C<< my @locations = $sprout->FormatLocations($prefix, \@locations, $oldFormat); >>      my @locations = $sprout->FormatLocations($prefix, \@locations, $oldFormat);
2237    
2238  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
2239  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
# Line 1864  Line 2298 
2298    
2299  =head3 DumpData  =head3 DumpData
2300    
2301  C<< $sprout->DumpData(); >>      $sprout->DumpData();
2302    
2303  Dump all the tables to tab-delimited DTX files. The files will be stored in the data directory.  Dump all the tables to tab-delimited DTX files. The files will be stored in the data directory.
2304    
# Line 1876  Line 2310 
2310      # Get the data directory name.      # Get the data directory name.
2311      my $outputDirectory = $self->{_options}->{dataDir};      my $outputDirectory = $self->{_options}->{dataDir};
2312      # Dump the relations.      # Dump the relations.
2313      $self->{_erdb}->DumpRelations($outputDirectory);      $self->DumpRelations($outputDirectory);
2314  }  }
2315    
2316  =head3 XMLFileName  =head3 XMLFileName
2317    
2318  C<< my $fileName = $sprout->XMLFileName(); >>      my $fileName = $sprout->XMLFileName();
2319    
2320  Return the name of this database's XML definition file.  Return the name of this database's XML definition file.
2321    
# Line 1892  Line 2326 
2326      return $self->{_xmlName};      return $self->{_xmlName};
2327  }  }
2328    
2329  =head3 Insert  =head3 GetGenomeNameData
   
 C<< $sprout->Insert($objectType, \%fieldHash); >>  
   
 Insert an entity or relationship instance into the database. The entity or relationship of interest  
 is defined by a type name and then a hash of field names to values. Field values in the primary  
 relation are represented by scalars. (Note that for relationships, the primary relation is  
 the B<only> relation.) Field values for the other relations comprising the entity are always  
 list references. For example, the following line inserts an inactive PEG feature named  
 C<fig|188.1.peg.1> with aliases C<ZP_00210270.1> and C<gi|46206278>.  
2330    
2331  C<< $sprout->Insert('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>      my ($genus, $species, $strain) = $sprout->GenomeNameData($genomeID);
   
 The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and  
 property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.  
2332    
2333  C<< $sprout->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>  Return the genus, species, and unique characterization for a genome. This
2334    is similar to L</GenusSpecies>, with the exception that it returns the
2335    values in three seperate fields.
2336    
2337  =over 4  =over 4
2338    
2339  =item newObjectType  =item genomeID
2340    
2341  Type name of the entity or relationship to insert.  ID of the genome whose name data is desired.
2342    
2343  =item fieldHash  =item RETURN
2344    
2345  Hash of field names to values.  Returns a three-element list, consisting of the genus, species, and strain
2346    of the specified genome. If the genome is not found, an error occurs.
2347    
2348  =back  =back
2349    
2350  =cut  =cut
2351  #: Return Type ;  
2352    sub GetGenomeNameData {
2353        # Get the parameters.
2354        my ($self, $genomeID) = @_;
2355        # Get the desired values.
2356        my ($genus, $species, $strain) = $self->GetEntityValues('Genome', $genomeID =>
2357                                                                [qw(Genome(genus) Genome(species) Genome(unique-characterization))]);
2358        # Throw an error if they were not found.
2359        if (! defined $genus) {
2360            Confess("Genome $genomeID not found in database.");
2361        }
2362        # Return the results.
2363        return ($genus, $species, $strain);
2364    }
2365    
2366    =head3 GetGenomeByNameData
2367    
2368        my @genomes = $sprout->GetGenomeByNameData($genus, $species, $strain);
2369    
2370    Return a list of the IDs of the genomes with the specified genus,
2371    species, and strain. In almost every case, there will be either zero or
2372    one IDs returned; however, two or more IDs could be returned if there are
2373    multiple versions of the genome in the database.
2374    
2375    =over 4
2376    
2377    =item genus
2378    
2379    Genus of the desired genome.
2380    
2381    =item species
2382    
2383    Species of the desired genome.
2384    
2385    =item strain
2386    
2387    Strain (unique characterization) of the desired genome. This may be an empty
2388    string, in which case it is presumed that the desired genome has no strain
2389    specified.
2390    
2391    =item RETURN
2392    
2393    Returns a list of the IDs of the genomes having the specified genus, species, and
2394    strain.
2395    
2396    =back
2397    
2398    =cut
2399    
2400    sub GetGenomeByNameData {
2401        # Get the parameters.
2402        my ($self, $genus, $species, $strain) = @_;
2403        # Try to find the genomes.
2404        my @retVal = $self->GetFlat(['Genome'], "Genome(genus) = ? AND Genome(species) = ? AND Genome(unique-characterization) = ?",
2405                                    [$genus, $species, $strain], 'Genome(id)');
2406        # Return the result.
2407        return @retVal;
2408    }
2409    
2410    =head3 Insert
2411    
2412        $sprout->Insert($objectType, \%fieldHash);
2413    
2414    Insert an entity or relationship instance into the database. The entity or relationship of interest
2415    is defined by a type name and then a hash of field names to values. Field values in the primary
2416    relation are represented by scalars. (Note that for relationships, the primary relation is
2417    the B<only> relation.) Field values for the other relations comprising the entity are always
2418    list references. For example, the following line inserts an inactive PEG feature named
2419    C<fig|188.1.peg.1> with aliases C<ZP_00210270.1> and C<gi|46206278>.
2420    
2421        $sprout->Insert('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']});
2422    
2423    The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
2424    property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
2425    
2426        $sprout->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'});
2427    
2428    =over 4
2429    
2430    =item newObjectType
2431    
2432    Type name of the entity or relationship to insert.
2433    
2434    =item fieldHash
2435    
2436    Hash of field names to values.
2437    
2438    =back
2439    
2440    =cut
2441    #: Return Type ;
2442  sub Insert {  sub Insert {
2443      # Get the parameters.      # Get the parameters.
2444      my ($self, $objectType, $fieldHash) = @_;      my ($self, $objectType, $fieldHash) = @_;
2445      # Call the underlying method.      # Call the underlying method.
2446      $self->{_erdb}->InsertObject($objectType, $fieldHash);      $self->InsertObject($objectType, $fieldHash);
2447  }  }
2448    
2449  =head3 Annotate  =head3 Annotate
2450    
2451  C<< my $ok = $sprout->Annotate($fid, $timestamp, $user, $text); >>      my $ok = $sprout->Annotate($fid, $timestamp, $user, $text);
2452    
2453  Annotate a feature. This inserts an Annotation record into the database and links it to the  Annotate a feature. This inserts an Annotation record into the database and links it to the
2454  specified feature and user.  specified feature and user.
# Line 1987  Line 2502 
2502    
2503  =head3 AssignFunction  =head3 AssignFunction
2504    
2505  C<< my $ok = $sprout->AssignFunction($featureID, $user, $function, $assigningUser); >>      my $ok = $sprout->AssignFunction($featureID, $user, $function, $assigningUser);
2506    
2507  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
2508  format is described in L</ParseAssignment>.  format is described in L</ParseAssignment>.
# Line 2047  Line 2562 
2562    
2563  =head3 FeaturesByAlias  =head3 FeaturesByAlias
2564    
2565  C<< my @features = $sprout->FeaturesByAlias($alias); >>      my @features = $sprout->FeaturesByAlias($alias);
2566    
2567  Returns a list of features with the specified alias. The alias is parsed to determine  Returns a list of features with the specified alias. The alias is parsed to determine
2568  the type of the alias. A string of digits is a GenBack ID and a string of exactly 6  the type of the alias. A string of digits is a GenBack ID and a string of exactly 6
# Line 2081  Line 2596 
2596          push @retVal, $mappedAlias;          push @retVal, $mappedAlias;
2597      } else {      } else {
2598          # Here we have a non-FIG alias. Get the features with the normalized alias.          # Here we have a non-FIG alias. Get the features with the normalized alias.
2599          @retVal = $self->GetFlat(['Feature'], 'Feature(alias) = ?', [$mappedAlias], 'Feature(id)');          @retVal = $self->GetFlat(['IsAliasOf'], 'IsAliasOf(from-link) = ?', [$mappedAlias], 'IsAliasOf(to-link)');
2600      }      }
2601      # Return the result.      # Return the result.
2602      return @retVal;      return @retVal;
2603  }  }
2604    
 =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  
 #: Return Type $;  
 sub Exists {  
     # Get the parameters.  
     my ($self, $entityName, $entityID) = @_;  
     # Check for the entity instance.  
     Trace("Checking existence of $entityName with ID=$entityID.") if T(4);  
     my $testInstance = $self->GetEntity($entityName, $entityID);  
     # Return an existence indicator.  
     my $retVal = ($testInstance ? 1 : 0);  
     return $retVal;  
 }  
   
