[Bio] / Sprout / Sprout.pm Repository:
ViewVC logotype

Diff of /Sprout/Sprout.pm

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.9, Mon Feb 7 00:32:07 2005 UTC revision 1.25, Sun Sep 11 17:29:52 2005 UTC
# Line 70  Line 70 
70    
71  * B<maxSequenceLength> maximum number of residues per sequence, (default C<8000>)  * B<maxSequenceLength> maximum number of residues per sequence, (default C<8000>)
72    
73    * B<noDBOpen> suppresses the connection to the database if TRUE, else FALSE
74    
75  =back  =back
76    
77  For example, the following constructor call specifies a database named I<Sprout> and a user name of  For example, the following constructor call specifies a database named I<Sprout> and a user name of
# Line 86  Line 88 
88          # 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
89          # the incoming data.          # the incoming data.
90          my $optionTable = Tracer::GetOptions({          my $optionTable = Tracer::GetOptions({
91                                             dbType               => 'mysql',                     # database type                         dbType       => $FIG_Config::dbms,
92                                             dataDir              => 'Data',                      # data file directory                                                          # database type
93                                             xmlFileName  => 'SproutDBD.xml', # database definition file name                         dataDir      => $FIG_Config::sproutData,
94                                             userData             => 'root/',                     # user name and password                                                          # data file directory
95                                             port                 => 0,                           # database connection port                         xmlFileName  => "$FIG_Config::sproutData/SproutDBD.xml",
96                                                            # database definition file name
97                           userData     => "$FIG_Config::dbuser/$FIG_Config::dbpass",
98                                                            # user name and password
99                           port         => $FIG_Config::dbport,
100                                                            # database connection port
101                                             maxSegmentLength => 4500,            # maximum feature segment length                                             maxSegmentLength => 4500,            # maximum feature segment length
102                                             maxSequenceLength => 8000,           # maximum contig sequence length                                             maxSequenceLength => 8000,           # maximum contig sequence length
103                           noDBOpen     => 0,               # 1 to suppress the database open
104                                            }, $options);                                            }, $options);
105          # Get the data directory.          # Get the data directory.
106          my $dataDir = $optionTable->{dataDir};          my $dataDir = $optionTable->{dataDir};
# Line 100  Line 108 
108          $optionTable->{userData} =~ m!([^/]*)/(.*)$!;          $optionTable->{userData} =~ m!([^/]*)/(.*)$!;
109          my ($userName, $password) = ($1, $2);          my ($userName, $password) = ($1, $2);
110          # Connect to the database.          # Connect to the database.
111          my $dbh = DBKernel->new($optionTable->{dbType}, $dbName, $userName, $password, $optionTable->{port});      my $dbh;
112        if (! $optionTable->{noDBOpen}) {
113            $dbh = DBKernel->new($optionTable->{dbType}, $dbName, $userName,
114                                    $password, $optionTable->{port});
115        }
116          # Create the ERDB object.          # Create the ERDB object.
117          my $xmlFileName = "$optionTable->{xmlFileName}";          my $xmlFileName = "$optionTable->{xmlFileName}";
118          my $erdb = ERDB->new($dbh, $xmlFileName);          my $erdb = ERDB->new($dbh, $xmlFileName);
# Line 124  Line 136 
136  =cut  =cut
137  #: Return Type $;  #: Return Type $;
138  sub MaxSegment {  sub MaxSegment {
139          my $self = shift @_;      my ($self) = @_;
140          return $self->{_options}->{maxSegmentLength};          return $self->{_options}->{maxSegmentLength};
141  }  }
142    
# Line 139  Line 151 
151  =cut  =cut
152  #: Return Type $;  #: Return Type $;
153  sub MaxSequence {  sub MaxSequence {
154          my $self = shift @_;      my ($self) = @_;
155          return $self->{_options}->{maxSequenceLength};          return $self->{_options}->{maxSequenceLength};
156  }  }
157    
# Line 232  Line 244 
244    
245  sub Get {  sub Get {
246          # Get the parameters.          # Get the parameters.
247          my $self = shift @_;      my ($self, $objectNames, $filterClause, $parameterList) = @_;
         my ($objectNames, $filterClause, $parameterList) = @_;  
248          # We differ from the ERDB Get method in that the parameter list is passed in as a list reference          # We differ from the ERDB Get method in that the parameter list is passed in as a list reference
249          # rather than a list of parameters. The next step is to convert the parameters from a reference          # rather than a list of parameters. The next step is to convert the parameters from a reference
250          # to a real list. We can only do this if the parameters have been specified.          # to a real list. We can only do this if the parameters have been specified.
# Line 269  Line 280 
280    
281  sub GetEntity {  sub GetEntity {
282          # Get the parameters.          # Get the parameters.
283          my $self = shift @_;      my ($self, $entityType, $ID) = @_;
284          my ($entityType, $ID) = @_;      # Call the ERDB method.
285          # Create a query.      return $self->{_erdb}->GetEntity($entityType, $ID);
         my $query = $self->Get([$entityType], "$entityType(id) = ?", [$ID]);  
         # Get the first (and only) object.  
         my $retVal = $query->Fetch();  
         # Return the result.  
         return $retVal;  
286  }  }
287    
288  =head3 GetEntityValues  =head3 GetEntityValues
# Line 309  Line 315 
315  #: Return Type @;  #: Return Type @;
316  sub GetEntityValues {  sub GetEntityValues {
317          # Get the parameters.          # Get the parameters.
318          my $self = shift @_;      my ($self, $entityType, $ID, $fields) = @_;
319          my ($entityType, $ID, $fields) = @_;      # Call the ERDB method.
320          # Get the specified entity.      return $self->{_erdb}->GetEntityValues($entityType, $ID, $fields);
         my $entity = $self->GetEntity($entityType, $ID);  
         # Declare the return list.  
         my @retVal = ();  
         # If we found the entity, push the values into the return list.  
         if ($entity) {  
                 push @retVal, $entity->Values($fields);  
         }  
         # Return the result.  
         return @retVal;  
321  }  }
322    
323  =head3 ShowMetaData  =head3 ShowMetaData
# Line 341  Line 338 
338    
339  sub ShowMetaData {  sub ShowMetaData {
340          # Get the parameters.          # Get the parameters.
341          my $self = shift @_;      my ($self, $fileName) = @_;
         my ($fileName) = @_;  
342          # Compute the file name.          # Compute the file name.
343          my $options = $self->{_options};          my $options = $self->{_options};
344          # Call the show method on the underlying ERDB object.          # Call the show method on the underlying ERDB object.
# Line 382  Line 378 
378  #: Return Type %;  #: Return Type %;
379  sub Load {  sub Load {
380          # Get the parameters.          # Get the parameters.
381          my $self = shift @_;      my ($self, $rebuild) = @_;
         my ($rebuild) = @_;  
382          # Get the database object.          # Get the database object.
383          my $erdb = $self->{_erdb};          my $erdb = $self->{_erdb};
384          # Load the tables from the data directory.          # Load the tables from the data directory.
# Line 426  Line 421 
421  #: Return Type $%;  #: Return Type $%;
422  sub LoadUpdate {  sub LoadUpdate {
423          # Get the parameters.          # Get the parameters.
424          my $self = shift @_;      my ($self, $truncateFlag, $tableList) = @_;
         my ($truncateFlag, $tableList) = @_;  
425          # Get the database object.          # Get the database object.
426          my $erdb = $self->{_erdb};          my $erdb = $self->{_erdb};
427          # Declare the return value.          # Declare the return value.
# Line 438  Line 432 
432          # Loop through the incoming table names.          # Loop through the incoming table names.
433          for my $tableName (@{$tableList}) {          for my $tableName (@{$tableList}) {
434                  # Find the table's file.                  # Find the table's file.
435                  my $fileName = "$dataDir/$tableName";          my $fileName = LoadFileName($dataDir, $tableName);
436                  if (! -e $fileName) {          if (! $fileName) {
437                          $fileName = "$fileName.dtx";              Trace("No load file found for $tableName in $dataDir.") if T(0);
438                  }          } else {
439                  # Attempt to load this table.                  # Attempt to load this table.
440                  my $result = $erdb->LoadTable($fileName, $tableName, $truncateFlag);                  my $result = $erdb->LoadTable($fileName, $tableName, $truncateFlag);
441                  # Accumulate the resulting statistics.                  # Accumulate the resulting statistics.
442                  $retVal->Accumulate($result);                  $retVal->Accumulate($result);
443          }          }
444        }
445          # Return the statistics.          # Return the statistics.
446          return $retVal;          return $retVal;
447  }  }
# Line 463  Line 458 
458  #: Return Type ;  #: Return Type ;
459  sub Build {  sub Build {
460          # Get the parameters.          # Get the parameters.
461          my $self = shift @_;      my ($self) = @_;
462          # Create the tables.          # Create the tables.
463          $self->{_erdb}->CreateTables;          $self->{_erdb}->CreateTables;
464  }  }
# Line 478  Line 473 
473  #: Return Type @;  #: Return Type @;
474  sub Genomes {  sub Genomes {
475          # Get the parameters.          # Get the parameters.
