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revision 1.15, Wed Jun 22 21:30:45 2005 UTC revision 1.29, Wed Sep 14 13:06:53 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 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 $retVal;
447  }  }
# Line 570  Line 583 
583  =item RETURN  =item RETURN
584    
585  Returns a list of the feature's contig segments. The locations are returned as a list in a list  Returns a list of the feature's contig segments. The locations are returned as a list in a list
586  context and as a space-delimited string in a scalar context.  context and as a comma-delimited string in a scalar context.
587    
588  =back  =back
589    
# Line 613  Line 626 
626          push @retVal, "${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 756  Line 769 
769              $start = $beg;              $start = $beg;
770              $stop = $beg + $len - 1;              $stop = $beg + $len - 1;
771          } else {          } else {
772              $start = $beg + $len + 1;              $start = $beg - $len + 1;
773              $stop = $beg;              $stop = $beg;
774          }          }
775            Trace("Looking for sequences containing $start through $stop.") if T(SDNA => 4);
776          my $query = $self->Get(['IsMadeUpOf','Sequence'],          my $query = $self->Get(['IsMadeUpOf','Sequence'],
777              "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .              "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .
778              " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",              " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",
# Line 770  Line 784 
784                  $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)',                  $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)',
785                                     'IsMadeUpOf(len)']);                                     'IsMadeUpOf(len)']);
786              my $stopPosition = $startPosition + $sequenceLength;              my $stopPosition = $startPosition + $sequenceLength;
787                Trace("Sequence is from $startPosition to $stopPosition.") if T(SDNA => 4);
788              # Figure out the start point and length of the relevant section.              # Figure out the start point and length of the relevant section.
789              my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);              my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);
790              my $len = ($stopPosition <= $stop ? $stopPosition : $stop) - $startPosition - $pos1;              my $len1 = ($stopPosition <= $stop ? $stopPosition : $stop) - $startPosition - $pos1;
791                Trace("Position is $pos1 for length $len1.") if T(SDNA => 4);
792              # Add the relevant data to the location data.              # Add the relevant data to the location data.
793              $locationDNA .= substr($sequenceData, $pos1, $len);              $locationDNA .= substr($sequenceData, $pos1, $len1);
794          }          }
795          # Add this location's data to the return string. Note that we may need to reverse it.          # Add this location's data to the return string. Note that we may need to reverse it.
796          if ($dir eq '+') {          if ($dir eq '+') {
797              $retVal .= $locationDNA;              $retVal .= $locationDNA;
798          } else {          } else {
799              $locationDNA = join('', reverse split //, $locationDNA);              $retVal .= FIG::reverse_comp($locationDNA);
             $retVal .= $locationDNA;  
800          }          }
801      }      }
802      # Return the result.      # Return the result.
# Line 1506  Line 1521 
1521      my ($self, $peg1, $peg2) = @_;      my ($self, $peg1, $peg2) = @_;
1522      # Declare the return variable.      # Declare the return variable.
1523      my @retVal = ();      my @retVal = ();
1524      # Our first task is to find out the nature of the coupling.      # Our first task is to find out the nature of the coupling: whether or not
1525        # it exists, its score, and whether the features are stored in the same
1526        # order as the ones coming in.
1527      my ($couplingID, $inverted, $score) = $self->GetCoupling($peg1, $peg2);      my ($couplingID, $inverted, $score) = $self->GetCoupling($peg1, $peg2);
1528      # Only proceed if a coupling exists.      # Only proceed if a coupling exists.
1529      if ($couplingID) {      if ($couplingID) {
1530          # Determine the ordering to place on the evidence items. If we're          # Determine the ordering to place on the evidence items. If we're
1531          # inverted, we want to see feature 2 before feature 1; otherwise,          # inverted, we want to see feature 2 before feature 1 (descending); otherwise,
1532          # we want the reverse.          # we want feature 1 before feature 2 (normal).
1533            Trace("Coupling evidence for ($peg1, $peg2) with inversion flag $inverted.") if T(Coupling => 4);
1534          my $ordering = ($inverted ? "DESC" : "");          my $ordering = ($inverted ? "DESC" : "");
1535          # Get the coupling evidence.          # Get the coupling evidence.
