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revision 1.16, Fri Jun 24 21:45:45 2005 UTC revision 1.56, Wed Apr 19 03:34:15 2006 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::fig/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 377  Line 389 
389    
390  =head3 LoadUpdate  =head3 LoadUpdate
391    
392  C<< my %stats = $sprout->LoadUpdate($truncateFlag, \@tableList); >>  C<< my $stats = $sprout->LoadUpdate($truncateFlag, \@tableList); >>
393    
394  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
395  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 420  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 $retVal;
447  }  }
# Line 570  Line 583 
583  =item RETURN  =item RETURN
584    
585  Returns a list of the feature's contig segments. The locations are returned as a list in a list  Returns a list of the feature's contig segments. The locations are returned as a list in a list
586  context and as a space-delimited string in a scalar context.  context and as a comma-delimited string in a scalar context.
587    
588  =back  =back
589    
# Line 597  Line 610 
610          if ($prevContig eq $contigID && $dir eq $prevDir) {          if ($prevContig eq $contigID && $dir eq $prevDir) {
611              # Here the new segment is in the same direction on the same contig. Insure the              # Here the new segment is in the same direction on the same contig. Insure the
612              # new segment's beginning is next to the old segment's end.              # new segment's beginning is next to the old segment's end.
613              if (($dir eq "-" && $beg == $prevBeg - $prevLen) ||              if ($dir eq "-" && $beg + $len == $prevBeg) {
614                  ($dir eq "+" && $beg == $prevBeg + $prevLen)) {                  # Here we're merging two backward blocks, so we keep the new begin point
615                  # Here we need to merge two segments. Adjust the beginning and length values                  # and adjust the length.
616                  # to include both segments.                  $len += $prevLen;
617                    # Pop the old segment off. The new one will replace it later.
618                    pop @retVal;
619                } elsif ($dir eq "+" && $beg == $prevBeg + $prevLen) {
620                    # Here we need to merge two forward blocks. Adjust the beginning and
621                    # length values to include both segments.
622                  $beg = $prevBeg;                  $beg = $prevBeg;
623                  $len += $prevLen;                  $len += $prevLen;
624                  # Pop the old segment off. The new one will replace it later.                  # Pop the old segment off. The new one will replace it later.
# Line 609  Line 627 
627          }          }
628          # Remember this specifier for the adjacent-segment test the next time through.          # Remember this specifier for the adjacent-segment test the next time through.
629          ($prevContig, $prevBeg, $prevDir, $prevLen) = ($contigID, $beg, $dir, $len);          ($prevContig, $prevBeg, $prevDir, $prevLen) = ($contigID, $beg, $dir, $len);
630            # Compute the initial base pair.
631            my $start = ($dir eq "+" ? $beg : $beg + $len - 1);
632          # Add the specifier to the list.          # Add the specifier to the list.
633          push @retVal, "${contigID}_$beg$dir$len";          push @retVal, "${contigID}_$start$dir$len";
634      }      }
635      # Return the list in the format indicated by the context.      # Return the list in the format indicated by the context.
636      return (wantarray ? @retVal : join(' ', @retVal));      return (wantarray ? @retVal : join(',', @retVal));
637  }  }
638    
639  =head3 ParseLocation  =head3 ParseLocation
# Line 644  Line 664 
664      shift if UNIVERSAL::isa($_[0],__PACKAGE__);      shift if UNIVERSAL::isa($_[0],__PACKAGE__);
665      my ($location) = @_;      my ($location) = @_;
666      # Parse it into segments.      # Parse it into segments.
667      $location =~ /^(.*)_(\d*)([+-_])(\d*)$/;      $location =~ /^(.+)_(\d+)([+\-_])(\d+)$/;
668      my ($contigID, $start, $dir, $len) = ($1, $2, $3, $4);      my ($contigID, $start, $dir, $len) = ($1, $2, $3, $4);
669      # If the direction is an underscore, convert it to a + or -.      # If the direction is an underscore, convert it to a + or -.
670      if ($dir eq "_") {      if ($dir eq "_") {
# Line 720  Line 740 
740  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,
741  each location is of the form I<contigID>C<_>I<begin>I<dir>I<end>.  each location is of the form I<contigID>C<_>I<begin>I<dir>I<end>.
742    
743    For example, the following would return the DNA sequence for contig C<83333.1:NC_000913>
744    between positions 1401 and 1532, inclusive.
745    
746        my $sequence = $sprout->DNASeq('83333.1:NC_000913_1401_1532');
747    
748  =over 4  =over 4
749    
750  =item locationList  =item locationList
751    
752  List of location specifiers, each in the form I<contigID>C<_>I<begin>I<dir>I<end> (see  List of location specifiers, each in the form I<contigID>C<_>I<begin>I<dir>I<len> or
753  L</FeatureLocation> for more about this format).  I<contigID>C<_>I<begin>C<_>I<end> (see L</FeatureLocation> for more about this format).
754    
755  =item RETURN  =item RETURN
756    
# Line 752  Line 777 
777          # the start point is the ending. Note that in the latter case we must reverse the DNA string          # the start point is the ending. Note that in the latter case we must reverse the DNA string
778          # before putting it in the return value.          # before putting it in the return value.