476          my $self = shift @_;      my ($self) = @_;
477          # Get all the genomes.          # Get all the genomes.
478          my @retVal = $self->GetFlat(['Genome'], "", [], 'Genome(id)');          my @retVal = $self->GetFlat(['Genome'], "", [], 'Genome(id)');
479          # Return the list of IDs.          # Return the list of IDs.
# Line 508  Line 503 
503  #: Return Type $;  #: Return Type $;
504  sub GenusSpecies {  sub GenusSpecies {
505          # Get the parameters.          # Get the parameters.
506          my $self = shift @_;      my ($self, $genomeID) = @_;
         my ($genomeID) = @_;  
507          # Get the data for the specified genome.          # Get the data for the specified genome.
508          my @values = $self->GetEntityValues('Genome', $genomeID, ['Genome(genus)', 'Genome(species)',          my @values = $self->GetEntityValues('Genome', $genomeID, ['Genome(genus)', 'Genome(species)',
509                                                                                                                            'Genome(unique-characterization)']);                                                                                                                            'Genome(unique-characterization)']);
# Line 545  Line 539 
539  #: Return Type @;  #: Return Type @;
540  sub FeaturesOf {  sub FeaturesOf {
541          # Get the parameters.          # Get the parameters.
542          my $self = shift @_;      my ($self, $genomeID,$ftype) = @_;
         my ($genomeID,$ftype) = @_;  
543          # Get the features we want.          # Get the features we want.
544          my @features;          my @features;
545          if (!$ftype) {          if (!$ftype) {
# Line 590  Line 583 
583  =item RETURN  =item RETURN
584    
585  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
586  context and as a space-delimited string in a scalar context.  context and as a comma-delimited string in a scalar context.
587    
588  =back  =back
589    
# Line 599  Line 592 
592  #: Return Type $;  #: Return Type $;
593  sub FeatureLocation {  sub FeatureLocation {
594          # Get the parameters.          # Get the parameters.
595          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
596          # Create a query for the feature locations.          # Create a query for the feature locations.
597          my $query = $self->Get(['IsLocatedIn'], "IsLocatedIn(from-link) = ? ORDER BY IsLocatedIn(locN)",          my $query = $self->Get(['IsLocatedIn'], "IsLocatedIn(from-link) = ? ORDER BY IsLocatedIn(locN)",
598                                                     [$featureID]);                                                     [$featureID]);
# Line 634  Line 626 
626                  push @retVal, "${contigID}_$beg$dir$len";                  push @retVal, "${contigID}_$beg$dir$len";
627          }          }
628          # Return the list in the format indicated by the context.          # Return the list in the format indicated by the context.
629          return (wantarray ? @retVal : join(' ', @retVal));      return (wantarray ? @retVal : join(',', @retVal));
630  }  }
631    
632  =head3 ParseLocation  =head3 ParseLocation
# Line 660  Line 652 
652  =cut  =cut
653  #: Return Type @;  #: Return Type @;
654  sub ParseLocation {  sub ParseLocation {
655          # Get the parameter.      # Get the parameter. Note that if we're called as an instance method, we ignore
656        # the first parameter.
657        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
658          my ($location) = @_;          my ($location) = @_;
659          # Parse it into segments.          # Parse it into segments.
660          $location =~ /^(.*)_(\d*)([+-_])(\d*)$/;          $location =~ /^(.*)_(\d*)([+-_])(\d*)$/;
# Line 679  Line 673 
673          return ($contigID, $start, $dir, $len);          return ($contigID, $start, $dir, $len);
674  }  }
675    
676    =head3 PointLocation
677    
678    C<< my $found = Sprout::PointLocation($location, $point); >>
679    
680    Return the offset into the specified location of the specified point on the contig. If
681    the specified point is before the location, a negative value will be returned. If it is
682    beyond the location, an undefined value will be returned. It is assumed that the offset
683    is for the location's contig. The location can either be new-style (using a C<+> or C<->
684    and a length) or old-style (using C<_> and start and end positions.
685    
686    =over 4
687    
688    =item location
689    
690    A location specifier (see L</FeatureLocation> for a description).
691    
692    =item point
693    
694    The offset into the contig of the point in which we're interested.
695    
696    =item RETURN
697    
698    Returns the offset inside the specified location of the specified point, a negative
699    number if the point is before the location, or an undefined value if the point is past
700    the location. If the length of the location is 0, this method will B<always> denote
701    that it is outside the location. The offset will always be relative to the left-most
702    position in the location.
703    
704    =back
705    
706    =cut
707    #: Return Type $;
708    sub PointLocation {
709        # Get the parameter. Note that if we're called as an instance method, we ignore
710        # the first parameter.
711        shift if UNIVERSAL::isa($_[0],__PACKAGE__);
712        my ($location, $point) = @_;
713        # Parse out the location elements. Note that this works on both old-style and new-style
714        # locations.
715        my ($contigID, $start, $dir, $len) = ParseLocation($location);
716        # Declare the return variable.
717        my $retVal;
718        # Compute the offset. The computation is dependent on the direction of the location.
719        my $offset = (($dir == '+') ? $point - $start : $point - ($start - $len + 1));
720        # Return the offset if it's valid.
721        if ($offset < $len) {
722            $retVal = $offset;
723        }
724        # Return the offset found.
725        return $retVal;
726    }
727    
728  =head3 DNASeq  =head3 DNASeq
729    
730  C<< my $sequence = $sprout->DNASeq(\@locationList); >>  C<< my $sequence = $sprout->DNASeq(\@locationList); >>
# Line 704  Line 750 
750  #: Return Type $;  #: Return Type $;
751  sub DNASeq {  sub DNASeq {
752          # Get the parameters.          # Get the parameters.
753          my $self = shift @_;      my ($self, $locationList) = @_;
         my ($locationList) = @_;  
754          # Create the return string.          # Create the return string.
755          my $retVal = "";          my $retVal = "";
756          # Loop through the locations.          # Loop through the locations.
# Line 778  Line 823 
823  #: Return Type @;  #: Return Type @;
824  sub AllContigs {  sub AllContigs {
825          # Get the parameters.          # Get the parameters.
826          my $self = shift @_;      my ($self, $genomeID) = @_;
         my ($genomeID) = @_;  
827          # Ask for the genome's Contigs.          # Ask for the genome's Contigs.
828          my @retVal = $self->GetFlat(['HasContig'], "HasContig(from-link) = ?", [$genomeID],          my @retVal = $self->GetFlat(['HasContig'], "HasContig(from-link) = ?", [$genomeID],
829                                                                  'HasContig(to-link)');                                                                  'HasContig(to-link)');
# Line 809  Line 853 
853  #: Return Type $;  #: Return Type $;
854  sub ContigLength {  sub ContigLength {
855          # Get the parameters.          # Get the parameters.
856          my $self = shift @_;      my ($self, $contigID) = @_;
         my ($contigID) = @_;  
857          # Get the contig's last sequence.          # Get the contig's last sequence.
858          my $query = $self->Get(['IsMadeUpOf'],          my $query = $self->Get(['IsMadeUpOf'],
859                  "IsMadeUpOf(from-link) = ? ORDER BY IsMadeUpOf(start-position) DESC",                  "IsMadeUpOf(from-link) = ? ORDER BY IsMadeUpOf(start-position) DESC",
# Line 861  Line 904 
904  #: Return Type @@;  #: Return Type @@;
905  sub GenesInRegion {  sub GenesInRegion {
906          # Get the parameters.          # Get the parameters.
907          my $self = shift @_;      my ($self, $contigID, $start, $stop) = @_;
         my ($contigID, $start, $stop) = @_;  
908          # Get the maximum segment length.          # Get the maximum segment length.
909          my $maximumSegmentLength = $self->MaxSegment;          my $maximumSegmentLength = $self->MaxSegment;
910          # Create a hash to receive the feature list. We use a hash so that we can eliminate          # Create a hash to receive the feature list. We use a hash so that we can eliminate
# Line 963  Line 1005 
1005  #: Return Type $;  #: Return Type $;
1006  sub FType {  sub FType {
1007          # Get the parameters.          # Get the parameters.
1008          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
1009          # Get the specified feature's type.          # Get the specified feature's type.
1010          my ($retVal) = $self->GetEntityValues('Feature', $featureID, ['Feature(feature-type)']);          my ($retVal) = $self->GetEntityValues('Feature', $featureID, ['Feature(feature-type)']);
1011          # Return the result.          # Return the result.
# Line 1001  Line 1042 
1042  #: Return Type @%;  #: Return Type @%;
1043  sub FeatureAnnotations {  sub FeatureAnnotations {
1044          # Get the parameters.          # Get the parameters.
1045          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
1046          # 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.