2605  =head3 FeatureTranslation  =head3 FeatureTranslation
2606    
2607  C<< my $translation = $sprout->FeatureTranslation($featureID); >>      my $translation = $sprout->FeatureTranslation($featureID);
2608    
2609  Return the translation of a feature.  Return the translation of a feature.
2610    
# Line 2152  Line 2632 
2632    
2633  =head3 Taxonomy  =head3 Taxonomy
2634    
2635  C<< my @taxonomyList = $sprout->Taxonomy($genome); >>      my @taxonomyList = $sprout->Taxonomy($genome);
2636    
2637  Return the taxonomy of the specified genome. This will be in the form of a list  Return the taxonomy of the specified genome. This will be in the form of a list
2638  containing the various classifications in order from domain (eg. C<Bacteria>, C<Archaea>,  containing the various classifications in order from domain (eg. C<Bacteria>, C<Archaea>,
2639  or C<Eukaryote>) to sub-species. For example,  or C<Eukaryote>) to sub-species. For example,
2640    
2641  C<< (Bacteria, Proteobacteria, Gammaproteobacteria, Enterobacteriales, Enterobacteriaceae, Escherichia, Escherichia coli, Escherichia coli K12) >>      (Bacteria, Proteobacteria, Gammaproteobacteria, Enterobacteriales, Enterobacteriaceae, Escherichia, Escherichia coli, Escherichia coli K12)
2642    
2643  =over 4  =over 4
2644    
# Line 2193  Line 2673 
2673    
2674  =head3 CrudeDistance  =head3 CrudeDistance
2675    
2676  C<< my $distance = $sprout->CrudeDistance($genome1, $genome2); >>      my $distance = $sprout->CrudeDistance($genome1, $genome2);
2677    
2678  Returns a crude estimate of the distance between two genomes. The distance is construed so  Returns a crude estimate of the distance between two genomes. The distance is construed so
2679  that it will be 0 for genomes with identical taxonomies and 1 for genomes from different domains.  that it will be 0 for genomes with identical taxonomies and 1 for genomes from different domains.
# Line 2245  Line 2725 
2725    
2726  =head3 RoleName  =head3 RoleName
2727    
2728  C<< my $roleName = $sprout->RoleName($roleID); >>      my $roleName = $sprout->RoleName($roleID);
2729    
2730  Return the descriptive name of the role with the specified ID. In general, a role  Return the descriptive name of the role with the specified ID. In general, a role
2731  will only have a descriptive name if it is coded as an EC number.  will only have a descriptive name if it is coded as an EC number.
# Line 2279  Line 2759 
2759    
2760  =head3 RoleDiagrams  =head3 RoleDiagrams
2761    
2762  C<< my @diagrams = $sprout->RoleDiagrams($roleID); >>      my @diagrams = $sprout->RoleDiagrams($roleID);
2763    
2764  Return a list of the diagrams containing a specified functional role.  Return a list of the diagrams containing a specified functional role.
2765    
# Line 2307  Line 2787 
2787      return @retVal;      return @retVal;
2788  }  }
2789    
 =head3 GetProperties  
   
 C<< my @list = $sprout->GetProperties($fid, $key, $value, $url); >>  
   
 Return a list of the properties with the specified characteristics.  
   
 Properties are arbitrary key-value pairs associated with a feature. (At some point they  
 will also be associated with genomes.) A property value is represented by a 4-tuple of  
 the form B<($fid, $key, $value, $url)>. These exactly correspond to the parameter  
   
 =over 4  
   
 =item fid  
   
 ID of the feature possessing the property.  
   
 =item key  
   
 Name or key of the property.  
   
 =item value  
   
 Value of the property.  
   
 =item url  
   
 URL of the document that indicated the property should have this particular value, or an  
 empty string if no such document exists.  
   
 =back  
   
 The parameters act as a filter for the desired data. Any non-null parameter will  
 automatically match all the tuples returned. So, specifying just the I<$fid> will  
 return all the properties of the specified feature; similarly, specifying the I<$key>  
 and I<$value> parameters will return all the features having the specified property  
 value.  
   
 A single property key can have many values, representing different ideas about the  
 feature in question. For example, one paper may declare that a feature C<fig|83333.1.peg.10> is  
 virulent, and another may declare that it is not virulent. A query about the virulence of  
 C<fig|83333.1.peg.10> would be coded as  
   
     my @list = $sprout->GetProperties('fig|83333.1.peg.10', 'virulence', '', '');  
   
 Here the I<$value> and I<$url> fields are left blank, indicating that those fields are  
 not to be filtered. The tuples returned would be  
   
     ('fig|83333.1.peg.10', 'virulence', 'yes', 'http://www.somewhere.edu/first.paper.pdf')  
     ('fig|83333.1.peg.10', 'virulence', 'no', 'http://www.somewhere.edu/second.paper.pdf')  
   
 =cut  
 #: Return Type @@;  
 sub GetProperties {  
     # Get the parameters.  
     my ($self, @parms) = @_;  
     # Declare the return variable.  
     my @retVal = ();  
     # Now we need to create a WHERE clause that will get us the data we want. First,  
     # we create a list of the columns containing the data for each parameter.  
     my @colNames = ('HasProperty(from-link)', 'Property(property-name)',  
                     'Property(property-value)', 'HasProperty(evidence)');  
     # Now we build the WHERE clause and the list of parameter values.  
     my @where = ();  
     my @values = ();  
     for (my $i = 0; $i <= $#colNames; $i++) {  
         my $parm = $parms[$i];  
         if (defined $parm && ($parm ne '')) {  
             push @where, "$colNames[$i] = ?";  
             push @values, $parm;  
         }  
     }  
     # Format the WHERE clause.  
     my $filter = (@values > 0 ? (join " AND ", @where) : undef);  
     # Ask for all the propertie values with the desired characteristics.  
     my $query = $self->Get(['HasProperty', 'Property'], $filter, \@values);  
     while (my $valueObject = $query->Fetch()) {  
         my @tuple = $valueObject->Values(\@colNames);  
         push @retVal, \@tuple;  
     }  
     # Return the result.  
     return @retVal;  
 }  
   
