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revision 1.100, Mon Jul 16 19:59:50 2007 UTC revision 1.111, Wed May 7 23:11:51 2008 UTC
# Line 1  Line 1 
1  package Sprout;  package Sprout;
2    
     require Exporter;  
     use ERDB;  
     @ISA = qw(Exporter ERDB);  
3      use Data::Dumper;      use Data::Dumper;
4      use strict;      use strict;
5      use DBKernel;      use DBKernel;
# Line 17  Line 14 
14      use BasicLocation;      use BasicLocation;
15      use CustomAttributes;      use CustomAttributes;
16      use RemoteCustomAttributes;      use RemoteCustomAttributes;
17        use CGI;
18        use WikiTools;
19        use base qw(ERDB);
20    
21  =head1 Sprout Database Manipulation Object  =head1 Sprout Database Manipulation Object
22    
# Line 29  Line 29 
29  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>
30  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>.
31    
32  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' });
33    
34  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
35  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
36  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
37  L</dna_seq> returns the DNA sequence for a specified genome location.  L</DNASeq> returns the DNA sequence for a specified genome location.
38    
39  The Sprout object is a subclass of the ERDB object and inherits all its properties and methods.  The Sprout object is a subclass of the ERDB object and inherits all its properties and methods.
40    
# Line 46  Line 46 
46    
47  =head3 new  =head3 new
48    
49  C<< my $sprout = Sprout->new($dbName, \%options); >>      my $sprout = Sprout->new($dbName, \%options);
50    
51  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
52  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 80  Line 80 
80    
81  * B<noDBOpen> suppresses the connection to the database if TRUE, else FALSE  * B<noDBOpen> suppresses the connection to the database if TRUE, else FALSE
82    
83    * B<host> name of the database host
84    
85  =back  =back
86    
87  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
88  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
89  F</usr/fig/SproutData>.  F</usr/fig/SproutData>.
90    
91  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' });
92    
93  =cut  =cut
94    
# Line 110  Line 112 
112                         port         => $FIG_Config::dbport,                         port         => $FIG_Config::dbport,
113                                                          # database connection port                                                          # database connection port
114                         sock         => $FIG_Config::dbsock,                         sock         => $FIG_Config::dbsock,
115                         host         => $FIG_Config::dbhost,                         host         => $FIG_Config::sprout_host,
116                         maxSegmentLength => 4500,        # maximum feature segment length                         maxSegmentLength => 4500,        # maximum feature segment length
117                         maxSequenceLength => 8000,       # maximum contig sequence length                         maxSequenceLength => 8000,       # maximum contig sequence length
118                         noDBOpen     => 0,               # 1 to suppress the database open                         noDBOpen     => 0,               # 1 to suppress the database open
# Line 123  Line 125 
125      # Connect to the database.      # Connect to the database.
126      my $dbh;      my $dbh;
127      if (! $optionTable->{noDBOpen}) {      if (! $optionTable->{noDBOpen}) {
128            Trace("Connect data: host = $optionTable->{host}, port = $optionTable->{port}.") if T(3);
129          $dbh = DBKernel->new($optionTable->{dbType}, $dbName, $userName,          $dbh = DBKernel->new($optionTable->{dbType}, $dbName, $userName,
130                                  $password, $optionTable->{port}, $optionTable->{host}, $optionTable->{sock});                                  $password, $optionTable->{port}, $optionTable->{host}, $optionTable->{sock});
131      }      }
# Line 145  Line 148 
148          my $user = ($FIG_Config::arch eq 'win' ? 'self' : scalar(getpwent()));          my $user = ($FIG_Config::arch eq 'win' ? 'self' : scalar(getpwent()));
149          $retVal->{_ca} = CustomAttributes->new(user => $user);          $retVal->{_ca} = CustomAttributes->new(user => $user);
150      }      }
151        # Insure we have access to the stem module.
152        WikiUse('Lingua::Stem');
153        $retVal->{stemmer} = Lingua::Stem->new();
154        $retVal->{stemmer}->stem_caching({ -level => 2 });
155      # Return it.      # Return it.
156      return $retVal;      return $retVal;
157  }  }
158    
159    =head3 CoreGenomes
160    
161        my @genomes = $sprout->CoreGenomes($scope);
162    
163    Return the IDs of NMPDR genomes in the specified scope.
164    
165    =over 4
166    
167    =item scope
168    
169    Scope of the desired genomes. C<core> covers the original core genomes,
170    C<nmpdr> covers all genomes in NMPDR groups, and C<all> covers all
171    genomes in the system.
172    
173    =item RETURN
174    
175    Returns a list of the IDs for the genomes in the specified scope.
176    
177    =back
178    
179    =cut
180    
181    sub CoreGenomes {
182        # Get the parameters.
183        my ($self, $scope) = @_;
184        # Declare the return variable.
185        my @retVal = ();
186        # If we want all genomes, then this is easy.
187        if ($scope eq 'all') {
188            @retVal = $self->Genomes();
189        } else {
190            # Here we're dealing with groups. Get the hash of all the
191            # genome groups.
192            my %groups = $self->GetGroups();
193            # Loop through the groups, keeping the ones that we want.
194            for my $group (keys %groups) {
195                # Decide if we want to keep this group.
196                my $keepGroup = 0;
197                if ($scope eq 'nmpdr') {
198                    # NMPDR mode: keep all groups.
199                    $keepGroup = 1;
200                } elsif ($scope eq 'core') {
201                    # CORE mode. Only keep real core groups.
202                    if (grep { $group =~ /$_/ } @{$FIG_Config::realCoreGroups}) {
203                        $keepGroup = 1;
204                    }
205                }
206                # Add this group if we're keeping it.
207                if ($keepGroup) {
208                    push @retVal, @{$groups{$group}};
209                }
210            }
211        }
212        # Return the result.
213        return @retVal;
214    }
215    
216    =head3 SuperGroup
217    
218        my $superGroup = $sprout->SuperGroup($groupName);
219    
220    Return the name of the super-group containing the specified NMPDR genome
221    group. If no appropriate super-group can be found, an error will be
222    thrown.
223    
224    =over 4
225    
226    =item groupName
227    
228    Name of the group whose super-group is desired.
229    
230    =item RETURN
231    
232    Returns the name of the super-group containing the incoming group.
233    
234    =back
235    
236    =cut
237    
238    sub SuperGroup {
239        # Get the parameters.
240        my ($self, $groupName) = @_;
241        # Declare the return variable.
242        my $retVal;
243        # Get the group hash.
244        my %groupHash = $self->CheckGroupFile();
245        # Find the super-group genus.
246        $groupName =~ /([A-Z]\w+)/;
247        my $nameThing = $1;
248        # See if it's directly in the group hash.
249        if (exists $groupHash{$nameThing}) {
250            # Yes, then it's our result.
251            $retVal = $nameThing;
252        } else {
253            # No, so we have to search.
254            for my $superGroup (keys %groupHash) {
255                # Get this super-group's item list.
256                my $list = $groupHash{$superGroup}->{contents};
257                # Search it.
258                if (grep { $_->[0] eq $nameThing } @{$list}) {
259                    $retVal = $superGroup;
260                }
261            }
262            # Make sure we found something.
263            if (! $retVal) {
264                Confess("No super-group found for \"$groupName\".");
265            }
266        }
267        # Return the result.
268        return $retVal;
269    }
270    
271  =head3 MaxSegment  =head3 MaxSegment
272    
273  C<< my $length = $sprout->MaxSegment(); >>      my $length = $sprout->MaxSegment();
274    
275  This method returns the maximum permissible length of a feature segment. The length is important  This method returns the maximum permissible length of a feature segment. The length is important
276  because it enables us to make reasonable guesses at how to find features inside a particular  because it enables us to make reasonable guesses at how to find features inside a particular
# Line 168  Line 287 
287    
288  =head3 MaxSequence  =head3 MaxSequence
289    
290  C<< my $length = $sprout->MaxSequence(); >>      my $length = $sprout->MaxSequence();
291    
292  This method returns the maximum permissible length of a contig sequence. A contig is broken  This method returns the maximum permissible length of a contig sequence. A contig is broken
293  into sequences in order to save memory resources. In particular, when manipulating features,  into sequences in order to save memory resources. In particular, when manipulating features,
# Line 183  Line 302 
302    
303  =head3 Load  =head3 Load
304    
305  C<< $sprout->Load($rebuild); >>;      $sprout->Load($rebuild);;
306    
307  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.