779          my ($start, $stop);          my ($start, $stop);
780            Trace("Parse of \"$location\" is $beg$dir$len.") if T(SDNA => 4);
781          if ($dir eq "+") {          if ($dir eq "+") {
782              $start = $beg;              $start = $beg;
783              $stop = $beg + $len - 1;              $stop = $beg + $len - 1;
784          } else {          } else {
785              $start = $beg + $len + 1;              $start = $beg - $len + 1;
786              $stop = $beg;              $stop = $beg;
787          }          }
788            Trace("Looking for sequences containing $start through $stop.") if T(SDNA => 4);
789          my $query = $self->Get(['IsMadeUpOf','Sequence'],          my $query = $self->Get(['IsMadeUpOf','Sequence'],
790              "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .              "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .
791              " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",              " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",
# Line 770  Line 797 
797                  $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)',                  $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)',
798                                     'IsMadeUpOf(len)']);                                     'IsMadeUpOf(len)']);
799              my $stopPosition = $startPosition + $sequenceLength;              my $stopPosition = $startPosition + $sequenceLength;
800                Trace("Sequence is from $startPosition to $stopPosition.") if T(SDNA => 4);
801              # Figure out the start point and length of the relevant section.              # Figure out the start point and length of the relevant section.
802              my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);              my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);
803              my $len = ($stopPosition <= $stop ? $stopPosition : $stop) - $startPosition - $pos1;              my $len1 = ($stopPosition < $stop ? $stopPosition : $stop) + 1 - $startPosition - $pos1;
804                Trace("Position is $pos1 for length $len1.") if T(SDNA => 4);
805              # Add the relevant data to the location data.              # Add the relevant data to the location data.
806              $locationDNA .= substr($sequenceData, $pos1, $len);              $locationDNA .= substr($sequenceData, $pos1, $len1);
807          }          }
808          # Add this location's data to the return string. Note that we may need to reverse it.          # Add this location's data to the return string. Note that we may need to reverse it.
809          if ($dir eq '+') {          if ($dir eq '+') {
810              $retVal .= $locationDNA;              $retVal .= $locationDNA;
811          } else {          } else {
812              $locationDNA = join('', reverse split //, $locationDNA);              $retVal .= FIG::reverse_comp($locationDNA);
             $retVal .= $locationDNA;  
813          }          }
814      }      }
815      # Return the result.      # Return the result.
# Line 851  Line 879 
879      # Set it from the sequence data, if any.      # Set it from the sequence data, if any.
880      if ($sequence) {      if ($sequence) {
881          my ($start, $len) = $sequence->Values(['IsMadeUpOf(start-position)', 'IsMadeUpOf(len)']);          my ($start, $len) = $sequence->Values(['IsMadeUpOf(start-position)', 'IsMadeUpOf(len)']);
882          $retVal = $start + $len;          $retVal = $start + $len - 1;
883        }
884        # Return the result.
885        return $retVal;
886    }
887    
888    =head3 ClusterPEGs
889    
890    C<< my $clusteredList = $sprout->ClusterPEGs($sub, \@pegs); >>
891    
892    Cluster the PEGs in a list according to the cluster coding scheme of the specified
893    subsystem. In order for this to work properly, the subsystem object must have
894    been used recently to retrieve the PEGs using the B<get_pegs_from_cell> method.
895    This causes the cluster numbers to be pulled into the subsystem's color hash.
896    If a PEG is not found in the color hash, it will not appear in the output
897    sequence.
898    
899    =over 4
900    
901    =item sub
902    
903    Sprout subsystem object for the relevant subsystem, from the L</get_subsystem>
904    method.
905    
906    =item pegs
907    
908    Reference to the list of PEGs to be clustered.
909    
910    =item RETURN
911    
912    Returns a list of the PEGs, grouped into smaller lists by cluster number.
913    
914    =back
915    
916    =cut
917    #: Return Type $@@;
918    sub ClusterPEGs {
919        # Get the parameters.
920        my ($self, $sub, $pegs) = @_;
921        # Declare the return variable.
922        my $retVal = [];
923        # Loop through the PEGs, creating arrays for each cluster.
924        for my $pegID (@{$pegs}) {
925            my $clusterNumber = $sub->get_cluster_number($pegID);
926            # Only proceed if the PEG is in a cluster.
927            if ($clusterNumber >= 0) {
928                # Push this PEG onto the sub-list for the specified cluster number.
929                push @{$retVal->[$clusterNumber]}, $pegID;
930            }
931      }      }
932      # Return the result.      # Return the result.
933      return $retVal;      return $retVal;
# Line 1001  Line 1077 
1077    
1078  =head3 FeatureAnnotations  =head3 FeatureAnnotations
1079    
1080  C<< my @descriptors = $sprout->FeatureAnnotations($featureID); >>  C<< my @descriptors = $sprout->FeatureAnnotations($featureID, $rawFlag); >>
1081    
1082  Return the annotations of a feature.  Return the annotations of a feature.
1083    
# Line 1011  Line 1087 
1087    
1088  ID of the feature whose annotations are desired.  ID of the feature whose annotations are desired.
1089    
1090    =item rawFlag
1091    
1092    If TRUE, the annotation timestamps will be returned in raw form; otherwise, they
1093    will be returned in human-readable form.
1094    
1095  =item RETURN  =item RETURN
1096    
1097  Returns a list of annotation descriptors. Each descriptor is a hash with the following fields.  Returns a list of annotation descriptors. Each descriptor is a hash with the following fields.
1098    
1099  * B<featureID> ID of the relevant feature.  * B<featureID> ID of the relevant feature.