2790  =head3 FeatureProperties  =head3 FeatureProperties
2791    
2792  C<< my @properties = $sprout->FeatureProperties($featureID); >>      my @properties = $sprout->FeatureProperties($featureID);
2793    
2794  Return a list of the properties for the specified feature. Properties are key-value pairs  Return a list of the properties for the specified feature. Properties are key-value pairs
2795  that specify special characteristics of the feature. For example, a property could indicate  that specify special characteristics of the feature. For example, a property could indicate
2796  that a feature is essential to the survival of the organism or that it has benign influence  that a feature is essential to the survival of the organism or that it has benign influence
2797  on the activities of a pathogen. Each property is returned as a triple of the form  on the activities of a pathogen. Each property is returned as a triple of the form
2798  C<($key,$value,$url)>, where C<$key> is the property name, C<$value> is its value (commonly  C<($key,@values)>, where C<$key> is the property name and  C<@values> are its values.
 a 1 or a 0, but possibly a string or a floating-point value), and C<$url> is a string describing  
 the web address or citation in which the property's value for the feature was identified.  
2799    
2800  =over 4  =over 4
2801    
# Line 2410  Line 2805 
2805    
2806  =item RETURN  =item RETURN
2807    
2808  Returns a list of triples, each triple containing the property name, its value, and a URL or  Returns a list of tuples, each tuple containing the property name and its values.
 citation.  
2809    
2810  =back  =back
2811    
# Line 2421  Line 2815 
2815      # Get the parameters.      # Get the parameters.
2816      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
2817      # Get the properties.      # Get the properties.
2818      my @retVal = $self->GetAll(['HasProperty', 'Property'], "HasProperty(from-link) = ?", [$featureID],      my @attributes = $self->{_ca}->GetAttributes($featureID);
2819                              ['Property(property-name)', 'Property(property-value)',      # Strip the feature ID off each tuple.
2820                               'HasProperty(evidence)']);      my @retVal = ();
2821        for my $attributeRow (@attributes) {
2822            shift @{$attributeRow};
2823            push @retVal, $attributeRow;
2824        }
2825      # Return the resulting list.      # Return the resulting list.
2826      return @retVal;      return @retVal;
2827  }  }
2828    
2829  =head3 DiagramName  =head3 DiagramName
2830    
2831  C<< my $diagramName = $sprout->DiagramName($diagramID); >>      my $diagramName = $sprout->DiagramName($diagramID);
2832    
2833  Return the descriptive name of a diagram.  Return the descriptive name of a diagram.
2834    
# Line 2456  Line 2854 
2854      return $retVal;      return $retVal;
2855  }  }
2856    
2857    =head3 PropertyID
2858    
2859        my $id = $sprout->PropertyID($propName, $propValue);
2860    
2861    Return the ID of the specified property name and value pair, if the
2862    pair exists. Only a small subset of the FIG attributes are stored as
2863    Sprout properties, mostly for use in search optimization.
2864    
2865    =over 4
2866    
2867    =item propName
2868    
2869    Name of the desired property.
2870    
2871    =item propValue
2872    
2873    Value expected for the desired property.
2874    
2875    =item RETURN
2876    
2877    Returns the ID of the name/value pair, or C<undef> if the pair does not exist.
2878    
2879    =back
2880    
2881    =cut
2882    
2883    sub PropertyID {
2884        # Get the parameters.
2885        my ($self, $propName, $propValue) = @_;
2886        # Try to find the ID.
2887        my ($retVal) = $self->GetFlat(['Property'],
2888                                      "Property(property-name) = ? AND Property(property-value) = ?",
2889                                      [$propName, $propValue], 'Property(id)');
2890        # Return the result.
2891        return $retVal;
2892    }
2893    
2894  =head3 MergedAnnotations  =head3 MergedAnnotations
2895    
2896  C<< my @annotationList = $sprout->MergedAnnotations(\@list); >>      my @annotationList = $sprout->MergedAnnotations(\@list);
2897    
2898  Returns a merged list of the annotations for the features in a list. Each annotation is  Returns a merged list of the annotations for the features in a list. Each annotation is
2899  represented by a 4-tuple of the form C<($fid, $timestamp, $userID, $annotation)>, where  represented by a 4-tuple of the form C<($fid, $timestamp, $userID, $annotation)>, where
# Line 2507  Line 2942 
2942    
2943  =head3 RoleNeighbors  =head3 RoleNeighbors
2944    
2945  C<< my @roleList = $sprout->RoleNeighbors($roleID); >>      my @roleList = $sprout->RoleNeighbors($roleID);
2946    
2947  Returns a list of the roles that occur in the same diagram as the specified role. Because  Returns a list of the roles that occur in the same diagram as the specified role. Because
2948  diagrams and roles are in a many-to-many relationship with each other, the list is  diagrams and roles are in a many-to-many relationship with each other, the list is
# Line 2550  Line 2985 
2985    
2986  =head3 FeatureLinks  =head3 FeatureLinks
2987    
2988  C<< my @links = $sprout->FeatureLinks($featureID); >>      my @links = $sprout->FeatureLinks($featureID);
2989    
2990  Return a list of the web hyperlinks associated with a feature. The web hyperlinks are  Return a list of the web hyperlinks associated with a feature. The web hyperlinks are
2991  to external websites describing either the feature itself or the organism containing it  to external websites describing either the feature itself or the organism containing it
# Line 2581  Line 3016 
3016    
3017  =head3 SubsystemsOf  =head3 SubsystemsOf
3018    
3019  C<< my %subsystems = $sprout->SubsystemsOf($featureID); >>      my %subsystems = $sprout->SubsystemsOf($featureID);
3020    
3021  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
3022  to the roles the feature performs.  to the roles the feature performs.
# Line 2629  Line 3064 
3064    
3065  =head3 SubsystemList  =head3 SubsystemList
3066    
3067  C<< my @subsystems = $sprout->SubsystemList($featureID); >>      my @subsystems = $sprout->SubsystemList($featureID);
3068    
3069  Return a list containing the names of the subsystems in which the specified  Return a list containing the names of the subsystems in which the specified
3070  feature participates. Unlike L</SubsystemsOf>, this method only returns the  feature participates. Unlike L</SubsystemsOf>, this method only returns the
# Line 2652  Line 3087 
3087  sub SubsystemList {  sub SubsystemList {
3088      # Get the parameters.      # Get the parameters.
3089      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
3090      # Get the list of names.      # Get the list of names. We do a join to the Subsystem table because we have missing subsystems in
3091      my @retVal = $self->GetFlat(['ContainsFeature', 'HasSSCell'], "ContainsFeature(to-link) = ?",      # the Sprout database!
3092                                  [$featureID], 'HasSSCell(from-link)');      my @retVal = $self->GetFlat(['HasRoleInSubsystem', 'Subsystem'], "HasRoleInSubsystem(from-link) = ?",
3093                                    [$featureID], 'HasRoleInSubsystem(to-link)');
3094        # Return the result, sorted.
3095        return sort @retVal;
3096    }
3097    
3098    =head3 GenomeSubsystemData
3099    
3100        my %featureData = $sprout->GenomeSubsystemData($genomeID);
3101    
3102    Return a hash mapping genome features to their subsystem roles.
3103    
3104    =over 4
3105    
3106    =item genomeID
3107    
3108    ID of the genome whose subsystem feature map is desired.
3109    
3110    =item RETURN
3111    
3112    Returns a hash mapping each feature of the genome to a list of 2-tuples. Eacb
3113    2-tuple contains a subsystem name followed by a role ID.
3114    
3115    =back
3116    
3117    =cut
3118    
3119    sub GenomeSubsystemData {
3120        # Get the parameters.
3121        my ($self, $genomeID) = @_;
3122        # Declare the return variable.
3123        my %retVal = ();
3124        # Get a list of the genome features that participate in subsystems. For each
3125        # feature we get its subsystem ID and the corresponding roles.
3126        my @roleData = $self->GetAll(['HasFeature', 'ContainsFeature', 'IsRoleOf', 'HasSSCell'],
3127                                     "HasFeature(from-link) = ?", [$genomeID],
3128                                     ['HasFeature(to-link)', 'IsRoleOf(from-link)',  'HasSSCell(from-link)']);
3129        # Now we get a list of valid subsystems. These are the subsystems connected to the genome with
3130        # a non-negative variant code.
3131        my %subs = map { $_ => 1 } $self->GetFlat(['ParticipatesIn'],
3132                                                    "ParticipatesIn(from-link) = ? AND ParticipatesIn(variant-code) >= 0",
3133                                                    [$genomeID], 'ParticipatesIn(to-link)');
3134        # We loop through @roleData to build the hash.
3135        for my $roleEntry (@roleData) {
3136            # Get the data for this feature and cell.
3137            my ($fid, $role, $subsys) = @{$roleEntry};
3138            Trace("Subsystem for $fid is $subsys.") if T(4);
3139            # Check the subsystem;
3140            if ($subs{$subsys}) {
3141                Trace("Subsystem found.") if T(4);
3142                # Insure this feature has an entry in the return hash.
3143                if (! exists $retVal{$fid}) { $retVal{$fid} = []; }
3144                # Merge in this new data.
3145                push @{$retVal{$fid}}, [$subsys, $role];
3146            }
3147        }
3148      # Return the result.      # Return the result.
3149      return @retVal;      return %retVal;
3150  }  }
3151    
3152  =head3 RelatedFeatures  =head3 RelatedFeatures
3153    
3154  C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>      my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID);
3155    
3156  Return a list of the features which are bi-directional best hits of the specified feature and  Return a list of the features which are bi-directional best hits of the specified feature and
3157  have been assigned the specified function by the specified user. If no such features exists,  have been assigned the specified function by the specified user. If no such features exists,
# Line 2694  Line 3184 
3184      # Get the parameters.      # Get the parameters.
3185      my ($self, $featureID, $function, $userID) = @_;      my ($self, $featureID, $function, $userID) = @_;
3186      # 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.
3187      my @bbhFeatures = $self->GetFlat(['IsBidirectionalBestHitOf'],      my @bbhFeatures = map { $_->[0] } FIGRules::BBHData($featureID);
                                      "IsBidirectionalBestHitOf(from-link) = ?", [$featureID],  
                                      'IsBidirectionalBestHitOf(to-link)');  
3188      # Now we loop through the features, pulling out the ones that have the correct      # Now we loop through the features, pulling out the ones that have the correct
3189      # functional assignment.      # functional assignment.
3190      my @retVal = ();      my @retVal = ();
# Line 2714  Line 3202 
3202    
3203  =head3 TaxonomySort  =head3 TaxonomySort
3204    
3205  C<< my @sortedFeatureIDs = $sprout->TaxonomySort(\@featureIDs); >>      my @sortedFeatureIDs = $sprout->TaxonomySort(\@featureIDs);
3206    
3207  Return a list formed by sorting the specified features by the taxonomy of the containing  Return a list formed by sorting the specified features by the taxonomy of the containing
3208  genome. This will cause genomes from similar organisms to float close to each other.  genome. This will cause genomes from similar organisms to float close to each other.
# Line 2749  Line 3237 
3237          my ($taxonomy) = $self->GetFlat(['IsLocatedIn', 'HasContig', 'Genome'], "IsLocatedIn(from-link) = ?",          my ($taxonomy) = $self->GetFlat(['IsLocatedIn', 'HasContig', 'Genome'], "IsLocatedIn(from-link) = ?",
3238                                          [$fid], 'Genome(taxonomy)');                                          [$fid], 'Genome(taxonomy)');
3239          # Add this feature to the hash buffer.          # Add this feature to the hash buffer.
3240          Tracer::AddToListMap(\%hashBuffer, $taxonomy, $fid);          push @{$hashBuffer{$taxonomy}}, $fid;
3241      }      }
3242      # Sort the keys and get the elements.      # Sort the keys and get the elements.
3243      my @retVal = ();      my @retVal = ();
# Line 2760  Line 3248 
3248      return @retVal;      return @retVal;
3249  }  }
3250    
 =head3 GetAll  
   