308    
# Line 223  Line 342 
342    
343  =head3 LoadUpdate  =head3 LoadUpdate
344    
345  C<< my $stats = $sprout->LoadUpdate($truncateFlag, \@tableList); >>      my $stats = $sprout->LoadUpdate($truncateFlag, \@tableList);
346    
347  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
348  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 269  Line 388 
388              Trace("No load file found for $tableName in $dataDir.") if T(0);              Trace("No load file found for $tableName in $dataDir.") if T(0);
389          } else {          } else {
390              # Attempt to load this table.              # Attempt to load this table.
391              my $result = $self->LoadTable($fileName, $tableName, $truncateFlag);              my $result = $self->LoadTable($fileName, $tableName, truncate => $truncateFlag);
392              # Accumulate the resulting statistics.              # Accumulate the resulting statistics.
393              $retVal->Accumulate($result);              $retVal->Accumulate($result);
394          }          }
# Line 280  Line 399 
399    
400  =head3 GenomeCounts  =head3 GenomeCounts
401    
402  C<< my ($arch, $bact, $euk, $vir, $env, $unk) = $sprout->GenomeCounts($complete); >>      my ($arch, $bact, $euk, $vir, $env, $unk) = $sprout->GenomeCounts($complete);
403    
404  Count the number of genomes in each domain. If I<$complete> is TRUE, only complete  Count the number of genomes in each domain. If I<$complete> is TRUE, only complete
405  genomes will be included in the counts.  genomes will be included in the counts.
# Line 325  Line 444 
444    
445  =head3 ContigCount  =head3 ContigCount
446    
447  C<< my $count = $sprout->ContigCount($genomeID); >>      my $count = $sprout->ContigCount($genomeID);
448    
449  Return the number of contigs for the specified genome ID.  Return the number of contigs for the specified genome ID.
450    
# Line 352  Line 471 
471      return $retVal;      return $retVal;
472  }  }
473    
474  =head3 GeneMenu  =head3 GenomeMenu
475    
476        my $html = $sprout->GenomeMenu(%options);
477    
478  C<< my $selectHtml = $sprout->GeneMenu(\%attributes, $filterString, \@params, $selected); >>  Generate a genome selection control with the specified name and options.
479    This control is almost but not quite the same as the genome control in the
480    B<SearchHelper> class. Eventually, the two will be combined.
481    
482  Return an HTML select menu of genomes. Each genome will be an option in the menu,  =over 4
483  and will be displayed by name with the ID and a contig count attached. The selection  
484  value will be the genome ID. The genomes will be sorted by genus/species name.  =item options
485    
486    Optional parameters for the control (see below).
487    
488    =item RETURN
489    
490    Returns the HTML for a genome selection control on a form (sometimes called a popup menu).
491    
492    =back
493    
494    The valid options are as follows.
495    
496  =over 4  =over 4
497    
498  =item attributes  =item name
499    
500  Reference to a hash mapping attributes to values for the SELECT tag generated.  Name to give this control for use in passing it to the form. The default is C<myGenomeControl>.
501    Terrible things will happen if you have two controls with the same name on the same page.
502    
503  =item filterString  =item filter
504    
505    If specified, a filter for the list of genomes to display. The filter should be in the form of a
506    list reference. The first element of the list should be the filter string, and the remaining elements
507    the filter parameters.
508    
509    =item multiSelect
510    
511    If TRUE, then the user can select multiple genomes. If FALSE, the user can only select one genome.
512    
513    =item size
514    
515    Number of rows to display in the control. The default is C<10>
516    
517    =item id
518    
519    ID to give this control. The default is the value of the C<name> option. Nothing will work correctly
520    unless this ID is unique.
521    
522    =item selected
523    
524    A comma-delimited list of selected genomes, or a reference to a list of selected genomes. The
525    default is none.
526    
527    =item class
528    
529    If specified, a style class to assign to the genome control.
530    
531    =back
532    
533    =cut
534    
535    sub GenomeMenu {
536        # Get the parameters.
537        my ($self, %options) = @_;
538        # Get the control's name and ID.
539        my $menuName = $options{name} || 'myGenomeControl';
540        my $menuID = $options{id} || $menuName;
541        # Compute the IDs for the status display.
542        my $divID = "${menuID}_status";
543        my $urlID = "${menuID}_url";
544        # Compute the code to show selected genomes in the status area.
545        my $showSelect = "showSelected('$menuID', '$divID', '$urlID', 1000)";
546        # Check for single-select or multi-select.
547        my $multiSelect = $options{multiSelect} || 0;
548        # Get the style data.
549        my $class = $options{class} || '';
550        # Get the list of pre-selected items.
551        my $selections = $options{selected} || [];
552        if (ref $selections ne 'ARRAY') {
553            $selections = [ split /\s*,\s*/, $selections ];
554        }
555        my %selected = map { $_ => } @{$selections};
556        # Extract the filter information. The default is no filtering. It can be passed as a tab-delimited
557        # string or a list reference.
558        my $filterParms = $options{filter} || "";
559        if (! ref $filterParms) {
560            $filterParms = [split /\t|\\t/, $filterParms];
561        }
562        my $filterString = shift @{$filterParms};
563        # Get a list of all the genomes in group order. In fact, we only need them ordered
564        # by name (genus,species,strain), but putting primary-group in front enables us to
565        # take advantage of an existing index.
566        my @genomeList = $self->GetAll(['Genome'], "$filterString ORDER BY Genome(primary-group), Genome(genus), Genome(species), Genome(unique-characterization)",
567                                       $filterParms,
568                                       [qw(Genome(primary-group) Genome(id) Genome(genus) Genome(species) Genome(unique-characterization) Genome(taxonomy) Genome(contigs))]);
569        # Create a hash to organize the genomes by group. Each group will contain a list of
570        # 2-tuples, the first element being the genome ID and the second being the genome
571        # name.
572        my %gHash = ();
573        for my $genome (@genomeList) {
574            # Get the genome data.
575            my ($group, $genomeID, $genus, $species, $strain, $taxonomy, $contigs) = @{$genome};
576            # Compute its name. This is the genus, species, strain (if any), and the contig count.
577            my $name = "$genus $species ";
578            $name .= "$strain " if $strain;
579            my $contigCount = ($contigs == 1 ? "" : ", $contigs contigs");
580            # Now we get the domain. The domain tells us the display style of the organism.
581            my ($domain) = split /\s*;\s*/, $taxonomy, 2;
582            # Now compute the display group. This is normally the primary group, but if the
583            # organism is supporting, we blank it out.
584            my $displayGroup = ($group eq $FIG_Config::otherGroup ? "" : $group);
585            # Push the genome into the group's list. Note that we use the real group
586            # name for the hash key here, not the display group name.
587            push @{$gHash{$group}}, [$genomeID, $name, $contigCount, $domain];
588        }
589        # We are almost ready to unroll the menu out of the group hash. The final step is to separate
590        # the supporting genomes by domain. First, we extract the NMPDR groups and sort them. They
591        # are sorted by the first capitalized word. Groups with "other" are sorted after groups
592        # that aren't "other". At some point, we will want to make this less complicated.
593        my %sortGroups = map { $_ =~ /(other)?(.*)([A-Z].+)/; "$3$1$2" => $_ }
594                             grep { $_ ne $FIG_Config::otherGroup } keys %gHash;
595        my @groups = map { $sortGroups{$_} } sort keys %sortGroups;
596        # Remember the number of NMPDR groups.
597        my $nmpdrGroupCount = scalar @groups;
598        # Loop through the supporting genomes, classifying them by domain. We'll also keep a list
599        # of the domains found.
600        my @otherGenomes = @{$gHash{$FIG_Config::otherGroup}};
601        my @domains = ();
602        for my $genomeData (@otherGenomes) {
603            my ($genomeID, $name, $contigCount, $domain) = @{$genomeData};
604            if (exists $gHash{$domain}) {
605                push @{$gHash{$domain}}, $genomeData;
606            } else {
607                $gHash{$domain} = [$genomeData];
608                push @domains, $domain;
609            }
610        }
611        # Add the domain groups at the end of the main group list. The main group list will now
612        # contain all the categories we need to display the genomes.
613        push @groups, sort @domains;
614        # Delete the supporting group.
615        delete $gHash{$FIG_Config::otherGroup};
616        # Now it gets complicated. We need a way to mark all the NMPDR genomes. We take advantage
617        # of the fact they come first in the list. We'll accumulate a count of the NMPDR genomes
618        # and use that to make the selections.
