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revision 1.22, Fri Sep 9 21:10:46 2005 UTC revision 1.124, Wed Mar 4 00:09:43 2009 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 ERDBQuery;
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 qw(-nosticky);
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  =cut  The Sprout object is a subclass of the ERDB object and inherits all its properties and methods.
41    
42  #: Constructor SFXlate->new_sprout_only();  =cut
43    
44  =head2 Public Methods  =head2 Public Methods
45    
46  =head3 new  =head3 new
47    
48  C<< my $sprout = Sprout->new($dbName, \%options); >>      my $sprout = Sprout->new($dbName, \%options);
49    
50  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
51  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 50  Line 55 
55    
56  =item dbName  =item dbName
57    
58  Name of the database.  Name of the database. If omitted, the default Sprout database name is used.
59    
60  =item options  =item options
61    
# Line 62  Line 67 
67    
68  * B<xmlFileName> name of the XML file containing the database definition (default C<SproutDBD.xml>)  * B<xmlFileName> name of the XML file containing the database definition (default C<SproutDBD.xml>)
69    
70  * B<userData> user name and password, delimited by a slash (default C<root/>)  * B<userData> user name and password, delimited by a slash (default same as SEED)
71    
72  * B<port> connection port (default C<0>)  * B<port> connection port (default C<0>)
73    
74    * B<sock> connection socket (default same as SEED)
75    
76  * B<maxSegmentLength> maximum number of residues per feature segment, (default C<4500>)  * B<maxSegmentLength> maximum number of residues per feature segment, (default C<4500>)
77    
78  * B<maxSequenceLength> maximum number of residues per sequence, (default C<8000>)  * B<maxSequenceLength> maximum number of residues per sequence, (default C<8000>)
79    
80    * B<noDBOpen> suppresses the connection to the database if TRUE, else FALSE
81    
82    * B<host> name of the database host
83    
84  =back  =back
85    
86  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
87  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
88  F</usr/fig/SproutData>.  F</usr/fig/SproutData>.
89    
90  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' });
91    
92    In order to work properly with [[ERDBGeneratorPl]], the constructor has an alternate
93    form.
94    
95        my $sprout = Sprout->new(dbd => $filename);
96    
97    Where I<$fileName> is the name of the DBD file. This enables us to specify an alternate
98    DBD for the loader, which is important when the database format changes.
99    
100  =cut  =cut
101    
102  sub new {  sub new {
103      # Get the parameters.      # Get the parameters.
104      my ($class, $dbName, $options) = @_;      my ($class, $dbName, $options) = @_;
105        # Check for the alternate signature, and default the database name if it is missing.
106        if ($dbName eq 'dbd') {
107            $dbName = $FIG_Config::sproutDB;
108            $options = { xmlFileName => $options };
109        } elsif (! defined $dbName) {
110            $dbName = $FIG_Config::sproutDB;
111        } elsif (ref $dbName eq 'HASH') {
112            $options = $dbName;
113            $dbName = $FIG_Config::sproutDB;
114        }
115        # Compute the DBD directory.
116        my $dbd_dir = (defined($FIG_Config::dbd_dir) ? $FIG_Config::dbd_dir :
117                                                      $FIG_Config::fig );
118      # 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
119      # the incoming data.      # the incoming data.
120      my $optionTable = Tracer::GetOptions({      my $optionTable = Tracer::GetOptions({
# Line 90  Line 122 
122                                                          # database type                                                          # database type
123                         dataDir      => $FIG_Config::sproutData,                         dataDir      => $FIG_Config::sproutData,
124                                                          # data file directory                                                          # data file directory
125                         xmlFileName  => "$FIG_Config::sproutData/SproutDBD.xml",                         xmlFileName  => "$dbd_dir/SproutDBD.xml",
126                                                          # database definition file name                                                          # database definition file name
127                         userData     => "$FIG_Config::dbuser/$FIG_Config::dbpass",                         userData     => "$FIG_Config::sproutUser/$FIG_Config::sproutPass",
128                                                          # user name and password                                                          # user name and password
129                         port         => $FIG_Config::dbport,                         port         => $FIG_Config::sproutPort,
130                                                          # database connection port                                                          # database connection port
131                           sock         => $FIG_Config::sproutSock,
132                           host         => $FIG_Config::sprout_host,
133                         maxSegmentLength => 4500,        # maximum feature segment length                         maxSegmentLength => 4500,        # maximum feature segment length
134                         maxSequenceLength => 8000,       # maximum contig sequence length                         maxSequenceLength => 8000,       # maximum contig sequence length
135                           noDBOpen     => 0,               # 1 to suppress the database open
136                           demandDriven => 0,               # 1 for forward-only queries
137                        }, $options);                        }, $options);
138      # Get the data directory.      # Get the data directory.
139      my $dataDir = $optionTable->{dataDir};      my $dataDir = $optionTable->{dataDir};
# Line 105  Line 141 
141      $optionTable->{userData} =~ m!([^/]*)/(.*)$!;      $optionTable->{userData} =~ m!([^/]*)/(.*)$!;
142      my ($userName, $password) = ($1, $2);      my ($userName, $password) = ($1, $2);
143      # Connect to the database.      # Connect to the database.
144      my $dbh = DBKernel->new($optionTable->{dbType}, $dbName, $userName, $password, $optionTable->{port});      my $dbh;
145        if (! $optionTable->{noDBOpen}) {
146            Trace("Connect data: host = $optionTable->{host}, port = $optionTable->{port}.") if T(3);
147            $dbh = DBKernel->new($optionTable->{dbType}, $dbName, $userName,
148                                    $password, $optionTable->{port}, $optionTable->{host}, $optionTable->{sock});
149        }
150      # Create the ERDB object.      # Create the ERDB object.
151      my $xmlFileName = "$optionTable->{xmlFileName}";      my $xmlFileName = "$optionTable->{xmlFileName}";
152      my $erdb = ERDB->new($dbh, $xmlFileName);      my $retVal = ERDB::new($class, $dbh, $xmlFileName, %$optionTable);
153      # Create this object.      # Add the option table and XML file name.
154      my $self = { _erdb => $erdb, _options => $optionTable, _xmlName => $xmlFileName };      $retVal->{_options} = $optionTable;
155      # Bless and return it.      $retVal->{_xmlName} = $xmlFileName;
156      bless $self;      # Set up space for the group file data.
157      return $self;      $retVal->{groupHash} = undef;
158        # Set up space for the genome hash. We use this to identify NMPDR genomes
159        # and remember genome data.
160        $retVal->{genomeHash} = {};
161        $retVal->{genomeHashFilled} = 0;
162        # Remember the data directory name.
163        $retVal->{dataDir} = $dataDir;
164        # Return it.
165        return $retVal;
166  }  }
167    
168  =head3 MaxSegment  =head3 ca
169    
170  C<< my $length = $sprout->MaxSegment(); >>      my $ca = $sprout->ca():;
171    
172  This method returns the maximum permissible length of a feature segment. The length is important  Return the [[CustomAttributesPm]] object for retrieving object
173  because it enables us to make reasonable guesses at how to find features inside a particular  properties.
 contig region. For example, if the maximum length is 4000 and we're looking for a feature that  
 overlaps the region from 6000 to 7000 we know that the starting position must be between 2001  
 and 10999.  
174    
175  =cut  =cut
 #: Return Type $;  
 sub MaxSegment {  
     my ($self) = @_;  
     return $self->{_options}->{maxSegmentLength};  
 }  
   
 =head3 MaxSequence  
176    
177  C<< my $length = $sprout->MaxSequence(); >>  sub ca {
178        # Get the parameters.
 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 $;  
 sub MaxSequence {  
179      my ($self) = @_;      my ($self) = @_;
180      return $self->{_options}->{maxSequenceLength};      # Do we already have an attribute object?
181        my $retVal = $self->{_ca};
182        if (! defined $retVal) {
183            # No, create one. How we do it depends on the configuration.
184            if ($FIG_Config::attrURL) {
185                Trace("Remote attribute server $FIG_Config::attrURL chosen.") if T(3);
186                $retVal = RemoteCustomAttributes->new($FIG_Config::attrURL);
187            } elsif ($FIG_Config::attrDbName) {
188                Trace("Local attribute database $FIG_Config::attrDbName chosen.") if T(3);
189                my $user = ($FIG_Config::arch eq 'win' ? 'self' : scalar(getpwent()));
190                $retVal = CustomAttributes->new(user => $user);
191            }
192            # Save it for next time.
193            $self->{_ca} = $retVal;
194        }
195        # Return the result.
196        return $retVal;
197  }  }
198    
199  =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.  
   
 C<< $query = $sprout->Get(['Genome'], "ORDER BY Genome(genus), Genome(species)"); >>  
200    
201  Odd things may happen if one of the ORDER BY fields is in a secondary relation. So, for example, an      my @genomes = $sprout->CoreGenomes($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.  
202    
203  If multiple names are specified, then the query processor will automatically determine a  Return the IDs of NMPDR genomes in the specified scope.
 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.  
204    
205  =over 4  =over 4
206    
207  =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.  
208    
209  =item parameterList  Scope of the desired genomes. C<core> covers the original core genomes,
210    C<nmpdr> covers all genomes in NMPDR groups, and C<all> covers all
211  List of the parameters to be substituted in for the parameters marks in the filter clause.  genomes in the system.
212    
213  =item RETURN  =item RETURN
214    
215  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.
216    
217  =back  =back
218    
219  =cut  =cut
220    
221  sub Get {  sub CoreGenomes {
222      # Get the parameters.      # Get the parameters.
223      my ($self, $objectNames, $filterClause, $parameterList) = @_;      my ($self, $scope) = @_;
224      # We differ from the ERDB Get method in that the parameter list is passed in as a list reference      # Declare the return variable.
225      # rather than a list of parameters. The next step is to convert the parameters from a reference      my @retVal = ();
226      # to a real list. We can only do this if the parameters have been specified.      # If we want all genomes, then this is easy.
227      my @parameters;      if ($scope eq 'all') {
228      if ($parameterList) { @parameters = @{$parameterList}; }          @retVal = $self->Genomes();
229      return $self->{_erdb}->Get($objectNames, $filterClause, @parameters);      } else {
230            # Here we're dealing with groups. Get the hash of all the
231            # genome groups.
232            my %groups = $self->GetGroups();
233            # Loop through the groups, keeping the ones that we want.
234            for my $group (keys %groups) {
235                # Decide if we want to keep this group.
236                my $keepGroup = 0;
237                if ($scope eq 'nmpdr') {
238                    # NMPDR mode: keep all groups.
239                    $keepGroup = 1;
240                } elsif ($scope eq 'core') {
241                    # CORE mode. Only keep real core groups.
242                    if (grep { $group =~ /$_/ } @{$FIG_Config::realCoreGroups}) {
243                        $keepGroup = 1;
244                    }
245                }
246                # Add this group if we're keeping it.
247                if ($keepGroup) {
248                    push @retVal, @{$groups{$group}};
249                }
250            }
251        }
252        # Return the result.
253        return @retVal;
254  }  }
255    
256  =head3 GetEntity  =head3 SuperGroup
257    
258  C<< my $entityObject = $sprout->GetEntity($entityType, $ID); >>      my $superGroup = $sprout->SuperGroup($groupName);
259    
260  Return an object describing the entity instance with a specified ID.  Return the name of the super-group containing the specified NMPDR genome
261    group. If no appropriate super-group can be found, an error will be
262    thrown.
263    
264  =over 4  =over 4
265    
266  =item entityType  =item groupName
   
 Entity type name.  
267    
268  =item ID  Name of the group whose super-group is desired.
   