 C<< my @list = $sprout->GetAll(\@objectNames, $filterClause, \@parameters, \@fields, $count); >>  
   
 Return a list of values taken from the objects returned by a query. The first three  
 parameters correspond to the parameters of the L</Get> method. The final parameter is  
 a list of the fields desired from each record found by the query. The field name  
 syntax is the standard syntax used for fields in the B<ERDB> system--  
 B<I<objectName>(I<fieldName>)>-- where I<objectName> is the name of the relevant entity  
 or relationship and I<fieldName> is the name of the field.  
   
 The list returned will be a list of lists. Each element of the list will contain  
 the values returned for the fields specified in the fourth parameter. If one of the  
 fields specified returns multiple values, they are flattened in with the rest. For  
 example, the following call will return a list of the features in a particular  
 spreadsheet cell, and each feature will be represented by a list containing the  
 feature ID followed by all of its aliases.  
   
 C<< $query = $sprout->Get(['ContainsFeature', 'Feature'], "ContainsFeature(from-link) = ?", [$ssCellID], ['Feature(id)', 'Feature(alias)']); >>  
   
 =over 4  
   
 =item objectNames  
   
 List containing the names of the entity and relationship objects to be retrieved.  
   
 =item filterClause  
   
 WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  
 be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form  
 B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the  
 parameter list as additional parameters. The fields in a filter clause can come from primary  
 entity relations, relationship relations, or secondary entity relations; however, all of the  
 entities and relationships involved must be included in the list of object names.  
   
 =item parameterList  
   
 List of the parameters to be substituted in for the parameters marks in the filter clause.  
   
 =item fields  
   
 List of the fields to be returned in each element of the list returned.  
   
 =item count  
   
 Maximum number of records to return. If omitted or 0, all available records will be returned.  
   
 =item RETURN  
   
 Returns a list of list references. Each element of the return list contains the values for the  
 fields specified in the B<fields> parameter.  
   
 =back  
   
 =cut  
 #: Return Type @@;  
 sub GetAll {  
     # Get the parameters.  
     my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;  
     # Call the ERDB method.  
     my @retVal = $self->{_erdb}->GetAll($objectNames, $filterClause, $parameterList,  
                                         $fields, $count);  
     # Return the resulting list.  
     return @retVal;  
 }  
   
 =head3 GetFlat  
   
 C<< my @list = $sprout->GetFlat(\@objectNames, $filterClause, $parameterList, $field); >>  
   
 This is a variation of L</GetAll> that asks for only a single field per record and  
 returns a single flattened list.  
   
 =over 4  
   
 =item objectNames  
   
 List containing the names of the entity and relationship objects to be retrieved.  
   
 =item filterClause  
   
 WHERE/ORDER BY clause (without the WHERE) to be used to filter and sort the query. The WHERE clause can  
 be parameterized with parameter markers (C<?>). Each field used must be specified in the standard form  
 B<I<objectName>(I<fieldName>)>. Any parameters specified in the filter clause should be added to the  
 parameter list as additional parameters. The fields in a filter clause can come from primary  
 entity relations, relationship relations, or secondary entity relations; however, all of the  
 entities and relationships involved must be included in the list of object names.  
   
 =item parameterList  
   
 List of the parameters to be substituted in for the parameters marks in the filter clause.  
   
 =item field  
   
 Name of the field to be used to get the elements of the list returned.  
   
 =item RETURN  
   
 Returns a list of values.  
   