1100    
1101  * B<timeStamp> time the annotation was made, in user-friendly format.  * B<timeStamp> time the annotation was made.
1102    
1103  * B<user> ID of the user who made the annotation  * B<user> ID of the user who made the annotation
1104    
# Line 1029  Line 1110 
1110  #: Return Type @%;  #: Return Type @%;
1111  sub FeatureAnnotations {  sub FeatureAnnotations {
1112      # Get the parameters.      # Get the parameters.
1113      my ($self, $featureID) = @_;      my ($self, $featureID, $rawFlag) = @_;
1114      # 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.
1115      my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],      my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1116                             "IsTargetOfAnnotation(from-link) = ?", [$featureID]);                             "IsTargetOfAnnotation(from-link) = ?", [$featureID]);
# Line 1042  Line 1123 
1123              $annotation->Values(['IsTargetOfAnnotation(from-link)',              $annotation->Values(['IsTargetOfAnnotation(from-link)',
1124                                   'Annotation(time)', 'MadeAnnotation(from-link)',                                   'Annotation(time)', 'MadeAnnotation(from-link)',
1125                                   'Annotation(annotation)']);                                   'Annotation(annotation)']);
1126            # Convert the time, if necessary.
1127            if (! $rawFlag) {
1128                $timeStamp = FriendlyTimestamp($timeStamp);
1129            }
1130          # Assemble them into a hash.          # Assemble them into a hash.
1131          my $annotationHash = { featureID => $featureID,          my $annotationHash = { featureID => $featureID,
1132                                 timeStamp => FriendlyTimestamp($timeStamp),                                 timeStamp => $timeStamp,
1133                                 user => $user, text => $text };                                 user => $user, text => $text };
1134          # Add it to the return list.          # Add it to the return list.
1135          push @retVal, $annotationHash;          push @retVal, $annotationHash;
# Line 1073  Line 1158 
1158    
1159  =item RETURN  =item RETURN
1160    
1161  Returns a hash mapping the functional assignment IDs to user IDs.  Returns a hash mapping the user IDs to functional assignment IDs.
1162    
1163  =back  =back
1164    
# Line 1083  Line 1168 
1168      # Get the parameters.      # Get the parameters.
1169      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
1170      # Get all of the feature's annotations.      # Get all of the feature's annotations.
1171      my @query = $self->GetAll(['IsTargetOfAnnotation', 'Annotation'],      my @query = $self->GetAll(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1172                              "IsTargetOfAnnotation(from-link) = ?",                              "IsTargetOfAnnotation(from-link) = ?",
1173                              [$featureID], ['Annotation(time)', 'Annotation(annotation)']);                              [$featureID], ['Annotation(time)', 'Annotation(annotation)',
1174                                               'MadeAnnotation(from-link)']);
1175      # Declare the return hash.      # Declare the return hash.
1176      my %retVal;      my %retVal;
     # Declare a hash for insuring we only make one assignment per user.  
     my %timeHash = ();  
1177      # Now we sort the assignments by timestamp in reverse.      # Now we sort the assignments by timestamp in reverse.
1178      my @sortedQuery = sort { -($a->[0] <=> $b->[0]) } @query;      my @sortedQuery = sort { -($a->[0] <=> $b->[0]) } @query;
1179      # Loop until we run out of annotations.      # Loop until we run out of annotations.
1180      for my $annotation (@sortedQuery) {      for my $annotation (@sortedQuery) {
1181          # Get the annotation fields.          # Get the annotation fields.
1182          my ($timeStamp, $text) = @{$annotation};          my ($timeStamp, $text, $user) = @{$annotation};
1183          # Check to see if this is a functional assignment.          # Check to see if this is a functional assignment.
1184          my ($user, $function) = _ParseAssignment($text);          my ($actualUser, $function) = _ParseAssignment($user, $text);
1185          if ($user && ! exists $timeHash{$user}) {          if ($actualUser && ! exists $retVal{$actualUser}) {
1186              # Here it is a functional assignment and there has been no              # Here it is a functional assignment and there has been no
1187              # previous assignment for this user, so we stuff it in the              # previous assignment for this user, so we stuff it in the
1188              # return hash.              # return hash.
1189              $retVal{$function} = $user;              $retVal{$actualUser} = $function;
             # Insure we don't assign to this user again.  
             $timeHash{$user} = 1;  
1190          }          }
1191      }      }
1192      # Return the hash of assignments found.      # Return the hash of assignments found.
# Line 1120  Line 1202 
1202  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
1203  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
1204  assignment is a type of annotation. The format of an assignment is described in  assignment is a type of annotation. The format of an assignment is described in
1205  L</ParseLocation>. Its worth noting that we cannot filter on the content of the  L</ParseAssignment>. Its worth noting that we cannot filter on the content of the
1206  annotation itself because it's a text field; however, this is not a big problem because  annotation itself because it's a text field; however, this is not a big problem because
1207  most features only have a small number of annotations.  most features only have a small number of annotations.
1208    
# Line 1182  Line 1264 
1264              }              }
1265          }          }
1266          # Build a query for all of the feature's annotations, sorted by date.          # Build a query for all of the feature's annotations, sorted by date.
1267          my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation'],          my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1268                                 "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",                                 "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1269                                 [$featureID]);                                 [$featureID]);
1270          my $timeSelected = 0;          my $timeSelected = 0;
1271          # Loop until we run out of annotations.          # Loop until we run out of annotations.