1047          my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],          my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1048                                                     "IsTargetOfAnnotation(from-link) = ?", [$featureID]);                                                     "IsTargetOfAnnotation(from-link) = ?", [$featureID]);
# Line 1031  Line 1071 
1071  C<< my %functions = $sprout->AllFunctionsOf($featureID); >>  C<< my %functions = $sprout->AllFunctionsOf($featureID); >>
1072    
1073  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
1074  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,
1075  It has the format "XXXX\nset XXXX function to\nYYYYY". In this instance, XXXX is the user ID  Functional assignments are described in the L</ParseAssignment> function. Its worth noting that
1076  and YYYYY is the functional assignment text. Its worth noting that we cannot filter on the content  we cannot filter on the content of the annotation itself because it's a text field; however,
1077  of the annotation itself because it's a text field; however, this is not a big problem because most  this is not a big problem because most features only have a small number of annotations.
1078  features only have a small number of annotations. Finally, if a single user has multiple  Finally, if a single user has multiple functional assignments, we will only keep the most
1079  functional assignments, we will only keep the most recent one.  recent one.
1080    
1081  =over 4  =over 4
1082    
# Line 1054  Line 1094 
1094  #: Return Type %;  #: Return Type %;
1095  sub AllFunctionsOf {  sub AllFunctionsOf {
1096          # Get the parameters.          # Get the parameters.
1097          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
1098          # Get all of the feature's annotations.          # Get all of the feature's annotations.
1099      my @query = $self->GetAll(['IsTargetOfAnnotation', 'Annotation'],      my @query = $self->GetAll(['IsTargetOfAnnotation', 'Annotation'],
1100                                                      "IsTargetOfAnnotation(from-link) = ?",                                                      "IsTargetOfAnnotation(from-link) = ?",
# Line 1071  Line 1110 
1110          # Get the annotation fields.          # Get the annotation fields.
1111          my ($timeStamp, $text) = @{$annotation};          my ($timeStamp, $text) = @{$annotation};
1112                  # Check to see if this is a functional assignment.                  # Check to see if this is a functional assignment.
1113                  my ($user, $function) = ParseAssignment($text);          my ($user, $function) = _ParseAssignment($text);
1114          if ($user && ! exists $timeHash{$user}) {          if ($user && ! exists $timeHash{$user}) {
1115              # Here it is a functional assignment and there has been no              # Here it is a functional assignment and there has been no
1116              # previous assignment for this user, so we stuff it in the              # previous assignment for this user, so we stuff it in the
# Line 1093  Line 1132 
1132    
1133  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
1134  the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional  the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional
1135  assignment is a type of annotation. It has the format "XXXX\nset XXXX function to\nYYYYY". In this  assignment is a type of annotation. The format of an assignment is described in
1136  instance, XXXX is the user ID and YYYYY is the functional assignment text. Its worth noting that  L</ParseLocation>. Its worth noting that we cannot filter on the content of the
1137  we cannot filter on the content of the annotation itself because it's a text field; however, this  annotation itself because it's a text field; however, this is not a big problem because
1138  is not a big problem because most features only have a small number of annotations.  most features only have a small number of annotations.
1139    
1140  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
1141  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
# Line 1128  Line 1167 
1167  #: Return Type $;  #: Return Type $;
1168  sub FunctionOf {  sub FunctionOf {
1169          # Get the parameters.          # Get the parameters.
1170          my $self = shift @_;      my ($self, $featureID, $userID) = @_;
         my ($featureID, $userID) = @_;  
1171      # Declare the return value.      # Declare the return value.
1172      my $retVal;      my $retVal;
1173      # Determine the ID type.      # Determine the ID type.
# Line 1166  Line 1204 
1204              # Get the annotation text.              # Get the annotation text.
1205              my ($text, $time) = $annotation->Values(['Annotation(annotation)','Annotation(time)']);              my ($text, $time) = $annotation->Values(['Annotation(annotation)','Annotation(time)']);
1206              # Check to see if this is a functional assignment for a trusted user.              # Check to see if this is a functional assignment for a trusted user.
1207              my ($user, $type, $function) = split(/\n/, $text);              my ($user, $function) = _ParseAssignment($text);
1208              if ($type =~ m/^set $user function to$/i) {              if ($user) {
1209                  # Here it is a functional assignment. Check the time and the user                  # Here it is a functional assignment. Check the time and the user
1210                  # name. The time must be recent and the user must be trusted.                  # name. The time must be recent and the user must be trusted.
1211                  if ((exists $trusteeTable{$user}) && ($time > $timeSelected)) {                  if ((exists $trusteeTable{$user}) && ($time > $timeSelected)) {
# Line 1205  Line 1243 
1243    
1244  =item RETURN  =item RETURN
1245    
1246  Returns a reference to a hash that maps the IDs of the incoming features to the IDs of  Returns a reference to a hash that maps the IDs of the incoming features to the best hits
1247  their best hits.  on the target genome.
1248    
1249  =back  =back
1250    
# Line 1214  Line 1252 
1252  #: Return Type %;  #: Return Type %;
1253  sub BBHList {  sub BBHList {
1254          # Get the parameters.          # Get the parameters.
1255          my $self = shift @_;      my ($self, $genomeID, $featureList) = @_;
         my ($genomeID, $featureList) = @_;  
1256          # Create the return structure.          # Create the return structure.
1257          my %retVal = ();          my %retVal = ();
1258          # Loop through the incoming features.          # Loop through the incoming features.
# Line 1235  Line 1272 
1272          return \%retVal;          return \%retVal;
1273  }  }
1274    
1275    =head3 SimList
1276    
1277    C<< my %similarities = $sprout->SimList($featureID, $count); >>
1278    
1279    Return a list of the similarities to the specified feature.
1280    
1281    Sprout does not support real similarities, so this method just returns the bidirectional
1282    best hits.
1283    
1284    =over 4
1285    
1286    =item featureID
1287    
1288    ID of the feature whose similarities are desired.
1289    
1290    =item count
1291    
1292    Maximum number of similar features to be returned, or C<0> to return them all.
1293    
1294    =back
1295    
1296    =cut
1297    #: Return Type %;
1298    sub SimList {
1299        # Get the parameters.
1300        my ($self, $featureID, $count) = @_;
1301        # Ask for the best hits.
1302        my @lists = $self->GetAll(['IsBidirectionalBestHitOf'],
1303                                  "IsBidirectionalBestHitOf(from-link) = ? ORDER BY IsBidirectionalBestHitOf(score) DESC",
1304                                  [$featureID], ['IsBidirectionalBestHitOf(to-link)', 'IsBidirectionalBestHitOf(score)'],
1305                                  $count);
1306        # Create the return value.
1307        my %retVal = ();
1308        for my $tuple (@lists) {
1309            $retVal{$tuple->[0]} = $tuple->[1];
1310        }
1311        # Return the result.
1312        return %retVal;
1313    }
1314    
1315    
1316    
1317    =head3 IsComplete
1318    
1319    C<< my $flag = $sprout->IsComplete($genomeID); >>
1320    
1321    Return TRUE if the specified genome is complete, else FALSE.
1322    
1323    =over 4
1324    
1325    =item genomeID
1326    
1327    ID of the genome whose completeness status is desired.
1328    
1329    =item RETURN
1330    
1331    Returns TRUE if the genome is complete, FALSE if it is incomplete, and C<undef> if it is
1332    not found.
1333    
1334    =back
1335    
1336    =cut
1337    #: Return Type $;
1338    sub IsComplete {
1339        # Get the parameters.
1340        my ($self, $genomeID) = @_;
1341        # Declare the return variable.
1342        my $retVal;
1343        # Get the genome's data.
1344        my $genomeData = $self->GetEntity('Genome', $genomeID);
1345        if ($genomeData) {
1346            # The genome exists, so get the completeness flag.
1347            ($retVal) = $genomeData->Value('complete');
1348        }
1349        # Return the result.
1350        return $retVal;
1351    }
1352    
1353  =head3 FeatureAliases  =head3 FeatureAliases
1354    
1355  C<< my @aliasList = $sprout->FeatureAliases($featureID); >>  C<< my @aliasList = $sprout->FeatureAliases($featureID); >>
# Line 1258  Line 1373 
1373  #: Return Type @;  #: Return Type @;
1374  sub FeatureAliases {  sub FeatureAliases {
1375          # Get the parameters.          # Get the parameters.
1376          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
1377          # Get the desired feature's aliases          # Get the desired feature's aliases
1378          my @retVal = $self->GetEntityValues('Feature', $featureID, ['Feature(alias)']);          my @retVal = $self->GetEntityValues('Feature', $featureID, ['Feature(alias)']);
1379          # Return the result.          # Return the result.
# Line 1289  Line 1403 
1403  #: Return Type $;  #: Return Type $;
1404  sub GenomeOf {  sub GenomeOf {
1405          # Get the parameters.          # Get the parameters.
1406          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
1407          # Create a query to find the genome associated with the feature.          # Create a query to find the genome associated with the feature.
1408          my $query = $self->Get(['IsLocatedIn', 'HasContig'], "IsLocatedIn(from-link) = ?", [$featureID]);          my $query = $self->Get(['IsLocatedIn', 'HasContig'], "IsLocatedIn(from-link) = ?", [$featureID]);
1409          # Declare the return value.          # Declare the return value.