619        my $nmpdrCount = 0;
620        # Create the type counters.
621        my $groupCount = 1;
622        # Get the number of rows to display.
623        my $rows = $options{size} || 10;
624        # If we're multi-row, create an onChange event.
625        my $onChangeTag = ( $rows > 1 ? " onChange=\"$showSelect;\" onFocus=\"$showSelect;\"" : "" );
626        # Set up the multiple-select flag.
627        my $multipleTag = ($multiSelect ? " multiple" : "" );
628        # Set up the style class.
629        my $classTag = ($class ? " class=\"$class\"" : "" );
630        # Create the SELECT tag and stuff it into the output array.
631        my @lines = ("<SELECT name=\"$menuID\" id=\"$menuID\" $onChangeTag$multipleTag$classTag size=\"$rows\">");
632        # Loop through the groups.
633        for my $group (@groups) {
634            # Get the genomes in the group.
635            for my $genome (@{$gHash{$group}}) {
636                # If this is an NMPDR organism, we add an extra style and count it.
637                my $nmpdrStyle = "";
638                if ($nmpdrGroupCount > 0) {
639                    $nmpdrCount++;
640                    $nmpdrStyle = " Core";
641                }
642                # Get the organism ID, name, contig count, and domain.
643                my ($genomeID, $name, $contigCount, $domain) = @{$genome};
644                # See if we're pre-selected.
645                my $selectTag = ($selected{$genomeID} ? " SELECTED" : "");
646                # Compute the display name.
647                my $nameString = "$name ($genomeID$contigCount)";
648                # Generate the option tag.
649                my $optionTag = "<OPTION class=\"$domain$nmpdrStyle\" title=\"$group\" value=\"$genomeID\"$selectTag>$nameString</OPTION>";
650                push @lines, "    $optionTag";
651            }
652            # Record this group in the nmpdrGroup count. When that gets to 0, we've finished the NMPDR
653            # groups.
654            $nmpdrGroupCount--;
655        }
656        # Close the SELECT tag.
657        push @lines, "</SELECT>";
658        if ($rows > 1) {
659            # We're in a non-compact mode, so we need to add some selection helpers. First is
660            # the search box. This allows the user to type text and change which genomes are
661            # displayed. For multiple-select mode, we include a button that selects the displayed
662            # genes. For single-select mode, we use a plain label instead.
663            my $searchThingName = "${menuID}_SearchThing";
664            my $searchThingLabel = ($multiSelect ? "<INPUT type=\"button\" name=\"MacroSearch\" class=\"button\" value=\"Select genomes containing\" onClick=\"selectShowing('$menuID', '$searchThingName'); $showSelect;\" />"
665                                                 : "Show genomes containing");
666            push @lines, "<br />$searchThingLabel&nbsp;" .
667                         "<INPUT type=\"text\" id=\"$searchThingName\" name=\"$searchThingName\" size=\"30\" onKeyup=\"showTyped('$menuID', '$searchThingName');\" />";
668            # For multi-select mode, we also have buttons to set and clear selections.
669            if ($multiSelect) {
670                push @lines, "<INPUT type=\"button\" name=\"ClearAll\" class=\"bigButton\"  value=\"Clear All\" onClick=\"clearAll('$menuID'); $showSelect\" />";
671                push @lines, "<INPUT type=\"button\" name=\"SelectAll\" class=\"bigButton\" value=\"Select All\" onClick=\"selectAll('$menuID'); $showSelect\" />";
672                push @lines, "<INPUT type=\"button\" name=\"NMPDROnly\" class=\"bigButton\"  value=\"Select NMPDR\" onClick=\"selectSome('$menuID', $nmpdrCount, true); $showSelect;\" />";
673            }
674            # Add a hidden field we can use to generate organism page hyperlinks.
675            push @lines, "<INPUT type=\"hidden\" id=\"$urlID\" value=\"$FIG_Config::cgi_url/seedviewer.cgi?page=Organism;organism=\" />";
676            # Add the status display. This tells the user what's selected no matter where the list is scrolled.
677            push @lines, "<DIV id=\"$divID\" class=\"Panel\"></DIV>";
678        }
679        # Assemble all the lines into a string.
680        my $retVal = join("\n", @lines, "");
681        # Return the result.
682        return $retVal;
683    }
684    
 A filter string for use in selecting the genomes. The filter string must conform  
 to the rules for the C<< ERDB->Get >> method.  
685    
686  =item params  =head3 Stem
687    
688  Reference to a list of values to be substituted in for the parameter marks in      my $stem = $sprout->Stem($word);
 the filter string.  
689    
690  =item selected (optional)  Return the stem of the specified word, or C<undef> if the word is not
691    stemmable. Note that even if the word is stemmable, the stem may be
692    the same as the original word.
693    
694  ID of the genome to be initially selected.  =over 4
695    
696  =item fast (optional)  =item word
697    
698  If specified and TRUE, the contig counts will be omitted to improve performance.  Word to convert into a stem.
699    
700  =item RETURN  =item RETURN
701    
702  Returns an HTML select menu with the specified genomes as selectable options.  Returns a stem of the word (which may be the word itself), or C<undef> if
703    the word is not stemmable.
704    
705  =back  =back
706    
707  =cut  =cut
708    
709  sub GeneMenu {  sub Stem {
710      # Get the parameters.      # Get the parameters.
711      my ($self, $attributes, $filterString, $params, $selected, $fast) = @_;      my ($self, $word) = @_;
712      my $slowMode = ! $fast;      # Declare the return variable.
713      # Default to nothing selected. This prevents an execution warning if "$selected"      my $retVal;
714      # is undefined.      # See if it's stemmable.
715      $selected = "" unless defined $selected;      if ($word =~ /^[A-Za-z]+$/) {
716      Trace("Gene Menu called with slow mode \"$slowMode\" and selection \"$selected\".") if T(3);          # Compute the stem.
717      # Start the menu.          my $stemList = $self->{stemmer}->stem($word);
718      my $retVal = "<select " .          my $stem = $stemList->[0];
719          join(" ", map { "$_=\"$attributes->{$_}\"" } keys %{$attributes}) .          # Check to see if it's long enough.
720          ">\n";          if (length $stem >= 3) {
721      # Get the genomes.              # Yes, keep it.
722      my @genomes = $self->GetAll(['Genome'], $filterString, $params, ['Genome(id)',              $retVal = $stem;
723                                                                       'Genome(genus)',          } else {
724                                                                       'Genome(species)',              # No, use the original word.
725                                                                       'Genome(unique-characterization)']);              $retVal = $word;
726      # Sort them by name.          }
     my @sorted = sort { lc("$a->[1] $a->[2]") cmp lc("$b->[1] $b->[2]") } @genomes;  
     # Loop through the genomes, creating the option tags.  
     for my $genomeData (@sorted) {  
         # Get the data for this genome.  
         my ($genomeID, $genus, $species, $strain) = @{$genomeData};  
         # Get the contig count.  
         my $contigInfo = "";  
         if ($slowMode) {  
             my $count = $self->ContigCount($genomeID);  
             my $counting = ($count == 1 ? "contig" : "contigs");  
             $contigInfo = "[$count $counting]";  
         }  
         # Find out if we're selected.  
         my $selectOption = ($selected eq $genomeID ? " selected" : "");  
         # Build the option tag.  
         $retVal .= "<option value=\"$genomeID\"$selectOption>$genus $species $strain ($genomeID)$contigInfo</option>\n";  
727      }      }
     # Close the SELECT tag.  
     $retVal .= "</select>\n";  
728      # Return the result.      # Return the result.
729      return $retVal;      return $retVal;
730  }  }
731    
732    
733  =head3 Build  =head3 Build
734    
735  C<< $sprout->Build(); >>      $sprout->Build();
736    
737  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.
738  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 452  Line 749 
749    
750  =head3 Genomes  =head3 Genomes
751    
752  C<< my @genomes = $sprout->Genomes(); >>      my @genomes = $sprout->Genomes();
753    
754  Return a list of all the genome IDs.  Return a list of all the genome IDs.
755    
# Line 469  Line 766 
766    
767  =head3 GenusSpecies  =head3 GenusSpecies
768    
769  C<< my $infoString = $sprout->GenusSpecies($genomeID); >>      my $infoString = $sprout->GenusSpecies($genomeID);
770    
771  Return the genus, species, and unique characterization for a genome.  Return the genus, species, and unique characterization for a genome.