1272          while (my $annotation = $query->Fetch()) {          while (my $annotation = $query->Fetch()) {
1273              # Get the annotation text.              # Get the annotation text.
1274              my ($text, $time) = $annotation->Values(['Annotation(annotation)','Annotation(time)']);              my ($text, $time, $user) = $annotation->Values(['Annotation(annotation)',
1275                                                         'Annotation(time)', 'MadeAnnotation(from-link)']);
1276              # Check to see if this is a functional assignment for a trusted user.              # Check to see if this is a functional assignment for a trusted user.
1277              my ($user, $function) = _ParseAssignment($text);              my ($actualUser, $function) = _ParseAssignment($user, $text);
1278              if ($user) {              Trace("Assignment user is $actualUser, text is $function.") if T(4);
1279                if ($actualUser) {
1280                  # Here it is a functional assignment. Check the time and the user                  # Here it is a functional assignment. Check the time and the user
1281                  # name. The time must be recent and the user must be trusted.                  # name. The time must be recent and the user must be trusted.
1282                  if ((exists $trusteeTable{$user}) && ($time > $timeSelected)) {                  if ((exists $trusteeTable{$actualUser}) && ($time > $timeSelected)) {
1283                      $retVal = $function;                      $retVal = $function;
1284                      $timeSelected = $time;                      $timeSelected = $time;
1285                  }                  }
# Line 1211  Line 1295 
1295      return $retVal;      return $retVal;
1296  }  }
1297    
1298    =head3 FunctionsOf
1299    
1300    C<< my @functionList = $sprout->FunctionOf($featureID, $userID); >>
1301    
1302    Return the functional assignments of a particular feature.
1303    
1304    The functional assignment is handled differently depending on the type of feature. If
1305    the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional
1306    assignment is a type of annotation. The format of an assignment is described in
1307    L</ParseAssignment>. Its worth noting that we cannot filter on the content of the
1308    annotation itself because it's a text field; however, this is not a big problem because
1309    most features only have a small number of annotations.
1310    
1311    If the feature is B<not> identified by a FIG ID, then the functional assignment
1312    information is taken from the B<ExternalAliasFunc> table. If the table does
1313    not contain an entry for the feature, an empty list is returned.
1314    
1315    =over 4
1316    
1317    =item featureID
1318    
1319    ID of the feature whose functional assignments are desired.
1320    
1321    =item RETURN
1322    
1323    Returns a list of 2-tuples, each consisting of a user ID and the text of an assignment by
1324    that user.
1325    
1326    =back
1327    
1328    =cut
1329    #: Return Type @@;
1330    sub FunctionsOf {
1331        # Get the parameters.
1332        my ($self, $featureID) = @_;
1333        # Declare the return value.
1334        my @retVal = ();
1335        # Determine the ID type.
1336        if ($featureID =~ m/^fig\|/) {
1337            # Here we have a FIG feature ID. We must build the list of trusted
1338            # users.
1339            my %trusteeTable = ();
1340            # Build a query for all of the feature's annotations, sorted by date.
1341            my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1342                                   "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1343                                   [$featureID]);
1344            my $timeSelected = 0;
1345            # Loop until we run out of annotations.
1346            while (my $annotation = $query->Fetch()) {
1347                # Get the annotation text.
1348                my ($text, $time, $user) = $annotation->Values(['Annotation(annotation)',
1349                                                                'Annotation(time)',
1350                                                                'MadeAnnotation(user)']);
1351                # Check to see if this is a functional assignment for a trusted user.
1352                my ($actualUser, $function) = _ParseAssignment($user, $text);
1353                if ($actualUser) {
1354                    # Here it is a functional assignment.
1355                    push @retVal, [$actualUser, $function];
1356                }
1357            }
1358        } else {
1359            # Here we have a non-FIG feature ID. In this case the user ID does not
1360            # matter. We simply get the information from the External Alias Function
1361            # table.
1362            my @assignments = $self->GetEntityValues('ExternalAliasFunc', $featureID,
1363                                                     ['ExternalAliasFunc(func)']);
1364            push @retVal, map { ['master', $_] } @assignments;
1365        }
1366        # Return the assignments found.
1367        return @retVal;
1368    }
1369    
1370  =head3 BBHList  =head3 BBHList
1371    
1372  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>
# Line 1248  Line 1404 
1404          my $query = $self->Get(['IsBidirectionalBestHitOf'],          my $query = $self->Get(['IsBidirectionalBestHitOf'],
1405                                 "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",                                 "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",
1406                                 [$featureID, $genomeID]);                                 [$featureID, $genomeID]);
1407          # Look for the best hit.          # Peel off the BBHs found.
1408          my $bbh = $query->Fetch;          my @found = ();
1409          if ($bbh) {          while (my $bbh = $query->Fetch) {
1410              my ($targetFeature) = $bbh->Value('IsBidirectionalBestHitOf(to-link)');              push @found, $bbh->Value('IsBidirectionalBestHitOf(to-link)');
             $retVal{$featureID} = $targetFeature;  
1411          }          }
1412            $retVal{$featureID} = \@found;
1413      }      }
1414      # Return the mapping.      # Return the mapping.
1415      return \%retVal;      return \%retVal;
# Line 1331  Line 1487 
1487      my $genomeData = $self->GetEntity('Genome', $genomeID);      my $genomeData = $self->GetEntity('Genome', $genomeID);
1488      if ($genomeData) {      if ($genomeData) {
1489          # The genome exists, so get the completeness flag.          # The genome exists, so get the completeness flag.