 =back  
   
 =cut  
 #: Return Type @;  
 sub GetFlat {  
     # Get the parameters.  
     my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;  
     # Construct the query.  
     my $query = $self->Get($objectNames, $filterClause, $parameterList);  
     # Create the result list.  
     my @retVal = ();  
     # Loop through the records, adding the field values found to the result list.  
     while (my $row = $query->Fetch()) {  
         push @retVal, $row->Value($field);  
     }  
     # Return the list created.  
     return @retVal;  
 }  
   
3251  =head3 Protein  =head3 Protein
3252    
3253  C<< my $protein = Sprout::Protein($sequence, $table); >>      my $protein = Sprout::Protein($sequence, $table);
3254    
3255  Translate a DNA sequence into a protein sequence.  Translate a DNA sequence into a protein sequence.
3256    
# Line 2951  Line 3320 
3320      # Loop through the input triples.      # Loop through the input triples.
3321      my $n = length $sequence;      my $n = length $sequence;
3322      for (my $i = 0; $i < $n; $i += 3) {      for (my $i = 0; $i < $n; $i += 3) {
3323          # Get the current triple from the sequence.          # Get the current triple from the sequence. Note we convert to
3324          my $triple = substr($sequence, $i, 3);          # upper case to insure a match.
3325            my $triple = uc substr($sequence, $i, 3);
3326          # Translate it using the table.          # Translate it using the table.
3327          my $protein = "X";          my $protein = "X";
3328          if (exists $table->{$triple}) { $protein = $table->{$triple}; }          if (exists $table->{$triple}) { $protein = $table->{$triple}; }
# Line 2966  Line 3336 
3336    
3337  =head3 LoadInfo  =head3 LoadInfo
3338    
3339  C<< my ($dirName, @relNames) = $sprout->LoadInfo(); >>      my ($dirName, @relNames) = $sprout->LoadInfo();
3340    
3341  Return the name of the directory from which data is to be loaded and a list of the relation  Return the name of the directory from which data is to be loaded and a list of the relation
3342  names. This information is useful when trying to analyze what needs to be put where in order  names. This information is useful when trying to analyze what needs to be put where in order
# Line 2980  Line 3350 
3350      # Create the return list, priming it with the name of the data directory.      # Create the return list, priming it with the name of the data directory.
3351      my @retVal = ($self->{_options}->{dataDir});      my @retVal = ($self->{_options}->{dataDir});
3352      # Concatenate the table names.      # Concatenate the table names.
3353      push @retVal, $self->{_erdb}->GetTableNames();      push @retVal, $self->GetTableNames();
3354      # Return the result.      # Return the result.
3355      return @retVal;      return @retVal;
3356  }  }
3357    
3358    =head3 BBHMatrix
3359    
3360        my %bbhMap = $sprout->BBHMatrix($genomeID, $cutoff, @targets);
3361    
3362    Find all the bidirectional best hits for the features of a genome in a
3363    specified list of target genomes. The return value will be a hash mapping
3364    features in the original genome to their bidirectional best hits in the
3365    target genomes.
3366    
3367    =over 4
3368    
3369    =item genomeID
3370    
3371    ID of the genome whose features are to be examined for bidirectional best hits.
3372    
3373    =item cutoff
3374    
3375    A cutoff value. Only hits with a score lower than the cutoff will be returned.
3376    
3377    =item targets
3378    
3379    List of target genomes. Only pairs originating in the original
3380    genome and landing in one of the target genomes will be returned.
3381    
3382    =item RETURN
3383    
3384    Returns a hash mapping each feature in the original genome to a hash mapping its
3385    BBH pegs in the target genomes to their scores.
3386    
3387    =back
3388    
3389    =cut
3390    
3391    sub BBHMatrix {
3392        # Get the parameters.
3393        my ($self, $genomeID, $cutoff, @targets) = @_;
3394        # Declare the return variable.
3395        my %retVal = ();
3396        # Ask for the BBHs.
3397        my @bbhList = FIGRules::BatchBBHs("fig|$genomeID.%", $cutoff, @targets);
3398        # We now have a set of 4-tuples that we need to convert into a hash of hashes.
3399        for my $bbhData (@bbhList) {
3400            my ($peg1, $peg2, $score) = @{$bbhData};
3401            if (! exists $retVal{$peg1}) {
3402                $retVal{$peg1} = { $peg2 => $score };
3403            } else {
3404                $retVal{$peg1}->{$peg2} = $score;
3405            }
3406        }
3407        # Return the result.
3408        return %retVal;
3409    }
3410    
3411    
3412    =head3 SimMatrix
3413    
3414        my %simMap = $sprout->SimMatrix($genomeID, $cutoff, @targets);
3415    
3416    Find all the similarities for the features of a genome in a
3417    specified list of target genomes. The return value will be a hash mapping
3418    features in the original genome to their similarites in the
3419    target genomes.
3420    
3421    =over 4
3422    
3423    =item genomeID
3424    
3425    ID of the genome whose features are to be examined for similarities.
3426    
3427    =item cutoff
3428    
3429    A cutoff value. Only hits with a score lower than the cutoff will be returned.
3430    
3431    =item targets
3432    
3433    List of target genomes. Only pairs originating in the original
3434    genome and landing in one of the target genomes will be returned.
3435    
3436    =item RETURN
3437    
3438    Returns a hash mapping each feature in the original genome to a hash mapping its
3439    similar pegs in the target genomes to their scores.
3440    
3441    =back
3442    
3443    =cut
3444    
3445    sub SimMatrix {
3446        # Get the parameters.
3447        my ($self, $genomeID, $cutoff, @targets) = @_;
3448        # Declare the return variable.
3449        my %retVal = ();
3450        # Get the list of features in the source organism.
3451        my @fids = $self->FeaturesOf($genomeID);
3452        # Ask for the sims. We only want similarities to fig features.
3453        my $simList = FIGRules::GetNetworkSims($self, \@fids, {}, 1000, $cutoff, "fig");
3454        if (! defined $simList) {
3455            Confess("Unable to retrieve similarities from server.");
3456        } else {
3457            Trace("Processing sims.") if T(3);
3458            # We now have a set of sims that we need to convert into a hash of hashes. First, we
3459            # Create a hash for the target genomes.
3460            my %targetHash = map { $_ => 1 } @targets;
3461            for my $simData (@{$simList}) {
3462                # Get the PEGs and the score.
3463                my ($peg1, $peg2, $score) = ($simData->id1, $simData->id2, $simData->psc);
3464                # Insure the second ID is in the target list.
3465                my ($genome2) = FIGRules::ParseFeatureID($peg2);
3466                if (exists $targetHash{$genome2}) {
3467                    # Here it is. Now we need to add it to the return hash. How we do that depends
3468                    # on whether or not $peg1 is new to us.
3469                    if (! exists $retVal{$peg1}) {
3470                        $retVal{$peg1} = { $peg2 => $score };
3471                    } else {
3472                        $retVal{$peg1}->{$peg2} = $score;
3473                    }
3474                }
3475            }
3476        }
3477        # Return the result.
3478        return %retVal;
3479    }
3480    
3481    
3482  =head3 LowBBHs  =head3 LowBBHs
3483    
3484  C<< my %bbhMap = $sprout->GoodBBHs($featureID, $cutoff); >>      my %bbhMap = $sprout->LowBBHs($featureID, $cutoff);
3485    
3486  Return the bidirectional best hits of a feature whose score is no greater than a  Return the bidirectional best hits of a feature whose score is no greater than a
3487  specified cutoff value. A higher cutoff value will allow inclusion of hits with  specified cutoff value. A higher cutoff value will allow inclusion of hits with
# Line 3016  Line 3510 
3510      my ($self, $featureID, $cutoff) = @_;      my ($self, $featureID, $cutoff) = @_;
3511      # Create the return hash.      # Create the return hash.
3512      my %retVal = ();      my %retVal = ();
3513      # Create a query to get the desired BBHs.      # Query for the desired BBHs.