 ID of the desired entity.  
269    
270  =item RETURN  =item RETURN
271    
272  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.  
273    
274  =back  =back
275    
276  =cut  =cut
277    
278  sub GetEntity {  sub SuperGroup {
279      # Get the parameters.      # Get the parameters.
280      my ($self, $entityType, $ID) = @_;      my ($self, $groupName) = @_;
281      # Call the ERDB method.      # Declare the return variable.
282      return $self->{_erdb}->GetEntity($entityType, $ID);      my $retVal;
283        # Get the group hash.
284        my %groupHash = $self->CheckGroupFile();
285        # Find the super-group genus.
286        $groupName =~ /([A-Z]\w+)/;
287        my $nameThing = $1;
288        # See if it's directly in the group hash.
289        if (exists $groupHash{$nameThing}) {
290            # Yes, then it's our result.
291            $retVal = $nameThing;
292        } else {
293            # No, so we have to search.
294            for my $superGroup (keys %groupHash) {
295                # Get this super-group's item list.
296                my $list = $groupHash{$superGroup}->{contents};
297                # Search it.
298                if (grep { $_->[0] eq $nameThing } @{$list}) {
299                    $retVal = $superGroup;
300                }
301            }
302            # Make sure we found something.
303            if (! $retVal) {
304                Confess("No super-group found for \"$groupName\".");
305            }
306        }
307        # Return the result.
308        return $retVal;
309  }  }
310    
311  =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  
312    
313  Returns a flattened list of the values of the specified fields for the specified entity.      my $length = $sprout->MaxSegment();
314    
315  =back  This method returns the maximum permissible length of a feature segment. The length is important
316    because it enables us to make reasonable guesses at how to find features inside a particular
317    contig region. For example, if the maximum length is 4000 and we're looking for a feature that
318    overlaps the region from 6000 to 7000 we know that the starting position must be between 2001
319    and 10999.
320    
321  =cut  =cut
322  #: Return Type @;  #: Return Type $;
323  sub GetEntityValues {  sub MaxSegment {
324      # Get the parameters.      my ($self) = @_;
325      my ($self, $entityType, $ID, $fields) = @_;      return $self->{_options}->{maxSegmentLength};
     # Call the ERDB method.  
     return $self->{_erdb}->GetEntityValues($entityType, $ID, $fields);  
326  }  }
327    
328  =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  
329    
330  Fully-qualified name to give to the output file.      my $length = $sprout->MaxSequence();
331    
332  =back  This method returns the maximum permissible length of a contig sequence. A contig is broken
333    into sequences in order to save memory resources. In particular, when manipulating features,
334    we generally only need a few sequences in memory rather than the entire contig.
335    
336  =cut  =cut
337    #: Return Type $;
338  sub ShowMetaData {  sub MaxSequence {
339      # Get the parameters.      my ($self) = @_;
340      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);  
341  }  }
342    
343  =head3 Load  =head3 Load
344    
345  C<< $sprout->Load($rebuild); >>;      $sprout->Load($rebuild);;
346    
347  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.
348    
# Line 352  Line 354 
354  The files are loaded based on the presumption that each line of the file is a record in the  The files are loaded based on the presumption that each line of the file is a record in the
355  relation, and the individual fields are delimited by tabs. Tab and new-line characters inside  relation, and the individual fields are delimited by tabs. Tab and new-line characters inside
356  fields must be represented by the escape sequences C<\t> and C<\n>, respectively. The fields must  fields must be represented by the escape sequences C<\t> and C<\n>, respectively. The fields must
357  be presented in the order given in the relation tables produced by the L</ShowMetaData> method.  be presented in the order given in the relation tables produced by the database documentation.
358    
359  =over 4  =over 4
360    
# Line 372  Line 374 
374  sub Load {  sub Load {
375      # Get the parameters.      # Get the parameters.
376      my ($self, $rebuild) = @_;      my ($self, $rebuild) = @_;
     # Get the database object.  
     my $erdb = $self->{_erdb};  
377      # Load the tables from the data directory.      # Load the tables from the data directory.
378      my $retVal = $erdb->LoadTables($self->{_options}->{dataDir}, $rebuild);      my $retVal = $self->LoadTables($self->{_options}->{dataDir}, $rebuild);
379      # Return the statistics.      # Return the statistics.
380      return $retVal;      return $retVal;
381  }  }
382    
383  =head3 LoadUpdate  =head3 LoadUpdate
384    
385  C<< my %stats = $sprout->LoadUpdate($truncateFlag, \@tableList); >>      my $stats = $sprout->LoadUpdate($truncateFlag, \@tableList);
386    
387  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
388  or two tables without reloading the whole database. For each table, there must be a corresponding  or two tables without reloading the whole database. For each table, there must be a corresponding
# Line 415  Line 415 
415  sub LoadUpdate {  sub LoadUpdate {
416      # Get the parameters.      # Get the parameters.
417      my ($self, $truncateFlag, $tableList) = @_;      my ($self, $truncateFlag, $tableList) = @_;
     # Get the database object.  
     my $erdb = $self->{_erdb};  
418      # Declare the return value.      # Declare the return value.
419      my $retVal = Stats->new();      my $retVal = Stats->new();
420      # Get the data directory.      # Get the data directory.
# Line 430  Line 428 
428              Trace("No load file found for $tableName in $dataDir.") if T(0);              Trace("No load file found for $tableName in $dataDir.") if T(0);
429          } else {          } else {
430              # Attempt to load this table.              # Attempt to load this table.
431              my $result = $erdb->LoadTable($fileName, $tableName, $truncateFlag);              my $result = $self->LoadTable($fileName, $tableName, truncate => $truncateFlag);
432              # Accumulate the resulting statistics.              # Accumulate the resulting statistics.
433              $retVal->Accumulate($result);              $retVal->Accumulate($result);
434          }          }
# Line 439  Line 437 
437      return $retVal;      return $retVal;
438  }  }
439    
440    =head3 GenomeCounts
441    
442        my ($arch, $bact, $euk, $vir, $env, $unk) = $sprout->GenomeCounts($complete);
443    
444    Count the number of genomes in each domain. If I<$complete> is TRUE, only complete
445    genomes will be included in the counts.
446    
447    =over 4
448    
449    =item complete
450    
451    TRUE if only complete genomes are to be counted, FALSE if all genomes are to be
452    counted
453    
454    =item RETURN
455    
456    A six-element list containing the number of genomes in each of six categories--
457    Archaea, Bacteria, Eukaryota, Viral, Environmental, and Unknown, respectively.
458    
459    =back
460    
461    =cut
462    
463    sub GenomeCounts {
464        # Get the parameters.
465        my ($self, $complete) = @_;
466        # Set the filter based on the completeness flag.
467        my $filter = ($complete ? "Genome(complete) = 1" : "");
468        # Get all the genomes and the related taxonomy information.
469        my @genomes = $self->GetAll(['Genome'], $filter, [], ['Genome(id)', 'Genome(taxonomy)']);
470        # Clear the counters.
471        my ($arch, $bact, $euk, $vir, $env, $unk) = (0, 0, 0, 0, 0, 0);
472        # Loop through, counting the domains.
473        for my $genome (@genomes) {
474            if    ($genome->[1] =~ /^archaea/i)  { ++$arch }
475            elsif ($genome->[1] =~ /^bacter/i)   { ++$bact }
476            elsif ($genome->[1] =~ /^eukar/i)    { ++$euk }
477            elsif ($genome->[1] =~ /^vir/i)      { ++$vir }
478            elsif ($genome->[1] =~ /^env/i)      { ++$env }
479            else  { ++$unk }
480        }
481        # Return the counts.
482        return ($arch, $bact, $euk, $vir, $env, $unk);
483    }
484    
485    =head3 ContigCount
486    
487        my $count = $sprout->ContigCount($genomeID);
488    
489    Return the number of contigs for the specified genome ID.
490    
491    =over 4
492    
493    =item genomeID
494    
495    ID of the genome whose contig count is desired.
496    
497    =item RETURN
498    
499    Returns the number of contigs for the specified genome.
500    
501    =back
502    
503    =cut
504    
505    sub ContigCount {
506        # Get the parameters.
507        my ($self, $genomeID) = @_;
508        # Get the contig count.
509        my $retVal = $self->GetCount(['Contig', 'HasContig'], "HasContig(from-link) = ?", [$genomeID]);
510        # Return the result.
511        return $retVal;
512    }
513    
514    =head3 GenomeMenu
515    
516        my $html = $sprout->GenomeMenu(%options);
517    
518    Generate a genome selection control with the specified name and options.
519    This control is almost but not quite the same as the genome control in the
520    B<SearchHelper> class. Eventually, the two will be combined.
521    
522    =over 4
523    
524    =item options
525    
526    Optional parameters for the control (see below).
527    
528    =item RETURN
529    
530    Returns the HTML for a genome selection control on a form (sometimes called a popup menu).
531    
532    =back
533    
534    The valid options are as follows.
535    
536    =over 4
537    
538    =item name
539    
540    Name to give this control for use in passing it to the form. The default is C<myGenomeControl>.
541    Terrible things will happen if you have two controls with the same name on the same page.
542    
543    =item filter
544    
545    If specified, a filter for the list of genomes to display. The filter should be in the form of a
546    list reference, a string, or a hash reference. If it is a list reference, the first element
547    of the list should be the filter string, and the remaining elements the filter parameters. If it is a
548    string, it will be split into a list at each included tab. If it is a hash reference, it should be
549    a hash that maps genomes which should be included to a TRUE value.
550    
551    =item multiSelect
552    
553    If TRUE, then the user can select multiple genomes. If FALSE, the user can only select one genome.
554    
555    =item size
556    
557    Number of rows to display in the control. The default is C<10>
558    
559    =item id
560    
561    ID to give this control. The default is the value of the C<name> option. Nothing will work correctly
562    unless this ID is unique.
563    
564    =item selected
565    
566    A comma-delimited list of selected genomes, or a reference to a list of selected genomes. The
567    default is none.
568    
569    =item class
570    
571    If specified, a style class to assign to the genome control.
572    
573    =back
574    
575    =cut
576    
577    sub GenomeMenu {
578        # Get the parameters.
579        my ($self, %options) = @_;
580        # Get the control's name and ID.
581        my $menuName = $options{name} || $options{id} || 'myGenomeControl';
582        my $menuID = $options{id} || $menuName;
583        Trace("Genome menu name = $menuName with ID $menuID.") if T(3);
584        # Compute the IDs for the status display.
585        my $divID = "${menuID}_status";
586        my $urlID = "${menuID}_url";
587        # Compute the code to show selected genomes in the status area.
588        my $showSelect = "showSelected('$menuID', '$divID', '$urlID', $FIG_Config::genome_control_cap)";
589        # Check for single-select or multi-select.
590        my $multiSelect = $options{multiSelect} || 0;
591        # Get the style data.
592        my $class = $options{class} || '';
593        # Get the list of pre-selected items.
594        my $selections = $options{selected} || [];
595        if (ref $selections ne 'ARRAY') {
596            $selections = [ split /\s*,\s*/, $selections ];
597        }
598        my %selected = map { $_ => 1 } @{$selections};
599        # Extract the filter information. The default is no filtering. It can be passed as a tab-delimited
600        # string, a hash reference, or a list reference.
601        my ($filterHash, $filterString);
602        my $filterParms = $options{filter} || "";
603        if (ref $filterParms eq 'HASH') {
604            $filterHash = $filterParms;
605            $filterParms = [];
606            $filterString = "";
607        } else {
608            if (! ref $filterParms) {
609                $filterParms = [split /\t|\\t/, $filterParms];
610            }
611            $filterString = shift @{$filterParms};
612        }
613        # Check for possible subsystem filtering. If there is one, we will tack the
614        # relationship onto the object name list.
615        my @objectNames = qw(Genome);
616        if ($filterString =~ /ParticipatesIn\(/) {
617            push @objectNames, 'ParticipatesIn';
618        }
619        # Get a list of all the genomes in group order. In fact, we only need them ordered
620        # by name (genus,species,strain), but putting primary-group in front enables us to
621        # take advantage of an existing index.
622        my @genomeList = $self->GetAll(\@objectNames, "$filterString ORDER BY Genome(primary-group), Genome(genus), Genome(species), Genome(unique-characterization)",
623                                       $filterParms,
624                                       [qw(Genome(primary-group) Genome(id) Genome(genus) Genome(species) Genome(unique-characterization) Genome(taxonomy) Genome(contigs))]);
625        # Apply the hash filter (if any).
626        if (defined $filterHash) {
627            @genomeList = grep { $filterHash->{$_->[1]} } @genomeList;
628        }
629        # Create a hash to organize the genomes by group. Each group will contain a list of
630        # 2-tuples, the first element being the genome ID and the second being the genome
631        # name.
632        my %gHash = ();
633        for my $genome (@genomeList) {
634            # Get the genome data.
635            my ($group, $genomeID, $genus, $species, $strain, $taxonomy, $contigs) = @{$genome};
636            # Compute its name. This is the genus, species, strain (if any), and the contig count.
637            my $name = "$genus $species ";
638            $name .= "$strain " if $strain;
639            my $contigCount = ($contigs == 1 ? "" : ", $contigs contigs");
640            # Now we get the domain. The domain tells us the display style of the organism.
641            my ($domain) = split /\s*;\s*/, $taxonomy, 2;
642            # Now compute the display group. This is normally the primary group, but if the
643            # organism is supporting, we blank it out.
644            my $displayGroup = ($group eq $FIG_Config::otherGroup ? "" : $group);
645            # Push the genome into the group's list. Note that we use the real group
646            # name for the hash key here, not the display group name.
647            push @{$gHash{$group}}, [$genomeID, $name, $contigCount, $domain];
648        }
649        # We are almost ready to unroll the menu out of the group hash. The final step is to separate
650        # the supporting genomes by domain. First, we extract the NMPDR groups and sort them. They
651        # are sorted by the first capitalized word. Groups with "other" are sorted after groups
652        # that aren't "other". At some point, we will want to make this less complicated.
653        my %sortGroups = map { $_ =~ /(other)?(.*)([A-Z].+)/; "$3$1$2" => $_ }
654                             grep { $_ ne $FIG_Config::otherGroup } keys %gHash;
655        my @groups = map { $sortGroups{$_} } sort keys %sortGroups;
656        # Remember the number of NMPDR groups.
657        my $nmpdrGroupCount = scalar @groups;
658        # Are there any supporting genomes?
659        if (exists $gHash{$FIG_Config::otherGroup}) {
660            # Loop through the supporting genomes, classifying them by domain. We'll also keep a list
661            # of the domains found.
662            my @otherGenomes = @{$gHash{$FIG_Config::otherGroup}};
663            my @domains = ();
664            for my $genomeData (@otherGenomes) {
665                my ($genomeID, $name, $contigCount, $domain) = @{$genomeData};
666                if (exists $gHash{$domain}) {
667                    push @{$gHash{$domain}}, $genomeData;
668                } else {
669                    $gHash{$domain} = [$genomeData];
670                    push @domains, $domain;
671                }
672            }
673            # Add the domain groups at the end of the main group list. The main group list will now
674            # contain all the categories we need to display the genomes.
675            push @groups, sort @domains;
676            # Delete the supporting group.
677            delete $gHash{$FIG_Config::otherGroup};
678        }
679        # Now it gets complicated. We need a way to mark all the NMPDR genomes. We take advantage
680        # of the fact they come first in the list. We'll accumulate a count of the NMPDR genomes
681        # and use that to make the selections.
682        my $nmpdrCount = 0;
683        # Create the type counters.
684        my $groupCount = 1;
685        # Get the number of rows to display.
686        my $rows = $options{size} || 10;
687        # If we're multi-row, create an onChange event.
688        my $onChangeTag = ( $rows > 1 ? " onChange=\"$showSelect;\" onFocus=\"$showSelect;\"" : "" );
689        # Set up the multiple-select flag.
690        my $multipleTag = ($multiSelect ? " multiple" : "" );
691        # Set up the style class.
692        my $classTag = ($class ? " $class" : "" );
693        # Create the SELECT tag and stuff it into the output array.
694        my @lines = qq(<SELECT name="$menuName" id="$menuID" class="genomeSelect $class" $onChangeTag$multipleTag$classTag size="$rows">);
695        # Loop through the groups.
696        for my $group (@groups) {
697            # Get the genomes in the group.
698            for my $genome (@{$gHash{$group}}) {
699                # If this is an NMPDR organism, we add an extra style and count it.
700                my $nmpdrStyle = "";
701                if ($nmpdrGroupCount > 0) {
702                    $nmpdrCount++;
703                    $nmpdrStyle = " Core";
704                }
705                # Get the organism ID, name, contig count, and domain.
706                my ($genomeID, $name, $contigCount, $domain) = @{$genome};
707                # See if we're pre-selected.
708                my $selectTag = ($selected{$genomeID} ? " SELECTED" : "");
709                # Compute the display name.
710                my $nameString = "$name ($genomeID$contigCount)";
711                # Generate the option tag.
712                my $optionTag = "<OPTION class=\"$domain$nmpdrStyle\" title=\"$group\" value=\"$genomeID\"$selectTag>$nameString</OPTION>";
713                push @lines, "    $optionTag";
714            }
715            # Record this group in the nmpdrGroup count. When that gets to 0, we've finished the NMPDR
716            # groups.
717            $nmpdrGroupCount--;
718        }
719        # Close the SELECT tag.
720        push @lines, "</SELECT>";
721        if ($rows > 1) {
722            # We're in a non-compact mode, so we need to add some selection helpers. First is
723            # the search box. This allows the user to type text and change which genomes are
724            # displayed. For multiple-select mode, we include a button that selects the displayed
725            # genes. For single-select mode, we use a plain label instead.
726            my $searchThingName = "${menuID}_SearchThing";
727            my $searchThingLabel = "Type to narrow selection";
728            my $searchThingButton = "";
729            my $goHint = "";
730            if ($multiSelect) {
731                $searchThingButton = qq(<INPUT type="button" name="MacroSearch" class="button" value="Go" onClick="selectShowing('$menuID', '$searchThingName'); $showSelect;" />);
732                $goHint = " Click <strong>Go</strong> to select them.";
733            }
734            push @lines, "<br />$searchThingLabel&nbsp;" .
735                         qq(<INPUT type="text" id="$searchThingName" name="$searchThingName" class="genomeSearchThing" onKeyup="showTyped('$menuID', '$searchThingName');" />) .
736                         $searchThingButton .
737                         Hint("GenomeControl", "Type a genome ID or part of an organism name to filter the genomes displayed.$goHint") . "<br />";
738            # For multi-select mode, we also have buttons to set and clear selections.
739            if ($multiSelect) {
740                push @lines, qq(<INPUT type="button" name="ClearAll" class="bigButton genomeButton" value="Clear All" onClick="clearAll(getElementById('$menuID')); $showSelect" />);
741                push @lines, qq(<INPUT type="button" name="SelectAll" class="bigButton genomeButton" value="Select All" onClick="selectAll(getElementById('$menuID')); $showSelect" />);
742                push @lines, qq(<INPUT type="button" name="NMPDROnly" class="bigButton genomeButton" value="Select NMPDR" onClick="selectSome(getElementById('$menuID'), $nmpdrCount, true); $showSelect;" />);
743            }
744            # Add a hidden field we can use to generate organism page hyperlinks.
745            push @lines, qq(<INPUT type="hidden" id="$urlID" value="$FIG_Config::cgi_url/wiki/rest.cgi/NmpdrPlugin/SeedViewer?page=Organism;organism=" />);
746            # Add the status display. This tells the user what's selected no matter where the list is scrolled.
747            push @lines, qq(<DIV id="$divID" class="Panel"></DIV>);
748        }
749        # Assemble all the lines into a string.
750        my $retVal = join("\n", @lines, "");
751        # Return the result.
752        return $retVal;
753    }
754    
755    
756    =head3 Stem
757    
758        my $stem = $sprout->Stem($word);
759    
760    Return the stem of the specified word, or C<undef> if the word is not
761    stemmable. Note that even if the word is stemmable, the stem may be
762    the same as the original word.
763    
764    =over 4
765    
766    =item word
767    
768    Word to convert into a stem.
769    
770    =item RETURN
771    
772    Returns a stem of the word (which may be the word itself), or C<undef> if
773    the word is not stemmable.
774    
775    =back