1490          ($retVal) = $genomeData->Value('complete');          ($retVal) = $genomeData->Value('Genome(complete)');
1491      }      }
1492      # Return the result.      # Return the result.
1493      return $retVal;      return $retVal;
# Line 1371  Line 1527 
1527    
1528  C<< my $genomeID = $sprout->GenomeOf($featureID); >>  C<< my $genomeID = $sprout->GenomeOf($featureID); >>
1529    
1530  Return the genome that contains a specified feature.  Return the genome that contains a specified feature or contig.
1531    
1532  =over 4  =over 4
1533    
1534  =item featureID  =item featureID
1535    
1536  ID of the feature whose genome is desired.  ID of the feature or contig whose genome is desired.
1537    
1538  =item RETURN  =item RETURN
1539    
1540  Returns the ID of the genome for the specified feature. If the feature is not found, returns  Returns the ID of the genome for the specified feature or contig. If the feature or contig is not
1541  an undefined value.  found, returns an undefined value.
1542    
1543  =back  =back
1544    
# Line 1391  Line 1547 
1547  sub GenomeOf {  sub GenomeOf {
1548      # Get the parameters.      # Get the parameters.
1549      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
1550      # Create a query to find the genome associated with the feature.      # Create a query to find the genome associated with the incoming ID.
1551      my $query = $self->Get(['IsLocatedIn', 'HasContig'], "IsLocatedIn(from-link) = ?", [$featureID]);      my $query = $self->Get(['IsLocatedIn', 'HasContig'], "IsLocatedIn(from-link) = ? OR HasContig(to-link) = ?",
1552                               [$featureID, $featureID]);
1553      # Declare the return value.      # Declare the return value.
1554      my $retVal;      my $retVal;
1555      # Get the genome ID.      # Get the genome ID.
# Line 1506  Line 1663 
1663      my ($self, $peg1, $peg2) = @_;      my ($self, $peg1, $peg2) = @_;
1664      # Declare the return variable.      # Declare the return variable.
1665      my @retVal = ();      my @retVal = ();
1666      # Our first task is to find out the nature of the coupling.      # Our first task is to find out the nature of the coupling: whether or not
1667        # it exists, its score, and whether the features are stored in the same
1668        # order as the ones coming in.
1669      my ($couplingID, $inverted, $score) = $self->GetCoupling($peg1, $peg2);      my ($couplingID, $inverted, $score) = $self->GetCoupling($peg1, $peg2);
1670      # Only proceed if a coupling exists.      # Only proceed if a coupling exists.
1671      if ($couplingID) {      if ($couplingID) {
1672          # Determine the ordering to place on the evidence items. If we're          # Determine the ordering to place on the evidence items. If we're
1673          # inverted, we want to see feature 2 before feature 1; otherwise,          # inverted, we want to see feature 2 before feature 1 (descending); otherwise,
1674          # we want the reverse.          # we want feature 1 before feature 2 (normal).
1675            Trace("Coupling evidence for ($peg1, $peg2) with inversion flag $inverted.") if T(Coupling => 4);
1676          my $ordering = ($inverted ? "DESC" : "");          my $ordering = ($inverted ? "DESC" : "");
1677          # Get the coupling evidence.          # Get the coupling evidence.
1678          my @evidenceList = $self->GetAll(['IsEvidencedBy', 'PCH', 'UsesAsEvidence'],          my @evidenceList = $self->GetAll(['IsEvidencedBy', 'PCH', 'UsesAsEvidence'],
1679                                            "IsEvidencedBy(from-link) = ? ORDER BY PCH(id), UsesAsEvidence(pos) $ordering",                                            "IsEvidencedBy(from-link) = ? ORDER BY PCH(id), UsesAsEvidence(pos) $ordering",
1680                                            [$couplingID],                                            [$couplingID],
1681                                            ['PCH(used)', 'UsesAsEvidence(pos)']);                                            ['PCH(used)', 'UsesAsEvidence(to-link)']);
1682          # Loop through the evidence items. Each piece of evidence is represented by two          # Loop through the evidence items. Each piece of evidence is represented by two
1683          # positions in the evidence list, one for each feature on the other side of the          # positions in the evidence list, one for each feature on the other side of the
1684          # evidence link. If at some point we want to generalize to couplings with          # evidence link. If at some point we want to generalize to couplings with
# Line 1526  Line 1686 
1686          while (@evidenceList > 0) {          while (@evidenceList > 0) {
1687              my $peg1Data = shift @evidenceList;              my $peg1Data = shift @evidenceList;
1688              my $peg2Data = shift @evidenceList;              my $peg2Data = shift @evidenceList;
1689                Trace("Peg 1 is " . $peg1Data->[1] . " and Peg 2 is " . $peg2Data->[1] . ".") if T(Coupling => 4);
1690              push @retVal, [$peg1Data->[1], $peg2Data->[1], $peg1Data->[0]];              push @retVal, [$peg1Data->[1], $peg2Data->[1], $peg1Data->[0]];
1691          }          }
1692            Trace("Last index in evidence result is is $#retVal.") if T(Coupling => 4);
1693      }      }
     # TODO: code  
1694      # Return the result.      # Return the result.
1695      return @retVal;      return @retVal;
1696  }  }
# Line 1575  Line 1736 
1736      # Find the coupling data.      # Find the coupling data.