# Line 1326  Line 1439 
1439  #: Return Type %;  #: Return Type %;
1440  sub CoupledFeatures {  sub CoupledFeatures {
1441          # Get the parameters.          # Get the parameters.
1442          my $self = shift @_;      my ($self, $featureID) = @_;
1443          my ($featureID) = @_;      # Create a query to retrieve the functionally-coupled features.
1444          # Create a query to retrieve the functionally-coupled features. Note that we depend on the      my $query = $self->Get(['ParticipatesInCoupling', 'Coupling'],
1445          # fact that the functional coupling is physically paired. If (A,B) is in the database, then                             "ParticipatesInCoupling(from-link) = ?", [$featureID]);
         # (B,A) will also be found.  
         my $query = $self->Get(['IsClusteredOnChromosomeWith'],  
                                                    "IsClusteredOnChromosomeWith(from-link) = ?", [$featureID]);  
1446          # This value will be set to TRUE if we find at least one coupled feature.          # This value will be set to TRUE if we find at least one coupled feature.
1447          my $found = 0;          my $found = 0;
1448          # Create the return hash.          # Create the return hash.
1449          my %retVal = ();          my %retVal = ();
1450          # Retrieve the relationship records and store them in the hash.          # Retrieve the relationship records and store them in the hash.
1451          while (my $clustering = $query->Fetch()) {          while (my $clustering = $query->Fetch()) {
1452                  my ($otherFeatureID, $score) = $clustering->Values(['IsClusteredOnChromosomeWith(to-link)',          # Get the ID and score of the coupling.
1453                                                                      'IsClusteredOnChromosomeWith(score)']);          my ($couplingID, $score) = $clustering->Values(['Coupling(id)',
1454                                                            'Coupling(score)']);
1455            # The coupling ID contains the two feature IDs separated by a space. We use
1456            # this information to find the ID of the other feature.
1457            my ($fid1, $fid2) = split / /, $couplingID;
1458            my $otherFeatureID = ($featureID eq $fid1 ? $fid2 : $fid1);
1459            # Attach the other feature's score to its ID.
1460                  $retVal{$otherFeatureID} = $score;                  $retVal{$otherFeatureID} = $score;
1461                  $found = 1;                  $found = 1;
1462          }          }
# Line 1353  Line 1469 
1469          return %retVal;          return %retVal;
1470  }  }
1471    
1472    =head3 CouplingEvidence
1473    
1474    C<< my @evidence = $sprout->CouplingEvidence($peg1, $peg2); >>
1475    
1476    Return the evidence for a functional coupling.
1477    
1478    A pair of features is considered evidence of a coupling between two other
1479    features if they occur close together on a contig and both are similar to
1480    the coupled features. So, if B<A1> and B<A2> are close together on a contig,
1481    B<B1> and B<B2> are considered evidence for the coupling if (1) B<B1> and
1482    B<B2> are close together, (2) B<B1> is similar to B<A1>, and (3) B<B2> is
1483    similar to B<A2>.
1484    
1485    The score of a coupling is determined by the number of pieces of evidence
1486    that are considered I<representative>. If several evidence items belong to
1487    a group of genomes that are close to each other, only one of those items
1488    is considered representative. The other evidence items are presumed to be
1489    there because of the relationship between the genomes rather than because
1490    the two proteins generated by the features have a related functionality.
1491    
1492    Each evidence item is returned as a three-tuple in the form C<[>I<$peg1a>C<,>
1493    I<$peg2a>C<,> I<$rep>C<]>, where I<$peg1a> is similar to I<$peg1>, I<$peg2a>
1494    is similar to I<$peg2>, and I<$rep> is TRUE if the evidence is representative
1495    and FALSE otherwise.
1496    
1497    =over 4
1498    
1499    =item peg1
1500    
1501    ID of the feature of interest.
1502    
1503    =item peg2
1504    
1505    ID of a feature functionally coupled to the feature of interest.
1506    
1507    =item RETURN
1508    
1509    Returns a list of 3-tuples. Each tuple consists of a feature similar to the feature
1510    of interest, a feature similar to the functionally coupled feature, and a flag
1511    that is TRUE for a representative piece of evidence and FALSE otherwise.
1512    
1513    =back
1514    
1515    =cut
1516    #: Return Type @@;
1517    sub CouplingEvidence {
1518        # Get the parameters.
1519        my ($self, $peg1, $peg2) = @_;
1520        # Declare the return variable.
1521        my @retVal = ();
1522        # Our first task is to find out the nature of the coupling: whether or not
1523        # it exists, its score, and whether the features are stored in the same
1524        # order as the ones coming in.
1525        my ($couplingID, $inverted, $score) = $self->GetCoupling($peg1, $peg2);
1526        # Only proceed if a coupling exists.
1527        if ($couplingID) {
1528            # Determine the ordering to place on the evidence items. If we're
1529            # inverted, we want to see feature 2 before feature 1 (descending); otherwise,
1530            # we want feature 1 before feature 2 (normal).
1531            Trace("Coupling evidence for ($peg1, $peg2) with inversion flag $inverted.") if T(Coupling => 4);
1532            my $ordering = ($inverted ? "DESC" : "");
1533            # Get the coupling evidence.
1534            my @evidenceList = $self->GetAll(['IsEvidencedBy', 'PCH', 'UsesAsEvidence'],
1535                                              "IsEvidencedBy(from-link) = ? ORDER BY PCH(id), UsesAsEvidence(pos) $ordering",
1536                                              [$couplingID],
1537                                              ['PCH(used)', 'UsesAsEvidence(to-link)']);
1538            # Loop through the evidence items. Each piece of evidence is represented by two
1539            # positions in the evidence list, one for each feature on the other side of the
1540            # evidence link. If at some point we want to generalize to couplings with
1541            # more than two positions, this section of code will need to be re-done.
1542            while (@evidenceList > 0) {
1543                my $peg1Data = shift @evidenceList;
1544                my $peg2Data = shift @evidenceList;
1545                Trace("Peg 1 is " . $peg1Data->[1] . " and Peg 2 is " . $peg2Data->[1] . ".") if T(Coupling => 4);
1546                push @retVal, [$peg1Data->[1], $peg2Data->[1], $peg1Data->[0]];
1547            }
1548            Trace("Last index in evidence result is is $#retVal.") if T(Coupling => 4);
1549        }
1550        # Return the result.
1551        return @retVal;
1552    }
1553    
1554    =head3 GetCoupling
1555    
1556    C<< my ($couplingID, $inverted, $score) = $sprout->GetCoupling($peg1, $peg2); >>
1557    
1558    Return the coupling (if any) for the specified pair of PEGs. If a coupling
1559    exists, we return the coupling ID along with an indicator of whether the
1560    coupling is stored as C<(>I<$peg1>C<, >I<$peg2>C<)> or C<(>I<$peg2>C<, >I<$peg1>C<)>.
1561    In the second case, we say the coupling is I<inverted>. The importance of an
1562    inverted coupling is that the PEGs in the evidence will appear in reverse order.
1563    
1564    =over 4
1565    
1566    =item peg1
1567    
1568    ID of the feature of interest.
1569    
1570    =item peg2
1571    
1572    ID of the potentially coupled feature.
1573    
1574    =item RETURN
1575    
1576    Returns a three-element list. The first element contains the database ID of
1577    the coupling. The second element is FALSE if the coupling is stored in the
1578    database in the caller specified order and TRUE if it is stored in the
1579    inverted order. The third element is the coupling's score. If the coupling
1580    does not exist, all three list elements will be C<undef>.
1581    
1582    =back
1583    
1584    =cut
1585    #: Return Type $%@;
1586    sub GetCoupling {
1587        # Get the parameters.
1588        my ($self, $peg1, $peg2) = @_;
1589        # Declare the return values. We'll start with the coupling ID and undefine the
1590        # flag and score until we have more information.
1591        my ($retVal, $inverted, $score) = (CouplingID($peg1, $peg2), undef, undef);
1592        # Find the coupling data.
1593        my @pegs = $self->GetAll(['Coupling', 'ParticipatesInCoupling'],
1594                                     "Coupling(id) = ? ORDER BY ParticipatesInCoupling(pos)",
1595                                     [$retVal], ["ParticipatesInCoupling(from-link)", "Coupling(score)"]);
1596        # Check to see if we found anything.
1597        if (!@pegs) {
1598            Trace("No coupling found.") if T(Coupling => 4);
1599            # No coupling, so undefine the return value.
1600            $retVal = undef;
1601        } else {
1602            # We have a coupling! Get the score and check for inversion.
1603            $score = $pegs[0]->[1];
1604            my $firstFound = $pegs[0]->[0];
1605            $inverted = ($firstFound ne $peg1);
1606            Trace("Coupling score is $score. First peg is $firstFound, peg 1 is $peg1.") if T(Coupling => 4);
1607        }
1608        # Return the result.