772    
# Line 501  Line 798 
798    
799  =head3 FeaturesOf  =head3 FeaturesOf
800    
801  C<< my @features = $sprout->FeaturesOf($genomeID, $ftype); >>      my @features = $sprout->FeaturesOf($genomeID, $ftype);
802    
803  Return a list of the features relevant to a specified genome.  Return a list of the features relevant to a specified genome.
804    
# Line 546  Line 843 
843    
844  =head3 FeatureLocation  =head3 FeatureLocation
845    
846  C<< my @locations = $sprout->FeatureLocation($featureID); >>      my @locations = $sprout->FeatureLocation($featureID);
847    
848  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
849  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 570  Line 867 
867  =item RETURN  =item RETURN
868    
869  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
870  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
871    wasn't found.
872    
873  =back  =back
874    
# Line 579  Line 877 
877  sub FeatureLocation {  sub FeatureLocation {
878      # Get the parameters.      # Get the parameters.
879      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
880        # Declare the return variable.
881        my @retVal = ();
882      # Get the feature record.      # Get the feature record.
883      my $object = $self->GetEntity('Feature', $featureID);      my $object = $self->GetEntity('Feature', $featureID);
884      Confess("Feature $featureID not found.") if ! defined($object);      # Only proceed if we found it.
885        if (defined $object) {
886      # Get the location string.      # Get the location string.
887      my $locString = $object->PrimaryValue('Feature(location-string)');      my $locString = $object->PrimaryValue('Feature(location-string)');
888      # Create the return list.      # Create the return list.
889      my @retVal = split /\s*,\s*/, $locString;          @retVal = split /\s*,\s*/, $locString;
890        }
891      # Return the list in the format indicated by the context.      # Return the list in the format indicated by the context.
892      return (wantarray ? @retVal : join(',', @retVal));      return (wantarray ? @retVal : join(',', @retVal));
893  }  }
894    
895  =head3 ParseLocation  =head3 ParseLocation
896    
897  C<< my ($contigID, $start, $dir, $len) = Sprout::ParseLocation($location); >>      my ($contigID, $start, $dir, $len) = Sprout::ParseLocation($location);
898    
899  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
900  length.  length.
# Line 638  Line 940 
940    
941  =head3 PointLocation  =head3 PointLocation
942    
943  C<< my $found = Sprout::PointLocation($location, $point); >>      my $found = Sprout::PointLocation($location, $point);
944    
945  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
946  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 690  Line 992 
992    
993  =head3 DNASeq  =head3 DNASeq
994    
995  C<< my $sequence = $sprout->DNASeq(\@locationList); >>      my $sequence = $sprout->DNASeq(\@locationList);
996    
997  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
998  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,
# Line 774  Line 1076 
1076    
1077  =head3 AllContigs  =head3 AllContigs
1078    
1079  C<< my @idList = $sprout->AllContigs($genomeID); >>      my @idList = $sprout->AllContigs($genomeID);
1080    
1081  Return a list of all the contigs for a genome.  Return a list of all the contigs for a genome.
1082    
# Line 804  Line 1106 
1106    
1107  =head3 GenomeLength  =head3 GenomeLength
1108    
1109  C<< my $length = $sprout->GenomeLength($genomeID); >>      my $length = $sprout->GenomeLength($genomeID);
1110    
1111  Return the length of the specified genome in base pairs.  Return the length of the specified genome in base pairs.
1112    
# Line 839  Line 1141 
1141    
1142  =head3 FeatureCount  =head3 FeatureCount
1143    
1144  C<< my $count = $sprout->FeatureCount($genomeID, $type); >>      my $count = $sprout->FeatureCount($genomeID, $type);
1145    
1146  Return the number of features of the specified type in the specified genome.  Return the number of features of the specified type in the specified genome.
1147    
# Line 874  Line 1176 
1176    
1177  =head3 GenomeAssignments  =head3 GenomeAssignments
1178    
1179  C<< my $fidHash = $sprout->GenomeAssignments($genomeID); >>      my $fidHash = $sprout->GenomeAssignments($genomeID);
1180    
1181  Return a list of a genome's assigned features. The return hash will contain each  Return a list of a genome's assigned features. The return hash will contain each
1182  assigned feature of the genome mapped to the text of its most recent functional  assigned feature of the genome mapped to the text of its most recent functional
# Line 917  Line 1219 
1219    
1220  =head3 ContigLength  =head3 ContigLength
1221    
1222  C<< my $length = $sprout->ContigLength($contigID); >>      my $length = $sprout->ContigLength($contigID);
1223    
1224  Compute the length of a contig.  Compute the length of a contig.
1225    
# Line 956  Line 1258 
1258    
1259  =head3 ClusterPEGs  =head3 ClusterPEGs
1260    
1261  C<< my $clusteredList = $sprout->ClusterPEGs($sub, \@pegs); >>      my $clusteredList = $sprout->ClusterPEGs($sub, \@pegs);
1262    
1263  Cluster the PEGs in a list according to the cluster coding scheme of the specified  Cluster the PEGs in a list according to the cluster coding scheme of the specified
1264  subsystem. In order for this to work properly, the subsystem object must have  subsystem. In order for this to work properly, the subsystem object must have
1265  been used recently to retrieve the PEGs using the B<get_pegs_from_cell> method.  been used recently to retrieve the PEGs using the B<get_pegs_from_cell> or
1266  This causes the cluster numbers to be pulled into the subsystem's color hash.  B<get_row> methods. This causes the cluster numbers to be pulled into the
1267  If a PEG is not found in the color hash, it will not appear in the output  subsystem's color hash. If a PEG is not found in the color hash, it will not
1268  sequence.  appear in the output sequence.
1269    
1270  =over 4  =over 4
1271    
# Line 1004  Line 1306 
1306    
1307  =head3 GenesInRegion  =head3 GenesInRegion
1308    
1309  C<< my (\@featureIDList, $beg, $end) = $sprout->GenesInRegion($contigID, $start, $stop); >>      my (\@featureIDList, $beg, $end) = $sprout->GenesInRegion($contigID, $start, $stop);
1310    
1311  List the features which overlap a specified region in a contig.  List the features which overlap a specified region in a contig.
1312    
# Line 1085  Line 1387 
1387    
1388  =head3 GeneDataInRegion  =head3 GeneDataInRegion
1389    
1390  C<< my @featureList = $sprout->GenesInRegion($contigID, $start, $stop); >>      my @featureList = $sprout->GenesInRegion($contigID, $start, $stop);
1391    
1392  List the features which overlap a specified region in a contig.  List the features which overlap a specified region in a contig.
1393    
# Line 1156  Line 1458 
1458    
1459  =head3 FType  =head3 FType
1460    
1461  C<< my $ftype = $sprout->FType($featureID); >>      my $ftype = $sprout->FType($featureID);
1462    
1463  Return the type of a feature.  Return the type of a feature.
1464    
# Line 1186  Line 1488 
1488    
1489  =head3 FeatureAnnotations  =head3 FeatureAnnotations
1490    
1491  C<< my @descriptors = $sprout->FeatureAnnotations($featureID, $rawFlag); >>      my @descriptors = $sprout->FeatureAnnotations($featureID, $rawFlag);
1492    
1493  Return the annotations of a feature.  Return the annotations of a feature.
1494    
# Line 1249  Line 1551 
1551    
1552  =head3 AllFunctionsOf  =head3 AllFunctionsOf
1553    
1554  C<< my %functions = $sprout->AllFunctionsOf($featureID); >>      my %functions = $sprout->AllFunctionsOf($featureID);
1555    
1556  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
1557  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 1304  Line 1606 
1606    
1607  =head3 FunctionOf  =head3 FunctionOf
1608    
1609  C<< my $functionText = $sprout->FunctionOf($featureID, $userID); >>      my $functionText = $sprout->FunctionOf($featureID, $userID);
1610    
1611  Return the most recently-determined functional assignment of a particular feature.  Return the most recently-determined functional assignment of a particular feature.
1612    
# Line 1408  Line 1710 
1710    
1711  =head3 FunctionsOf  =head3 FunctionsOf
1712    
1713  C<< my @functionList = $sprout->FunctionOf($featureID, $userID); >>      my @functionList = $sprout->FunctionOf($featureID, $userID);
1714    
1715  Return the functional assignments of a particular feature.  Return the functional assignments of a particular feature.