1737      my @pegs = $self->GetAll(['Coupling', 'ParticipatesInCoupling'],      my @pegs = $self->GetAll(['Coupling', 'ParticipatesInCoupling'],
1738                                   "Coupling(id) = ? ORDER BY ParticipatesInCoupling(pos)",                                   "Coupling(id) = ? ORDER BY ParticipatesInCoupling(pos)",
1739                                   [$retVal], "ParticipatesInCoupling(from-link), Coupling(score)");                                   [$retVal], ["ParticipatesInCoupling(from-link)", "Coupling(score)"]);
1740      # Check to see if we found anything.      # Check to see if we found anything.
1741      if (!@pegs) {      if (!@pegs) {
1742            Trace("No coupling found.") if T(Coupling => 4);
1743          # No coupling, so undefine the return value.          # No coupling, so undefine the return value.
1744          $retVal = undef;          $retVal = undef;
1745      } else {      } else {
1746          # We have a coupling! Get the score and check for inversion.          # We have a coupling! Get the score and check for inversion.
1747          $score = $pegs[0]->[1];          $score = $pegs[0]->[1];
1748          $inverted = ($pegs[0]->[0] eq $peg1);          my $firstFound = $pegs[0]->[0];
1749            $inverted = ($firstFound ne $peg1);
1750            Trace("Coupling score is $score. First peg is $firstFound, peg 1 is $peg1.") if T(Coupling => 4);
1751      }      }
1752      # Return the result.      # Return the result.
1753      return ($retVal, $inverted, $score);      return ($retVal, $inverted, $score);
# Line 1688  Line 1852 
1852          if ($line =~ m/^>\s*(.+?)(\s|\n)/) {          if ($line =~ m/^>\s*(.+?)(\s|\n)/) {
1853              # Here we have a new header. Store the current sequence if we have one.              # Here we have a new header. Store the current sequence if we have one.
1854              if ($id) {              if ($id) {
1855                  $retVal{$id} = uc $sequence;                  $retVal{$id} = lc $sequence;
1856              }              }
1857              # Clear the sequence accumulator and save the new ID.              # Clear the sequence accumulator and save the new ID.
1858              ($id, $sequence) = ("$prefix$1", "");              ($id, $sequence) = ("$prefix$1", "");
1859          } else {          } else {
1860              # 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.
1861              # First, we get the actual data out. Note that we normalize to upper              # First, we get the actual data out. Note that we normalize to lower
1862              # case.              # case.
1863              $line =~ /^\s*(.*?)(\s|\n)/;              $line =~ /^\s*(.*?)(\s|\n)/;
1864              $sequence .= $1;              $sequence .= $1;
# Line 1702  Line 1866 
1866      }      }
1867      # Flush out the last sequence (if any).      # Flush out the last sequence (if any).
1868      if ($sequence) {      if ($sequence) {
1869          $retVal{$id} = uc $sequence;          $retVal{$id} = lc $sequence;
1870      }      }
1871      # Close the file.      # Close the file.
1872      close FASTAFILE;      close FASTAFILE;
# Line 2028  Line 2192 
2192      # Get the parameters.      # Get the parameters.
2193      my ($self, $entityName, $entityID) = @_;      my ($self, $entityName, $entityID) = @_;
2194      # Check for the entity instance.      # Check for the entity instance.
2195        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
2196      my $testInstance = $self->GetEntity($entityName, $entityID);      my $testInstance = $self->GetEntity($entityName, $entityID);
2197      # Return an existence indicator.      # Return an existence indicator.
2198      my $retVal = ($testInstance ? 1 : 0);      my $retVal = ($testInstance ? 1 : 0);
# Line 2219  Line 2384 
2384      return @retVal;      return @retVal;
2385  }  }
2386    
2387    =head3 GetProperties
2388    
2389    C<< my @list = $sprout->GetProperties($fid, $key, $value, $url); >>
2390    
2391    Return a list of the properties with the specified characteristics.
2392    
2393    Properties are arbitrary key-value pairs associated with a feature. (At some point they
2394    will also be associated with genomes.) A property value is represented by a 4-tuple of
2395    the form B<($fid, $key, $value, $url)>. These exactly correspond to the parameter
2396    
2397    =over 4
2398    
2399    =item fid
2400    
2401    ID of the feature possessing the property.
2402    
2403    =item key
2404    
2405    Name or key of the property.
2406    
2407    =item value
2408    
2409    Value of the property.
2410    
2411    =item url
2412    
2413    URL of the document that indicated the property should have this particular value, or an
2414    empty string if no such document exists.
2415    
2416    =back
2417    
2418    The parameters act as a filter for the desired data. Any non-null parameter will
2419    automatically match all the tuples returned. So, specifying just the I<$fid> will
2420    return all the properties of the specified feature; similarly, specifying the I<$key>
2421    and I<$value> parameters will return all the features having the specified property
2422    value.
2423    
2424    A single property key can have many values, representing different ideas about the
2425    feature in question. For example, one paper may declare that a feature C<fig|83333.1.peg.10> is
2426    virulent, and another may declare that it is not virulent. A query about the virulence of
2427    C<fig|83333.1.peg.10> would be coded as
2428    
2429        my @list = $sprout->GetProperties('fig|83333.1.peg.10', 'virulence', '', '');
2430    
2431    Here the I<$value> and I<$url> fields are left blank, indicating that those fields are
2432    not to be filtered. The tuples returned would be
2433    
2434        ('fig|83333.1.peg.10', 'virulence', 'yes', 'http://www.somewhere.edu/first.paper.pdf')
2435        ('fig|83333.1.peg.10', 'virulence', 'no', 'http://www.somewhere.edu/second.paper.pdf')
2436    
2437    =cut
2438    #: Return Type @@;
2439    sub GetProperties {
2440        # Get the parameters.