776    
777    =cut
778    
779    sub Stem {
780        # Get the parameters.
781        my ($self, $word) = @_;
782        # Get the stemmer object.
783        my $stemmer = $self->{stemmer};
784        if (! defined $stemmer) {
785            # We don't have one pre-built, so we build and save it now.
786            $stemmer = BioWords->new(exceptions => "$FIG_Config::sproutData/Exceptions.txt",
787                                     stops => "$FIG_Config::sproutData/StopWords.txt",
788                                     cache => 0);
789            $self->{stemmer} = $stemmer;
790        }
791        # Try to stem the word.
792        my $retVal = $stemmer->Process($word);
793        # Return the result.
794        return $retVal;
795    }
796    
797    
798  =head3 Build  =head3 Build
799    
800  C<< $sprout->Build(); >>      $sprout->Build();
801    
802  Build the database. The database will be cleared and the tables re-created from the metadata.  Build the database. The database will be cleared and the tables re-created from the metadata.
803  This method is useful when a database is brand new or when the database definition has  This method is useful when a database is brand new or when the database definition has
# Line 453  Line 809 
809      # Get the parameters.      # Get the parameters.
810      my ($self) = @_;      my ($self) = @_;
811      # Create the tables.      # Create the tables.
812      $self->{_erdb}->CreateTables;      $self->CreateTables();
813  }  }
814    
815  =head3 Genomes  =head3 Genomes
816    
817  C<< my @genomes = $sprout->Genomes(); >>      my @genomes = $sprout->Genomes();
818    
819  Return a list of all the genome IDs.  Return a list of all the genome IDs.
820    
# Line 475  Line 831 
831    
832  =head3 GenusSpecies  =head3 GenusSpecies
833    
834  C<< my $infoString = $sprout->GenusSpecies($genomeID); >>      my $infoString = $sprout->GenusSpecies($genomeID);
835    
836  Return the genus, species, and unique characterization for a genome.  Return the genus, species, and unique characterization for a genome.
837    
# Line 497  Line 853 
853  sub GenusSpecies {  sub GenusSpecies {
854      # Get the parameters.      # Get the parameters.
855      my ($self, $genomeID) = @_;      my ($self, $genomeID) = @_;
856      # Get the data for the specified genome.      # Declare the return value.
857      my @values = $self->GetEntityValues('Genome', $genomeID, ['Genome(genus)', 'Genome(species)',      my $retVal;
858                                                                'Genome(unique-characterization)']);      # Get the genome data.
859      # Format the result and return it.      my $genomeData = $self->_GenomeData($genomeID);
860      my $retVal = join(' ', @values);      # Only proceed if we found the genome.
861        if (defined $genomeData) {
862            $retVal = $genomeData->PrimaryValue('Genome(scientific-name)');
863        }
864        # Return it.
865      return $retVal;      return $retVal;
866  }  }
867    
868  =head3 FeaturesOf  =head3 FeaturesOf
869    
870  C<< my @features = $sprout->FeaturesOf($genomeID, $ftype); >>      my @features = $sprout->FeaturesOf($genomeID, $ftype);
871    
872  Return a list of the features relevant to a specified genome.  Return a list of the features relevant to a specified genome.
873    
# Line 552  Line 912 
912    
913  =head3 FeatureLocation  =head3 FeatureLocation
914    
915  C<< my @locations = $sprout->FeatureLocation($featureID); >>      my @locations = $sprout->FeatureLocation($featureID);
916    
917  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
918  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 576  Line 936 
936  =item RETURN  =item RETURN
937    
938  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
939  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
940    wasn't found.
941    
942  =back  =back
943    
944  =cut  =cut
945  #: Return Type @;  
 #: Return Type $;  
946  sub FeatureLocation {  sub FeatureLocation {
947      # Get the parameters.      # Get the parameters.
948      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
949      # 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.  
950      my @retVal = ();      my @retVal = ();
951      # Set up the variables used to determine if we have adjacent segments. This initial setup will      # Get the feature record.
952      # not match anything.      my $object = $self->GetEntity('Feature', $featureID);
953      my ($prevContig, $prevBeg, $prevDir, $prevLen) = ("", 0, "0", 0);      # Only proceed if we found it.
954      # Loop through the query results, creating location specifiers.      if (defined $object) {
955      while (my $location = $query->Fetch()) {          # Get the location string.
956          # Get the location parameters.          my $locString = $object->PrimaryValue('Feature(location-string)');
957          my ($contigID, $beg, $dir, $len) = $location->Values(['IsLocatedIn(to-link)',          # Create the return list.
958              '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 == $prevBeg - $prevLen) ||  
                 ($dir eq "+" && $beg == $prevBeg + $prevLen)) {  
                 # Here we need to merge two segments. 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, $len);  
         # Add the specifier to the list.  
         push @retVal, "${contigID}_$beg$dir$len";  
959      }      }
960      # Return the list in the format indicated by the context.      # Return the list in the format indicated by the context.
961      return (wantarray ? @retVal : join(',', @retVal));      return (wantarray ? @retVal : join(',', @retVal));
# Line 624  Line 963 
963    
964  =head3 ParseLocation  =head3 ParseLocation
965    
966  C<< my ($contigID, $start, $dir, $len) = Sprout::ParseLocation($location); >>      my ($contigID, $start, $dir, $len) = Sprout::ParseLocation($location);
967    
968  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
969  length.  length.
# Line 643  Line 982 
982  =back  =back
983    
984  =cut  =cut
985  #: Return Type @;  
986  sub ParseLocation {  sub ParseLocation {
987      # 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
988      # the first parameter.      # the first parameter.
989      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
990      my ($location) = @_;      my ($location) = @_;
991      # Parse it into segments.      # Parse it into segments.
992      $location =~ /^(.*)_(\d*)([+-_])(\d*)$/;      $location =~ /^(.+)_(\d+)([+\-_])(\d+)$/;
993      my ($contigID, $start, $dir, $len) = ($1, $2, $3, $4);      my ($contigID, $start, $dir, $len) = ($1, $2, $3, $4);
994      # If the direction is an underscore, convert it to a + or -.      # If the direction is an underscore, convert it to a + or -.
995      if ($dir eq "_") {      if ($dir eq "_") {
# Line 666  Line 1005 
1005      return ($contigID, $start, $dir, $len);      return ($contigID, $start, $dir, $len);
1006  }  }
1007    
1008    
1009    
1010  =head3 PointLocation  =head3 PointLocation
1011    
1012  C<< my $found = Sprout::PointLocation($location, $point); >>      my $found = Sprout::PointLocation($location, $point);
1013    
1014  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
1015  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 697  Line 1038 
1038  =back  =back
1039    
1040  =cut  =cut
1041  #: Return Type $;  
1042  sub PointLocation {  sub PointLocation {
1043      # 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
1044      # the first parameter.      # the first parameter.
# Line 720  Line 1061 
1061    
1062  =head3 DNASeq  =head3 DNASeq
1063    
1064  C<< my $sequence = $sprout->DNASeq(\@locationList); >>      my $sequence = $sprout->DNASeq(\@locationList);
1065    
1066  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
1067  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,
1068  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>.
1069    
1070    For example, the following would return the DNA sequence for contig C<83333.1:NC_000913>
1071    between positions 1401 and 1532, inclusive.
1072    
1073        my $sequence = $sprout->DNASeq('83333.1:NC_000913_1401_1532');
1074    
1075  =over 4  =over 4
1076    
1077  =item locationList  =item locationList
1078    
1079  List of location specifiers, each in the form I<contigID>C<_>I<begin>I<dir>I<end> (see  List of location specifiers, each in the form I<contigID>C<_>I<begin>I<dir>I<len> or
1080  L</FeatureLocation> for more about this format).  I<contigID>C<_>I<begin>C<_>I<end> (see L</FeatureLocation> for more about this format).
1081    
1082  =item RETURN  =item RETURN
1083    
# Line 758  Line 1104 
1104          # the start point is the ending. Note that in the latter case we must reverse the DNA string          # the start point is the ending. Note that in the latter case we must reverse the DNA string
1105          # before putting it in the return value.          # before putting it in the return value.
1106          my ($start, $stop);          my ($start, $stop);
1107            Trace("Parse of \"$location\" is $beg$dir$len.") if T(SDNA => 4);
1108          if ($dir eq "+") {          if ($dir eq "+") {
1109              $start = $beg;              $start = $beg;
1110              $stop = $beg + $len - 1;              $stop = $beg + $len - 1;
1111          } else {          } else {
1112              $start = $beg + $len + 1;              $start = $beg - $len + 1;
1113              $stop = $beg;              $stop = $beg;
1114          }          }
1115            Trace("Looking for sequences containing $start through $stop.") if T(SDNA => 4);
1116          my $query = $self->Get(['IsMadeUpOf','Sequence'],          my $query = $self->Get(['IsMadeUpOf','Sequence'],
1117              "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .              "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .
1118              " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",              " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",
# Line 776  Line 1124 
1124                  $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)',                  $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)',
1125                                     'IsMadeUpOf(len)']);                                     'IsMadeUpOf(len)']);
1126              my $stopPosition = $startPosition + $sequenceLength;              my $stopPosition = $startPosition + $sequenceLength;
1127                Trace("Sequence is from $startPosition to $stopPosition.") if T(SDNA => 4);
1128              # Figure out the start point and length of the relevant section.              # Figure out the start point and length of the relevant section.
1129              my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);              my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);
1130              my $len = ($stopPosition <= $stop ? $stopPosition : $stop) - $startPosition - $pos1;              my $len1 = ($stopPosition < $stop ? $stopPosition : $stop) + 1 - $startPosition - $pos1;
1131                Trace("Position is $pos1 for length $len1.") if T(SDNA => 4);
1132              # Add the relevant data to the location data.              # Add the relevant data to the location data.
1133              $locationDNA .= substr($sequenceData, $pos1, $len);              $locationDNA .= substr($sequenceData, $pos1, $len1);
1134          }          }
1135          # Add this location's data to the return string. Note that we may need to reverse it.          # Add this location's data to the return string. Note that we may need to reverse it.
1136          if ($dir eq '+') {          if ($dir eq '+') {
1137              $retVal .= $locationDNA;              $retVal .= $locationDNA;
1138          } else {          } else {
1139              $locationDNA = join('', reverse split //, $locationDNA);              $retVal .= FIG::reverse_comp($locationDNA);
             $retVal .= $locationDNA;  
1140          }          }
1141      }      }
1142      # Return the result.      # Return the result.
# Line 796  Line 1145 
1145    
1146  =head3 AllContigs  =head3 AllContigs
1147    
1148  C<< my @idList = $sprout->AllContigs($genomeID); >>      my @idList = $sprout->AllContigs($genomeID);
1149    
1150  Return a list of all the contigs for a genome.  Return a list of all the contigs for a genome.
1151    
# Line 824  Line 1173 
1173      return @retVal;      return @retVal;
1174  }  }
1175    
1176  =head3 ContigLength  =head3 GenomeLength
1177    
1178  C<< my $length = $sprout->ContigLength($contigID); >>      my $length = $sprout->GenomeLength($genomeID);
1179    
1180  Compute the length of a contig.  Return the length of the specified genome in base pairs.
1181    
1182  =over 4  =over 4
1183    
1184  =item contigID  =item genomeID
1185    
1186  ID of the contig whose length is desired.  ID of the genome whose base pair count is desired.
1187    
1188  =item RETURN  =item RETURN
1189    
1190  Returns the number of positions in the contig.  Returns the number of base pairs in all the contigs of the specified
1191    genome.
1192    
1193  =back  =back
1194    
1195  =cut  =cut
1196  #: Return Type $;  
1197  sub ContigLength {  sub GenomeLength {
1198        # Get the parameters.
1199        my ($self, $genomeID) = @_;
1200        # Declare the return variable.
1201        my $retVal = 0;
1202        # Get the genome data.
1203        my $genomeData = $self->_GenomeData($genomeID);
1204        # Only proceed if it exists.
1205        if (defined $genomeData) {
1206            $retVal = $genomeData->PrimaryValue('Genome(dna-size)');
1207        }
1208        # Return the result.
1209        return $retVal;
1210    }
1211    
1212    =head3 FeatureCount
1213    
1214        my $count = $sprout->FeatureCount($genomeID, $type);
1215    
1216    Return the number of features of the specified type in the specified genome.
1217    
1218    =over 4
1219    
1220    =item genomeID
1221    
1222    ID of the genome whose feature count is desired.
1223    
1224    =item type
1225    
1226    Type of feature to count (eg. C<peg>, C<rna>, etc.).
1227    
1228    =item RETURN
1229    
1230    Returns the number of features of the specified type for the specified genome.
1231    
1232    =back
1233    
1234    =cut
1235    
1236    sub FeatureCount {
1237        # Get the parameters.
1238        my ($self, $genomeID, $type) = @_;
1239        # Compute the count.
1240        my $retVal = $self->GetCount(['HasFeature', 'Feature'],
1241                                    "HasFeature(from-link) = ? AND Feature(feature-type) = ?",
1242                                    [$genomeID, $type]);
1243        # Return the result.
1244        return $retVal;
1245    }
1246    
1247    =head3 GenomeAssignments
1248    
1249        my $fidHash = $sprout->GenomeAssignments($genomeID);
1250    
1251    Return a list of a genome's assigned features. The return hash will contain each
1252    assigned feature of the genome mapped to the text of its most recent functional
1253    assignment.
1254    
1255    =over 4
1256    
1257    =item genomeID
1258    
1259    ID of the genome whose functional assignments are desired.
1260    
1261    =item RETURN
1262    
1263    Returns a reference to a hash which maps each feature to its most recent
1264    functional assignment.
1265    
1266    =back
1267    
1268    =cut
1269    
1270    sub GenomeAssignments {
1271        # Get the parameters.
1272        my ($self, $genomeID) = @_;
1273        # Declare the return variable.
1274        my $retVal = {};
1275        # Query the genome's features.
1276        my $query = $self->Get(['HasFeature', 'Feature'], "HasFeature(from-link) = ?",
1277                               [$genomeID]);
1278        # Loop through the features.
1279        while (my $data = $query->Fetch) {
1280            # Get the feature ID and assignment.
1281            my ($fid, $assignment) = $data->Values(['Feature(id)', 'Feature(assignment)']);
1282            if ($assignment) {
1283                $retVal->{$fid} = $assignment;
1284            }
1285        }
1286        # Return the result.
1287        return $retVal;
1288    }
1289    
1290    =head3 ContigLength
1291    
1292        my $length = $sprout->ContigLength($contigID);
1293    
1294    Compute the length of a contig.
1295    
1296    =over 4
1297    
1298    =item contigID
1299    
1300    ID of the contig whose length is desired.
1301    
1302    =item RETURN
1303    
1304    Returns the number of positions in the contig.
1305    
1306    =back
1307    
1308    =cut
1309    #: Return Type $;
1310    sub ContigLength {
1311      # Get the parameters.      # Get the parameters.
1312      my ($self, $contigID) = @_;      my ($self, $contigID) = @_;
1313      # Get the contig's last sequence.      # Get the contig's last sequence.
# Line 857  Line 1320 
1320      # Set it from the sequence data, if any.      # Set it from the sequence data, if any.
1321      if ($sequence) {      if ($sequence) {
1322          my ($start, $len) = $sequence->Values(['IsMadeUpOf(start-position)', 'IsMadeUpOf(len)']);          my ($start, $len) = $sequence->Values(['IsMadeUpOf(start-position)', 'IsMadeUpOf(len)']);
1323          $retVal = $start + $len;          $retVal = $start + $len - 1;
1324        }
1325        # Return the result.
1326        return $retVal;
1327    }
1328    
1329    =head3 ClusterPEGs
1330    
1331        my $clusteredList = $sprout->ClusterPEGs($sub, \@pegs);
1332    
1333    Cluster the PEGs in a list according to the cluster coding scheme of the specified
1334    subsystem. In order for this to work properly, the subsystem object must have
1335    been used recently to retrieve the PEGs using the B<get_pegs_from_cell> or
1336    B<get_row> methods. This causes the cluster numbers to be pulled into the
1337    subsystem's color hash. If a PEG is not found in the color hash, it will not
1338    appear in the output sequence.
1339    
1340    =over 4
1341    
1342    =item sub
1343    
1344    Sprout subsystem object for the relevant subsystem, from the L</get_subsystem>
1345    method.
1346    
1347    =item pegs
1348    
1349    Reference to the list of PEGs to be clustered.
1350    
1351    =item RETURN
1352    
1353    Returns a list of the PEGs, grouped into smaller lists by cluster number.
1354    
1355    =back
1356    
1357    =cut
1358    #: Return Type $@@;
1359    sub ClusterPEGs {
1360        # Get the parameters.
1361        my ($self, $sub, $pegs) = @_;
1362        # Declare the return variable.
1363        my $retVal = [];
1364        # Loop through the PEGs, creating arrays for each cluster.
1365        for my $pegID (@{$pegs}) {
1366            my $clusterNumber = $sub->get_cluster_number($pegID);
1367            # Only proceed if the PEG is in a cluster.
1368            if ($clusterNumber >= 0) {
1369                # Push this PEG onto the sub-list for the specified cluster number.
1370                push @{$retVal->[$clusterNumber]}, $pegID;
1371            }
1372      }      }
1373      # Return the result.      # Return the result.
1374      return $retVal;      return $retVal;
# Line 865  Line 1376 
1376    
1377  =head3 GenesInRegion  =head3 GenesInRegion
1378    
1379  C<< my (\@featureIDList, $beg, $end) = $sprout->GenesInRegion($contigID, $start, $stop); >>      my (\@featureIDList, $beg, $end) = $sprout->GenesInRegion($contigID, $start, $stop);
1380    
1381  List the features which overlap a specified region in a contig.  List the features which overlap a specified region in a contig.
1382    
# Line 894  Line 1405 
1405  =back  =back
1406    
1407  =cut  =cut
1408  #: Return Type @@;  
1409  sub GenesInRegion {  sub GenesInRegion {
1410      # Get the parameters.      # Get the parameters.
1411      my ($self, $contigID, $start, $stop) = @_;      my ($self, $contigID, $start, $stop) = @_;
1412      # Get the maximum segment length.      # Get the maximum segment length.
1413      my $maximumSegmentLength = $self->MaxSegment;      my $maximumSegmentLength = $self->MaxSegment;
     # Create a hash to receive the feature list. We use a hash so that we can eliminate  
     # duplicates easily. The hash key will be the feature ID. The value will be a two-element  
     # containing the minimum and maximum offsets. We will use the offsets to sort the results  
     # when we're building the result set.  
     my %featuresFound = ();  
1414      # Prime the values we'll use for the returned beginning and end.      # Prime the values we'll use for the returned beginning and end.
1415      my @initialMinMax = ($self->ContigLength($contigID), 0);      my @initialMinMax = ($self->ContigLength($contigID), 0);
1416      my ($min, $max) = @initialMinMax;      my ($min, $max) = @initialMinMax;
1417      # Create a table of parameters for each query. Each query looks for features travelling in      # Get the overlapping features.
1418        my @featureObjects = $self->GeneDataInRegion($contigID, $start, $stop);
1419        # We'l use this hash to help us track the feature IDs and sort them. The key is the
1420        # feature ID and the value is a [$left,$right] pair indicating the maximum extent
1421        # of the feature's locations.
1422        my %featureMap = ();
1423        # Loop through them to do the begin/end analysis.
1424        for my $featureObject (@featureObjects) {
1425            # Get the feature's location string. This may contain multiple actual locations.
1426            my ($locations, $fid) = $featureObject->Values([qw(Feature(location-string) Feature(id))]);
1427            my @locationSegments = split /\s*,\s*/, $locations;
1428            # Loop through the locations.
1429            for my $locationSegment (@locationSegments) {
1430                # Construct an object for the location.
1431                my $locationObject = BasicLocation->new($locationSegment);
1432                # Merge the current segment's begin and end into the min and max.
1433                my ($left, $right) = ($locationObject->Left, $locationObject->Right);
1434                my ($beg, $end);
1435                if (exists $featureMap{$fid}) {
1436                    ($beg, $end) = @{$featureMap{$fid}};
1437                    $beg = $left if $left < $beg;
1438                    $end = $right if $right > $end;
1439                } else {
1440                    ($beg, $end) = ($left, $right);
1441                }
1442                $min = $beg if $beg < $min;
1443                $max = $end if $end > $max;
1444                # Store the feature's new extent back into the hash table.
1445                $featureMap{$fid} = [$beg, $end];
1446            }
1447        }
1448        # Now we must compute the list of the IDs for the features found. We start with a list
1449        # of midpoints / feature ID pairs. (It's not really a midpoint, it's twice the midpoint,