1536          my @evidenceList = $self->GetAll(['IsEvidencedBy', 'PCH', 'UsesAsEvidence'],          my @evidenceList = $self->GetAll(['IsEvidencedBy', 'PCH', 'UsesAsEvidence'],
1537                                            "IsEvidencedBy(from-link) = ? ORDER BY PCH(id), UsesAsEvidence(pos) $ordering",                                            "IsEvidencedBy(from-link) = ? ORDER BY PCH(id), UsesAsEvidence(pos) $ordering",
1538                                            [$couplingID],                                            [$couplingID],
1539                                            ['PCH(used)', 'UsesAsEvidence(pos)']);                                            ['PCH(used)', 'UsesAsEvidence(to-link)']);
1540          # 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
1541          # 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
1542          # 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 1544 
1544          while (@evidenceList > 0) {          while (@evidenceList > 0) {
1545              my $peg1Data = shift @evidenceList;              my $peg1Data = shift @evidenceList;
1546              my $peg2Data = shift @evidenceList;              my $peg2Data = shift @evidenceList;
1547                Trace("Peg 1 is " . $peg1Data->[1] . " and Peg 2 is " . $peg2Data->[1] . ".") if T(Coupling => 4);
1548              push @retVal, [$peg1Data->[1], $peg2Data->[1], $peg1Data->[0]];              push @retVal, [$peg1Data->[1], $peg2Data->[1], $peg1Data->[0]];
1549          }          }
1550            Trace("Last index in evidence result is is $#retVal.") if T(Coupling => 4);
1551      }      }
     # TODO: code  
1552      # Return the result.      # Return the result.
1553      return @retVal;      return @retVal;
1554  }  }
# Line 1575  Line 1594 
1594      # Find the coupling data.      # Find the coupling data.
1595      my @pegs = $self->GetAll(['Coupling', 'ParticipatesInCoupling'],      my @pegs = $self->GetAll(['Coupling', 'ParticipatesInCoupling'],
1596                                   "Coupling(id) = ? ORDER BY ParticipatesInCoupling(pos)",                                   "Coupling(id) = ? ORDER BY ParticipatesInCoupling(pos)",
1597                                   [$retVal], "ParticipatesInCoupling(from-link), Coupling(score)");                                   [$retVal], ["ParticipatesInCoupling(from-link)", "Coupling(score)"]);
1598      # Check to see if we found anything.      # Check to see if we found anything.
1599      if (!@pegs) {      if (!@pegs) {
1600            Trace("No coupling found.") if T(Coupling => 4);
1601          # No coupling, so undefine the return value.          # No coupling, so undefine the return value.
1602          $retVal = undef;          $retVal = undef;
1603      } else {      } else {
1604          # We have a coupling! Get the score and check for inversion.          # We have a coupling! Get the score and check for inversion.
1605          $score = $pegs[0]->[1];          $score = $pegs[0]->[1];
1606          $inverted = ($pegs[0]->[0] eq $peg1);          my $firstFound = $pegs[0]->[0];
1607            $inverted = ($firstFound ne $peg1);
1608            Trace("Coupling score is $score. First peg is $firstFound, peg 1 is $peg1.") if T(Coupling => 4);
1609      }      }
1610      # Return the result.      # Return the result.
1611      return ($retVal, $inverted, $score);      return ($retVal, $inverted, $score);
# Line 1688  Line 1710 
1710          if ($line =~ m/^>\s*(.+?)(\s|\n)/) {          if ($line =~ m/^>\s*(.+?)(\s|\n)/) {
1711              # Here we have a new header. Store the current sequence if we have one.              # Here we have a new header. Store the current sequence if we have one.
1712              if ($id) {              if ($id) {
1713                  $retVal{$id} = uc $sequence;                  $retVal{$id} = lc $sequence;
1714              }              }
1715              # Clear the sequence accumulator and save the new ID.              # Clear the sequence accumulator and save the new ID.
1716              ($id, $sequence) = ("$prefix$1", "");              ($id, $sequence) = ("$prefix$1", "");
1717          } else {          } else {
1718              # 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.
1719              # 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
1720              # case.              # case.
1721              $line =~ /^\s*(.*?)(\s|\n)/;              $line =~ /^\s*(.*?)(\s|\n)/;
1722              $sequence .= $1;              $sequence .= $1;
# Line 1702  Line 1724 
1724      }      }
1725      # Flush out the last sequence (if any).      # Flush out the last sequence (if any).
1726      if ($sequence) {      if ($sequence) {
1727          $retVal{$id} = uc $sequence;          $retVal{$id} = lc $sequence;
1728      }      }
1729      # Close the file.      # Close the file.
1730      close FASTAFILE;      close FASTAFILE;
# Line 2028  Line 2050 
2050      # Get the parameters.      # Get the parameters.
2051      my ($self, $entityName, $entityID) = @_;      my ($self, $entityName, $entityID) = @_;
2052      # Check for the entity instance.      # Check for the entity instance.
2053        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
2054      my $testInstance = $self->GetEntity($entityName, $entityID);      my $testInstance = $self->GetEntity($entityName, $entityID);
2055      # Return an existence indicator.      # Return an existence indicator.