1716    
# Line 1480  Line 1782 
1782    
1783  =head3 BBHList  =head3 BBHList
1784    
1785  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>      my $bbhHash = $sprout->BBHList($genomeID, \@featureList);
1786    
1787  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
1788  on a specified target genome.  on a specified target genome.
# Line 1530  Line 1832 
1832    
1833  =head3 SimList  =head3 SimList
1834    
1835  C<< my %similarities = $sprout->SimList($featureID, $count); >>      my %similarities = $sprout->SimList($featureID, $count);
1836    
1837  Return a list of the similarities to the specified feature.  Return a list of the similarities to the specified feature.
1838    
# Line 1566  Line 1868 
1868    
1869  =head3 IsComplete  =head3 IsComplete
1870    
1871  C<< my $flag = $sprout->IsComplete($genomeID); >>      my $flag = $sprout->IsComplete($genomeID);
1872    
1873  Return TRUE if the specified genome is complete, else FALSE.  Return TRUE if the specified genome is complete, else FALSE.
1874    
# Line 1602  Line 1904 
1904    
1905  =head3 FeatureAliases  =head3 FeatureAliases
1906    
1907  C<< my @aliasList = $sprout->FeatureAliases($featureID); >>      my @aliasList = $sprout->FeatureAliases($featureID);
1908    
1909  Return a list of the aliases for a specified feature.  Return a list of the aliases for a specified feature.
1910    
# Line 1632  Line 1934 
1934    
1935  =head3 GenomeOf  =head3 GenomeOf
1936    
1937  C<< my $genomeID = $sprout->GenomeOf($featureID); >>      my $genomeID = $sprout->GenomeOf($featureID);
1938    
1939  Return the genome that contains a specified feature or contig.  Return the genome that contains a specified feature or contig.
1940    
# Line 1668  Line 1970 
1970    
1971  =head3 CoupledFeatures  =head3 CoupledFeatures
1972    
1973  C<< my %coupleHash = $sprout->CoupledFeatures($featureID); >>      my %coupleHash = $sprout->CoupledFeatures($featureID);
1974    
1975  Return the features functionally coupled with a specified feature. Features are considered  Return the features functionally coupled with a specified feature. Features are considered
1976  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 1715  Line 2017 
2017    
2018  =head3 CouplingEvidence  =head3 CouplingEvidence
2019    
2020  C<< my @evidence = $sprout->CouplingEvidence($peg1, $peg2); >>      my @evidence = $sprout->CouplingEvidence($peg1, $peg2);
2021    
2022  Return the evidence for a functional coupling.  Return the evidence for a functional coupling.
2023    
# Line 1777  Line 2079 
2079    
2080  =head3 GetSynonymGroup  =head3 GetSynonymGroup
2081    
2082  C<< my $id = $sprout->GetSynonymGroup($fid); >>      my $id = $sprout->GetSynonymGroup($fid);
2083    
2084  Return the synonym group name for the specified feature.  Return the synonym group name for the specified feature.
2085    
# Line 1816  Line 2118 
2118    
2119  =head3 GetBoundaries  =head3 GetBoundaries
2120    
2121  C<< my ($contig, $beg, $end) = $sprout->GetBoundaries(@locList); >>      my ($contig, $beg, $end) = $sprout->GetBoundaries(@locList);
2122    
2123  Determine the begin and end boundaries for the locations in a list. All of the  Determine the begin and end boundaries for the locations in a list. All of the
2124  locations must belong to the same contig and have mostly the same direction in  locations must belong to the same contig and have mostly the same direction in
# Line 1880  Line 2182 
2182    
2183  =head3 ReadFasta  =head3 ReadFasta
2184    
2185  C<< my %sequenceData = Sprout::ReadFasta($fileName, $prefix); >>      my %sequenceData = Sprout::ReadFasta($fileName, $prefix);
2186    
2187  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
2188  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 1946  Line 2248 
2248    
2249  =head3 FormatLocations  =head3 FormatLocations
2250    
2251  C<< my @locations = $sprout->FormatLocations($prefix, \@locations, $oldFormat); >>      my @locations = $sprout->FormatLocations($prefix, \@locations, $oldFormat);
2252    
2253  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
2254  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 2011  Line 2313 
2313    
2314  =head3 DumpData  =head3 DumpData
2315    
2316  C<< $sprout->DumpData(); >>      $sprout->DumpData();
2317    
2318  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.
2319    
# Line 2028  Line 2330 
2330    
2331  =head3 XMLFileName  =head3 XMLFileName
2332    
2333  C<< my $fileName = $sprout->XMLFileName(); >>      my $fileName = $sprout->XMLFileName();
2334    
2335  Return the name of this database's XML definition file.  Return the name of this database's XML definition file.
2336    
# Line 2039  Line 2341 
2341      return $self->{_xmlName};      return $self->{_xmlName};
2342  }  }
2343    
2344    =head3 GetGenomeNameData
2345    
2346        my ($genus, $species, $strain) = $sprout->GenomeNameData($genomeID);
2347    
2348    Return the genus, species, and unique characterization for a genome. This
2349    is similar to L</GenusSpecies>, with the exception that it returns the
2350    values in three seperate fields.
2351    
2352    =over 4
2353    
2354    =item genomeID
2355    
2356    ID of the genome whose name data is desired.
2357    
2358    =item RETURN
2359    
2360    Returns a three-element list, consisting of the genus, species, and strain
2361    of the specified genome. If the genome is not found, an error occurs.
2362    
2363    =back
2364    
2365    =cut
2366    
2367    sub GetGenomeNameData {
2368        # Get the parameters.
2369        my ($self, $genomeID) = @_;
2370        # Get the desired values.
2371        my ($genus, $species, $strain) = $self->GetEntityValues('Genome', $genomeID =>
2372                                                                [qw(Genome(genus) Genome(species) Genome(unique-characterization))]);
2373        # Throw an error if they were not found.
2374        if (! defined $genus) {
2375            Confess("Genome $genomeID not found in database.");
2376        }
2377        # Return the results.
2378        return ($genus, $species, $strain);
2379    }
2380    
2381    =head3 GetGenomeByNameData
2382    
2383        my @genomes = $sprout->GetGenomeByNameData($genus, $species, $strain);
2384    
2385    Return a list of the IDs of the genomes with the specified genus,
2386    species, and strain. In almost every case, there will be either zero or
2387    one IDs returned; however, two or more IDs could be returned if there are
2388    multiple versions of the genome in the database.
2389    
2390    =over 4
2391    
2392    =item genus
2393    
2394    Genus of the desired genome.
2395    
2396    =item species
2397    
2398    Species of the desired genome.
2399    
2400    =item strain
2401    
2402    Strain (unique characterization) of the desired genome. This may be an empty
2403    string, in which case it is presumed that the desired genome has no strain
2404    specified.
2405    
2406    =item RETURN
2407    
2408    Returns a list of the IDs of the genomes having the specified genus, species, and
2409    strain.
2410    
2411    =back
2412    
2413    =cut
2414    
2415    sub GetGenomeByNameData {
2416        # Get the parameters.
2417        my ($self, $genus, $species, $strain) = @_;
2418        # Try to find the genomes.
2419        my @retVal = $self->GetFlat(['Genome'], "Genome(genus) = ? AND Genome(species) = ? AND Genome(unique-characterization) = ?",
2420                                    [$genus, $species, $strain], 'Genome(id)');
2421        # Return the result.
2422        return @retVal;
2423    }
2424    
2425  =head3 Insert  =head3 Insert
2426    
2427  C<< $sprout->Insert($objectType, \%fieldHash); >>      $sprout->Insert($objectType, \%fieldHash);
2428    
2429  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
2430  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 2050  Line 2433 
2433  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
2434  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>.
2435    
2436  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']});
2437    
2438  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
2439  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>.
2440    
2441  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'});
2442    
2443  =over 4  =over 4
2444    
# Line 2080  Line 2463 
2463    
2464  =head3 Annotate  =head3 Annotate
2465    
2466  C<< my $ok = $sprout->Annotate($fid, $timestamp, $user, $text); >>      my $ok = $sprout->Annotate($fid, $timestamp, $user, $text);
2467    
2468  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
2469  specified feature and user.  specified feature and user.
# Line 2134  Line 2517 
2517    
2518  =head3 AssignFunction  =head3 AssignFunction
2519    
2520  C<< my $ok = $sprout->AssignFunction($featureID, $user, $function, $assigningUser); >>      my $ok = $sprout->AssignFunction($featureID, $user, $function, $assigningUser);
2521    
2522  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
2523  format is described in L</ParseAssignment>.  format is described in L</ParseAssignment>.