1450        # but the result of the sort will be the same.)
1451        my @list = map { [$featureMap{$_}->[0] + $featureMap{$_}->[1], $_] } keys %featureMap;
1452        # Now we sort by midpoint and yank out the feature IDs.
1453        my @retVal = map { $_->[1] } sort { $a->[0] <=> $b->[0] } @list;
1454        # Return it along with the min and max.
1455        return (\@retVal, $min, $max);
1456    }
1457    
1458    =head3 GeneDataInRegion
1459    
1460        my @featureList = $sprout->GenesInRegion($contigID, $start, $stop);
1461    
1462    List the features which overlap a specified region in a contig.
1463    
1464    =over 4
1465    
1466    =item contigID
1467    
1468    ID of the contig containing the region of interest.
1469    
1470    =item start
1471    
1472    Offset of the first residue in the region of interest.
1473    
1474    =item stop
1475    
1476    Offset of the last residue in the region of interest.
1477    
1478    =item RETURN
1479    
1480    Returns a list of B<ERDBObjects> for the desired features. Each object will
1481    contain a B<Feature> record.
1482    
1483    =back
1484    
1485    =cut
1486    
1487    sub GeneDataInRegion {
1488        # Get the parameters.
1489        my ($self, $contigID, $start, $stop) = @_;
1490        # Get the maximum segment length.
1491        my $maximumSegmentLength = $self->MaxSegment;
1492        # Create a hash to receive the feature list. We use a hash so that we can eliminate
1493        # duplicates easily. The hash key will be the feature ID. The value will be the feature's
1494        # ERDBObject from the query.
1495        my %featuresFound = ();
1496        # Create a table of parameters for the queries. Each query looks for features travelling in
1497      # 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,
1498      # 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
1499      # 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 917  Line 1502 
1502      # Loop through the query parameters.      # Loop through the query parameters.
1503      for my $parms (values %queryParms) {      for my $parms (values %queryParms) {
1504          # Create the query.          # Create the query.
1505          my $query = $self->Get(['IsLocatedIn'],          my $query = $self->Get([qw(Feature IsLocatedIn)],
1506              "IsLocatedIn(to-link)= ? AND IsLocatedIn(dir) = ? AND IsLocatedIn(beg) >= ? AND IsLocatedIn(beg) <= ?",              "IsLocatedIn(to-link)= ? AND IsLocatedIn(dir) = ? AND IsLocatedIn(beg) >= ? AND IsLocatedIn(beg) <= ?",
1507              $parms);              $parms);
1508          # Loop through the feature segments found.          # Loop through the feature segments found.
1509          while (my $segment = $query->Fetch) {          while (my $segment = $query->Fetch) {
1510              # Get the data about this segment.              # Get the data about this segment.
1511              my ($featureID, $dir, $beg, $len) = $segment->Values(['IsLocatedIn(from-link)',              my ($featureID, $contig, $dir, $beg, $len) = $segment->Values([qw(IsLocatedIn(from-link)
1512                  'IsLocatedIn(dir)', 'IsLocatedIn(beg)', 'IsLocatedIn(len)']);                  IsLocatedIn(to-link) IsLocatedIn(dir) IsLocatedIn(beg) IsLocatedIn(len))]);
1513              # Determine if this feature actually overlaps the region. The query insures that              # Determine if this feature segment actually overlaps the region. The query insures that
1514              # this will be the case if the segment is the maximum length, so to fine-tune              # this will be the case if the segment is the maximum length, so to fine-tune
1515              # the results we insure that the inequality from the query holds using the actual              # the results we insure that the inequality from the query holds using the actual
1516              # length.              # length.
1517              my ($found, $end) = (0, 0);              my $loc = BasicLocation->new($contig, $beg, $dir, $len);
1518              if ($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.  
                     $found = 1;  
                 }  
             }  
1519              if ($found) {              if ($found) {
1520                  # Here we need to record the feature and update the minima and maxima. First,                  # Save this feature in the result list.
1521                  # 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, $loc2];  
1522              }              }
1523          }          }
1524      }      }
1525      # Now we must compute the list of the IDs for the features found. We start with a list      # Return the ERDB objects for the features found.
1526      # of midpoints / feature ID pairs. (It's not really a midpoint, it's twice the midpoint,      return values %featuresFound;
     # but the result of the sort will be the same.)  
     my @list = map { [$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);  
1527  }  }
1528    
1529  =head3 FType  =head3 FType
1530    
1531  C<< my $ftype = $sprout->FType($featureID); >>      my $ftype = $sprout->FType($featureID);
1532    
1533  Return the type of a feature.  Return the type of a feature.
1534    
# Line 1007  Line 1558 
1558    
1559  =head3 FeatureAnnotations  =head3 FeatureAnnotations
1560    
1561  C<< my @descriptors = $sprout->FeatureAnnotations($featureID); >>      my @descriptors = $sprout->FeatureAnnotations($featureID, $rawFlag);
1562    
1563  Return the annotations of a feature.  Return the annotations of a feature.
1564    
# Line 1017  Line 1568 
1568    
1569  ID of the feature whose annotations are desired.  ID of the feature whose annotations are desired.
1570    
1571    =item rawFlag
1572    
1573    If TRUE, the annotation timestamps will be returned in raw form; otherwise, they
1574    will be returned in human-readable form.
1575    
1576  =item RETURN  =item RETURN
1577    
1578  Returns a list of annotation descriptors. Each descriptor is a hash with the following fields.  Returns a list of annotation descriptors. Each descriptor is a hash with the following fields.
1579    
1580  * B<featureID> ID of the relevant feature.  * B<featureID> ID of the relevant feature.
1581    
1582  * B<timeStamp> time the annotation was made, in user-friendly format.  * B<timeStamp> time the annotation was made.
1583    
1584  * B<user> ID of the user who made the annotation  * B<user> ID of the user who made the annotation
1585    
# Line 1035  Line 1591 
1591  #: Return Type @%;  #: Return Type @%;
1592  sub FeatureAnnotations {  sub FeatureAnnotations {
1593      # Get the parameters.      # Get the parameters.
1594      my ($self, $featureID) = @_;      my ($self, $featureID, $rawFlag) = @_;
1595      # Create a query to get the feature's annotations and the associated users.      # Create a query to get the feature's annotations and the associated users.
1596      my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],      my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1597                             "IsTargetOfAnnotation(from-link) = ?", [$featureID]);                             "IsTargetOfAnnotation(from-link) = ?", [$featureID]);
# Line 1048  Line 1604 
1604              $annotation->Values(['IsTargetOfAnnotation(from-link)',              $annotation->Values(['IsTargetOfAnnotation(from-link)',
1605                                   'Annotation(time)', 'MadeAnnotation(from-link)',                                   'Annotation(time)', 'MadeAnnotation(from-link)',
1606                                   'Annotation(annotation)']);                                   'Annotation(annotation)']);
1607            # Convert the time, if necessary.
1608            if (! $rawFlag) {
1609                $timeStamp = FriendlyTimestamp($timeStamp);
1610            }
1611          # Assemble them into a hash.          # Assemble them into a hash.
1612          my $annotationHash = { featureID => $featureID,          my $annotationHash = { featureID => $featureID,
1613                                 timeStamp => FriendlyTimestamp($timeStamp),                                 timeStamp => $timeStamp,
1614                                 user => $user, text => $text };                                 user => $user, text => $text };
1615          # Add it to the return list.          # Add it to the return list.
1616          push @retVal, $annotationHash;          push @retVal, $annotationHash;
# Line 1061  Line 1621 
1621    
1622  =head3 AllFunctionsOf  =head3 AllFunctionsOf
1623    
1624  C<< my %functions = $sprout->AllFunctionsOf($featureID); >>      my %functions = $sprout->AllFunctionsOf($featureID);
1625    
1626  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
1627  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 1079  Line 1639 
1639    
1640  =item RETURN  =item RETURN
1641    
1642  Returns a hash mapping the functional assignment IDs to user IDs.  Returns a hash mapping the user IDs to functional assignment IDs.
1643    
1644  =back  =back
1645    
# Line 1089  Line 1649 
1649      # Get the parameters.      # Get the parameters.
1650      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
1651      # Get all of the feature's annotations.      # Get all of the feature's annotations.
1652      my @query = $self->GetAll(['IsTargetOfAnnotation', 'Annotation'],      my @query = $self->GetAll(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1653                              "IsTargetOfAnnotation(from-link) = ?",                              "IsTargetOfAnnotation(from-link) = ?",
1654                              [$featureID], ['Annotation(time)', 'Annotation(annotation)']);                              [$featureID], ['Annotation(time)', 'Annotation(annotation)',
1655                                               'MadeAnnotation(from-link)']);
1656      # Declare the return hash.      # Declare the return hash.
1657      my %retVal;      my %retVal;
     # Declare a hash for insuring we only make one assignment per user.  
     my %timeHash = ();  
1658      # Now we sort the assignments by timestamp in reverse.      # Now we sort the assignments by timestamp in reverse.
1659      my @sortedQuery = sort { -($a->[0] <=> $b->[0]) } @query;      my @sortedQuery = sort { -($a->[0] <=> $b->[0]) } @query;
1660      # Loop until we run out of annotations.      # Loop until we run out of annotations.
1661      for my $annotation (@sortedQuery) {      for my $annotation (@sortedQuery) {
1662          # Get the annotation fields.          # Get the annotation fields.
1663          my ($timeStamp, $text) = @{$annotation};          my ($timeStamp, $text, $user) = @{$annotation};
1664          # Check to see if this is a functional assignment.          # Check to see if this is a functional assignment.
1665          my ($user, $function) = _ParseAssignment($text);          my ($actualUser, $function) = _ParseAssignment($user, $text);
1666          if ($user && ! exists $timeHash{$user}) {          if ($actualUser && ! exists $retVal{$actualUser}) {
1667              # Here it is a functional assignment and there has been no              # Here it is a functional assignment and there has been no
1668              # previous assignment for this user, so we stuff it in the              # previous assignment for this user, so we stuff it in the
1669              # return hash.              # return hash.
1670              $retVal{$function} = $user;              $retVal{$actualUser} = $function;
             # Insure we don't assign to this user again.  
             $timeHash{$user} = 1;  
1671          }          }
1672      }      }
1673      # Return the hash of assignments found.      # Return the hash of assignments found.
# Line 1119  Line 1676 
1676    
1677  =head3 FunctionOf  =head3 FunctionOf
1678    
1679  C<< my $functionText = $sprout->FunctionOf($featureID, $userID); >>      my $functionText = $sprout->FunctionOf($featureID, $userID);
1680    
1681  Return the most recently-determined functional assignment of a particular feature.  Return the most recently-determined functional assignment of a particular feature.
1682    
1683  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
1684  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
1685  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.  
1686    
1687  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
1688  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
1689  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
1690  is trusted.  is trusted.
1691    
1692  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.
1693  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.  
1694    
1695  =over 4  =over 4
1696    
# Line 1147  Line 1700 
1700    
1701  =item userID (optional)  =item userID (optional)
1702    
1703  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
1704  C<FIG> assignment will be returned.  functional assignment in the B<Feature> table will be returned.
1705    
1706  =item RETURN  =item RETURN
1707    
# Line 1163  Line 1716 
1716      my ($self, $featureID, $userID) = @_;      my ($self, $featureID, $userID) = @_;
1717      # Declare the return value.      # Declare the return value.
1718      my $retVal;      my $retVal;
1719      # Determine the ID type.      # Find a FIG ID for this feature.
1720      if ($featureID =~ m/^fig\|/) {      my ($fid) = $self->FeaturesByAlias($featureID);
1721          # Here we have a FIG feature ID. We must build the list of trusted      # Only proceed if we have an ID.
1722          # users.      if ($fid) {
1723            # Here we have a FIG feature ID.
1724            if (!$userID) {
1725                # Use the primary assignment.
1726                ($retVal) = $self->GetEntityValues('Feature', $fid, ['Feature(assignment)']);
1727            } else {
1728                # We must build the list of trusted users.
1729          my %trusteeTable = ();          my %trusteeTable = ();
1730          # Check the user ID.          # Check the user ID.
1731          if (!$userID) {          if (!$userID) {
# Line 1188  Line 1747 
1747              }              }
1748          }          }
1749          # 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.
1750          my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation'],              my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1751                                 "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",                                 "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1752                                 [$featureID]);                                     [$fid]);
1753          my $timeSelected = 0;          my $timeSelected = 0;
1754          # Loop until we run out of annotations.          # Loop until we run out of annotations.
1755          while (my $annotation = $query->Fetch()) {          while (my $annotation = $query->Fetch()) {
1756              # Get the annotation text.              # Get the annotation text.
1757              my ($text, $time) = $annotation->Values(['Annotation(annotation)','Annotation(time)']);                  my ($text, $time, $user) = $annotation->Values(['Annotation(annotation)',
1758                                                             'Annotation(time)', 'MadeAnnotation(from-link)']);
1759              # Check to see if this is a functional assignment for a trusted user.              # Check to see if this is a functional assignment for a trusted user.
1760              my ($user, $function) = _ParseAssignment($text);                  my ($actualUser, $function) = _ParseAssignment($user, $text);
1761              if ($user) {                  Trace("Assignment user is $actualUser, text is $function.") if T(4);
1762                    if ($actualUser) {
1763                  # Here it is a functional assignment. Check the time and the user                  # Here it is a functional assignment. Check the time and the user
1764                  # name. The time must be recent and the user must be trusted.                  # name. The time must be recent and the user must be trusted.
1765                  if ((exists $trusteeTable{$user}) && ($time > $timeSelected)) {                      if ((exists $trusteeTable{$actualUser}) && ($time > $timeSelected)) {
1766                      $retVal = $function;                      $retVal = $function;
1767                      $timeSelected = $time;                      $timeSelected = $time;
1768                  }                  }
1769              }              }
1770          }          }
1771      } else {          }
         # Here we have a non-FIG feature ID. In this case the user ID does not  
         # matter. We simply get the information from the External Alias Function  
         # table.  
         ($retVal) = $self->GetEntityValues('ExternalAliasFunc', $featureID, ['ExternalAliasFunc(func)']);  
1772      }      }
1773      # Return the assignment found.      # Return the assignment found.
1774      return $retVal;      return $retVal;
1775  }  }
1776    
1777    =head3 FunctionsOf
1778    
1779        my @functionList = $sprout->FunctionOf($featureID, $userID);
1780    
1781    Return the functional assignments of a particular feature.
1782    
1783    The functional assignment is handled differently depending on the type of feature. If
1784    the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional
1785    assignment is a type of annotation. The format of an assignment is described in
1786    L</ParseAssignment>. Its worth noting that we cannot filter on the content of the
1787    annotation itself because it's a text field; however, this is not a big problem because
1788    most features only have a small number of annotations.
1789    
1790    =over 4
1791    
1792    =item featureID
1793    
1794    ID of the feature whose functional assignments are desired.
1795    
1796    =item RETURN
1797    
1798    Returns a list of 2-tuples, each consisting of a user ID and the text of an assignment by
1799    that user.
1800    
1801    =back
1802    
1803    =cut
1804    #: Return Type @@;
1805    sub FunctionsOf {
1806        # Get the parameters.
1807        my ($self, $featureID) = @_;
1808        # Declare the return value.
1809        my @retVal = ();
1810        # Convert to a FIG ID.
1811        my ($fid) = $self->FeaturesByAlias($featureID);
1812        # Only proceed if we found one.
1813        if ($fid) {
1814            # Here we have a FIG feature ID. We must build the list of trusted
1815            # users.
1816            my %trusteeTable = ();
1817            # Build a query for all of the feature's annotations, sorted by date.
1818            my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1819                                   "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1820                                   [$fid]);
1821            my $timeSelected = 0;
1822            # Loop until we run out of annotations.
1823            while (my $annotation = $query->Fetch()) {
1824                # Get the annotation text.
1825                my ($text, $time, $user) = $annotation->Values(['Annotation(annotation)',
1826                                                                'Annotation(time)',
1827                                                                'MadeAnnotation(user)']);
1828                # Check to see if this is a functional assignment for a trusted user.
1829                my ($actualUser, $function) = _ParseAssignment($user, $text);
1830                if ($actualUser) {
1831                    # Here it is a functional assignment.
1832                    push @retVal, [$actualUser, $function];
1833                }
1834            }
1835        }
1836        # Return the assignments found.
1837        return @retVal;
1838    }
1839    
1840  =head3 BBHList  =head3 BBHList
1841    
1842  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>      my $bbhHash = $sprout->BBHList($genomeID, \@featureList);
1843    
1844  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
1845  on a specified target genome.  on a specified target genome.
# Line 1250  Line 1870 
1870      my %retVal = ();      my %retVal = ();
1871      # Loop through the incoming features.      # Loop through the incoming features.
1872      for my $featureID (@{$featureList}) {      for my $featureID (@{$featureList}) {
1873          # Create a query to get the feature's best hit.          # Ask the server for the feature's best hit.
1874          my $query = $self->Get(['IsBidirectionalBestHitOf'],          my $bbhData = FIGRules::BBHData($featureID);
1875                                 "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",          # Peel off the BBHs found.
1876                                 [$featureID, $genomeID]);          my @found = ();
1877          # Look for the best hit.          for my $bbh (@$bbhData) {
1878          my $bbh = $query->Fetch;              my $fid = $bbh->[0];
1879          if ($bbh) {              my $bbGenome = $self->GenomeOf($fid);
1880              my ($targetFeature) = $bbh->Value('IsBidirectionalBestHitOf(to-link)');              if ($bbGenome eq $genomeID) {
1881              $retVal{$featureID} = $targetFeature;                  push @found, $fid;
1882                }
1883          }          }
1884            $retVal{$featureID} = \@found;
1885      }      }
1886      # Return the mapping.      # Return the mapping.
1887      return \%retVal;      return \%retVal;
# Line 1267  Line 1889 
1889    
1890  =head3 SimList  =head3 SimList
1891    
1892  C<< my %similarities = $sprout->SimList($featureID, $count); >>      my %similarities = $sprout->SimList($featureID, $count);
1893    
1894  Return a list of the similarities to the specified feature.  Return a list of the similarities to the specified feature.
1895    
1896  Sprout does not support real similarities, so this method just returns the bidirectional  This method just returns the bidirectional best hits for performance reasons.
 best hits.  
1897    
1898  =over 4  =over 4
1899    
# Line 1292  Line 1913 
1913      # Get the parameters.      # Get the parameters.
1914      my ($self, $featureID, $count) = @_;      my ($self, $featureID, $count) = @_;
1915      # Ask for the best hits.      # Ask for the best hits.
1916      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);  
1917      # Create the return value.      # Create the return value.
1918      my %retVal = ();      my %retVal = ();
1919      for my $tuple (@lists) {      for my $tuple (@$lists) {
1920          $retVal{$tuple->[0]} = $tuple->[1];          $retVal{$tuple->[0]} = $tuple->[1];
1921      }      }
1922      # Return the result.      # Return the result.
1923      return %retVal;      return %retVal;
1924  }  }
1925    
   