3514      my @bbhList = $self->GetAll(['IsBidirectionalBestHitOf'],      my @bbhList = FIGRules::BBHData($featureID, $cutoff);
                                 'IsBidirectionalBestHitOf(sc) <= ? AND IsBidirectionalBestHitOf(from-link) = ?',  
                                 [$cutoff, $featureID],  
                                 ['IsBidirectionalBestHitOf(to-link)', 'IsBidirectionalBestHitOf(sc)']);  
3515      # Form the results into the return hash.      # Form the results into the return hash.
3516      for my $pair (@bbhList) {      for my $pair (@bbhList) {
3517          $retVal{$pair->[0]} = $pair->[1];          my $fid = $pair->[0];
3518            if ($self->Exists('Feature', $fid)) {
3519                $retVal{$fid} = $pair->[1];
3520            }
3521      }      }
3522      # Return the result.      # Return the result.
3523      return %retVal;      return %retVal;
3524  }  }
3525    
3526    =head3 Sims
3527    
3528        my $simList = $sprout->Sims($fid, $maxN, $maxP, $select, $max_expand, $filters);
3529    
3530    Get a list of similarities for a specified feature. Similarity information is not kept in the
3531    Sprout database; rather, they are retrieved from a network server. The similarities are
3532    returned as B<Sim> objects. A Sim object is actually a list reference that has been blessed
3533    so that its elements can be accessed by name.
3534    
3535    Similarities can be either raw or expanded. The raw similarities are basic
3536    hits between features with similar DNA. Expanding a raw similarity drags in any
3537    features considered substantially identical. So, for example, if features B<A1>,
3538    B<A2>, and B<A3> are all substantially identical to B<A>, then a raw similarity
3539    B<[C,A]> would be expanded to B<[C,A] [C,A1] [C,A2] [C,A3]>.
3540    
3541    =over 4
3542    
3543    =item fid
3544    
3545    ID of the feature whose similarities are desired, or reference to a list of IDs
3546    of features whose similarities are desired.
3547    
3548    =item maxN
3549    
3550    Maximum number of similarities to return.
3551    
3552    =item maxP
3553    
3554    Minumum allowable similarity score.
3555    
3556    =item select
3557    
3558    Selection criterion: C<raw> means only raw similarities are returned; C<fig>
3559    means only similarities to FIG features are returned; C<all> means all expanded
3560    similarities are returned; and C<figx> means similarities are expanded until the
3561    number of FIG features equals the maximum.
3562    
3563    =item max_expand
3564    
3565    The maximum number of features to expand.
3566    
3567    =item filters
3568    
3569    Reference to a hash containing filter information, or a subroutine that can be
3570    used to filter the sims.
3571    
3572    =item RETURN
3573    
3574    Returns a reference to a list of similarity objects, or C<undef> if an error
3575    occurred.
3576    
3577    =back
3578    
3579    =cut
3580    
3581    sub Sims {
3582        # Get the parameters.
3583        my ($self, $fid, $maxN, $maxP, $select, $max_expand, $filters) = @_;
3584        # Create the shim object to test for deleted FIDs.
3585        my $shim = FidCheck->new($self);
3586        # Ask the network for sims.
3587        my $retVal = FIGRules::GetNetworkSims($shim, $fid, {}, $maxN, $maxP, $select, $max_expand, $filters);
3588        # Return the result.
3589        return $retVal;
3590    }
3591    
3592    =head3 IsAllGenomes
3593    
3594        my $flag = $sprout->IsAllGenomes(\@list, \@checkList);
3595    
3596    Return TRUE if all genomes in the second list are represented in the first list at
3597    least one. Otherwise, return FALSE. If the second list is omitted, the first list is
3598    compared to a list of all the genomes.
3599    
3600    =over 4
3601    
3602    =item list
3603    
3604    Reference to the list to be compared to the second list.
3605    
3606    =item checkList (optional)
3607    
3608    Reference to the comparison target list. Every genome ID in this list must occur at
3609    least once in the first list. If this parameter is omitted, a list of all the genomes
3610    is used.
3611    
3612    =item RETURN
3613    
3614    Returns TRUE if every item in the second list appears at least once in the
3615    first list, else FALSE.
3616    
3617    =back
3618    
3619    =cut
3620    
3621    sub IsAllGenomes {
3622        # Get the parameters.
3623        my ($self, $list, $checkList) = @_;
3624        # Supply the checklist if it was omitted.
3625        $checkList = [$self->Genomes()] if ! defined($checkList);
3626        # Create a hash of the original list.
3627        my %testList = map { $_ => 1 } @{$list};
3628        # Declare the return variable. We assume that the representation
3629        # is complete and stop at the first failure.
3630        my $retVal = 1;
3631        my $n = scalar @{$checkList};
3632        for (my $i = 0; $retVal && $i < $n; $i++) {
3633            if (! $testList{$checkList->[$i]}) {
3634                $retVal = 0;
3635            }
3636        }
3637        # Return the result.
3638        return $retVal;
3639    }
3640    
3641  =head3 GetGroups  =head3 GetGroups
3642    
3643  C<< my %groups = $sprout->GetGroups(\@groupList); >>      my %groups = $sprout->GetGroups(\@groupList);
3644    
3645  Return a hash mapping each group to the IDs of the genomes in the group.  Return a hash mapping each group to the IDs of the genomes in the group.
3646  A list of groups may be specified, in which case only those groups will be  A list of groups may be specified, in which case only those groups will be
# Line 3050  Line 3659 
3659          # Here we have a group list. Loop through them individually,          # Here we have a group list. Loop through them individually,
3660          # getting a list of the relevant genomes.          # getting a list of the relevant genomes.
3661          for my $group (@{$groupList}) {          for my $group (@{$groupList}) {
3662              my @genomeIDs = $self->GetFlat(['Genome'], "Genome(group-name) = ?",              my @genomeIDs = $self->GetFlat(['Genome'], "Genome(primary-group) = ?",
3663                  [$group], "Genome(id)");                  [$group], "Genome(id)");
3664              $retVal{$group} = \@genomeIDs;              $retVal{$group} = \@genomeIDs;
3665          }          }
# Line 3058  Line 3667 
3667          # Here we need all of the groups. In this case, we run through all          # Here we need all of the groups. In this case, we run through all
3668          # of the genome records, putting each one found into the appropriate          # of the genome records, putting each one found into the appropriate
3669          # group. Note that we use a filter clause to insure that only genomes          # group. Note that we use a filter clause to insure that only genomes
3670          # in groups are included in the return set.          # in real NMPDR groups are included in the return set.
3671          my @genomes = $self->GetAll(['Genome'], "Genome(group-name) > ' '", [],          my @genomes = $self->GetAll(['Genome'], "Genome(primary-group) <> ?",
3672                                      ['Genome(id)', 'Genome(group-name)']);                                      [$FIG_Config::otherGroup], ['Genome(id)', 'Genome(primary-group)']);
3673          # Loop through the genomes found.          # Loop through the genomes found.
3674          for my $genome (@genomes) {          for my $genome (@genomes) {
3675              # Pop this genome's ID off the current list.              # Get the genome ID and group, and add this genome to the group's list.
3676              my @groups = @{$genome};              my ($genomeID, $group) = @{$genome};
3677              my $genomeID = shift @groups;              push @{$retVal{$group}}, $genomeID;
             # Loop through the groups, adding the genome ID to each group's  
             # list.  
             for my $group (@groups) {  
                 Tracer::AddToListMap(\%retVal, $group, $genomeID);  
             }  
3678          }          }
3679      }      }
3680      # Return the hash we just built.      # Return the hash we just built.
# Line 3079  Line 3683 
3683    
3684  =head3 MyGenomes  =head3 MyGenomes
3685    
3686  C<< my @genomes = Sprout::MyGenomes($dataDir); >>      my @genomes = Sprout::MyGenomes($dataDir);
3687    