1609        return ($retVal, $inverted, $score);
1610    }
1611    
1612    =head3 CouplingID
1613    
1614    C<< my $couplingID = Sprout::CouplingID($peg1, $peg2); >>
1615    
1616    Return the coupling ID for a pair of feature IDs.
1617    
1618    The coupling ID is currently computed by joining the feature IDs in
1619    sorted order with a space. Client modules (that is, modules which
1620    use Sprout) should not, however, count on this always being the
1621    case. This method provides a way for abstracting the concept of a
1622    coupling ID. All that we know for sure about it is that it can be
1623    generated easily from the feature IDs and the order of the IDs
1624    in the parameter list does not matter (i.e. C<CouplingID("a1", "b1")>
1625    will have the same value as C<CouplingID("b1", "a1")>.
1626    
1627    =over 4
1628    
1629    =item peg1
1630    
1631    First feature of interest.
1632    
1633    =item peg2
1634    
1635    Second feature of interest.
1636    
1637    =item RETURN
1638    
1639    Returns the ID that would be used to represent a functional coupling of
1640    the two specified PEGs.
1641    
1642    =back
1643    
1644    =cut
1645    #: Return Type $;
1646    sub CouplingID {
1647        return join " ", sort @_;
1648    }
1649    
1650  =head3 GetEntityTypes  =head3 GetEntityTypes
1651    
1652  C<< my @entityList = $sprout->GetEntityTypes(); >>  C<< my @entityList = $sprout->GetEntityTypes(); >>
# Line 1363  Line 1657 
1657  #: Return Type @;  #: Return Type @;
1658  sub GetEntityTypes {  sub GetEntityTypes {
1659          # Get the parameters.          # Get the parameters.
1660          my $self = shift @_;      my ($self) = @_;
1661          # Get the underlying database object.          # Get the underlying database object.
1662          my $erdb = $self->{_erdb};          my $erdb = $self->{_erdb};
1663          # Get its entity type list.          # Get its entity type list.
# Line 1414  Line 1708 
1708                  if ($line =~ m/^>\s*(.+?)(\s|\n)/) {                  if ($line =~ m/^>\s*(.+?)(\s|\n)/) {
1709                          # Here we have a new header. Store the current sequence if we have one.                          # Here we have a new header. Store the current sequence if we have one.
1710                          if ($id) {                          if ($id) {
1711                                  $retVal{$id} = $sequence;                  $retVal{$id} = lc $sequence;
1712                          }                          }
1713                          # Clear the sequence accumulator and save the new ID.                          # Clear the sequence accumulator and save the new ID.
1714                          ($id, $sequence) = ("$prefix$1", "");                          ($id, $sequence) = ("$prefix$1", "");
1715                  } else {                  } else {
1716                          # 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.
1717                          # First, we get the actual data out.              # First, we get the actual data out. Note that we normalize to lower
1718                # case.
1719                          $line =~ /^\s*(.*?)(\s|\n)/;                          $line =~ /^\s*(.*?)(\s|\n)/;
1720                          $sequence .= $1;                          $sequence .= $1;
1721                  }                  }
1722          }          }
1723          # Flush out the last sequence (if any).          # Flush out the last sequence (if any).
1724          if ($sequence) {          if ($sequence) {
1725                  $retVal {$id} = $sequence;          $retVal{$id} = lc $sequence;
1726          }          }
1727        # Close the file.
1728        close FASTAFILE;
1729          # Return the hash constructed from the file.          # Return the hash constructed from the file.
1730          return %retVal;          return %retVal;
1731  }  }
# Line 1439  Line 1736 
1736    
1737  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
1738  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
1739  gene. The old format is I<contig>_I<beg>_I<end>.  gene. The old format is I<contig>_I<beg>_I<end>. If a feature is in the new format already,
1740    it will not be changed; otherwise, it will be converted. This method can also be used to
1741    perform the reverse task-- insuring that all the locations are in the old format.
1742    
1743  =over 4  =over 4
1744    
# Line 1466  Line 1765 
1765  #: Return Type @;  #: Return Type @;
1766  sub FormatLocations {  sub FormatLocations {
1767          # Get the parameters.          # Get the parameters.
1768          my $self = shift @_;      my ($self, $prefix, $locations, $oldFormat) = @_;
         my ($prefix, $locations, $oldFormat) = @_;  
1769          # Create the return list.          # Create the return list.
1770          my @retVal = ();          my @retVal = ();
1771          # Check to see if any locations were passed in.          # Check to see if any locations were passed in.
1772          if ($locations eq '') {          if ($locations eq '') {
1773              confess "No locations specified.";          Confess("No locations specified.");
1774          } else {          } else {
1775                  # Loop through the locations, converting them to the new format.                  # Loop through the locations, converting them to the new format.
1776                  for my $location (@{$locations}) {                  for my $location (@{$locations}) {
# Line 1507  Line 1805 
1805    
1806  sub DumpData {  sub DumpData {
1807          # Get the parameters.          # Get the parameters.
1808          my $self = shift @_;      my ($self) = @_;
1809          # Get the data directory name.          # Get the data directory name.
1810          my $outputDirectory = $self->{_options}->{dataDir};          my $outputDirectory = $self->{_options}->{dataDir};
1811          # Dump the relations.          # Dump the relations.
# Line 1523  Line 1821 
1821  =cut  =cut
1822  #: Return Type $;  #: Return Type $;
1823  sub XMLFileName {  sub XMLFileName {
1824          my $self = shift @_;      my ($self) = @_;
1825          return $self->{_xmlName};          return $self->{_xmlName};
1826  }  }
1827    
# Line 1543  Line 1841 
1841  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
1842  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>.
1843    
1844  C<< $sprout->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence = 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>  C<< $sprout->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>
1845    
1846  =over 4  =over 4
1847    
# Line 1561  Line 1859 
1859  #: Return Type ;  #: Return Type ;
1860  sub Insert {  sub Insert {
1861          # Get the parameters.          # Get the parameters.
1862          my $self = shift @_;      my ($self, $objectType, $fieldHash) = @_;
         my ($objectType, $fieldHash) = @_;  
1863          # Call the underlying method.          # Call the underlying method.
1864          $self->{_erdb}->InsertObject($objectType, $fieldHash);          $self->{_erdb}->InsertObject($objectType, $fieldHash);
1865  }  }
# Line 1603  Line 1900 
1900  #: Return Type $;  #: Return Type $;
1901  sub Annotate {  sub Annotate {
1902          # Get the parameters.          # Get the parameters.
1903          my $self = shift @_;      my ($self, $fid, $timestamp, $user, $text) = @_;
         my ($fid, $timestamp, $user, $text) = @_;  
1904          # Create the annotation ID.          # Create the annotation ID.
1905          my $aid = "$fid:$timestamp";          my $aid = "$fid:$timestamp";
1906          # Insert the Annotation object.          # Insert the Annotation object.
# Line 1624  Line 1920 
1920    
1921  =head3 AssignFunction  =head3 AssignFunction
1922    
1923  C<< my $ok = $sprout->AssignFunction($featureID, $user, $function); >>  C<< my $ok = $sprout->AssignFunction($featureID, $user, $function, $assigningUser); >>
1924    
1925  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
1926  format is "XXXX\nset XXXX function to\nYYYYY" where XXXX is the feature type and YYYY is the functional  format is described in L</ParseAssignment>.
 assignment text.  
1927    
1928  =over 4  =over 4
1929    
# Line 1638  Line 1933 
1933    
1934  =item user  =item user
1935    
1936  Name of the user making the assignment. This is frequently a group name, like C<kegg> or C<fig>.  Name of the user group making the assignment, such as C<kegg> or C<fig>.
1937    
1938  =item function  =item function
1939    
1940  Text of the function being assigned.  Text of the function being assigned.
1941    
1942    =item assigningUser (optional)
1943    
1944    Name of the individual user making the assignment. If omitted, defaults to the user group.
1945    
1946  =item RETURN  =item RETURN
1947    
1948  Returns 1 if successful, 0 if an error occurred.  Returns 1 if successful, 0 if an error occurred.
# Line 1654  Line 1953 
1953  #: Return Type $;  #: Return Type $;
1954  sub AssignFunction {  sub AssignFunction {
1955          # Get the parameters.          # Get the parameters.
1956          my $self = shift @_;      my ($self, $featureID, $user, $function, $assigningUser) = @_;
1957          my ($featureID, $user, $function) = @_;      # Default the assigning user.
1958        if (! $assigningUser) {
1959            $assigningUser = $user;
1960        }
1961          # Create an annotation string from the parameters.          # Create an annotation string from the parameters.
1962          my $annotationText = "$user\nset $user function to\n$function";      my $annotationText = "$assigningUser\nset $user function to\n$function";
1963          # Get the current time.          # Get the current time.
1964          my $now = time;          my $now = time;
1965          # Declare the return variable.          # Declare the return variable.
# Line 1702  Line 2004 
2004  #: Return Type @;  #: Return Type @;
2005  sub FeaturesByAlias {  sub FeaturesByAlias {
2006          # Get the parameters.          # Get the parameters.