   
1926  =head3 IsComplete  =head3 IsComplete
1927    
1928  C<< my $flag = $sprout->IsComplete($genomeID); >>      my $flag = $sprout->IsComplete($genomeID);
1929    
1930  Return TRUE if the specified genome is complete, else FALSE.  Return TRUE if the specified genome is complete, else FALSE.
1931    
# Line 1334  Line 1950 
1950      # Declare the return variable.      # Declare the return variable.
1951      my $retVal;      my $retVal;
1952      # Get the genome's data.      # Get the genome's data.
1953      my $genomeData = $self->GetEntity('Genome', $genomeID);      my $genomeData = $self->_GenomeData($genomeID);
1954      if ($genomeData) {      # Only proceed if it exists.
1955        if (defined $genomeData) {
1956          # The genome exists, so get the completeness flag.          # The genome exists, so get the completeness flag.
1957          ($retVal) = $genomeData->Value('complete');          $retVal = $genomeData->PrimaryValue('Genome(complete)');
1958      }      }
1959      # Return the result.      # Return the result.
1960      return $retVal;      return $retVal;
# Line 1345  Line 1962 
1962    
1963  =head3 FeatureAliases  =head3 FeatureAliases
1964    
1965  C<< my @aliasList = $sprout->FeatureAliases($featureID); >>      my @aliasList = $sprout->FeatureAliases($featureID);
1966    
1967  Return a list of the aliases for a specified feature.  Return a list of the aliases for a specified feature.
1968    
# Line 1368  Line 1985 
1985      # Get the parameters.      # Get the parameters.
1986      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
1987      # Get the desired feature's aliases      # Get the desired feature's aliases
1988      my @retVal = $self->GetEntityValues('Feature', $featureID, ['Feature(alias)']);      my @retVal = $self->GetFlat(['IsAliasOf'], "IsAliasOf(to-link) = ?", [$featureID], 'IsAliasOf(from-link)');
1989      # Return the result.      # Return the result.
1990      return @retVal;      return @retVal;
1991  }  }
1992    
1993  =head3 GenomeOf  =head3 GenomeOf
1994    
1995  C<< my $genomeID = $sprout->GenomeOf($featureID); >>      my $genomeID = $sprout->GenomeOf($featureID);
1996    
1997  Return the genome that contains a specified feature.  Return the genome that contains a specified feature or contig.
1998    
1999  =over 4  =over 4
2000    
2001  =item featureID  =item featureID
2002    
2003  ID of the feature whose genome is desired.  ID of the feature or contig whose genome is desired.
2004    
2005  =item RETURN  =item RETURN
2006    
2007  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
2008  an undefined value.  found, returns an undefined value.
2009    
2010  =back  =back
2011    
# Line 1397  Line 2014 
2014  sub GenomeOf {  sub GenomeOf {
2015      # Get the parameters.      # Get the parameters.
2016      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]);  
2017      # Declare the return value.      # Declare the return value.
2018      my $retVal;      my $retVal;
2019      # Get the genome ID.      # Parse the genome ID from the feature ID.
2020      if (my $relationship = $query->Fetch()) {      if ($featureID =~ /^fig\|(\d+\.\d+)/) {
2021          ($retVal) = $relationship->Value('HasContig(from-link)');          $retVal = $1;
2022        } else {
2023            # Find the feature by alias.
2024            my ($realFeatureID) = $self->FeaturesByAlias($featureID);
2025            if ($realFeatureID && $realFeatureID =~ /^fig\|(\d+\.\d+)/) {
2026                $retVal = $1;
2027            }
2028      }      }
2029      # Return the value found.      # Return the value found.
2030      return $retVal;      return $retVal;
# Line 1411  Line 2032 
2032    
2033  =head3 CoupledFeatures  =head3 CoupledFeatures
2034    
2035  C<< my %coupleHash = $sprout->CoupledFeatures($featureID); >>      my %coupleHash = $sprout->CoupledFeatures($featureID);
2036    
2037  Return the features functionally coupled with a specified feature. Features are considered  Return the features functionally coupled with a specified feature. Features are considered
2038  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 1433  Line 2054 
2054  sub CoupledFeatures {  sub CoupledFeatures {
2055      # Get the parameters.      # Get the parameters.
2056      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
2057      # Create a query to retrieve the functionally-coupled features.      # Ask the coupling server for the data.
2058      my $query = $self->Get(['ParticipatesInCoupling', 'Coupling'],      Trace("Looking for features coupled to $featureID.") if T(coupling => 3);
2059                             "ParticipatesInCoupling(from-link) = ?", [$featureID]);      my @rawPairs = FIGRules::NetCouplingData('coupled_to', id1 => $featureID);
2060      # This value will be set to TRUE if we find at least one coupled feature.      Trace(scalar(@rawPairs) . " couplings returned.") if T(coupling => 3);
2061      my $found = 0;      # Form them into a hash.
     # Create the return hash.  
2062      my %retVal = ();      my %retVal = ();
2063      # Retrieve the relationship records and store them in the hash.      for my $pair (@rawPairs) {
2064      while (my $clustering = $query->Fetch()) {          # Get the feature ID and score.
2065          # Get the ID and score of the coupling.          my ($featureID2, $score) = @{$pair};
2066          my ($couplingID, $score) = $clustering->Values(['Coupling(id)',          # Only proceed if the feature is in NMPDR.
2067                                                          'Coupling(score)']);          if ($self->_CheckFeature($featureID2)) {
2068          # The coupling ID contains the two feature IDs separated by a space. We use              $retVal{$featureID2} = $score;
         # this information to find the ID of the other feature.  
         my ($fid1, $fid2) = split / /, $couplingID;  
         my $otherFeatureID = ($featureID eq $fid1 ? $fid2 : $fid1);  
         # Attach the other feature's score to its ID.  
         $retVal{$otherFeatureID} = $score;  
         $found = 1;  
2069      }      }
     # Functional coupling is reflexive. If we found at least one coupled feature, we must add  
     # the incoming feature as well.  
     if ($found) {  
         $retVal{$featureID} = 9999;  
2070      }      }
2071      # Return the hash.      # Return the hash.
2072      return %retVal;      return %retVal;
# Line 1464  Line 2074 
2074    
2075  =head3 CouplingEvidence  =head3 CouplingEvidence
2076    
2077  C<< my @evidence = $sprout->CouplingEvidence($peg1, $peg2); >>      my @evidence = $sprout->CouplingEvidence($peg1, $peg2);
2078    
2079  Return the evidence for a functional coupling.  Return the evidence for a functional coupling.
2080    
# Line 1512  Line 2122 
2122      my ($self, $peg1, $peg2) = @_;      my ($self, $peg1, $peg2) = @_;
2123      # Declare the return variable.      # Declare the return variable.
2124      my @retVal = ();      my @retVal = ();
2125      # Our first task is to find out the nature of the coupling: whether or not      # Get the coupling and evidence data.
2126      # it exists, its score, and whether the features are stored in the same      my @rawData = FIGRules::NetCouplingData('coupling_evidence', id1 => $peg1, id2 => $peg2);
2127      # order as the ones coming in.      # Loop through the raw data, saving the ones that are in NMPDR genomes.
2128      my ($couplingID, $inverted, $score) = $self->GetCoupling($peg1, $peg2);      for my $rawTuple (@rawData) {
2129      # Only proceed if a coupling exists.          if ($self->_CheckFeature($rawTuple->[0]) && $self->_CheckFeature($rawTuple->[1])) {
2130      if ($couplingID) {              push @retVal, $rawTuple;
2131          # Determine the ordering to place on the evidence items. If we're          }
         # inverted, we want to see feature 2 before feature 1 (descending); otherwise,  
         # we want feature 1 before feature 2 (normal).  
         Trace("Coupling evidence for ($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);  
2132      }      }
2133      # Return the result.      # Return the result.
2134      return @retVal;      return @retVal;
2135  }  }
2136    
2137  =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.  
2138    
2139  =over 4      my $id = $sprout->GetSynonymGroup($fid);
2140    
2141  =item peg1  Return the synonym group name for the specified feature.
2142    
2143  ID of the feature of interest.  =over 4
2144    
2145  =item peg2  =item fid
2146    
2147  ID of the potentially coupled feature.  ID of the feature whose synonym group is desired.
2148    
2149  =item RETURN  =item RETURN
2150    
2151  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
2152  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>.  
2153    
2154  =back  =back
2155    
2156  =cut  =cut
2157  #: Return Type $%@;  
2158  sub GetCoupling {  sub GetSynonymGroup {
2159      # Get the parameters.      # Get the parameters.
2160      my ($self, $peg1, $peg2) = @_;      my ($self, $fid) = @_;
2161      # Declare the return values. We'll start with the coupling ID and undefine the      # Declare the return variable.
2162      # flag and score until we have more information.      my $retVal;
2163      my ($retVal, $inverted, $score) = (CouplingID($peg1, $peg2), undef, undef);      # Find the synonym group.
2164      # Find the coupling data.      my @groups = $self->GetFlat(['IsSynonymGroupFor'], "IsSynonymGroupFor(to-link) = ?",
2165      my @pegs = $self->GetAll(['Coupling', 'ParticipatesInCoupling'],                                     [$fid], 'IsSynonymGroupFor(from-link)');
                                  "Coupling(id) = ? ORDER BY ParticipatesInCoupling(pos)",  
                                  [$retVal], ["ParticipatesInCoupling(from-link)", "Coupling(score)"]);  
2166      # Check to see if we found anything.      # Check to see if we found anything.
2167      if (!@pegs) {      if (@groups) {
2168          # No coupling, so undefine the return value.          $retVal = $groups[0];
         $retVal = undef;  
2169      } else {      } else {
2170          # We have a coupling! Get the score and check for inversion.          $retVal = $fid;
         $score = $pegs[0]->[1];  
         $inverted = ($pegs[0]->[0] eq $peg1);  
2171      }      }
2172      # Return the result.      # Return the result.
2173      return ($retVal, $inverted, $score);      return $retVal;
2174  }  }
2175    
2176  =head3 CouplingID  =head3 GetBoundaries
2177    
2178  C<< my $couplingID = Sprout::CouplingID($peg1, $peg2); >>      my ($contig, $beg, $end) = $sprout->GetBoundaries(@locList);
2179    
2180  Return the coupling ID for a pair of feature IDs.  Determine the begin and end boundaries for the locations in a list. All of the
2181    locations must belong to the same contig and have mostly the same direction in
2182  The coupling ID is currently computed by joining the feature IDs in  order for this method to produce a meaningful result. The resulting
2183  sorted order with a space. Client modules (that is, modules which  begin/end pair will contain all of the bases in any of the locations.
 use Sprout) should not, however, count on this always being the  
 case. This method provides a way for abstracting the concept of a  
 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")>.  
2184    
2185  =over 4  =over 4
2186    
2187  =item peg1  =item locList
   