# Line 2194  Line 2577 
2577    
2578  =head3 FeaturesByAlias  =head3 FeaturesByAlias
2579    
2580  C<< my @features = $sprout->FeaturesByAlias($alias); >>      my @features = $sprout->FeaturesByAlias($alias);
2581    
2582  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
2583  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 2236  Line 2619 
2619    
2620  =head3 FeatureTranslation  =head3 FeatureTranslation
2621    
2622  C<< my $translation = $sprout->FeatureTranslation($featureID); >>      my $translation = $sprout->FeatureTranslation($featureID);
2623    
2624  Return the translation of a feature.  Return the translation of a feature.
2625    
# Line 2264  Line 2647 
2647    
2648  =head3 Taxonomy  =head3 Taxonomy
2649    
2650  C<< my @taxonomyList = $sprout->Taxonomy($genome); >>      my @taxonomyList = $sprout->Taxonomy($genome);
2651    
2652  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
2653  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>,
2654  or C<Eukaryote>) to sub-species. For example,  or C<Eukaryote>) to sub-species. For example,
2655    
2656  C<< (Bacteria, Proteobacteria, Gammaproteobacteria, Enterobacteriales, Enterobacteriaceae, Escherichia, Escherichia coli, Escherichia coli K12) >>      (Bacteria, Proteobacteria, Gammaproteobacteria, Enterobacteriales, Enterobacteriaceae, Escherichia, Escherichia coli, Escherichia coli K12)
2657    
2658  =over 4  =over 4
2659    
# Line 2305  Line 2688 
2688    
2689  =head3 CrudeDistance  =head3 CrudeDistance
2690    
2691  C<< my $distance = $sprout->CrudeDistance($genome1, $genome2); >>      my $distance = $sprout->CrudeDistance($genome1, $genome2);
2692    
2693  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
2694  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 2357  Line 2740 
2740    
2741  =head3 RoleName  =head3 RoleName
2742    
2743  C<< my $roleName = $sprout->RoleName($roleID); >>      my $roleName = $sprout->RoleName($roleID);
2744    
2745  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
2746  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 2391  Line 2774 
2774    
2775  =head3 RoleDiagrams  =head3 RoleDiagrams
2776    
2777  C<< my @diagrams = $sprout->RoleDiagrams($roleID); >>      my @diagrams = $sprout->RoleDiagrams($roleID);
2778    
2779  Return a list of the diagrams containing a specified functional role.  Return a list of the diagrams containing a specified functional role.
2780    
# Line 2421  Line 2804 
2804    
2805  =head3 GetProperties  =head3 GetProperties
2806    
2807  C<< my @list = $sprout->GetProperties($fid, $key, $value, $url); >>      my @list = $sprout->GetProperties($fid, $key, $value, $url);
2808    
2809  Return a list of the properties with the specified characteristics.  Return a list of the properties with the specified characteristics.
2810    
# Line 2507  Line 2890 
2890    
2891  =head3 FeatureProperties  =head3 FeatureProperties
2892    
2893  C<< my @properties = $sprout->FeatureProperties($featureID); >>      my @properties = $sprout->FeatureProperties($featureID);
2894    
2895  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
2896  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
# Line 2546  Line 2929 
2929    
2930  =head3 DiagramName  =head3 DiagramName
2931    
2932  C<< my $diagramName = $sprout->DiagramName($diagramID); >>      my $diagramName = $sprout->DiagramName($diagramID);
2933    
2934  Return the descriptive name of a diagram.  Return the descriptive name of a diagram.
2935    
# Line 2574  Line 2957 
2957    
2958  =head3 PropertyID  =head3 PropertyID
2959    
2960  C<< my $id = $sprout->PropertyID($propName, $propValue); >>      my $id = $sprout->PropertyID($propName, $propValue);
2961    
2962  Return the ID of the specified property name and value pair, if the  Return the ID of the specified property name and value pair, if the
2963  pair exists. Only a small subset of the FIG attributes are stored as  pair exists. Only a small subset of the FIG attributes are stored as
# Line 2611  Line 2994 
2994    
2995  =head3 MergedAnnotations  =head3 MergedAnnotations
2996    
2997  C<< my @annotationList = $sprout->MergedAnnotations(\@list); >>      my @annotationList = $sprout->MergedAnnotations(\@list);
2998    
2999  Returns a merged list of the annotations for the features in a list. Each annotation is  Returns a merged list of the annotations for the features in a list. Each annotation is
3000  represented by a 4-tuple of the form C<($fid, $timestamp, $userID, $annotation)>, where  represented by a 4-tuple of the form C<($fid, $timestamp, $userID, $annotation)>, where
# Line 2660  Line 3043 
3043    
3044  =head3 RoleNeighbors  =head3 RoleNeighbors
3045    
3046  C<< my @roleList = $sprout->RoleNeighbors($roleID); >>      my @roleList = $sprout->RoleNeighbors($roleID);
3047    
3048  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
3049  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 2703  Line 3086 
3086    
3087  =head3 FeatureLinks  =head3 FeatureLinks
3088    
3089  C<< my @links = $sprout->FeatureLinks($featureID); >>      my @links = $sprout->FeatureLinks($featureID);
3090    
3091  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
3092  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 2734  Line 3117 
3117    
3118  =head3 SubsystemsOf  =head3 SubsystemsOf
3119    
3120  C<< my %subsystems = $sprout->SubsystemsOf($featureID); >>      my %subsystems = $sprout->SubsystemsOf($featureID);
3121    
3122  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
3123  to the roles the feature performs.  to the roles the feature performs.
# Line 2782  Line 3165 
3165    
3166  =head3 SubsystemList  =head3 SubsystemList
3167    
3168  C<< my @subsystems = $sprout->SubsystemList($featureID); >>      my @subsystems = $sprout->SubsystemList($featureID);
3169    
3170  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
3171  feature participates. Unlike L</SubsystemsOf>, this method only returns the  feature participates. Unlike L</SubsystemsOf>, this method only returns the
# Line 2814  Line 3197 
3197    
3198  =head3 GenomeSubsystemData  =head3 GenomeSubsystemData
3199    
3200  C<< my %featureData = $sprout->GenomeSubsystemData($genomeID); >>      my %featureData = $sprout->GenomeSubsystemData($genomeID);
3201    
3202  Return a hash mapping genome features to their subsystem roles.  Return a hash mapping genome features to their subsystem roles.
3203    
# Line 2874  Line 3257 
3257    
3258  =head3 RelatedFeatures  =head3 RelatedFeatures
3259    
3260  C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>      my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID);
3261    
3262  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
3263  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 2925  Line 3308 
3308    
3309  =head3 TaxonomySort  =head3 TaxonomySort
3310    
3311  C<< my @sortedFeatureIDs = $sprout->TaxonomySort(\@featureIDs); >>      my @sortedFeatureIDs = $sprout->TaxonomySort(\@featureIDs);
3312    
3313  Return a list formed by sorting the specified features by the taxonomy of the containing  Return a list formed by sorting the specified features by the taxonomy of the containing
3314  genome. This will cause genomes from similar organisms to float close to each other.  genome. This will cause genomes from similar organisms to float close to each other.
# Line 2960  Line 3343 
3343          my ($taxonomy) = $self->GetFlat(['IsLocatedIn', 'HasContig', 'Genome'], "IsLocatedIn(from-link) = ?",          my ($taxonomy) = $self->GetFlat(['IsLocatedIn', 'HasContig', 'Genome'], "IsLocatedIn(from-link) = ?",
3344                                          [$fid], 'Genome(taxonomy)');                                          [$fid], 'Genome(taxonomy)');
3345          # Add this feature to the hash buffer.          # Add this feature to the hash buffer.
3346          Tracer::AddToListMap(\%hashBuffer, $taxonomy, $fid);          push @{$hashBuffer{$taxonomy}}, $fid;
3347      }      }
3348      # Sort the keys and get the elements.      # Sort the keys and get the elements.