2007          my $self = shift @_;      my ($self, $alias) = @_;
         my ($alias) = @_;  
2008          # Declare the return variable.          # Declare the return variable.
2009          my @retVal = ();          my @retVal = ();
2010          # Parse the alias.          # Parse the alias.
# Line 1745  Line 2046 
2046  #: Return Type $;  #: Return Type $;
2047  sub Exists {  sub Exists {
2048          # Get the parameters.          # Get the parameters.
2049          my $self = shift @_;      my ($self, $entityName, $entityID) = @_;
         my ($entityName, $entityID) = @_;  
2050          # Check for the entity instance.          # Check for the entity instance.
2051          my $testInstance = $self->GetEntity($entityName, $entityID);          my $testInstance = $self->GetEntity($entityName, $entityID);
2052          # Return an existence indicator.          # Return an existence indicator.
# Line 1776  Line 2076 
2076  #: Return Type $;  #: Return Type $;
2077  sub FeatureTranslation {  sub FeatureTranslation {
2078          # Get the parameters.          # Get the parameters.
2079          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
2080          # Get the specified feature's translation.          # Get the specified feature's translation.
2081          my ($retVal) = $self->GetEntityValues("Feature", $featureID, ['Feature(translation)']);          my ($retVal) = $self->GetEntityValues("Feature", $featureID, ['Feature(translation)']);
2082          return $retVal;          return $retVal;
# Line 1809  Line 2108 
2108  #: Return Type @;  #: Return Type @;
2109  sub Taxonomy {  sub Taxonomy {
2110          # Get the parameters.          # Get the parameters.
2111          my $self = shift @_;      my ($self, $genome) = @_;
         my ($genome) = @_;  
2112          # Find the specified genome's taxonomy string.          # Find the specified genome's taxonomy string.
2113          my ($list) = $self->GetEntityValues('Genome', $genome, ['Genome(taxonomy)']);          my ($list) = $self->GetEntityValues('Genome', $genome, ['Genome(taxonomy)']);
2114          # Declare the return variable.          # Declare the return variable.
# Line 1853  Line 2151 
2151  #: Return Type $;  #: Return Type $;
2152  sub CrudeDistance {  sub CrudeDistance {
2153          # Get the parameters.          # Get the parameters.
2154          my $self = shift @_;      my ($self, $genome1, $genome2) = @_;
         my ($genome1, $genome2) = @_;  
2155          # Insure that the distance is commutative by sorting the genome IDs.          # Insure that the distance is commutative by sorting the genome IDs.
2156          my ($genomeA, $genomeB);          my ($genomeA, $genomeB);
2157          if ($genome2 < $genome2) {          if ($genome2 < $genome2) {
# Line 1901  Line 2198 
2198  #: Return Type $;  #: Return Type $;
2199  sub RoleName {  sub RoleName {
2200          # Get the parameters.          # Get the parameters.
2201          my $self = shift @_;      my ($self, $roleID) = @_;
         my ($roleID) = @_;  
2202          # Get the specified role's name.          # Get the specified role's name.
2203          my ($retVal) = $self->GetEntityValues('Role', $roleID, ['Role(name)']);          my ($retVal) = $self->GetEntityValues('Role', $roleID, ['Role(name)']);
2204          # Use the ID if the role has no name.          # Use the ID if the role has no name.
# Line 1935  Line 2231 
2231  #: Return Type @;  #: Return Type @;
2232  sub RoleDiagrams {  sub RoleDiagrams {
2233          # Get the parameters.          # Get the parameters.
2234          my $self = shift @_;      my ($self, $roleID) = @_;
         my ($roleID) = @_;  
2235          # Query for the diagrams.          # Query for the diagrams.
2236          my @retVal = $self->GetFlat(['RoleOccursIn'], "RoleOccursIn(from-link) = ?", [$roleID],          my @retVal = $self->GetFlat(['RoleOccursIn'], "RoleOccursIn(from-link) = ?", [$roleID],
2237                                                                  'RoleOccursIn(to-link)');                                                                  'RoleOccursIn(to-link)');
# Line 1944  Line 2239 
2239          return @retVal;          return @retVal;
2240  }  }
2241    
2242    =head3 GetProperties
2243    
2244    C<< my @list = $sprout->GetProperties($fid, $key, $value, $url); >>
2245    
2246    Return a list of the properties with the specified characteristics.
2247    
2248    Properties are arbitrary key-value pairs associated with a feature. (At some point they
2249    will also be associated with genomes.) A property value is represented by a 4-tuple of
2250    the form B<($fid, $key, $value, $url)>. These exactly correspond to the parameter
2251    
2252    =over 4
2253    
2254    =item fid
2255    
2256    ID of the feature possessing the property.
2257    
2258    =item key
2259    
2260    Name or key of the property.
2261    
2262    =item value
2263    
2264    Value of the property.
2265    
2266    =item url
2267    
2268    URL of the document that indicated the property should have this particular value, or an
2269    empty string if no such document exists.
2270    
2271    =back
2272    
2273    The parameters act as a filter for the desired data. Any non-null parameter will
2274    automatically match all the tuples returned. So, specifying just the I<$fid> will
2275    return all the properties of the specified feature; similarly, specifying the I<$key>
2276    and I<$value> parameters will return all the features having the specified property
2277    value.
2278    
2279    A single property key can have many values, representing different ideas about the
2280    feature in question. For example, one paper may declare that a feature C<fig|83333.1.peg.10> is
2281    virulent, and another may declare that it is not virulent. A query about the virulence of
2282    C<fig|83333.1.peg.10> would be coded as
2283    
2284        my @list = $sprout->GetProperties('fig|83333.1.peg.10', 'virulence', '', '');
2285    
2286    Here the I<$value> and I<$url> fields are left blank, indicating that those fields are
2287    not to be filtered. The tuples returned would be
2288    
2289        ('fig|83333.1.peg.10', 'virulence', 'yes', 'http://www.somewhere.edu/first.paper.pdf')
2290        ('fig|83333.1.peg.10', 'virulence', 'no', 'http://www.somewhere.edu/second.paper.pdf')
2291    
2292    =cut
2293    #: Return Type @@;
2294    sub GetProperties {
2295        # Get the parameters.
2296        my ($self, @parms) = @_;
2297        # Declare the return variable.
2298        my @retVal = ();
2299        # Now we need to create a WHERE clause that will get us the data we want. First,
2300        # we create a list of the columns containing the data for each parameter.
2301        my @colNames = ('HasProperty(from-link)', 'Property(property-name)',
2302                        'Property(property-value)', 'HasProperty(evidence)');
2303        # Now we build the WHERE clause and the list of parameter values.
2304        my @where = ();
2305        my @values = ();
2306        for (my $i = 0; $i <= $#colNames; $i++) {
2307            my $parm = $parms[$i];
2308            if (defined $parm && ($parm ne '')) {
2309                push @where, "$colNames[$i] = ?";
2310                push @values, $parm;
2311            }
2312        }
2313        # Format the WHERE clause.
2314        my $filter = (@values > 0 ? (join " AND ", @where) : undef);
2315        # Ask for all the propertie values with the desired characteristics.
2316        my $query = $self->Get(['HasProperty', 'Property'], $filter, \@values);
2317        while (my $valueObject = $query->Fetch()) {
2318            my @tuple = $valueObject->Values(\@colNames);
2319            push @retVal, \@tuple;
2320        }
2321        # Return the result.
2322        return @retVal;
2323    }
2324    
2325  =head3 FeatureProperties  =head3 FeatureProperties
2326    
2327  C<< my @properties = $sprout->FeatureProperties($featureID); >>  C<< my @properties = $sprout->FeatureProperties($featureID); >>
# Line 1973  Line 2351 
2351  #: Return Type @@;  #: Return Type @@;
2352  sub FeatureProperties {  sub FeatureProperties {
2353          # Get the parameters.          # Get the parameters.
2354          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
2355          # Get the properties.          # Get the properties.
2356          my @retVal = $self->GetAll(['HasProperty', 'Property'], "HasProperty(from-link) = ?", [$featureID],          my @retVal = $self->GetAll(['HasProperty', 'Property'], "HasProperty(from-link) = ?", [$featureID],
2357                                                          ['Property(property-name)', 'Property(property-value)',                                                          ['Property(property-name)', 'Property(property-value)',
# Line 2005  Line 2382 
2382  #: Return Type $;  #: Return Type $;
2383  sub DiagramName {  sub DiagramName {
2384          # Get the parameters.          # Get the parameters.
2385          my $self = shift @_;      my ($self, $diagramID) = @_;
         my ($diagramID) = @_;  
2386          # Get the specified diagram's name and return it.          # Get the specified diagram's name and return it.
2387          my ($retVal) = $self->GetEntityValues('Diagram', $diagramID, ['Diagram(name)']);          my ($retVal) = $self->GetEntityValues('Diagram', $diagramID, ['Diagram(name)']);
2388          return $retVal;          return $retVal;
# Line 2038  Line 2414 
2414  #: Return Type @;  #: Return Type @;
2415  sub MergedAnnotations {  sub MergedAnnotations {
2416          # Get the parameters.          # Get the parameters.