 First feature of interest.  
   
 =item peg2  
2188    
2189  Second feature of interest.  List of locations to process.
2190    
2191  =item RETURN  =item RETURN
2192    
2193  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,
2194  the two specified PEGs.  and the ending boundary. The beginning boundary will be left of the
2195    end for mostly-forward locations and right of the end for mostly-backward
2196    locations.
2197    
2198  =back  =back
2199    
2200  =cut  =cut
2201  #: Return Type $;  
2202  sub CouplingID {  sub GetBoundaries {
2203      return join " ", sort @_;      # Get the parameters.
2204        my ($self, @locList) = @_;
2205        # Set up the counters used to determine the most popular direction.
2206        my %counts = ( '+' => 0, '-' => 0 );
2207        # Get the last location and parse it.
2208        my $locObject = BasicLocation->new(pop @locList);
2209        # Prime the loop with its data.
2210        my ($contig, $beg, $end) = ($locObject->Contig, $locObject->Left, $locObject->Right);
2211        # Count its direction.
2212        $counts{$locObject->Dir}++;
2213        # Loop through the remaining locations. Note that in most situations, this loop
2214        # will not iterate at all, because most of the time we will be dealing with a
2215        # singleton list.
2216        for my $loc (@locList) {
2217            # Create a location object.
2218            my $locObject = BasicLocation->new($loc);
2219            # Count the direction.
2220            $counts{$locObject->Dir}++;
2221            # Get the left end and the right end.
2222            my $left = $locObject->Left;
2223            my $right = $locObject->Right;
2224            # Merge them into the return variables.
2225            if ($left < $beg) {
2226                $beg = $left;
2227            }
2228            if ($right > $end) {
2229                $end = $right;
2230            }
2231        }
2232        # If the most common direction is reverse, flip the begin and end markers.
2233        if ($counts{'-'} > $counts{'+'}) {
2234            ($beg, $end) = ($end, $beg);
2235        }
2236        # Return the result.
2237        return ($contig, $beg, $end);
2238  }  }
2239    
2240  =head3 GetEntityTypes  =head3 ReadFasta
2241    
2242  C<< my @entityList = $sprout->GetEntityTypes(); >>      my %sequenceData = Sprout::ReadFasta($fileName, $prefix);
   
 Return the list of supported entity types.  
   
 =cut  
 #: Return Type @;  
 sub GetEntityTypes {  
     # Get the parameters.  
     my ($self) = @_;  
     # Get the underlying database object.  
     my $erdb = $self->{_erdb};  
     # Get its entity type list.  
     my @retVal = $erdb->GetEntityTypes();  
 }  
   
 =head3 ReadFasta  
   
 C<< my %sequenceData = Sprout::ReadFasta($fileName, $prefix); >>  
2243    
2244  Read sequence data from a FASTA-format file. Each sequence in a FASTA file is represented by  Read sequence data from a FASTA-format file. Each sequence in a FASTA file is represented by
2245  one or more lines of data. The first line begins with a > character and contains an ID.  one or more lines of data. The first line begins with a > character and contains an ID.
# Line 1698  Line 2281 
2281          if ($line =~ m/^>\s*(.+?)(\s|\n)/) {          if ($line =~ m/^>\s*(.+?)(\s|\n)/) {
2282              # Here we have a new header. Store the current sequence if we have one.              # Here we have a new header. Store the current sequence if we have one.
2283              if ($id) {              if ($id) {
2284                  $retVal{$id} = uc $sequence;                  $retVal{$id} = lc $sequence;
2285              }              }
2286              # Clear the sequence accumulator and save the new ID.              # Clear the sequence accumulator and save the new ID.
2287              ($id, $sequence) = ("$prefix$1", "");              ($id, $sequence) = ("$prefix$1", "");
2288          } else {          } else {
2289              # Here we have a data line, so we add it to the sequence accumulator.              # Here we have a data line, so we add it to the sequence accumulator.
2290              # First, we get the actual data out. Note that we normalize to upper              # First, we get the actual data out. Note that we normalize to lower
2291              # case.              # case.
2292              $line =~ /^\s*(.*?)(\s|\n)/;              $line =~ /^\s*(.*?)(\s|\n)/;
2293              $sequence .= $1;              $sequence .= $1;
# Line 1712  Line 2295 
2295      }      }
2296      # Flush out the last sequence (if any).      # Flush out the last sequence (if any).
2297      if ($sequence) {      if ($sequence) {
2298          $retVal{$id} = uc $sequence;          $retVal{$id} = lc $sequence;
2299      }      }
2300      # Close the file.      # Close the file.
2301      close FASTAFILE;      close FASTAFILE;
# Line 1722  Line 2305 
2305    
2306  =head3 FormatLocations  =head3 FormatLocations
2307    
2308  C<< my @locations = $sprout->FormatLocations($prefix, \@locations, $oldFormat); >>      my @locations = $sprout->FormatLocations($prefix, \@locations, $oldFormat);
2309    
2310  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
2311  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 1787  Line 2370 
2370    
2371  =head3 DumpData  =head3 DumpData
2372    
2373  C<< $sprout->DumpData(); >>      $sprout->DumpData();
2374    
2375  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.
2376    
# Line 1799  Line 2382 
2382      # Get the data directory name.      # Get the data directory name.
2383      my $outputDirectory = $self->{_options}->{dataDir};      my $outputDirectory = $self->{_options}->{dataDir};
2384      # Dump the relations.      # Dump the relations.
2385      $self->{_erdb}->DumpRelations($outputDirectory);      $self->DumpRelations($outputDirectory);
2386  }  }
2387    
2388  =head3 XMLFileName  =head3 XMLFileName
2389    
2390  C<< my $fileName = $sprout->XMLFileName(); >>      my $fileName = $sprout->XMLFileName();
2391    
2392  Return the name of this database's XML definition file.  Return the name of this database's XML definition file.
2393    
# Line 1815  Line 2398 
2398      return $self->{_xmlName};      return $self->{_xmlName};
2399  }  }
2400    
2401    =head3 GetGenomeNameData
2402    
2403        my ($genus, $species, $strain) = $sprout->GenomeNameData($genomeID);
2404    
2405    Return the genus, species, and unique characterization for a genome. This
2406    is similar to L</GenusSpecies>, with the exception that it returns the
2407    values in three seperate fields.
2408    
2409    =over 4
2410    
2411    =item genomeID
2412    
2413    ID of the genome whose name data is desired.
2414    
2415    =item RETURN
2416    
2417    Returns a three-element list, consisting of the genus, species, and strain
2418    of the specified genome. If the genome is not found, an error occurs.
2419    
2420    =back
2421    
2422    =cut
2423    
2424    sub GetGenomeNameData {
2425        # Get the parameters.
2426        my ($self, $genomeID) = @_;
2427        # Declare the return variables.
2428        my ($genus, $species, $strain);
2429        # Get the genome's data.
2430        my $genomeData = $self->_GenomeData($genomeID);
2431        # Only proceed if the genome exists.
2432        if (defined $genomeData) {
2433            # Get the desired values.
2434            ($genus, $species, $strain) = $genomeData->Values(['Genome(genus)',
2435                                                               'Genome(species)',
2436                                                               'Genome(unique-characterization)']);
2437        } else {
2438            # Throw an error because they were not found.
2439            Confess("Genome $genomeID not found in database.");
2440        }
2441        # Return the results.
2442        return ($genus, $species, $strain);
2443    }
2444    
2445    =head3 GetGenomeByNameData
2446    
2447        my @genomes = $sprout->GetGenomeByNameData($genus, $species, $strain);
2448    
2449    Return a list of the IDs of the genomes with the specified genus,
2450    species, and strain. In almost every case, there will be either zero or
2451    one IDs returned; however, two or more IDs could be returned if there are
2452    multiple versions of the genome in the database.
2453    
2454    =over 4
2455    
2456    =item genus
2457    
2458    Genus of the desired genome.
2459    
2460    =item species
2461    
2462    Species of the desired genome.
2463    
2464    =item strain
2465    
2466    Strain (unique characterization) of the desired genome. This may be an empty
2467    string, in which case it is presumed that the desired genome has no strain
2468    specified.
2469    
2470    =item RETURN
2471    
2472    Returns a list of the IDs of the genomes having the specified genus, species, and
2473    strain.
2474    
2475    =back
2476    
2477    =cut
2478    
2479    sub GetGenomeByNameData {
2480        # Get the parameters.
2481        my ($self, $genus, $species, $strain) = @_;
2482        # Try to find the genomes.
2483        my @retVal = $self->GetFlat(['Genome'], "Genome(genus) = ? AND Genome(species) = ? AND Genome(unique-characterization) = ?",
2484                                    [$genus, $species, $strain], 'Genome(id)');
2485        # Return the result.
2486        return @retVal;
2487    }
2488    
2489  =head3 Insert  =head3 Insert
2490    
2491  C<< $sprout->Insert($objectType, \%fieldHash); >>      $sprout->Insert($objectType, \%fieldHash);
2492    
2493  Insert an entity or relationship instance into the database. The entity or relationship of interest  Insert an entity or relationship instance into the database. The entity or relationship of interest
2494  is defined by a type name and then a hash of field names to values. Field values in the primary  is defined by a type name and then a hash of field names to values. Field values in the primary
# Line 1826  Line 2497 
2497  list references. For example, the following line inserts an inactive PEG feature named  list references. For example, the following line inserts an inactive PEG feature named
2498  C<fig|188.1.peg.1> with aliases C<ZP_00210270.1> and C<gi|46206278>.  C<fig|188.1.peg.1> with aliases C<ZP_00210270.1> and C<gi|46206278>.
2499    
2500  C<< $sprout->Insert('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']}); >>      $sprout->Insert('Feature', { id => 'fig|188.1.peg.1', active => 0, feature-type => 'peg', alias => ['ZP_00210270.1', 'gi|46206278']});
2501    
2502  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and  The next statement inserts a C<HasProperty> relationship between feature C<fig|158879.1.peg.1> and
2503  property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.  property C<4> with an evidence URL of C<http://seedu.uchicago.edu/query.cgi?article_id=142>.
2504    
2505  C<< $sprout->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>      $sprout->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'});
2506    
2507  =over 4  =over 4
2508    
# Line 1851  Line 2522 
2522      # Get the parameters.      # Get the parameters.
2523      my ($self, $objectType, $fieldHash) = @_;      my ($self, $objectType, $fieldHash) = @_;
2524      # Call the underlying method.      # Call the underlying method.
2525      $self->{_erdb}->InsertObject($objectType, $fieldHash);      $self->InsertObject($objectType, $fieldHash);
2526  }  }
2527    
2528  =head3 Annotate  =head3 Annotate
2529    
2530  C<< my $ok = $sprout->Annotate($fid, $timestamp, $user, $text); >>      my $ok = $sprout->Annotate($fid, $timestamp, $user, $text);
2531    
2532  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
2533  specified feature and user.  specified feature and user.
# Line 1910  Line 2581 
2581    
2582  =head3 AssignFunction  =head3 AssignFunction
2583    
2584  C<< my $ok = $sprout->AssignFunction($featureID, $user, $function, $assigningUser); >>      my $ok = $sprout->AssignFunction($featureID, $user, $function, $assigningUser);
2585    
2586  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
2587  format is described in L</ParseAssignment>.  format is described in L</ParseAssignment>.
# Line 1970  Line 2641 
2641    
2642  =head3 FeaturesByAlias  =head3 FeaturesByAlias
2643    
2644  C<< my @features = $sprout->FeaturesByAlias($alias); >>      my @features = $sprout->FeaturesByAlias($alias);
2645    
2646  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
2647  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 2004  Line 2675 
2675          push @retVal, $mappedAlias;          push @retVal, $mappedAlias;
2676      } else {      } else {
2677          # 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.
2678          @retVal = $self->GetFlat(['Feature'], 'Feature(alias) = ?', [$mappedAlias], 'Feature(id)');          @retVal = $self->GetFlat(['IsAliasOf'], 'IsAliasOf(from-link) = ?', [$mappedAlias], 'IsAliasOf(to-link)');
2679      }      }
2680      # Return the result.      # Return the result.
2681      return @retVal;      return @retVal;
2682  }  }
2683    
 =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.  
     my $testInstance = $self->GetEntity($entityName, $entityID);  
     # Return an existence indicator.  
     my $retVal = ($testInstance ? 1 : 0);  
     return $retVal;  
 }  
   