2441        my ($self, @parms) = @_;
2442        # Declare the return variable.
2443        my @retVal = ();
2444        # Now we need to create a WHERE clause that will get us the data we want. First,
2445        # we create a list of the columns containing the data for each parameter.
2446        my @colNames = ('HasProperty(from-link)', 'Property(property-name)',
2447                        'Property(property-value)', 'HasProperty(evidence)');
2448        # Now we build the WHERE clause and the list of parameter values.
2449        my @where = ();
2450        my @values = ();
2451        for (my $i = 0; $i <= $#colNames; $i++) {
2452            my $parm = $parms[$i];
2453            if (defined $parm && ($parm ne '')) {
2454                push @where, "$colNames[$i] = ?";
2455                push @values, $parm;
2456            }
2457        }
2458        # Format the WHERE clause.
2459        my $filter = (@values > 0 ? (join " AND ", @where) : undef);
2460        # Ask for all the propertie values with the desired characteristics.
2461        my $query = $self->Get(['HasProperty', 'Property'], $filter, \@values);
2462        while (my $valueObject = $query->Fetch()) {
2463            my @tuple = $valueObject->Values(\@colNames);
2464            push @retVal, \@tuple;
2465        }
2466        # Return the result.
2467        return @retVal;
2468    }
2469    
2470  =head3 FeatureProperties  =head3 FeatureProperties
2471    
2472  C<< my @properties = $sprout->FeatureProperties($featureID); >>  C<< my @properties = $sprout->FeatureProperties($featureID); >>
# Line 2413  Line 2661 
2661  C<< my %subsystems = $sprout->SubsystemsOf($featureID); >>  C<< my %subsystems = $sprout->SubsystemsOf($featureID); >>
2662    
2663  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
2664  to the role the feature performs.  to the roles the feature performs.
2665    
2666  =over 4  =over 4
2667    
# Line 2423  Line 2671 
2671    
2672  =item RETURN  =item RETURN
2673    
2674  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.
2675    
2676  =back  =back
2677    
2678  =cut  =cut
2679  #: Return Type %;  #: Return Type %@;
2680  sub SubsystemsOf {  sub SubsystemsOf {
2681      # Get the parameters.      # Get the parameters.
2682      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
# Line 2438  Line 2686 
2686                                      ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);                                      ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);
2687      # Create the return value.      # Create the return value.
2688      my %retVal = ();      my %retVal = ();
2689        # Build a hash to weed out duplicates. Sometimes the same PEG and role appears
2690        # in two spreadsheet cells.
2691        my %dupHash = ();
2692      # Loop through the results, adding them to the hash.      # Loop through the results, adding them to the hash.
2693      for my $record (@subsystems) {      for my $record (@subsystems) {
2694          $retVal{$record->[0]} = $record->[1];          # Get this subsystem and role.
2695            my ($subsys, $role) = @{$record};
2696            # Insure it's the first time for both.
2697            my $dupKey = "$subsys\n$role";
2698            if (! exists $dupHash{"$subsys\n$role"}) {
2699                $dupHash{$dupKey} = 1;
2700                push @{$retVal{$subsys}}, $role;
2701            }
2702      }      }
2703      # Return the hash.      # Return the hash.
2704      return %retVal;      return %retVal;
# Line 2478  Line 2736 
2736      return @retVal;      return @retVal;
2737  }  }
2738    
2739    
2740    
2741  =head3 RelatedFeatures  =head3 RelatedFeatures
2742    
2743  C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>  C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>
# Line 2896  Line 3156 
3156      return %retVal;      return %retVal;
3157  }  }
3158    
3159    =head3 MyGenomes
3160    
3161    C<< my @genomes = Sprout::MyGenomes($dataDir); >>
3162    
3163    Return a list of the genomes to be included in the Sprout.
3164    
3165    This method is provided for use during the Sprout load. It presumes the Genome load file has
3166    already been created. (It will be in the Sprout data directory and called either C<Genome>
3167    or C<Genome.dtx>.) Essentially, it reads in the Genome load file and strips out the genome
3168    IDs.
3169    
3170    =over 4
3171    
3172    =item dataDir
3173    
3174    Directory containing the Sprout load files.
3175    
3176    =back
3177    
3178    =cut
3179    #: Return Type @;
3180    sub MyGenomes {
3181        # Get the parameters.
3182        my ($dataDir) = @_;
3183        # Compute the genome file name.
3184        my $genomeFileName = LoadFileName($dataDir, "Genome");
3185        # Extract the genome IDs from the files.
3186        my @retVal = map { $_ =~ /^(\S+)/; $1 } Tracer::GetFile($genomeFileName);
3187        # Return the result.
3188        return @retVal;
3189    }
3190    
3191    =head3 LoadFileName
3192    
3193    C<< my $fileName = Sprout::LoadFileName($dataDir, $tableName); >>
3194    
3195    Return the name of the load file for the specified table in the specified data
3196    directory.