2417          my $self = shift @_;      my ($self, $list) = @_;
         my ($list) = @_;  
2418          # Create a list to hold the annotation tuples found.          # Create a list to hold the annotation tuples found.
2419          my @tuples = ();          my @tuples = ();
2420          # Loop through the features in the input list.          # Loop through the features in the input list.
# Line 2087  Line 2462 
2462  #: Return Type @;  #: Return Type @;
2463  sub RoleNeighbors {  sub RoleNeighbors {
2464          # Get the parameters.          # Get the parameters.
2465          my $self = shift @_;      my ($self, $roleID) = @_;
         my ($roleID) = @_;  
2466          # Get all the diagrams containing this role.          # Get all the diagrams containing this role.
2467          my @diagrams = $self->GetFlat(['RoleOccursIn'], "RoleOccursIn(from-link) = ?", [$roleID],          my @diagrams = $self->GetFlat(['RoleOccursIn'], "RoleOccursIn(from-link) = ?", [$roleID],
2468                                                                    'RoleOccursIn(to-link)');                                                                    'RoleOccursIn(to-link)');
# Line 2130  Line 2504 
2504  #: Return Type @;  #: Return Type @;
2505  sub FeatureLinks {  sub FeatureLinks {
2506          # Get the parameters.          # Get the parameters.
2507          my $self = shift @_;      my ($self, $featureID) = @_;
         my ($featureID) = @_;  
2508          # Get the feature's links.          # Get the feature's links.
2509          my @retVal = $self->GetEntityValues('Feature', $featureID, ['Feature(link)']);          my @retVal = $self->GetEntityValues('Feature', $featureID, ['Feature(link)']);
2510          # Return the feature's links.          # Return the feature's links.
# Line 2143  Line 2516 
2516  C<< my %subsystems = $sprout->SubsystemsOf($featureID); >>  C<< my %subsystems = $sprout->SubsystemsOf($featureID); >>
2517    
2518  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
2519  to the role the feature performs.  to the roles the feature performs.
2520    
2521  =over 4  =over 4
2522    
# Line 2153  Line 2526 
2526    
2527  =item RETURN  =item RETURN
2528    
2529  Returns a hash mapping all the feature's subsystems to the feature's role.  Returns a hash mapping all the feature's subsystems to a list of the feature's roles.
2530    
2531  =back  =back
2532    
2533  =cut  =cut
2534  #: Return Type %;  #: Return Type %@;
2535  sub SubsystemsOf {  sub SubsystemsOf {
2536          # Get the parameters.          # Get the parameters.
2537          my $self = shift @_;      my ($self, $featureID) = @_;
2538          my ($featureID) = @_;      # Get the subsystem list.
         # Use the SSCell to connect features to subsystems.  
2539          my @subsystems = $self->GetAll(['ContainsFeature', 'HasSSCell', 'IsRoleOf'],          my @subsystems = $self->GetAll(['ContainsFeature', 'HasSSCell', 'IsRoleOf'],
2540                                                                          "ContainsFeature(to-link) = ?", [$featureID],                                                                          "ContainsFeature(to-link) = ?", [$featureID],
2541                                                                          ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);                                                                          ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);
# Line 2171  Line 2543 
2543          my %retVal = ();          my %retVal = ();
2544          # Loop through the results, adding them to the hash.          # Loop through the results, adding them to the hash.
2545          for my $record (@subsystems) {          for my $record (@subsystems) {
2546                  $retVal{$record->[0]} = $record->[1];          my ($subsys, $role) = @{$record};
2547            if (exists $retVal{$subsys}) {
2548                push @{$retVal{$subsys}}, $role;
2549            } else {
2550                $retVal{$subsys} = [$role];
2551            }
2552          }          }
2553          # Return the hash.          # Return the hash.
2554          return %retVal;          return %retVal;
2555  }  }
2556    
2557    =head3 SubsystemList
2558    
2559    C<< my @subsystems = $sprout->SubsystemList($featureID); >>
2560    
2561    Return a list containing the names of the subsystems in which the specified
2562    feature participates. Unlike L</SubsystemsOf>, this method only returns the
2563    subsystem names, not the roles.
2564    
2565    =over 4
2566    
2567    =item featureID
2568    
2569    ID of the feature whose subsystem names are desired.
2570    
2571    =item RETURN
2572    
2573    Returns a list of the names of the subsystems in which the feature participates.
2574    
2575    =back
2576    
2577    =cut
2578    #: Return Type @;
2579    sub SubsystemList {
2580        # Get the parameters.
2581        my ($self, $featureID) = @_;
2582        # Get the list of names.
2583        my @retVal = $self->GetFlat(['ContainsFeature', 'HasSSCell'], "ContainsFeature(to-link) = ?",
2584                                    [$featureID], 'HasSSCell(from-link)');
2585        # Return the result.
2586        return @retVal;
2587    }
2588    
2589  =head3 RelatedFeatures  =head3 RelatedFeatures
2590    
2591  C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>  C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>
# Line 2210  Line 2619 
2619  #: Return Type @;  #: Return Type @;
2620  sub RelatedFeatures {  sub RelatedFeatures {
2621          # Get the parameters.          # Get the parameters.
2622          my $self = shift @_;      my ($self, $featureID, $function, $userID) = @_;
         my ($featureID, $function, $userID) = @_;  
2623          # 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.
2624          my @bbhFeatures = $self->GetFlat(['IsBidirectionalBestHitOf'],          my @bbhFeatures = $self->GetFlat(['IsBidirectionalBestHitOf'],
2625                                                                           "IsBidirectionalBestHitOf(from-link) = ?", [$featureID],                                                                           "IsBidirectionalBestHitOf(from-link) = ?", [$featureID],
# Line 2259  Line 2667 
2667  #: Return Type @;  #: Return Type @;
2668  sub TaxonomySort {  sub TaxonomySort {
2669          # Get the parameters.          # Get the parameters.
2670          my $self = shift @_;      my ($self, $featureIDs) = @_;
         my ($featureIDs) = @_;  
2671          # Create the working hash table.          # Create the working hash table.
2672          my %hashBuffer = ();          my %hashBuffer = ();
2673          # Loop through the features.          # Loop through the features.
# Line 2269  Line 2676 
2676                  my ($taxonomy) = $self->GetFlat(['IsLocatedIn', 'HasContig', 'Genome'], "IsLocatedIn(from-link) = ?",                  my ($taxonomy) = $self->GetFlat(['IsLocatedIn', 'HasContig', 'Genome'], "IsLocatedIn(from-link) = ?",
2677                                                                                  [$fid], 'Genome(taxonomy)');                                                                                  [$fid], 'Genome(taxonomy)');
2678                  # Add this feature to the hash buffer.                  # Add this feature to the hash buffer.
2679                  if (exists $hashBuffer{$taxonomy}) {          Tracer::AddToListMap(\%hashBuffer, $taxonomy, $fid);
                         push @{$hashBuffer{$taxonomy}}, $fid;  
                 } else {  
                         $hashBuffer{$taxonomy} = [$fid];  
                 }  
2680          }          }
2681          # Sort the keys and get the elements.          # Sort the keys and get the elements.
2682          my @retVal = ();          my @retVal = ();
# Line 2342  Line 2745 
2745  #: Return Type @@;  #: Return Type @@;
2746  sub GetAll {  sub GetAll {
2747          # Get the parameters.          # Get the parameters.
2748          my $self = shift @_;      my ($self, $objectNames, $filterClause, $parameterList, $fields, $count) = @_;
2749          my ($objectNames, $filterClause, $parameterList, $fields, $count) = @_;      # Call the ERDB method.
2750          # Create the query.      my @retVal = $self->{_erdb}->GetAll($objectNames, $filterClause, $parameterList,
2751          my $query = $self->Get($objectNames, $filterClause, $parameterList);                                          $fields, $count);
         # Set up a counter of the number of records read.  
         my $fetched = 0;  
         # Insure the counter has a value.  
         if (!defined $count) {  
                 $count = 0;  
         }  
         # Loop through the records returned, extracting the fields. Note that if the  
         # counter is non-zero, we stop when the number of records read hits the count.  
         my @retVal = ();  
         while (($count == 0 || $fetched < $count) && (my $row = $query->Fetch())) {  
                 my @rowData = $row->Values($fields);  
                 push @retVal, \@rowData;  
                 $fetched++;  
         }  
2752          # Return the resulting list.          # Return the resulting list.
2753          return @retVal;          return @retVal;
2754  }  }
# Line 2404  Line 2793 
2793  #: Return Type @;  #: Return Type @;
2794  sub GetFlat {  sub GetFlat {
2795          # Get the parameters.          # Get the parameters.
2796          my $self = shift @_;      my ($self, $objectNames, $filterClause, $parameterList, $field) = @_;
         my ($objectNames, $filterClause, $parameterList, $field) = @_;  
2797          # Construct the query.          # Construct the query.