2684  =head3 FeatureTranslation  =head3 FeatureTranslation
2685    
2686  C<< my $translation = $sprout->FeatureTranslation($featureID); >>      my $translation = $sprout->FeatureTranslation($featureID);
2687    
2688  Return the translation of a feature.  Return the translation of a feature.
2689    
# Line 2074  Line 2711 
2711    
2712  =head3 Taxonomy  =head3 Taxonomy
2713    
2714  C<< my @taxonomyList = $sprout->Taxonomy($genome); >>      my @taxonomyList = $sprout->Taxonomy($genome);
2715    
2716  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
2717  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>,
2718  or C<Eukaryote>) to sub-species. For example,  or C<Eukaryote>) to sub-species. For example,
2719    
2720  C<< (Bacteria, Proteobacteria, Gammaproteobacteria, Enterobacteriales, Enterobacteriaceae, Escherichia, Escherichia coli, Escherichia coli K12) >>      (Bacteria, Proteobacteria, Gammaproteobacteria, Enterobacteriales, Enterobacteriaceae, Escherichia, Escherichia coli, Escherichia coli K12)
2721    
2722  =over 4  =over 4
2723    
# Line 2099  Line 2736 
2736  sub Taxonomy {  sub Taxonomy {
2737      # Get the parameters.      # Get the parameters.
2738      my ($self, $genome) = @_;      my ($self, $genome) = @_;
     # Find the specified genome's taxonomy string.  
     my ($list) = $self->GetEntityValues('Genome', $genome, ['Genome(taxonomy)']);  
2739      # Declare the return variable.      # Declare the return variable.
2740      my @retVal = ();      my @retVal = ();
2741      # If we found the genome, return its taxonomy string.      # Get the genome data.
2742      if ($list) {      my $genomeData = $self->_GenomeData($genome);
2743          @retVal = split /\s*;\s*/, $list;      # Only proceed if it exists.
2744        if (defined $genomeData) {
2745            # Create the taxonomy from the taxonomy string.
2746            @retVal = split /\s*;\s*/, $genomeData->PrimaryValue('Genome(taxonomy)');
2747      } else {      } else {
2748            # Genome doesn't exist, so emit a warning.
2749          Trace("Genome \"$genome\" does not have a taxonomy in the database.\n") if T(0);          Trace("Genome \"$genome\" does not have a taxonomy in the database.\n") if T(0);
2750      }      }
2751      # Return the value found.      # Return the value found.
# Line 2115  Line 2754 
2754    
2755  =head3 CrudeDistance  =head3 CrudeDistance
2756    
2757  C<< my $distance = $sprout->CrudeDistance($genome1, $genome2); >>      my $distance = $sprout->CrudeDistance($genome1, $genome2);
2758    
2759  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
2760  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 2151  Line 2790 
2790      }      }
2791      my @taxA = $self->Taxonomy($genomeA);      my @taxA = $self->Taxonomy($genomeA);
2792      my @taxB = $self->Taxonomy($genomeB);      my @taxB = $self->Taxonomy($genomeB);
2793      # Initialize the distance to 1. We'll reduce it each time we find a match between the      # Compute the distance.
2794      # taxonomies.      my $retVal = FIGRules::CrudeDistanceFormula(\@taxA, \@taxB);
     my $retVal = 1.0;  
     # Initialize the subtraction amount. This amount determines the distance reduction caused  
     # by a mismatch at the current level.  
     my $v = 0.5;  
     # Loop through the taxonomies.  
     for (my $i = 0; ($i < @taxA) && ($i < @taxB) && ($taxA[$i] eq $taxB[$i]); $i++) {  
         $retVal -= $v;  
         $v /= 2;  
     }  
2795      return $retVal;      return $retVal;
2796  }  }
2797    
2798  =head3 RoleName  =head3 RoleName
2799    
2800  C<< my $roleName = $sprout->RoleName($roleID); >>      my $roleName = $sprout->RoleName($roleID);
2801    
2802  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
2803  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 2201  Line 2831 
2831    
2832  =head3 RoleDiagrams  =head3 RoleDiagrams
2833    
2834  C<< my @diagrams = $sprout->RoleDiagrams($roleID); >>      my @diagrams = $sprout->RoleDiagrams($roleID);
2835    
2836  Return a list of the diagrams containing a specified functional role.  Return a list of the diagrams containing a specified functional role.
2837    
# Line 2229  Line 2859 
2859      return @retVal;      return @retVal;
2860  }  }
2861    
 =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;  
 }  
   
2862  =head3 FeatureProperties  =head3 FeatureProperties
2863    
2864  C<< my @properties = $sprout->FeatureProperties($featureID); >>      my @properties = $sprout->FeatureProperties($featureID);
2865    
2866  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
2867  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
2868  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
2869  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
2870  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.  
2871    
2872  =over 4  =over 4
2873    
# Line 2332  Line 2877 
2877    
2878  =item RETURN  =item RETURN
2879    
2880  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.  
2881    
2882  =back  =back
2883    
# Line 2343  Line 2887 
2887      # Get the parameters.      # Get the parameters.
2888      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
2889      # Get the properties.      # Get the properties.
2890      my @retVal = $self->GetAll(['HasProperty', 'Property'], "HasProperty(from-link) = ?", [$featureID],      my @attributes = $self->ca->GetAttributes($featureID);
2891                              ['Property(property-name)', 'Property(property-value)',      # Strip the feature ID off each tuple.
2892                               'HasProperty(evidence)']);      my @retVal = ();
2893        for my $attributeRow (@attributes) {
2894            shift @{$attributeRow};
2895            push @retVal, $attributeRow;
2896        }
2897      # Return the resulting list.      # Return the resulting list.
2898      return @retVal;      return @retVal;
2899  }  }
2900    
2901  =head3 DiagramName  =head3 DiagramName
2902    
2903  C<< my $diagramName = $sprout->DiagramName($diagramID); >>      my $diagramName = $sprout->DiagramName($diagramID);
2904    
2905  Return the descriptive name of a diagram.  Return the descriptive name of a diagram.
2906    
# Line 2378  Line 2926 
2926      return $retVal;      return $retVal;
2927  }  }
2928    
2929    =head3 PropertyID
2930    
2931        my $id = $sprout->PropertyID($propName, $propValue);
2932    
2933    Return the ID of the specified property name and value pair, if the
2934    pair exists. Only a small subset of the FIG attributes are stored as
2935    Sprout properties, mostly for use in search optimization.
2936    
2937    =over 4
2938    
2939    =item propName
2940    
2941    Name of the desired property.
2942    
2943    =item propValue
2944    
2945    Value expected for the desired property.
2946    
2947    =item RETURN
2948    
2949    Returns the ID of the name/value pair, or C<undef> if the pair does not exist.
2950    
2951    =back
2952    
2953    =cut
2954    
2955    sub PropertyID {
2956        # Get the parameters.
2957        my ($self, $propName, $propValue) = @_;
2958        # Try to find the ID.
2959        my ($retVal) = $self->GetFlat(['Property'],
2960                                      "Property(property-name) = ? AND Property(property-value) = ?",
2961                                      [$propName, $propValue], 'Property(id)');
2962        # Return the result.
2963        return $retVal;
2964    }
2965    
2966  =head3 MergedAnnotations  =head3 MergedAnnotations
2967    
2968  C<< my @annotationList = $sprout->MergedAnnotations(\@list); >>      my @annotationList = $sprout->MergedAnnotations(\@list);
2969    
2970  Returns a merged list of the annotations for the features in a list. Each annotation is  Returns a merged list of the annotations for the features in a list. Each annotation is
2971  represented by a 4-tuple of the form C<($fid, $timestamp, $userID, $annotation)>, where  represented by a 4-tuple of the form C<($fid, $timestamp, $userID, $annotation)>, where
# Line 2429  Line 3014 
3014    
3015  =head3 RoleNeighbors  =head3 RoleNeighbors
3016    
3017  C<< my @roleList = $sprout->RoleNeighbors($roleID); >>      my @roleList = $sprout->RoleNeighbors($roleID);
3018    
3019  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
3020  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 2472  Line 3057 
3057    
3058  =head3 FeatureLinks  =head3 FeatureLinks
3059    
3060  C<< my @links = $sprout->FeatureLinks($featureID); >>      my @links = $sprout->FeatureLinks($featureID);
3061    
3062  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
3063  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 2503  Line 3088 
3088    
3089  =head3 SubsystemsOf  =head3 SubsystemsOf
3090    
3091  C<< my %subsystems = $sprout->SubsystemsOf($featureID); >>      my %subsystems = $sprout->SubsystemsOf($featureID);
3092    
3093  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
3094  to the roles the feature performs.  to the roles the feature performs.
# Line 2531  Line 3116 
3116                                      ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);                                      ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);
3117      # Create the return value.      # Create the return value.
3118      my %retVal = ();      my %retVal = ();
3119        # Build a hash to weed out duplicates. Sometimes the same PEG and role appears
3120        # in two spreadsheet cells.
3121        my %dupHash = ();
3122      # Loop through the results, adding them to the hash.      # Loop through the results, adding them to the hash.
3123      for my $record (@subsystems) {      for my $record (@subsystems) {
3124            # Get this subsystem and role.
3125          my ($subsys, $role) = @{$record};          my ($subsys, $role) = @{$record};
3126          if (exists $retVal{$subsys}) {          # Insure it's the first time for both.
3127            my $dupKey = "$subsys\n$role";
3128            if (! exists $dupHash{"$subsys\n$role"}) {
3129                $dupHash{$dupKey} = 1;
3130              push @{$retVal{$subsys}}, $role;              push @{$retVal{$subsys}}, $role;
         } else {  
             $retVal{$subsys} = [$role];  
3131          }          }
3132      }      }
3133      # Return the hash.      # Return the hash.
# Line 2546  Line 3136 
3136    
3137  =head3 SubsystemList  =head3 SubsystemList
3138    
3139  C<< my @subsystems = $sprout->SubsystemList($featureID); >>      my @subsystems = $sprout->SubsystemList($featureID);
3140    
3141  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
3142  feature participates. Unlike L</SubsystemsOf>, this method only returns the  feature participates. Unlike L</SubsystemsOf>, this method only returns the
# Line 2569  Line 3159 
3159  sub SubsystemList {  sub SubsystemList {
3160      # Get the parameters.      # Get the parameters.
3161      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
3162      # Get the list of names.      # Get the list of names. We do a join to the Subsystem table because we have missing subsystems in
3163      my @retVal = $self->GetFlat(['ContainsFeature', 'HasSSCell'], "ContainsFeature(to-link) = ?",      # the Sprout database!
3164                                  [$featureID], 'HasSSCell(from-link)');      my @retVal = $self->GetFlat(['HasRoleInSubsystem', 'Subsystem'], "HasRoleInSubsystem(from-link) = ?",
3165                                    [$featureID], 'HasRoleInSubsystem(to-link)');
3166        # Return the result, sorted.
3167        return sort @retVal;
3168    }
3169    
3170    =head3 GenomeSubsystemData
3171    
3172        my %featureData = $sprout->GenomeSubsystemData($genomeID);
3173    
3174    Return a hash mapping genome features to their subsystem roles.
3175    
3176    =over 4
3177    
3178    =item genomeID
3179    
3180    ID of the genome whose subsystem feature map is desired.
3181    
3182    =item RETURN
3183    
3184    Returns a hash mapping each feature of the genome to a list of 2-tuples. Eacb
3185    2-tuple contains a subsystem name followed by a role ID.
3186    
3187    =back
3188    
3189    =cut
3190    
3191    sub GenomeSubsystemData {
3192        # Get the parameters.
3193        my ($self, $genomeID) = @_;
3194        # Declare the return variable.
3195        my %retVal = ();
3196        # Get a list of the genome features that participate in subsystems. For each
3197        # feature we get its subsystem ID and the corresponding roles.
3198        my @roleData = $self->GetAll(['HasFeature', 'ContainsFeature', 'IsRoleOf', 'HasSSCell'],
3199                                     "HasFeature(from-link) = ?", [$genomeID],
3200                                     ['HasFeature(to-link)', 'IsRoleOf(from-link)',  'HasSSCell(from-link)']);
3201        # Now we get a list of valid subsystems. These are the subsystems connected to the genome with
3202        # a non-negative variant code.
3203        my %subs = map { $_ => 1 } $self->GetFlat(['ParticipatesIn'],
3204                                                    "ParticipatesIn(from-link) = ? AND ParticipatesIn(variant-code) >= 0",
3205                                                    [$genomeID], 'ParticipatesIn(to-link)');
3206        # We loop through @roleData to build the hash.
3207        for my $roleEntry (@roleData) {
3208            # Get the data for this feature and cell.
3209            my ($fid, $role, $subsys) = @{$roleEntry};
3210            Trace("Subsystem for $fid is $subsys.") if T(4);
3211            # Check the subsystem;
3212            if ($subs{$subsys}) {
3213                Trace("Subsystem found.") if T(4);
3214                # Insure this feature has an entry in the return hash.
3215                if (! exists $retVal{$fid}) { $retVal{$fid} = []; }
3216                # Merge in this new data.
3217                push @{$retVal{$fid}}, [$subsys, $role];
3218            }
3219        }
3220      # Return the result.      # Return the result.
3221      return @retVal;      return %retVal;
3222  }  }
3223    
3224  =head3 RelatedFeatures  =head3 RelatedFeatures
3225    
3226  C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>      my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID);
3227    
3228  Return a list of the features which are bi-directional best hits of the specified feature and  Return a list of the features which are bi-directional best hits of the specified feature and
3229  have been assigned the specified function by the specified user. If no such features exists,  have been assigned the specified function by the specified user. If no such features exists,
# Line 2611  Line 3256 
3256      # Get the parameters.      # Get the parameters.
3257      my ($self, $featureID, $function, $userID) = @_;      my ($self, $featureID, $function, $userID) = @_;
3258      # 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.
3259      my @bbhFeatures = $self->GetFlat(['IsBidirectionalBestHitOf'],      my $bbhData = FIGRules::BBHData($featureID);
3260                                       "IsBidirectionalBestHitOf(from-link) = ?", [$featureID],      my @bbhFeatures = map { $_->[0] } @$bbhData;
                                      'IsBidirectionalBestHitOf(to-link)');  
3261      # 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
3262      # functional assignment.      # functional assignment.
3263      my @retVal = ();      my @retVal = ();
# Line 2631  Line 3275 
3275    
3276  =head3 TaxonomySort  =head3 TaxonomySort
3277    
3278  C<< my @sortedFeatureIDs = $sprout->TaxonomySort(\@featureIDs); >>      my @sortedFeatureIDs = $sprout->TaxonomySort(\@featureIDs);
3279    
3280  Return a list formed by sorting the specified features by the taxonomy of the containing  Return a list formed by sorting the specified features by the taxonomy of the containing
3281  genome. This will cause genomes from similar organisms to float close to each other.  genome. This will cause genomes from similar organisms to float close to each other.
# Line 2666  Line 3310 
3310          my ($taxonomy) = $self->GetFlat(['IsLocatedIn', 'HasContig', 'Genome'], "IsLocatedIn(from-link) = ?",          my ($taxonomy) = $self->GetFlat(['IsLocatedIn', 'HasContig', 'Genome'], "IsLocatedIn(from-link) = ?",
3311                                          [$fid], 'Genome(taxonomy)');                                          [$fid], 'Genome(taxonomy)');
3312          # Add this feature to the hash buffer.          # Add this feature to the hash buffer.
3313          Tracer::AddToListMap(\%hashBuffer, $taxonomy, $fid);          push @{$hashBuffer{$taxonomy}}, $fid;
3314      }      }
3315      # Sort the keys and get the elements.      # Sort the keys and get the elements.
3316      my @retVal = ();      my @retVal = ();
# Line 2677  Line 3321 
3321      return @retVal;      return @retVal;
3322  }  }
3323    
 =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;  
 }  
   