3349      my @retVal = ();      my @retVal = ();
# Line 2973  Line 3356 
3356    
3357  =head3 Protein  =head3 Protein
3358    
3359  C<< my $protein = Sprout::Protein($sequence, $table); >>      my $protein = Sprout::Protein($sequence, $table);
3360    
3361  Translate a DNA sequence into a protein sequence.  Translate a DNA sequence into a protein sequence.
3362    
# Line 3059  Line 3442 
3442    
3443  =head3 LoadInfo  =head3 LoadInfo
3444    
3445  C<< my ($dirName, @relNames) = $sprout->LoadInfo(); >>      my ($dirName, @relNames) = $sprout->LoadInfo();
3446    
3447  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
3448  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 3080  Line 3463 
3463    
3464  =head3 BBHMatrix  =head3 BBHMatrix
3465    
3466  C<< my %bbhMap = $sprout->BBHMatrix($genomeID, $cutoff, @targets); >>      my %bbhMap = $sprout->BBHMatrix($genomeID, $cutoff, @targets);
3467    
3468  Find all the bidirectional best hits for the features of a genome in a  Find all the bidirectional best hits for the features of a genome in a
3469  specified list of target genomes. The return value will be a hash mapping  specified list of target genomes. The return value will be a hash mapping
# Line 3134  Line 3517 
3517    
3518  =head3 SimMatrix  =head3 SimMatrix
3519    
3520  C<< my %simMap = $sprout->SimMatrix($genomeID, $cutoff, @targets); >>      my %simMap = $sprout->SimMatrix($genomeID, $cutoff, @targets);
3521    
3522  Find all the similarities for the features of a genome in a  Find all the similarities for the features of a genome in a
3523  specified list of target genomes. The return value will be a hash mapping  specified list of target genomes. The return value will be a hash mapping
# Line 3204  Line 3587 
3587    
3588  =head3 LowBBHs  =head3 LowBBHs
3589    
3590  C<< my %bbhMap = $sprout->LowBBHs($featureID, $cutoff); >>      my %bbhMap = $sprout->LowBBHs($featureID, $cutoff);
3591    
3592  Return the bidirectional best hits of a feature whose score is no greater than a  Return the bidirectional best hits of a feature whose score is no greater than a
3593  specified cutoff value. A higher cutoff value will allow inclusion of hits with  specified cutoff value. A higher cutoff value will allow inclusion of hits with
# Line 3248  Line 3631 
3631    
3632  =head3 Sims  =head3 Sims
3633    
3634  C<< my $simList = $sprout->Sims($fid, $maxN, $maxP, $select, $max_expand, $filters); >>      my $simList = $sprout->Sims($fid, $maxN, $maxP, $select, $max_expand, $filters);
3635    
3636  Get a list of similarities for a specified feature. Similarity information is not kept in the  Get a list of similarities for a specified feature. Similarity information is not kept in the
3637  Sprout database; rather, they are retrieved from a network server. The similarities are  Sprout database; rather, they are retrieved from a network server. The similarities are
# Line 3314  Line 3697 
3697    
3698  =head3 IsAllGenomes  =head3 IsAllGenomes
3699    
3700  C<< my $flag = $sprout->IsAllGenomes(\@list, \@checkList); >>      my $flag = $sprout->IsAllGenomes(\@list, \@checkList);
3701    
3702  Return TRUE if all genomes in the second list are represented in the first list at  Return TRUE if all genomes in the second list are represented in the first list at
3703  least one. Otherwise, return FALSE. If the second list is omitted, the first list is  least one. Otherwise, return FALSE. If the second list is omitted, the first list is
# Line 3363  Line 3746 
3746    
3747  =head3 GetGroups  =head3 GetGroups
3748    
3749  C<< my %groups = $sprout->GetGroups(\@groupList); >>      my %groups = $sprout->GetGroups(\@groupList);
3750    
3751  Return a hash mapping each group to the IDs of the genomes in the group.  Return a hash mapping each group to the IDs of the genomes in the group.
3752  A list of groups may be specified, in which case only those groups will be  A list of groups may be specified, in which case only those groups will be
# Line 3395  Line 3778 
3778                                      [$FIG_Config::otherGroup], ['Genome(id)', 'Genome(primary-group)']);                                      [$FIG_Config::otherGroup], ['Genome(id)', 'Genome(primary-group)']);
3779          # Loop through the genomes found.          # Loop through the genomes found.
3780          for my $genome (@genomes) {          for my $genome (@genomes) {
3781              # Pop this genome's ID off the current list.              # Get the genome ID and group, and add this genome to the group's list.
3782              my @groups = @{$genome};              my ($genomeID, $group) = @{$genome};
3783              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, $genomeID);  
             }  
3784          }          }
3785      }      }
3786      # Return the hash we just built.      # Return the hash we just built.
# Line 3411  Line 3789 
3789    
3790  =head3 MyGenomes  =head3 MyGenomes
3791    
3792  C<< my @genomes = Sprout::MyGenomes($dataDir); >>      my @genomes = Sprout::MyGenomes($dataDir);
3793    
3794  Return a list of the genomes to be included in the Sprout.  Return a list of the genomes to be included in the Sprout.
3795    
# Line 3443  Line 3821 
3821    
3822  =head3 LoadFileName  =head3 LoadFileName
3823    
3824  C<< my $fileName = Sprout::LoadFileName($dataDir, $tableName); >>      my $fileName = Sprout::LoadFileName($dataDir, $tableName);
3825    
3826  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
3827  directory.  directory.
# Line 3484  Line 3862 
3862    
3863  =head3 DeleteGenome  =head3 DeleteGenome
3864    
3865  C<< my $stats = $sprout->DeleteGenome($genomeID, $testFlag); >>      my $stats = $sprout->DeleteGenome($genomeID, $testFlag);
3866    
3867  Delete a genome from the database.  Delete a genome from the database.
3868    
# Line 3520  Line 3898 
3898    
3899  =head3 Fix  =head3 Fix
3900    
3901  C<< my %fixedHash = Sprout::Fix(%groupHash); >>      my %fixedHash = $sprout->Fix(%groupHash);
3902    
3903  Prepare a genome group hash (like that returned by L</GetGroups> for processing.  Prepare a genome group hash (like that returned by L</GetGroups>) for processing.
3904  Groups with the same primary name will be combined. The primary name is the  The groups will be combined into the appropriate super-groups.
 first capitalized word in the group name.  
3905    
3906  =over 4  =over 4
3907    
# Line 3542  Line 3919 
3919    
3920  sub Fix {  sub Fix {
3921      # Get the parameters.      # Get the parameters.
3922      my (%groupHash) = @_;      my ($self, %groupHash) = @_;
3923      # Create the result hash.      # Create the result hash.
3924      my %retVal = ();      my %retVal = ();
3925      # Copy over the genomes.      # Copy over the genomes.
3926      for my $groupID (keys %groupHash) {      for my $groupID (keys %groupHash) {
3927          # Make a safety copy of the group ID.          # Get the super-group name.
3928          my $realGroupID = $groupID;          my $realGroupID = $self->SuperGroup($groupID);
3929          # Yank the primary name.          # Append this group's genomes into the result hash
3930          if ($groupID =~ /([A-Z]\w+)/) {          # using the super-group name.
3931              $realGroupID = $1;          push @{$retVal{$realGroupID}}, @{$groupHash{$groupID}};
         }  
         # Append this group's genomes into the result hash.  
         Tracer::AddToListMap(\%retVal, $realGroupID, @{$groupHash{$groupID}});  
3932      }      }
3933      # Return the result hash.      # Return the result hash.
3934      return %retVal;      return %retVal;
# Line 3562  Line 3936 
3936    
3937  =head3 GroupPageName  =head3 GroupPageName
3938    
3939  C<< my $name = $sprout->GroupPageName($group); >>      my $name = $sprout->GroupPageName($group);
3940    
3941  Return the name of the page for the specified NMPDR group.  Return the name of the page for the specified NMPDR group.
3942    
# Line 3584  Line 3958 
3958  sub GroupPageName {  sub GroupPageName {
3959      # Get the parameters.      # Get the parameters.
3960      my ($self, $group) = @_;      my ($self, $group) = @_;
     # Declare the return variable.  
     my $retVal;  
3961      # Check for the group file data.      # Check for the group file data.
3962      if (! defined $self->{groupHash}) {      my %superTable = $self->CheckGroupFile();
         # Read the group file.  
         my %groupData = Sprout::ReadGroupFile($self->{_options}->{dataDir} . "/groups.tbl");  
         # Store it in our object.  
         $self->{groupHash} = \%groupData;  
     }  
3963      # Compute the real group name.      # Compute the real group name.
3964      my $realGroup = $group;      my $realGroup = $self->SuperGroup($group);
3965      if ($group =~ /([A-Z]\w+)/) {      # Get the associated page name.