2798          my $query = $self->Get($objectNames, $filterClause, $parameterList);          my $query = $self->Get($objectNames, $filterClause, $parameterList);
2799          # Create the result list.          # Create the result list.
# Line 2515  Line 2903 
2903  #: Return Type @;  #: Return Type @;
2904  sub LoadInfo {  sub LoadInfo {
2905          # Get the parameters.          # Get the parameters.
2906          my $self = shift @_;      my ($self) = @_;
2907          # 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.
2908          my @retVal = ($self->{_options}->{dataDir});          my @retVal = ($self->{_options}->{dataDir});
2909          # Concatenate the table names.          # Concatenate the table names.
# Line 2552  Line 2940 
2940  #: Return Type %;  #: Return Type %;
2941  sub LowBBHs {  sub LowBBHs {
2942          # Get the parsameters.          # Get the parsameters.
2943          my $self = shift @_;      my ($self, $featureID, $cutoff) = @_;
         my ($featureID, $cutoff) = @_;  
2944          # Create the return hash.          # Create the return hash.
2945          my %retVal = ();          my %retVal = ();
2946          # Create a query to get the desired BBHs.          # Create a query to get the desired BBHs.
# Line 2582  Line 2969 
2969  #: Return Type %@;  #: Return Type %@;
2970  sub GetGroups {  sub GetGroups {
2971      # Get the parameters.      # Get the parameters.
2972      my $self = shift @_;      my ($self, $groupList) = @_;
     my ($groupList) = @_;  
2973      # Declare the return value.      # Declare the return value.
2974      my %retVal = ();      my %retVal = ();
2975      # Determine whether we are getting all the groups or just some.      # Determine whether we are getting all the groups or just some.
# Line 2610  Line 2996 
2996              # Loop through the groups, adding the genome ID to each group's              # Loop through the groups, adding the genome ID to each group's
2997              # list.              # list.
2998              for my $group (@groups) {              for my $group (@groups) {
2999                  if (exists $retVal{$group}) {                  Tracer::AddToListMap(\%retVal, $group, $genomeID);
                     push @{$retVal{$group}}, $genomeID;  
                 } else {  
                     $retVal{$group} = [$genomeID];  
                 }  
3000              }              }
3001          }          }
3002      }      }
# Line 2622  Line 3004 
3004      return %retVal;      return %retVal;
3005  }  }
3006    
3007    =head3 MyGenomes
3008    
3009    C<< my @genomes = Sprout::MyGenomes($dataDir); >>
3010    
3011    Return a list of the genomes to be included in the Sprout.
3012    
3013    This method is provided for use during the Sprout load. It presumes the Genome load file has
3014    already been created. (It will be in the Sprout data directory and called either C<Genome>
3015    or C<Genome.dtx>.) Essentially, it reads in the Genome load file and strips out the genome
3016    IDs.
3017    
3018    =over 4
3019    
3020    =item dataDir
3021    
3022    Directory containing the Sprout load files.
3023    
3024    =back
3025    
3026    =cut
3027    #: Return Type @;
3028    sub MyGenomes {
3029        # Get the parameters.
3030        my ($dataDir) = @_;
3031        # Compute the genome file name.
3032        my $genomeFileName = LoadFileName($dataDir, "Genome");
3033        # Extract the genome IDs from the files.
3034        my @retVal = map { $_ =~ /^(\S+)/; $1 } Tracer::GetFile($genomeFileName);
3035        # Return the result.
3036        return @retVal;
3037    }
3038    
3039    =head3 LoadFileName
3040    
3041    C<< my $fileName = Sprout::LoadFileName($dataDir, $tableName); >>
3042    
3043    Return the name of the load file for the specified table in the specified data
3044    directory.
3045    
3046    =over 4
3047    
3048    =item dataDir
3049    
3050    Directory containing the Sprout load files.
3051    
3052    =item tableName
3053    
3054    Name of the table whose load file is desired.
3055    
3056    =item RETURN
3057    
3058    Returns the name of the file containing the load data for the specified table, or
3059    C<undef> if no load file is present.
3060    
3061    =back
3062    
3063    =cut
3064    #: Return Type $;
3065    sub LoadFileName {
3066        # Get the parameters.
3067        my ($dataDir, $tableName) = @_;
3068        # Declare the return variable.
3069        my $retVal;
3070        # Check for the various file names.
3071        if (-e "$dataDir/$tableName") {
3072            $retVal = "$dataDir/$tableName";
3073        } elsif (-e "$dataDir/$tableName.dtx") {
3074            $retVal = "$dataDir/$tableName.dtx";
3075        }
3076        # Return the result.
3077        return $retVal;
3078    }
3079    
3080  =head2 Internal Utility Methods  =head2 Internal Utility Methods
3081    
3082  =head3 ParseAssignment  =head3 ParseAssignment
3083    
3084  Parse annotation text to determine whether or not it is a functional assignment. If it is,  Parse annotation text to determine whether or not it is a functional assignment. If it is,
3085  the user and function text will be returned as a 2-element list. If it isn't, an empty list  the user, function text, and assigning user will be returned as a 3-element list. If it
3086  will be returned.  isn't, an empty list will be returned.
3087    
3088    A functional assignment is always of the form
3089    
3090        I<XXXX>C<\nset >I<YYYY>C< function to\n>I<ZZZZZ>
3091    
3092    where I<XXXX> is the B<assigning user>, I<YYYY> is the B<user>, and I<ZZZZ> is the
3093    actual functional role. In most cases, the user and the assigning user will be the
3094    same, but that is not always the case.
3095    
3096  This is a static method.  This is a static method.
3097    
# Line 2647  Line 3110 
3110    
3111  =cut  =cut
3112    
3113  sub ParseAssignment {  sub _ParseAssignment {
3114          # Get the parameters.          # Get the parameters.
3115          my ($text) = @_;          my ($text) = @_;
3116          # Declare the return value.          # Declare the return value.
3117          my @retVal = ();          my @retVal = ();
3118          # Check to see if this is a functional assignment.          # Check to see if this is a functional assignment.
3119          my ($user, $type, $function) = split(/\n/, $text);          my ($user, $type, $function) = split(/\n/, $text);
3120          if ($type =~ m/^set $user function to$/i) {      if ($type =~ m/^set ([^ ]+) function to$/i) {
3121                  # Here it is, so we return the user name and function text.          # Here it is, so we return the user name (which is in $1), the functional role text,
3122                  @retVal = ($user, $function);          # and the assigning user.
3123            @retVal = ($1, $function, $user);
3124          }          }
3125          # Return the result list.          # Return the result list.
3126          return @retVal;          return @retVal;
# Line 2688  Line 3152 
3152      return $retVal;      return $retVal;
3153  }  }
3154    
3155    =head3 AddProperty
3156    
3157    C<< my  = $sprout->AddProperty($featureID, $key, $value, $url); >>
3158    
3159    Add a new attribute value (Property) to a feature. In the SEED system, attributes can
3160    be added to almost any object. In Sprout, they can only be added to features. In
3161    Sprout, attributes are implemented using I<properties>. A property represents a key/value
3162    pair. If the particular key/value pair coming in is not already in the database, a new
3163    B<Property> record is created to hold it.
3164    
3165    =over 4
3166    
3167    =item peg
3168    
3169    ID of the feature to which the attribute is to be replied.
3170    
3171    =item key
3172    
3173    Name of the attribute (key).
3174    
3175    =item value
3176    
3177    Value of the attribute.
3178    
3179    =item url
3180    
3181    URL or text citation from which the property was obtained.
3182    
3183    =back
3184    
3185    =cut
3186    #: Return Type ;
3187    sub AddProperty {
3188        # Get the parameters.
3189        my ($self, $featureID, $key, $value, $url) = @_;
3190        # Declare the variable to hold the desired property ID.
3191        my $propID;
3192        # Attempt to find a property record for this key/value pair.
3193        my @properties = $self->GetFlat(['Property'],
3194                                       "Property(property-name) = ? AND Property(property-value) = ?",
3195                                       [$key, $value], 'Property(id)');
3196        if (@properties) {
3197            # Here the property is already in the database. We save its ID.
3198            $propID = $properties[0];
3199            # Here the property value does not exist. We need to generate an ID. It will be set
3200            # to a number one greater than the maximum value in the database. This call to
3201            # GetAll will stop after one record.
3202            my @maxProperty = $self->GetAll(['Property'], "ORDER BY Property(id) DESC", [], ['Property(id)'],
3203                                            1);
3204            $propID = $maxProperty[0]->[0] + 1;
3205            # Insert the new property value.
3206            $self->Insert('Property', { 'property-name' => $key, 'property-value' => $value, id => $propID });
3207        }
3208        # Now we connect the incoming feature to the property.
3209        $self->Insert('HasProperty', { 'from-link' => $featureID, 'to-link' => $propID, evidence => $url });
3210    }
3211    
3212    
3213    
3214  1;  1;

Legend:
Removed from v.1.9  
changed lines
  Added in v.1.25

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3