3688  Return a list of the genomes to be included in the Sprout.  Return a list of the genomes to be included in the Sprout.
3689    
# Line 3111  Line 3715 
3715    
3716  =head3 LoadFileName  =head3 LoadFileName
3717    
3718  C<< my $fileName = Sprout::LoadFileName($dataDir, $tableName); >>      my $fileName = Sprout::LoadFileName($dataDir, $tableName);
3719    
3720  Return the name of the load file for the specified table in the specified data  Return the name of the load file for the specified table in the specified data
3721  directory.  directory.
# Line 3150  Line 3754 
3754      return $retVal;      return $retVal;
3755  }  }
3756    
3757    =head3 DeleteGenome
3758    
3759        my $stats = $sprout->DeleteGenome($genomeID, $testFlag);
3760    
3761    Delete a genome from the database.
3762    
3763    =over 4
3764    
3765    =item genomeID
3766    
3767    ID of the genome to delete
3768    
3769    =item testFlag
3770    
3771    If TRUE, then the DELETE statements will be traced, but no deletions will occur.
3772    
3773    =item RETURN
3774    
3775    Returns a statistics object describing the rows deleted.
3776    
3777    =back
3778    
3779    =cut
3780    #: Return Type $%;
3781    sub DeleteGenome {
3782        # Get the parameters.
3783        my ($self, $genomeID, $testFlag) = @_;
3784        # Perform the delete for the genome's features.
3785        my $retVal = $self->Delete('Feature', "fig|$genomeID.%", testMode => $testFlag);
3786        # Perform the delete for the primary genome data.
3787        my $stats = $self->Delete('Genome', $genomeID, testMode => $testFlag);
3788        $retVal->Accumulate($stats);
3789        # Return the result.
3790        return $retVal;
3791    }
3792    
3793    =head3 Fix
3794    
3795        my %fixedHash = $sprout->Fix(%groupHash);
3796    
3797    Prepare a genome group hash (like that returned by L</GetGroups>) for processing.
3798    The groups will be combined into the appropriate super-groups.
3799    
3800    =over 4
3801    
3802    =item groupHash
3803    
3804    Hash to be fixed up.
3805    
3806    =item RETURN
3807    
3808    Returns a fixed-up version of the hash.
3809    
3810    =back
3811    
3812    =cut
3813    
3814    sub Fix {
3815        # Get the parameters.
3816        my ($self, %groupHash) = @_;
3817        # Create the result hash.
3818        my %retVal = ();
3819        # Copy over the genomes.
3820        for my $groupID (keys %groupHash) {
3821            # Get the super-group name.
3822            my $realGroupID = $self->SuperGroup($groupID);
3823            # Append this group's genomes into the result hash
3824            # using the super-group name.
3825            push @{$retVal{$realGroupID}}, @{$groupHash{$groupID}};
3826        }
3827        # Return the result hash.
3828        return %retVal;
3829    }
3830    
3831    =head3 GroupPageName
3832    
3833        my $name = $sprout->GroupPageName($group);
3834    
3835    Return the name of the page for the specified NMPDR group.
3836    
3837    =over 4
3838    
3839    =item group
3840    
3841    Name of the relevant group.
3842    
3843    =item RETURN
3844    
3845    Returns the relative page name (e.g. C<../content/campy.php>). If the group file is not in
3846    memory it will be read in.
3847    
3848    =back
3849    
3850    =cut
3851    
3852    sub GroupPageName {
3853        # Get the parameters.
3854        my ($self, $group) = @_;
3855        # Check for the group file data.
3856        my %superTable = $self->CheckGroupFile();
3857        # Compute the real group name.
3858        my $realGroup = $self->SuperGroup($group);
3859        # Get the associated page name.
3860        my $retVal = "../content/$superTable{$realGroup}->{page}";
3861        # Return the result.
3862        return $retVal;
3863    }
3864    
3865    
3866    =head3 AddProperty
3867    
3868        $sprout->AddProperty($featureID, $key, @values);
3869    
3870    Add a new attribute value (Property) to a feature.
3871    
3872    =over 4
3873    
3874    =item peg
3875    
3876    ID of the feature to which the attribute is to be added.
3877    
3878    =item key
3879    
3880    Name of the attribute (key).
3881    
3882    =item values
3883    
3884    Values of the attribute.
3885    
3886    =back
3887    
3888    =cut
3889    #: Return Type ;
3890    sub AddProperty {
3891        # Get the parameters.
3892        my ($self, $featureID, $key, @values) = @_;
3893        # Add the property using the attached attributes object.
3894        $self->{_ca}->AddAttribute($featureID, $key, @values);
3895    }
3896    
3897    =head3 CheckGroupFile
3898    
3899        my %groupData = $sprout->CheckGroupFile();
3900    
3901    Get the group file hash. The group file hash describes the relationship
3902    between a group and the super-group to which it belongs for purposes of
3903    display. The super-group name is computed from the first capitalized word
3904    in the actual group name. For each super-group, the group file contains
3905    the page name and a list of the species expected to be in the group.
3906    Each species is specified by a genus and a species name. A species name
3907    of C<0> implies an entire genus.
3908    
3909    This method returns a hash from super-group names to a hash reference. Each
3910    resulting hash reference contains the following fields.
3911    
3912    =over 4
3913    
3914    =item page
3915    
3916    The super-group's web page in the NMPDR.
3917    
3918    =item contents
3919    
3920    A list of 2-tuples, each containing a genus name followed by a species name
3921    (or 0, indicating all species). This list indicates which organisms belong
3922    in the super-group.
3923    
3924    =back
3925    
3926    =cut
3927    
3928    sub CheckGroupFile {
3929        # Get the parameters.
3930        my ($self) = @_;
3931        # Check to see if we already have this hash.
3932        if (! defined $self->{groupHash}) {
3933            # We don't, so we need to read it in.
3934            my %groupHash;
3935            # Read the group file.
3936            my @groupLines = Tracer::GetFile("$FIG_Config::sproutData/groups.tbl");
3937            # Loop through the list of sort-of groups.
3938            for my $groupLine (@groupLines) {
3939                my ($name, $page, @contents) = split /\t/, $groupLine;
3940                $groupHash{$name} = { page => $page,
3941                                      contents => [ map { [ split /\s*,\s*/, $_ ] } @contents ]
3942                                    };
3943            }
3944            # Save the hash.
3945            $self->{groupHash} = \%groupHash;
3946        }
3947        # Return the result.
3948        return %{$self->{groupHash}};
3949    }
3950    
3951    =head2 Virtual Methods
3952    
3953    =head3 CleanKeywords
3954    
3955        my $cleanedString = $sprout->CleanKeywords($searchExpression);
3956    
3957    Clean up a search expression or keyword list. This involves converting the periods
3958    in EC numbers to underscores, converting non-leading minus signs to underscores,
3959    a vertical bar or colon to an apostrophe, and forcing lower case for all alphabetic
3960    characters. In addition, any extra spaces are removed.
3961    
3962    =over 4
3963    
3964    =item searchExpression
3965    
3966    Search expression or keyword list to clean. Note that a search expression may
3967    contain boolean operators which need to be preserved. This includes leading
3968    minus signs.
3969    
3970    =item RETURN
3971    
3972    Cleaned expression or keyword list.
3973    
3974    =back
3975    
3976    =cut
3977    
3978    sub CleanKeywords {
3979        # Get the parameters.
3980        my ($self, $searchExpression) = @_;
3981        # Perform the standard cleanup.
3982        my $words = $self->ERDB::CleanKeywords($searchExpression);
3983        # Fix the periods in EC and TC numbers.
3984        $words =~ s/(\d+|\-)\.(\d+|-)\.(\d+|-)\.(\d+|-)/$1_$2_$3_$4/g;
3985        # Fix non-trailing periods.
3986        $words =~ s/\.(\w)/_$1/g;
3987        # Fix non-leading minus signs.
3988        $words =~ s/(\w)[\-]/$1_/g;
3989        # Fix the vertical bars and colons
3990        $words =~ s/(\w)[|:](\w)/$1'$2/g;
3991        # Now split up the list so that each keyword is in its own string. We keep the delimiters
3992        # because they may contain boolean expression data.
3993        my @words = split /([^A-Za-z'0-9_]+)/, $words;