3966          $realGroup = $1;      my $retVal = "../content/$superTable{$realGroup}->{page}";
     }  
     # Return the page name.  
     $retVal = "../content/" . $self->{groupHash}->{$realGroup}->[1];  
3967      # Return the result.      # Return the result.
3968      return $retVal;      return $retVal;
3969  }  }
3970    
 =head3 ReadGroupFile  
   
 C<< my %groupData = Sprout::ReadGroupFile($groupFileName); >>  
   
 Read in the data from the specified group file. The group file contains information  
 about each of the NMPDR groups.  
3971    
3972  =over 4  =head3 AddProperty
   
 =item name  
   
 Name of the group.  
   
 =item page  
   
 Name of the group's page on the web site (e.g. C<campy.php> for  
 Campylobacter)  
   
 =item genus  
   
 Genus of the group  
3973    
3974  =item species      $sprout->AddProperty($featureID, $key, @values);
3975    
3976  Species of the group, or an empty string if the group is for an entire  Add a new attribute value (Property) to a feature.
 genus. If the group contains more than one species, the species names  
 should be separated by commas.  
3977    
3978  =back  =over 4
3979    
3980  The parameters to this method are as follows  =item peg
3981    
3982  =over 4  ID of the feature to which the attribute is to be added.
3983    
3984  =item groupFile  =item key
3985    
3986  Name of the file containing the group data.  Name of the attribute (key).
3987    
3988  =item RETURN  =item values
3989    
3990  Returns a hash keyed on group name. The value of each hash  Values of the attribute.
3991    
3992  =back  =back
3993    
3994  =cut  =cut
3995    #: Return Type ;
3996  sub ReadGroupFile {  sub AddProperty {
3997      # Get the parameters.      # Get the parameters.
3998      my ($groupFileName) = @_;      my ($self, $featureID, $key, @values) = @_;
3999      # Declare the return variable.      # Add the property using the attached attributes object.
4000      my %retVal;      $self->{_ca}->AddAttribute($featureID, $key, @values);
     # Read the group file.  
     my @groupLines = Tracer::GetFile($groupFileName);  
     for my $groupLine (@groupLines) {  
         my ($name, $page, $genus, $species) = split(/\t/, $groupLine);  
         $retVal{$name} = [$page, $genus, $species];  
     }  
     # Return the result.  
     return %retVal;  
4001  }  }
4002    
4003  =head3 AddProperty  =head3 CheckGroupFile
4004    
4005  C<< my  = $sprout->AddProperty($featureID, $key, @values); >>      my %groupData = $sprout->CheckGroupFile();
4006    
4007  Add a new attribute value (Property) to a feature.  Get the group file hash. The group file hash describes the relationship
4008    between a group and the super-group to which it belongs for purposes of
4009    display. The super-group name is computed from the first capitalized word
4010    in the actual group name. For each super-group, the group file contains
4011    the page name and a list of the species expected to be in the group.
4012    Each species is specified by a genus and a species name. A species name
4013    of C<0> implies an entire genus.
4014    
4015  =over 4  This method returns a hash from super-group names to a hash reference. Each
4016    resulting hash reference contains the following fields.
4017    
4018  =item peg  =over 4
4019    
4020  ID of the feature to which the attribute is to be added.  =item page
4021    
4022  =item key  The super-group's web page in the NMPDR.
4023    
4024  Name of the attribute (key).  =item contents
4025    
4026  =item values  A list of 2-tuples, each containing a genus name followed by a species name
4027    (or 0, indicating all species). This list indicates which organisms belong
4028  Values of the attribute.  in the super-group.
4029    
4030  =back  =back
4031    
4032  =cut  =cut
4033  #: Return Type ;  
4034  sub AddProperty {  sub CheckGroupFile {
4035      # Get the parameters.      # Get the parameters.
4036      my ($self, $featureID, $key, @values) = @_;      my ($self) = @_;
4037      # Add the property using the attached attributes object.      # Check to see if we already have this hash.
4038      $self->{_ca}->AddAttribute($featureID, $key, @values);      if (! defined $self->{groupHash}) {
4039            # We don't, so we need to read it in.
4040            my %groupHash;
4041            # Read the group file.
4042            my @groupLines = Tracer::GetFile("$FIG_Config::sproutData/groups.tbl");
4043            # Loop through the list of sort-of groups.
4044            for my $groupLine (@groupLines) {
4045                my ($name, $page, @contents) = split /\t/, $groupLine;
4046                $groupHash{$name} = { page => $page,
4047                                      contents => [ map { [ split /\s*,\s*/, $_ ] } @contents ]
4048                                    };
4049            }
4050            # Save the hash.
4051            $self->{groupHash} = \%groupHash;
4052        }
4053        # Return the result.
4054        return %{$self->{groupHash}};
4055  }  }
4056    
4057  =head2 Virtual Methods  =head2 Virtual Methods
4058    
4059  =head3 CleanKeywords  =head3 CleanKeywords
4060    
4061  C<< my $cleanedString = $sprout->CleanKeywords($searchExpression); >>      my $cleanedString = $sprout->CleanKeywords($searchExpression);
4062    
4063  Clean up a search expression or keyword list. This involves converting the periods  Clean up a search expression or keyword list. This involves converting the periods
4064  in EC numbers to underscores, converting non-leading minus signs to underscores,  in EC numbers to underscores, converting non-leading minus signs to underscores,
# Line 3727  Line 4085 
4085      # Get the parameters.      # Get the parameters.
4086      my ($self, $searchExpression) = @_;      my ($self, $searchExpression) = @_;
4087      # Perform the standard cleanup.      # Perform the standard cleanup.
4088      my $retVal = $self->ERDB::CleanKeywords($searchExpression);      my $words = $self->ERDB::CleanKeywords($searchExpression);
4089      # Fix the periods in EC and TC numbers.      # Fix the periods in EC and TC numbers.
4090      $retVal =~ s/(\d+|\-)\.(\d+|-)\.(\d+|-)\.(\d+|-)/$1_$2_$3_$4/g;      $words =~ s/(\d+|\-)\.(\d+|-)\.(\d+|-)\.(\d+|-)/$1_$2_$3_$4/g;
4091      # Fix non-trailing periods.      # Fix non-trailing periods.
4092      $retVal =~ s/\.(\w)/_$1/g;      $words =~ s/\.(\w)/_$1/g;
4093      # Fix non-leading minus signs.      # Fix non-leading minus signs.
4094      $retVal =~ s/(\w)[\-]/$1_/g;      $words =~ s/(\w)[\-]/$1_/g;
4095      # Fix the vertical bars and colons      # Fix the vertical bars and colons
4096      $retVal =~ s/(\w)[|:](\w)/$1'$2/g;      $words =~ s/(\w)[|:](\w)/$1'$2/g;
4097        # Now split up the list so that each keyword is in its own string. We keep the delimiters
4098        # because they may contain boolean expression data.
4099        my @words = split /([^A-Za-z'0-9_]+)/, $words;
4100        # We'll convert the stemmable words into stems and re-assemble the result.
4101        my $retVal = "";
4102        for my $word (@words) {
4103            my $stem = $self->Stem($word);
4104            if (defined $stem) {
4105                $retVal .= $stem;
4106            } else {
4107                $retVal .= $word;
4108            }
4109        }
4110        Trace("Cleaned keyword list for \"$searchExpression\" is \"$retVal\".") if T(3);
4111      # Return the result.      # Return the result.
4112      return $retVal;      return $retVal;
4113  }  }
# Line 3750  Line 4122 
4122    
4123  A functional assignment is always of the form  A functional assignment is always of the form
4124    
4125      C<set >I<YYYY>C< function to\n>I<ZZZZZ>      set YYYY function to
4126        ZZZZ
4127    
4128  where I<YYYY> is the B<user>, and I<ZZZZ> is the actual functional role. In most cases,  where I<YYYY> is the B<user>, and I<ZZZZ> is the actual functional role. In most cases,
4129  the user and the assigning user (from MadeAnnotation) will be the same, but that is  the user and the assigning user (from MadeAnnotation) will be the same, but that is
# Line 3805  Line 4178 
4178    
4179  =head3 _CheckFeature  =head3 _CheckFeature
4180    
4181  C<< my $flag = $sprout->_CheckFeature($fid); >>      my $flag = $sprout->_CheckFeature($fid);
4182    
4183  Return TRUE if the specified FID is probably an NMPDR feature ID, else FALSE.  Return TRUE if the specified FID is probably an NMPDR feature ID, else FALSE.
4184    

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