3197    
3198    =over 4
3199    
3200    =item dataDir
3201    
3202    Directory containing the Sprout load files.
3203    
3204    =item tableName
3205    
3206    Name of the table whose load file is desired.
3207    
3208    =item RETURN
3209    
3210    Returns the name of the file containing the load data for the specified table, or
3211    C<undef> if no load file is present.
3212    
3213    =back
3214    
3215    =cut
3216    #: Return Type $;
3217    sub LoadFileName {
3218        # Get the parameters.
3219        my ($dataDir, $tableName) = @_;
3220        # Declare the return variable.
3221        my $retVal;
3222        # Check for the various file names.
3223        if (-e "$dataDir/$tableName") {
3224            $retVal = "$dataDir/$tableName";
3225        } elsif (-e "$dataDir/$tableName.dtx") {
3226            $retVal = "$dataDir/$tableName.dtx";
3227        }
3228        # Return the result.
3229        return $retVal;
3230    }
3231    
3232    =head3 DeleteGenome
3233    
3234    C<< my $stats = $sprout->DeleteGenome($genomeID, $testFlag); >>
3235    
3236    Delete a genome from the database.
3237    
3238    =over 4
3239    
3240    =item genomeID
3241    
3242    ID of the genome to delete
3243    
3244    =item testFlag
3245    
3246    If TRUE, then the DELETE statements will be traced, but no deletions will occur.
3247    
3248    =item RETURN
3249    
3250    Returns a statistics object describing the rows deleted.
3251    
3252    =back
3253    
3254    =cut
3255    #: Return Type $%;
3256    sub DeleteGenome {
3257        # Get the parameters.
3258        my ($self, $genomeID, $testFlag) = @_;
3259        # Perform the delete for the genome's features.
3260        my $retVal = $self->{_erdb}->Delete('Feature', "fig|$genomeID.%", $testFlag);
3261        # Perform the delete for the primary genome data.
3262        my $stats = $self->{_erdb}->Delete('Genome', $genomeID, $testFlag);
3263        $retVal->Accumulate($stats);
3264        # Return the result.
3265        return $retVal;
3266    }
3267    
3268  =head2 Internal Utility Methods  =head2 Internal Utility Methods
3269    
3270  =head3 ParseAssignment  =head3 ParseAssignment
# Line 2906  Line 3275 
3275    
3276  A functional assignment is always of the form  A functional assignment is always of the form
3277    
3278      I<XXXX>C<\nset >I<YYYY>C< function to\n>I<ZZZZZ>      C<set >I<YYYY>C< function to\n>I<ZZZZZ>
3279    
3280    where I<YYYY> is the B<user>, and I<ZZZZ> is the actual functional role. In most cases,
3281    the user and the assigning user (from MadeAnnotation) will be the same, but that is
3282    not always the case.
3283    
3284  where I<XXXX> is the B<assigning user>, I<YYYY> is the B<user>, and I<ZZZZ> is the  In addition, the functional role may contain extra data that is stripped, such as
3285  actual functional role. In most cases, the user and the assigning user will be the  terminating spaces or a comment separated from the rest of the text by a tab.
 same, but that is not always the case.  
3286    
3287  This is a static method.  This is a static method.
3288    
3289  =over 4  =over 4
3290    
3291    =item user
3292    
3293    Name of the assigning user.
3294    
3295  =item text  =item text
3296    
3297  Text of the annotation.  Text of the annotation.
# Line 2931  Line 3307 
3307    
3308  sub _ParseAssignment {  sub _ParseAssignment {
3309      # Get the parameters.      # Get the parameters.
3310      my ($text) = @_;      my ($user, $text) = @_;
3311      # Declare the return value.      # Declare the return value.
3312      my @retVal = ();      my @retVal = ();
3313      # Check to see if this is a functional assignment.      # Check to see if this is a functional assignment.
3314      my ($user, $type, $function) = split(/\n/, $text);      my ($type, $function) = split(/\n/, $text);
3315      if ($type =~ m/^set ([^ ]+) function to$/i) {      if ($type =~ m/^set function to$/i) {
3316          # Here it is, so we return the user name (which is in $1), the functional role text,          # Here we have an assignment without a user, so we use the incoming user ID.
3317          # and the assigning user.          @retVal = ($user, $function);
3318          @retVal = ($1, $function, $user);      } elsif ($type =~ m/^set (\S+) function to$/i) {
3319            # Here we have an assignment with a user that is passed back to the caller.
3320            @retVal = ($1, $function);
3321        }
3322        # If we have an assignment, we need to clean the function text. There may be
3323        # extra junk at the end added as a note from the user.
3324        if (@retVal) {
3325            $retVal[1] =~ s/(\t\S)?\s*$//;
3326      }      }
3327      # Return the result list.      # Return the result list.
3328      return @retVal;      return @retVal;
# Line 2967  Line 3350 
3350    
3351  sub FriendlyTimestamp {  sub FriendlyTimestamp {
3352      my ($timeValue) = @_;      my ($timeValue) = @_;
3353      my $retVal = strftime("%a %b %e %H:%M:%S %Y", localtime($timeValue));      my $retVal = localtime($timeValue);
3354      return $retVal;      return $retVal;
3355  }  }
3356    
# Line 3028  Line 3411 
3411      $self->Insert('HasProperty', { 'from-link' => $featureID, 'to-link' => $propID, evidence => $url });      $self->Insert('HasProperty', { 'from-link' => $featureID, 'to-link' => $propID, evidence => $url });
3412  }  }
3413    
3414    
3415  1;  1;

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