3324  =head3 Protein  =head3 Protein
3325    
3326  C<< my $protein = Sprout::Protein($sequence, $table); >>      my $protein = Sprout::Protein($sequence, $table);
3327    
3328  Translate a DNA sequence into a protein sequence.  Translate a DNA sequence into a protein sequence.
3329    
# Line 2868  Line 3393 
3393      # Loop through the input triples.      # Loop through the input triples.
3394      my $n = length $sequence;      my $n = length $sequence;
3395      for (my $i = 0; $i < $n; $i += 3) {      for (my $i = 0; $i < $n; $i += 3) {
3396          # Get the current triple from the sequence.          # Get the current triple from the sequence. Note we convert to
3397          my $triple = substr($sequence, $i, 3);          # upper case to insure a match.
3398            my $triple = uc substr($sequence, $i, 3);
3399          # Translate it using the table.          # Translate it using the table.
3400          my $protein = "X";          my $protein = "X";
3401          if (exists $table->{$triple}) { $protein = $table->{$triple}; }          if (exists $table->{$triple}) { $protein = $table->{$triple}; }
# Line 2883  Line 3409 
3409    
3410  =head3 LoadInfo  =head3 LoadInfo
3411    
3412  C<< my ($dirName, @relNames) = $sprout->LoadInfo(); >>      my ($dirName, @relNames) = $sprout->LoadInfo();
3413    
3414  Return the name of the directory from which data is to be loaded and a list of the relation  Return the name of the directory from which data is to be loaded and a list of the relation
3415  names. This information is useful when trying to analyze what needs to be put where in order  names. This information is useful when trying to analyze what needs to be put where in order
# Line 2897  Line 3423 
3423      # Create the return list, priming it with the name of the data directory.      # Create the return list, priming it with the name of the data directory.
3424      my @retVal = ($self->{_options}->{dataDir});      my @retVal = ($self->{_options}->{dataDir});
3425      # Concatenate the table names.      # Concatenate the table names.
3426      push @retVal, $self->{_erdb}->GetTableNames();      push @retVal, $self->GetTableNames();
3427      # Return the result.      # Return the result.
3428      return @retVal;      return @retVal;
3429  }  }
3430    
3431  =head3 LowBBHs  =head3 BBHMatrix
3432    
3433  C<< my %bbhMap = $sprout->GoodBBHs($featureID, $cutoff); >>      my $bbhMap = $sprout->BBHMatrix($genomeID, $cutoff, @targets);
3434    
3435  Return the bidirectional best hits of a feature whose score is no greater than a  Find all the bidirectional best hits for the features of a genome in a
3436  specified cutoff value. A higher cutoff value will allow inclusion of hits with  specified list of target genomes. The return value will be a hash mapping
3437  a greater score. The value returned is a map of feature IDs to scores.  features in the original genome to their bidirectional best hits in the
3438    target genomes.
3439    
3440  =over 4  =over 4
3441    
3442  =item featureID  =item genomeID
3443    
3444  ID of the feature whose best hits are desired.  ID of the genome whose features are to be examined for bidirectional best hits.
3445    
3446  =item cutoff  =item cutoff
3447    
3448  Maximum permissible score for inclusion in the results.  A cutoff value. Only hits with a score lower than the cutoff will be returned.
3449    
3450    =item targets
3451    
3452    List of target genomes. Only pairs originating in the original
3453    genome and landing in one of the target genomes will be returned.
3454    
3455  =item RETURN  =item RETURN
3456    
3457  Returns a hash mapping feature IDs to scores.  Returns a reference to a hash mapping each feature in the original genome
3458    to a sub-hash mapping its BBH pegs in the target genomes to their scores.
3459    
3460  =back  =back
3461    
3462  =cut  =cut
3463  #: Return Type %;  
3464  sub LowBBHs {  sub BBHMatrix {
3465      # Get the parsameters.      # Get the parameters.
3466      my ($self, $featureID, $cutoff) = @_;      my ($self, $genomeID, $cutoff, @targets) = @_;
3467      # Create the return hash.      # Declare the return variable.
3468      my %retVal = ();      my %retVal = ();
3469      # Create a query to get the desired BBHs.      # Ask for the BBHs.
3470      my @bbhList = $self->GetAll(['IsBidirectionalBestHitOf'],      my @bbhList = FIGRules::BatchBBHs("fig|$genomeID.%", $cutoff, @targets);
3471                                  'IsBidirectionalBestHitOf(sc) <= ? AND IsBidirectionalBestHitOf(from-link) = ?',      Trace("Retrieved " . scalar(@bbhList) . " BBH results.") if T(3);
3472                                  [$cutoff, $featureID],      # We now have a set of 4-tuples that we need to convert into a hash of hashes.
3473                                  ['IsBidirectionalBestHitOf(to-link)', 'IsBidirectionalBestHitOf(sc)']);      for my $bbhData (@bbhList) {
3474      # Form the results into the return hash.          my ($peg1, $peg2, $score) = @{$bbhData};
3475      for my $pair (@bbhList) {          if (! exists $retVal{$peg1}) {
3476          $retVal{$pair->[0]} = $pair->[1];              $retVal{$peg1} = { $peg2 => $score };
3477            } else {
3478                $retVal{$peg1}->{$peg2} = $score;
3479            }
3480      }      }
3481      # Return the result.      # Return the result.
3482      return %retVal;      return \%retVal;
3483  }  }
3484    
 =head3 GetGroups  
3485    
3486  C<< my %groups = $sprout->GetGroups(\@groupList); >>  =head3 SimMatrix
3487    
3488  Return a hash mapping each group to the IDs of the genomes in the group.      my %simMap = $sprout->SimMatrix($genomeID, $cutoff, @targets);
 A list of groups may be specified, in which case only those groups will be  
 shown. Alternatively, if no parameter is supplied, all groups will be  
 included. Genomes that are not in any group are omitted.  
3489    
3490  =cut  Find all the similarities for the features of a genome in a
3491  #: Return Type %@;  specified list of target genomes. The return value will be a hash mapping
3492  sub GetGroups {  features in the original genome to their similarites in the
3493      # Get the parameters.  target genomes.
3494      my ($self, $groupList) = @_;  
3495      # Declare the return value.  =over 4
3496      my %retVal = ();  
3497      # Determine whether we are getting all the groups or just some.  =item genomeID
3498      if (defined $groupList) {  
3499          # Here we have a group list. Loop through them individually,  ID of the genome whose features are to be examined for similarities.
3500          # getting a list of the relevant genomes.  
3501    =item cutoff
3502    
3503    A cutoff value. Only hits with a score lower than the cutoff will be returned.
3504    
3505    =item targets
3506    
3507    List of target genomes. Only pairs originating in the original
3508    genome and landing in one of the target genomes will be returned.
3509    
3510    =item RETURN
3511    
3512    Returns a hash mapping each feature in the original genome to a hash mapping its
3513    similar pegs in the target genomes to their scores.
3514    
3515    =back
3516    
3517    =cut
3518    
3519    sub SimMatrix {
3520        # Get the parameters.
3521        my ($self, $genomeID, $cutoff, @targets) = @_;
3522        # Declare the return variable.
3523        my %retVal = ();
3524        # Get the list of features in the source organism.
3525        my @fids = $self->FeaturesOf($genomeID);
3526        # Ask for the sims. We only want similarities to fig features.
3527        my $simList = FIGRules::GetNetworkSims($self, \@fids, {}, 1000, $cutoff, "fig");
3528        if (! defined $simList) {
3529            Confess("Unable to retrieve similarities from server.");
3530        } else {
3531            Trace("Processing sims.") if T(3);
3532            # We now have a set of sims that we need to convert into a hash of hashes. First, we
3533            # Create a hash for the target genomes.
3534            my %targetHash = map { $_ => 1 } @targets;
3535            for my $simData (@{$simList}) {
3536                # Get the PEGs and the score.
3537                my ($peg1, $peg2, $score) = ($simData->id1, $simData->id2, $simData->psc);
3538                # Insure the second ID is in the target list.
3539                my ($genome2) = FIGRules::ParseFeatureID($peg2);
3540                if (exists $targetHash{$genome2}) {
3541                    # Here it is. Now we need to add it to the return hash. How we do that depends
3542                    # on whether or not $peg1 is new to us.
3543                    if (! exists $retVal{$peg1}) {
3544                        $retVal{$peg1} = { $peg2 => $score };
3545                    } else {
3546                        $retVal{$peg1}->{$peg2} = $score;
3547                    }
3548                }
3549            }
3550        }
3551        # Return the result.
3552        return %retVal;
3553    }
3554    
3555    
3556    =head3 LowBBHs
3557    
3558        my %bbhMap = $sprout->LowBBHs($featureID, $cutoff);
3559    
3560    Return the bidirectional best hits of a feature whose score is no greater than a
3561    specified cutoff value. A higher cutoff value will allow inclusion of hits with
3562    a greater score. The value returned is a map of feature IDs to scores.
3563    
3564    =over 4
3565    
3566    =item featureID
3567    
3568    ID of the feature whose best hits are desired.
3569    
3570    =item cutoff
3571    
3572    Maximum permissible score for inclusion in the results.
3573    
3574    =item RETURN
3575    
3576    Returns a hash mapping feature IDs to scores.
3577    
3578    =back
3579    
3580    =cut
3581    #: Return Type %;
3582    sub LowBBHs {
3583        # Get the parsameters.
3584        my ($self, $featureID, $cutoff) = @_;
3585        # Create the return hash.
3586        my %retVal = ();
3587        # Query for the desired BBHs.
3588        my $bbhList = FIGRules::BBHData($featureID, $cutoff);
3589        # Form the results into the return hash.
3590        for my $pair (@$bbhList) {
3591            my $fid = $pair->[0];
3592            if ($self->Exists('Feature', $fid)) {
3593                $retVal{$fid} = $pair->[1];
3594            }
3595        }
3596        # Return the result.
3597        return %retVal;
3598    }
3599    
3600    =head3 Sims
3601    
3602        my $simList = $sprout->Sims($fid, $maxN, $maxP, $select, $max_expand, $filters);
3603    
3604    Get a list of similarities for a specified feature. Similarity information is not kept in the
3605    Sprout database; rather, they are retrieved from a network server. The similarities are
3606    returned as B<Sim> objects. A Sim object is actually a list reference that has been blessed
3607    so that its elements can be accessed by name.
3608    
3609    Similarities can be either raw or expanded. The raw similarities are basic
3610    hits between features with similar DNA. Expanding a raw similarity drags in any
3611    features considered substantially identical. So, for example, if features B<A1>,
3612    B<A2>, and B<A3> are all substantially identical to B<A>, then a raw similarity
3613    B<[C,A]> would be expanded to B<[C,A] [C,A1] [C,A2] [C,A3]>.
3614    
3615    =over 4
3616    
3617    =item fid
3618    
3619    ID of the feature whose similarities are desired, or reference to a list of IDs
3620    of features whose similarities are desired.
3621    
3622    =item maxN
3623    
3624    Maximum number of similarities to return.
3625    
3626    =item maxP
3627    
3628    Minumum allowable similarity score.
3629    
3630    =item select
3631    
3632    Selection criterion: C<raw> means only raw similarities are returned; C<fig>
3633    means only similarities to FIG features are returned; C<all> means all expanded
3634    similarities are returned; and C<figx> means similarities are expanded until the
3635    number of FIG features equals the maximum.
3636    
3637    =item max_expand
3638    
3639    The maximum number of features to expand.
3640    
3641    =item filters
3642    
3643    Reference to a hash containing filter information, or a subroutine that can be
3644    used to filter the sims.
3645    
3646    =item RETURN
3647    
3648    Returns a reference to a list of similarity objects, or C<undef> if an error
3649    occurred.
3650    
3651    =back
3652    
3653    =cut
3654    
3655    sub Sims {
3656        # Get the parameters.
3657        my ($self, $fid, $maxN, $maxP, $select, $max_expand, $filters) = @_;
3658        # Create the shim object to test for deleted FIDs.
3659        my $shim = FidCheck->new($self);
3660        # Ask the network for sims.
3661        my $retVal = FIGRules::GetNetworkSims($shim, $fid, {}, $maxN, $maxP, $select, $max_expand, $filters);
3662        # Return the result.
3663        return $retVal;
3664    }
3665    
3666    =head3 IsAllGenomes
3667    
3668        my $flag = $sprout->IsAllGenomes(\@list, \@checkList);
3669    
3670    Return TRUE if all genomes in the second list are represented in the first list at
3671    least one. Otherwise, return FALSE. If the second list is omitted, the first list is
3672    compared to a list of all the genomes.
3673    
3674    =over 4
3675    
3676    =item list
3677    
3678    Reference to the list to be compared to the second list.
3679    
3680    =item checkList (optional)
3681    
3682    Reference to the comparison target list. Every genome ID in this list must occur at
3683    least once in the first list. If this parameter is omitted, a list of all the genomes
3684    is used.
3685    
3686    =item RETURN
3687    
3688    Returns TRUE if every item in the second list appears at least once in the
3689    first list, else FALSE.
3690    
3691    =back
3692    
3693    =cut
3694    
3695    sub IsAllGenomes {
3696        # Get the parameters.
3697        my ($self, $list, $checkList) = @_;
3698        # Supply the checklist if it was omitted.
3699        $checkList = [$self->Genomes()] if ! defined($checkList);
3700        # Create a hash of the original list.
3701        my %testList = map { $_ => 1 } @{$list};
3702        # Declare the return variable. We assume that the representation
3703        # is complete and stop at the first failure.
3704        my $retVal = 1;
3705        my $n = scalar @{$checkList};
3706        for (my $i = 0; $retVal && $i < $n; $i++) {
3707            if (! $testList{$checkList->[$i]}) {
3708                $retVal = 0;
3709            }
3710        }
3711        # Return the result.
3712        return $retVal;
3713    }
3714    
3715    =head3 GetGroups
3716    
3717        my %groups = $sprout->GetGroups(\@groupList);
3718    
3719    Return a hash mapping each group to the IDs of the genomes in the group.
3720    A list of groups may be specified, in which case only those groups will be
3721    shown. Alternatively, if no parameter is supplied, all groups will be
3722    included. Genomes that are not in any group are omitted.
3723    
3724    =cut
3725    #: Return Type %@;
3726    sub GetGroups {
3727        # Get the parameters.
3728        my ($self, $groupList) = @_;
3729        # Declare the return value.
3730        my %retVal = ();
3731        # Determine whether we are getting all the groups or just some.
3732        if (defined $groupList) {
3733            # Here we have a group list. Loop through them individually,
3734            # getting a list of the relevant genomes.
3735          for my $group (@{$groupList}) {          for my $group (@{$groupList}) {
3736              my @genomeIDs = $self->GetFlat(['Genome'], "Genome(group-name) = ?",              my @genomeIDs = $self->GetFlat(['Genome'], "Genome(primary-group) = ?",
3737                  [$group], "Genome(id)");                  [$group], "Genome(id)");
3738              $retVal{$group} = \@genomeIDs;              $retVal{$group} = \@genomeIDs;
3739          }          }
# Line 2975  Line 3741 
3741          # 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
3742          # of the genome records, putting each one found into the appropriate          # of the genome records, putting each one found into the appropriate
3743          # 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
3744          # in groups are included in the return set.          # in real NMPDR groups are included in the return set.
3745          my @genomes = $self->GetAll(['Genome'], "Genome(group-name) > ' '", [],          my @genomes = $self->GetAll(['Genome'], "Genome(primary-group) <> ?",
3746                                      ['Genome(id)', 'Genome(group-name)']);                                      [$FIG_Config::otherGroup], ['Genome(id)', 'Genome(primary-group)']);
3747          # Loop through the genomes found.          # Loop through the genomes found.
3748          for my $genome (@genomes) {          for my $genome (@genomes) {
3749              # Pop this genome's ID off the current list.              # Get the genome ID and group, and add this genome to the group's list.
3750              my @groups = @{$genome};              my ($genomeID, $group) = @{$genome};
3751              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, $genomeID);  
             }  
3752          }          }
3753      }      }
3754      # Return the hash we just built.      # Return the hash we just built.
# Line 2996  Line 3757 
3757    
3758  =head3 MyGenomes  =head3 MyGenomes
3759    
3760  C<< my @genomes = Sprout::MyGenomes($dataDir); >>      my @genomes = Sprout::MyGenomes($dataDir);
3761    
3762  Return a list of the genomes to be included in the Sprout.  Return a list of the genomes to be included in the Sprout.
3763    
# Line 3028  Line 3789 
3789    
3790  =head3 LoadFileName  =head3 LoadFileName
3791    
3792  C<< my $fileName = Sprout::LoadFileName($dataDir, $tableName); >>      my $fileName = Sprout::LoadFileName($dataDir, $tableName);
3793    
3794  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
3795  directory.  directory.
# Line 3067  Line 3828 
3828      return $retVal;      return $retVal;
3829  }  }
3830    
3831    =head3 DeleteGenome
3832    
3833        my $stats = $sprout->DeleteGenome($genomeID, $testFlag);
3834    
3835    Delete a genome from the database.
3836    
3837    =over 4
3838    
3839    =item genomeID
3840    
3841    ID of the genome to delete
3842    
3843    =item testFlag
3844    
3845    If TRUE, then the DELETE statements will be traced, but no deletions will occur.
3846    
3847    =item RETURN
3848    
3849    Returns a statistics object describing the rows deleted.
3850    
3851    =back
3852    
3853    =cut
3854    #: Return Type $%;
3855    sub DeleteGenome {
3856        # Get the parameters.
3857        my ($self, $genomeID, $testFlag) = @_;
3858        # Perform the delete for the genome's features.
3859        my $retVal = $self->Delete('Feature', "fig|$genomeID.%", testMode => $testFlag);
3860        # Perform the delete for the primary genome data.
3861        my $stats = $self->Delete('Genome', $genomeID, testMode => $testFlag);
3862        $retVal->Accumulate($stats);
3863        # Return the result.
3864        return $retVal;
3865    }
3866    
3867    =head3 Fix
3868    
3869        my %fixedHash = $sprout->Fix(%groupHash);
3870    
3871    Prepare a genome group hash (like that returned by L</GetGroups>) for processing.
3872    The groups will be combined into the appropriate super-groups.
3873    
3874    =over 4
3875    
3876    =item groupHash
3877    
3878    Hash to be fixed up.
3879    
3880    =item RETURN
3881    
3882    Returns a fixed-up version of the hash.
3883    
3884    =back
3885    
3886    =cut
3887    
3888    sub Fix {
3889        # Get the parameters.
3890        my ($self, %groupHash) = @_;
3891        # Create the result hash.
3892        my %retVal = ();
3893        # Copy over the genomes.
3894        for my $groupID (keys %groupHash) {
3895            # Get the super-group name.
3896            my $realGroupID = $self->SuperGroup($groupID);
3897            # Append this group's genomes into the result hash
3898            # using the super-group name.
3899            push @{$retVal{$realGroupID}}, @{$groupHash{$groupID}};
3900        }
3901        # Return the result hash.
3902        return %retVal;
3903    }
3904    
3905    =head3 GroupPageName
3906    
3907        my $name = $sprout->GroupPageName($group);
3908    
3909    Return the name of the page for the specified NMPDR group.
3910    
3911    =over 4
3912    
3913    =item group
3914    
3915    Name of the relevant group.
3916    
3917    =item RETURN
3918    
3919    Returns the relative page name (e.g. C<../content/campy.php>). If the group file is not in
3920    memory it will be read in.
3921    
3922    =back
3923    
3924    =cut
3925    
3926    sub GroupPageName {
3927        # Get the parameters.
3928        my ($self, $group) = @_;
3929        # Check for the group file data.
3930        my %superTable = $self->CheckGroupFile();
3931        # Compute the real group name.
3932        my $realGroup = $self->SuperGroup($group);
3933        # Get the associated page name.
3934        my $retVal = "../content/$superTable{$realGroup}->{page}";
3935        # Return the result.
3936        return $retVal;
3937    }
3938    
3939    
3940    =head3 AddProperty
3941    
3942        $sprout->AddProperty($featureID, $key, @values);
3943    
3944    Add a new attribute value (Property) to a feature.
3945    
3946    =over 4
3947    
3948    =item peg
3949    
3950    ID of the feature to which the attribute is to be added.
3951    
3952    =item key
3953    
3954    Name of the attribute (key).
3955    
3956    =item values
3957    
3958    Values of the attribute.
3959    
3960    =back
3961    
3962    =cut
3963    #: Return Type ;
3964    sub AddProperty {
3965        # Get the parameters.
3966        my ($self, $featureID, $key, @values) = @_;
3967        # Add the property using the attached attributes object.
3968        $self->ca->AddAttribute($featureID, $key, @values);
3969    }
3970    
3971    =head3 CheckGroupFile
3972    
3973        my %groupData = $sprout->CheckGroupFile();
3974    
3975    Get the group file hash. The group file hash describes the relationship
3976    between a group and the super-group to which it belongs for purposes of
3977    display. The super-group name is computed from the first capitalized word
3978    in the actual group name. For each super-group, the group file contains
3979    the page name and a list of the species expected to be in the group.
3980    Each species is specified by a genus and a species name. A species name
3981    of C<0> implies an entire genus.
3982    
3983    This method returns a hash from super-group names to a hash reference. Each
3984    resulting hash reference contains the following fields.
3985    
3986    =over 4
3987    
3988    =item page
3989    
3990    The super-group's web page in the NMPDR.
3991    
3992    =item contents
3993    
3994    A list of 2-tuples, each containing a genus name followed by a species name
3995    (or 0, indicating all species). This list indicates which organisms belong
3996    in the super-group.
3997    
3998    =back
3999    
4000    =cut
4001    
4002    sub CheckGroupFile {
4003        # Get the parameters.
4004        my ($self) = @_;
4005        # Check to see if we already have this hash.
4006        if (! defined $self->{groupHash}) {
4007            # We don't, so we need to read it in.
4008            my %groupHash;
4009            # Read the group file.
4010            my @groupLines = Tracer::GetFile("$FIG_Config::sproutData/groups.tbl");
4011            # Loop through the list of sort-of groups.
4012            for my $groupLine (@groupLines) {
4013                my ($name, $page, @contents) = split /\t/, $groupLine;
4014                $groupHash{$name} = { page => $page,
4015                                      contents => [ map { [ split /\s*,\s*/, $_ ] } @contents ]
4016                                    };
4017            }
4018            # Save the hash.
4019            $self->{groupHash} = \%groupHash;
4020        }
4021        # Return the result.
4022        return %{$self->{groupHash}};
4023    }
4024    
4025    =head2 Virtual Methods
4026    
4027    =head3 CleanKeywords
4028    
4029        my $cleanedString = $sprout->CleanKeywords($searchExpression);
4030    
4031    Clean up a search expression or keyword list. This involves converting the periods
4032    in EC numbers to underscores, converting non-leading minus signs to underscores,
4033    a vertical bar or colon to an apostrophe, and forcing lower case for all alphabetic
4034    characters. In addition, any extra spaces are removed.
4035    
4036    =over 4
4037    
4038    =item searchExpression
4039    
4040    Search expression or keyword list to clean. Note that a search expression may
4041    contain boolean operators which need to be preserved. This includes leading
4042    minus signs.
4043    
4044    =item RETURN
4045    
4046    Cleaned expression or keyword list.
4047    
4048    =back
4049    
4050    =cut
4051    
4052    sub CleanKeywords {
4053        # Get the parameters.
4054        my ($self, $searchExpression) = @_;
4055        # Get the stemmer.
4056        my $stemmer = $self->GetStemmer();
4057        # Convert the search expression using the stemmer.
4058        my $retVal = $stemmer->PrepareSearchExpression($searchExpression);
4059        Trace("Cleaned keyword list for \"$searchExpression\" is \"$retVal\".") if T(3);
4060        # Return the result.
4061        return $retVal;
4062    }
4063    
4064    =head3 GetSourceObject
4065    
4066        my $source = $erdb->GetSourceObject();
4067    
4068    Return the object to be used in creating load files for this database.
4069    
4070    =cut
4071    
4072    sub GetSourceObject {
4073        # Get the parameters.
4074        my ($self) = @_;
4075        # Check to see if we already have a source object.
4076        my $retVal = $self->{_fig};
4077        if (! defined $retVal) {
4078            # No, so create one.
4079            require FIG;
4080            $retVal = FIG->new();
4081        }
4082        # Return the object.
4083        return $retVal;
4084    }
4085    
4086    =head3 SectionList
4087    
4088        my @sections = $erdb->SectionList();
4089    
4090    Return a list of the names for the different data sections used when loading this database.
4091    The default is a single string, in which case there is only one section representing the
4092    entire database.
4093    
4094    =cut
4095    
4096    sub SectionList {
4097        # Get the parameters.
4098        my ($self, $source) = @_;
4099        # Ask the BaseSproutLoader for a section list.
4100        require BaseSproutLoader;
4101        my @retVal = BaseSproutLoader::GetSectionList($self);
4102        # Return the list.
4103        return @retVal;
4104    }
4105    
4106    =head3 Loader
4107    
4108        my $groupLoader = $erdb->Loader($groupName, $options);
4109    
4110    Return an [[ERDBLoadGroupPm]] object for the specified load group. This method is used
4111    by [[ERDBGeneratorPl]] to create the load group objects. If you are not using
4112    [[ERDBGeneratorPl]], you don't need to override this method.
4113    
4114    =over 4
4115    
4116    =item groupName
4117    
4118    Name of the load group whose object is to be returned. The group name is
4119    guaranteed to be a single word with only the first letter capitalized.
4120    
4121    =item options
4122    
4123    Reference to a hash of command-line options.
4124    
4125    =item RETURN
4126    
4127    Returns an [[ERDBLoadGroupPm]] object that can be used to process the specified load group
4128    for this database.
4129    
4130    =back
4131    
4132    =cut
4133    
4134    sub Loader {
4135        # Get the parameters.
4136        my ($self, $groupName, $options) = @_;
4137        # Compute the loader name.
4138        my $loaderClass = "${groupName}SproutLoader";
4139        # Pull in its definition.
4140        require "$loaderClass.pm";
4141        # Create an object for it.
4142        my $retVal = eval("$loaderClass->new(\$self, \$options)");
4143        # Insure it worked.
4144        Confess("Could not create $loaderClass object: $@") if $@;
4145        # Return it to the caller.
4146        return $retVal;
4147    }
4148    
4149    
4150    =head3 LoadGroupList
4151    
4152        my @groups = $erdb->LoadGroupList();
4153    
4154    Returns a list of the names for this database's load groups. This method is used
4155    by [[ERDBGeneratorPl]] when the user wishes to load all table groups. The default
4156    is a single group called 'All' that loads everything.
4157    
4158    =cut
4159    
4160    sub LoadGroupList {
4161        # Return the list.
4162        return qw(Genome Subsystem Annotation Property Source Reaction Synonym Feature Drug);
4163    }
4164    
4165    =head3 LoadDirectory
4166    
4167        my $dirName = $erdb->LoadDirectory();
4168    
4169    Return the name of the directory in which load files are kept. The default is
4170    the FIG temporary directory, which is a really bad choice, but it's always there.
4171    
4172    =cut
4173    
4174    sub LoadDirectory {
4175        # Get the parameters.
4176        my ($self) = @_;
4177        # Return the directory name.
4178        return $self->{dataDir};
4179    }
4180    
4181  =head2 Internal Utility Methods  =head2 Internal Utility Methods
4182    
4183    =head3 GetStemmer
4184    
4185        my $stermmer = $sprout->GetStemmer();
4186    
4187    Return the stemmer object for this database.
4188    
4189    =cut
4190    
4191    sub GetStemmer {
4192        # Get the parameters.
4193        my ($self) = @_;
4194        # Declare the return variable.
4195        my $retVal = $self->{stemmer};
4196        if (! defined $retVal) {
4197            # We don't have one pre-built, so we build and save it now.
4198            $retVal = BioWords->new(exceptions => "$FIG_Config::sproutData/Exceptions.txt",
4199                                     stops => "$FIG_Config::sproutData/StopWords.txt",
4200                                     cache => 0);
4201            $self->{stemmer} = $retVal;
4202        }
4203        # Return the result.
4204        return $retVal;
4205    }
4206    
4207  =head3 ParseAssignment  =head3 ParseAssignment
4208    
4209  Parse annotation text to determine whether or not it is a functional assignment. If it is,  Parse annotation text to determine whether or not it is a functional assignment. If it is,
# Line 3077  Line 4212 
4212    
4213  A functional assignment is always of the form  A functional assignment is always of the form
4214    
4215      I<XXXX>C<\nset >I<YYYY>C< function to\n>I<ZZZZZ>      set YYYY function to
4216        ZZZZ
4217    
4218  where I<XXXX> is the B<assigning user>, I<YYYY> is the B<user>, and I<ZZZZ> is the  where I<YYYY> is the B<user>, and I<ZZZZ> is the actual functional role. In most cases,
4219  actual functional role. In most cases, the user and the assigning user will be the  the user and the assigning user (from MadeAnnotation) will be the same, but that is
4220  same, but that is not always the case.  not always the case.
4221    
4222    In addition, the functional role may contain extra data that is stripped, such as
4223    terminating spaces or a comment separated from the rest of the text by a tab.
4224    
4225  This is a static method.  This is a static method.
4226    
4227  =over 4  =over 4
4228    
4229    =item user
4230    
4231    Name of the assigning user.
4232    
4233  =item text  =item text
4234    
4235  Text of the annotation.  Text of the annotation.
# Line 3102  Line 4245 
4245    
4246  sub _ParseAssignment {  sub _ParseAssignment {
4247      # Get the parameters.      # Get the parameters.
4248      my ($text) = @_;      my ($user, $text) = @_;
4249      # Declare the return value.      # Declare the return value.
4250      my @retVal = ();      my @retVal = ();
4251      # Check to see if this is a functional assignment.      # Check to see if this is a functional assignment.
4252      my ($user, $type, $function) = split(/\n/, $text);      my ($type, $function) = split(/\n/, $text);
4253      if ($type =~ m/^set ([^ ]+) function to$/i) {      if ($type =~ m/^set function to$/i) {
4254          # Here it is, so we return the user name (which is in $1), the functional role text,          # Here we have an assignment without a user, so we use the incoming user ID.
4255          # and the assigning user.          @retVal = ($user, $function);
4256          @retVal = ($1, $function, $user);      } elsif ($type =~ m/^set (\S+) function to$/i) {
4257            # Here we have an assignment with a user that is passed back to the caller.
4258            @retVal = ($1, $function);
4259        }
4260        # If we have an assignment, we need to clean the function text. There may be
4261        # extra junk at the end added as a note from the user.
4262        if (defined( $retVal[1] )) {
4263            $retVal[1] =~ s/(\t\S)?\s*$//;
4264      }      }
4265      # Return the result list.      # Return the result list.
4266      return @retVal;      return @retVal;
4267  }  }
4268    
4269    =head3 _CheckFeature
4270    
4271        my $flag = $sprout->_CheckFeature($fid);
4272    
4273    Return TRUE if the specified FID is probably an NMPDR feature ID, else FALSE.
4274    
4275    =over 4
4276    
4277    =item fid
4278    
4279    Feature ID to check.
4280    
4281    =item RETURN
4282    
4283    Returns TRUE if the FID is for one of the NMPDR genomes, else FALSE.
4284    
4285    =back
4286    
4287    =cut
4288    
4289    sub _CheckFeature {
4290        # Get the parameters.
4291        my ($self, $fid) = @_;
4292        # Insure we have a genome hash.
4293        my $genomes = $self->_GenomeHash();
4294        # Get the feature's genome ID.
4295        my ($genomeID) = FIGRules::ParseFeatureID($fid);
4296        # Return an indicator of whether or not the genome ID is in the hash.
4297        return ($self->{genomeHash}->{$genomeID} ? 1 : 0);
4298    }
4299    
4300  =head3 FriendlyTimestamp  =head3 FriendlyTimestamp
4301    
4302  Convert a time number to a user-friendly time stamp for display.  Convert a time number to a user-friendly time stamp for display.
# Line 3138  Line 4319 
4319    
4320  sub FriendlyTimestamp {  sub FriendlyTimestamp {
4321      my ($timeValue) = @_;      my ($timeValue) = @_;
4322      my $retVal = strftime("%a %b %e %H:%M:%S %Y", localtime($timeValue));      my $retVal = localtime($timeValue);
4323      return $retVal;      return $retVal;
4324  }  }
4325    
 =head3 AddProperty  
4326    
4327  C<< my  = $sprout->AddProperty($featureID, $key, $value, $url); >>  =head3 Hint
4328    
4329  Add a new attribute value (Property) to a feature. In the SEED system, attributes can      my $htmlText = SearchHelper::Hint($wikiPage, $hintText);
4330  be added to almost any object. In Sprout, they can only be added to features. In  
4331  Sprout, attributes are implemented using I<properties>. A property represents a key/value  Return the HTML for a small question mark that displays the specified hint text when it is clicked.
4332  pair. If the particular key/value pair coming in is not already in the database, a new  This HTML can be put in forms to provide a useful hinting mechanism.
 B<Property> record is created to hold it.  
4333    
4334  =over 4  =over 4
4335    
4336  =item peg  =item wikiPage
4337    
4338  ID of the feature to which the attribute is to be replied.  Name of the wiki page to be popped up when the hint mark is clicked.
4339    
4340  =item key  =item hintText
4341    
4342  Name of the attribute (key).  Text to display for the hint. It is raw html, but may not contain any double quotes.
4343    
4344    =item RETURN
4345    
4346    Returns the html for the hint facility. The resulting html shows a small button-like thing that
4347    uses the standard FIG popup technology.
4348    
4349    =back
4350    
4351    =cut
4352    
4353    sub Hint {
4354        # Get the parameters.
4355        my ($wikiPage, $hintText) = @_;
4356        # Escape the single quotes in the hint text.
4357        my $quotedText = $hintText;
4358        $quotedText =~ s/'/\\'/g;
4359        # Convert the wiki page name to a URL.
4360        my $wikiURL = join("", map { ucfirst $_ } split /\s+/, $wikiPage);
4361        $wikiURL = "$FIG_Config::cgi_url/wiki/view.cgi/FIG/$wikiURL";
4362        # Compute the mouseover script.
4363        my $mouseOver = "doTooltip(this, '$quotedText')";
4364        # Create the html.
4365        my $retVal = "&nbsp;<a href=\"$wikiURL\"><img src=\"$FIG_Config::cgi_url/Html/button-h.png\" class=\"helpicon\" onmouseover=\"$mouseOver\"/></a>";
4366        # Return it.
4367        return $retVal;
4368    }
4369    
4370    =head3 _GenomeHash
4371    
4372        my $gHash = $sprout->_GenomeHash();
4373    
4374    Return a hash mapping all NMPDR genome IDs to [[ERDBObjectPm]] genome objects.
4375    
4376    =cut
4377    
4378    sub _GenomeHash {
4379        # Get the parameters.
4380        my ($self) = @_;
4381        # Do we already have a filled hash?
4382        if (! $self->{genomeHashFilled}) {
4383            # No, create it.
4384            my %gHash = map { $_->PrimaryValue('id') => $_ } $self->GetList("Genome", "", []);
4385            $self->{genomeHash} = \%gHash;
4386            # Denote we have it.
4387            $self->{genomeHashFilled} = 1;
4388        }
4389        # Return the hash.
4390        return $self->{genomeHash};
4391    }
4392    
4393    =head3 _GenomeData
4394    
4395        my $genomeData = $sprout->_GenomeData($genomeID);
4396    
4397    Return an [[ERDBObjectPm]] object for the specified genome, or an undefined
4398    value if the genome does not exist.
4399    
4400  =item value  =over 4
4401    
4402    =item genomeID
4403    
4404  Value of the attribute.  ID of the desired genome.
4405    
4406  =item url  =item RETURN
4407    
4408  URL or text citation from which the property was obtained.  Returns either an [[ERDBObjectPm]] containing the genome, or an undefined value.
4409    If the genome exists, it will have been read into the genome cache.
4410    
4411  =back  =back
4412    
4413  =cut  =cut
4414  #: Return Type ;  
4415  sub AddProperty {  sub _GenomeData {
4416      # Get the parameters.      # Get the parameters.
4417      my ($self, $featureID, $key, $value, $url) = @_;      my ($self, $genomeID) = @_;
4418      # Declare the variable to hold the desired property ID.      # Are we in the genome hash?
4419      my $propID;      if (! exists $self->{genomeHash}->{$genomeID} && ! $self->{genomeHashFilled}) {
4420      # Attempt to find a property record for this key/value pair.          # The genome isn't in the hash, and the hash is not complete, so we try to
4421      my @properties = $self->GetFlat(['Property'],          # read it.
4422                                     "Property(property-name) = ? AND Property(property-value) = ?",          $self->{genomeHash}->{$genomeID} = $self->GetEntity(Genome => $genomeID);
                                    [$key, $value], 'Property(id)');  
     if (@properties) {  
         # Here the property is already in the database. We save its ID.  
         $propID = $properties[0];  
         # Here the property value does not exist. We need to generate an ID. It will be set  
         # to a number one greater than the maximum value in the database. This call to  
         # GetAll will stop after one record.  
         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 });  
4423      }      }
4424      # Now we connect the incoming feature to the property.      # Return the result.
4425      $self->Insert('HasProperty', { 'from-link' => $featureID, 'to-link' => $propID, evidence => $url });      return $self->{genomeHash}->{$genomeID};
4426  }  }
4427    
4428    =head3 _CacheGenome
4429    
4430        $sprout->_CacheGenome($genomeID, $genomeData);
4431    
4432    Store the specified genome object in the genome cache if it is already there.
4433    
4434    =over 4
4435    
4436    =item genomeID
4437    
4438    ID of the genome to store in the cache.
4439    
4440    =item genomeData
4441    
4442    An [[ERDBObjectPm]] containing at least the data for the specified genome.
4443    Note that the Genome may not be the primary object in it, so a fully-qualified
4444    field name has to be used to retrieve data from it.
4445    
4446    =back
4447    
4448    =cut
4449    
4450    sub _CacheGenome {
4451        # Get the parameters.
4452        my ($self, $genomeID, $genomeData) = @_;
4453        # Only proceed if we don't already have the genome.
4454        if (! exists $self->{genomeHash}->{$genomeID}) {
4455            $self->{genomeHash}->{$genomeID} = $genomeData;
4456        }
4457    }
4458    
4459  1;  1;

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