3994        # We'll convert the stemmable words into stems and re-assemble the result.
3995        my $retVal = "";
3996        for my $word (@words) {
3997            my $stem = $self->Stem($word);
3998            if (defined $stem) {
3999                $retVal .= $stem;
4000            } else {
4001                $retVal .= $word;
4002            }
4003        }
4004        Trace("Cleaned keyword list for \"$searchExpression\" is \"$retVal\".") if T(3);
4005        # Return the result.
4006        return $retVal;
4007    }
4008    
4009  =head2 Internal Utility Methods  =head2 Internal Utility Methods
4010    
4011  =head3 ParseAssignment  =head3 ParseAssignment
# Line 3160  Line 4016 
4016    
4017  A functional assignment is always of the form  A functional assignment is always of the form
4018    
4019      I<XXXX>C<\nset >I<YYYY>C< function to\n>I<ZZZZZ>      set YYYY function to
4020        ZZZZ
4021    
4022    where I<YYYY> is the B<user>, and I<ZZZZ> is the actual functional role. In most cases,
4023    the user and the assigning user (from MadeAnnotation) will be the same, but that is
4024    not always the case.
4025    
4026  where I<XXXX> is the B<assigning user>, I<YYYY> is the B<user>, and I<ZZZZ> is the  In addition, the functional role may contain extra data that is stripped, such as
4027  actual functional role. In most cases, the user and the assigning user will be the  terminating spaces or a comment separated from the rest of the text by a tab.
 same, but that is not always the case.  
4028    
4029  This is a static method.  This is a static method.
4030    
4031  =over 4  =over 4
4032    
4033    =item user
4034    
4035    Name of the assigning user.
4036    
4037  =item text  =item text
4038    
4039  Text of the annotation.  Text of the annotation.
# Line 3185  Line 4049 
4049    
4050  sub _ParseAssignment {  sub _ParseAssignment {
4051      # Get the parameters.      # Get the parameters.
4052      my ($text) = @_;      my ($user, $text) = @_;
4053      # Declare the return value.      # Declare the return value.
4054      my @retVal = ();      my @retVal = ();
4055      # Check to see if this is a functional assignment.      # Check to see if this is a functional assignment.
4056      my ($type, $function) = split(/\n/, $text);      my ($type, $function) = split(/\n/, $text);
4057      if ($type =~ m/^set ([^ ]+) function to$/i) {      if ($type =~ m/^set function to$/i) {
4058          # Here it is, so we return the user name (which is in $1), the functional role text,          # Here we have an assignment without a user, so we use the incoming user ID.
4059          # and the assigning user.          @retVal = ($user, $function);
4060        } elsif ($type =~ m/^set (\S+) function to$/i) {
4061            # Here we have an assignment with a user that is passed back to the caller.
4062          @retVal = ($1, $function);          @retVal = ($1, $function);
4063      }      }
4064        # If we have an assignment, we need to clean the function text. There may be
4065        # extra junk at the end added as a note from the user.
4066        if (defined( $retVal[1] )) {
4067            $retVal[1] =~ s/(\t\S)?\s*$//;
4068        }
4069      # Return the result list.      # Return the result list.
4070      return @retVal;      return @retVal;
4071  }  }
4072    
4073    =head3 _CheckFeature
4074    
4075        my $flag = $sprout->_CheckFeature($fid);
4076    
4077    Return TRUE if the specified FID is probably an NMPDR feature ID, else FALSE.
4078    
4079    =over 4
4080    
4081    =item fid
4082    
4083    Feature ID to check.
4084    
4085    =item RETURN
4086    
4087    Returns TRUE if the FID is for one of the NMPDR genomes, else FALSE.
4088    
4089    =back
4090    
4091    =cut
4092    
4093    sub _CheckFeature {
4094        # Get the parameters.
4095        my ($self, $fid) = @_;
4096        # Insure we have a genome hash.
4097        if (! defined $self->{genomeHash}) {
4098            my %genomeHash = map { $_ => 1 } $self->GetFlat(['Genome'], "", [], 'Genome(id)');
4099            $self->{genomeHash} = \%genomeHash;
4100        }
4101        # Get the feature's genome ID.
4102        my ($genomeID) = FIGRules::ParseFeatureID($fid);
4103        # Return an indicator of whether or not the genome ID is in the hash.
4104        return ($self->{genomeHash}->{$genomeID} ? 1 : 0);
4105    }
4106    
4107  =head3 FriendlyTimestamp  =head3 FriendlyTimestamp
4108    
4109  Convert a time number to a user-friendly time stamp for display.  Convert a time number to a user-friendly time stamp for display.
# Line 3225  Line 4130 
4130      return $retVal;      return $retVal;
4131  }  }
4132    
 =head3 AddProperty  
4133    
4134  C<< my  = $sprout->AddProperty($featureID, $key, $value, $url); >>  =head3 Hint
4135    
4136  Add a new attribute value (Property) to a feature. In the SEED system, attributes can      my $htmlText = SearchHelper::Hint($wikiPage, $hintText);
 be added to almost any object. In Sprout, they can only be added to features. In  
 Sprout, attributes are implemented using I<properties>. A property represents a key/value  
 pair. If the particular key/value pair coming in is not already in the database, a new  
 B<Property> record is created to hold it.  
4137    
4138  =over 4  Return the HTML for a small question mark that displays the specified hint text when it is clicked.
4139    This HTML can be put in forms to provide a useful hinting mechanism.
 =item peg  
4140    
4141  ID of the feature to which the attribute is to be replied.  =over 4
4142    
4143  =item key  =item wikiPage
4144    
4145  Name of the attribute (key).  Name of the wiki page to be popped up when the hint mark is clicked.
4146    
4147  =item value  =item hintText
4148    
4149  Value of the attribute.  Text to display for the hint. It is raw html, but may not contain any double quotes.
4150    
4151  =item url  =item RETURN
4152    
4153  URL or text citation from which the property was obtained.  Returns the html for the hint facility. The resulting html shows a small button-like thing that
4154    uses the standard FIG popup technology.
4155    
4156  =back  =back
4157    
4158  =cut  =cut
4159  #: Return Type ;  
4160  sub AddProperty {  sub Hint {
4161      # Get the parameters.      # Get the parameters.
4162      my ($self, $featureID, $key, $value, $url) = @_;      my ($wikiPage, $hintText) = @_;
4163      # Declare the variable to hold the desired property ID.      # Escape the single quotes in the hint text.
4164      my $propID;      my $quotedText = $hintText;
4165      # Attempt to find a property record for this key/value pair.      $quotedText =~ s/'/\\'/g;
4166      my @properties = $self->GetFlat(['Property'],      # Convert the wiki page name to a URL.
4167                                     "Property(property-name) = ? AND Property(property-value) = ?",      my $wikiURL = join("", map { ucfirst $_ } split /\s+/, $wikiPage);
4168                                     [$key, $value], 'Property(id)');      $wikiURL = "$FIG_Config::cgi_url/wiki/view.cgi/FIG/$wikiURL";
4169      if (@properties) {      # Compute the mouseover script.
4170          # Here the property is already in the database. We save its ID.      my $mouseOver = "doTooltip(this, '$quotedText')";
4171          $propID = $properties[0];      # Create the html.
4172          # Here the property value does not exist. We need to generate an ID. It will be set      my $retVal = "&nbsp;<a href=\"$wikiURL\"><img src=\"$FIG_Config::cgi_url/Html/button-h.png\" class=\"helpicon\" onmouseover=\"$mouseOver\"/></a>";
4173          # to a number one greater than the maximum value in the database. This call to      # Return it.
4174          # GetAll will stop after one record.      return $retVal;
         my @maxProperty = $self->GetAll(['Property'], "ORDER BY Property(id) DESC", [], ['Property(id)'],  
                                         1);  
         $propID = $maxProperty[0]->[0] + 1;  
         # Insert the new property value.  
         $self->Insert('Property', { 'property-name' => $key, 'property-value' => $value, id => $propID });  
     }  
     # Now we connect the incoming feature to the property.  
     $self->Insert('HasProperty', { 'from-link' => $featureID, 'to-link' => $propID, evidence => $url });  
4175  }  }
4176    
   
   
4177  1;  1;

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