2056      my $retVal = ($testInstance ? 1 : 0);      my $retVal = ($testInstance ? 1 : 0);
# Line 2219  Line 2242 
2242      return @retVal;      return @retVal;
2243  }  }
2244    
2245    =head3 GetProperties
2246    
2247    C<< my @list = $sprout->GetProperties($fid, $key, $value, $url); >>
2248    
2249    Return a list of the properties with the specified characteristics.
2250    
2251    Properties are arbitrary key-value pairs associated with a feature. (At some point they
2252    will also be associated with genomes.) A property value is represented by a 4-tuple of
2253    the form B<($fid, $key, $value, $url)>. These exactly correspond to the parameter
2254    
2255    =over 4
2256    
2257    =item fid
2258    
2259    ID of the feature possessing the property.
2260    
2261    =item key
2262    
2263    Name or key of the property.
2264    
2265    =item value
2266    
2267    Value of the property.
2268    
2269    =item url
2270    
2271    URL of the document that indicated the property should have this particular value, or an
2272    empty string if no such document exists.
2273    
2274    =back
2275    
2276    The parameters act as a filter for the desired data. Any non-null parameter will
2277    automatically match all the tuples returned. So, specifying just the I<$fid> will
2278    return all the properties of the specified feature; similarly, specifying the I<$key>
2279    and I<$value> parameters will return all the features having the specified property
2280    value.
2281    
2282    A single property key can have many values, representing different ideas about the
2283    feature in question. For example, one paper may declare that a feature C<fig|83333.1.peg.10> is
2284    virulent, and another may declare that it is not virulent. A query about the virulence of
2285    C<fig|83333.1.peg.10> would be coded as
2286    
2287        my @list = $sprout->GetProperties('fig|83333.1.peg.10', 'virulence', '', '');
2288    
2289    Here the I<$value> and I<$url> fields are left blank, indicating that those fields are
2290    not to be filtered. The tuples returned would be
2291    
2292        ('fig|83333.1.peg.10', 'virulence', 'yes', 'http://www.somewhere.edu/first.paper.pdf')
2293        ('fig|83333.1.peg.10', 'virulence', 'no', 'http://www.somewhere.edu/second.paper.pdf')
2294    
2295    =cut
2296    #: Return Type @@;
2297    sub GetProperties {
2298        # Get the parameters.
2299        my ($self, @parms) = @_;
2300        # Declare the return variable.
2301        my @retVal = ();
2302        # Now we need to create a WHERE clause that will get us the data we want. First,
2303        # we create a list of the columns containing the data for each parameter.
2304        my @colNames = ('HasProperty(from-link)', 'Property(property-name)',
2305                        'Property(property-value)', 'HasProperty(evidence)');
2306        # Now we build the WHERE clause and the list of parameter values.
2307        my @where = ();
2308        my @values = ();
2309        for (my $i = 0; $i <= $#colNames; $i++) {
2310            my $parm = $parms[$i];
2311            if (defined $parm && ($parm ne '')) {
2312                push @where, "$colNames[$i] = ?";
2313                push @values, $parm;
2314            }
2315        }
2316        # Format the WHERE clause.
2317        my $filter = (@values > 0 ? (join " AND ", @where) : undef);
2318        # Ask for all the propertie values with the desired characteristics.
2319        my $query = $self->Get(['HasProperty', 'Property'], $filter, \@values);
2320        while (my $valueObject = $query->Fetch()) {
2321            my @tuple = $valueObject->Values(\@colNames);
2322            push @retVal, \@tuple;
2323        }
2324        # Return the result.
2325        return @retVal;
2326    }
2327    
2328  =head3 FeatureProperties  =head3 FeatureProperties
2329    
2330  C<< my @properties = $sprout->FeatureProperties($featureID); >>  C<< my @properties = $sprout->FeatureProperties($featureID); >>
# Line 2413  Line 2519 
2519  C<< my %subsystems = $sprout->SubsystemsOf($featureID); >>  C<< my %subsystems = $sprout->SubsystemsOf($featureID); >>
2520    
2521  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
2522  to the role the feature performs.  to the roles the feature performs.
2523    
2524  =over 4  =over 4
2525    
# Line 2423  Line 2529 
2529    
2530  =item RETURN  =item RETURN
2531    
2532  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.
2533    
2534  =back  =back
2535    
2536  =cut  =cut
2537  #: Return Type %;  #: Return Type %@;
2538  sub SubsystemsOf {  sub SubsystemsOf {
2539      # Get the parameters.      # Get the parameters.
2540      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
2541      # Use the SSCell to connect features to subsystems.      # Get the subsystem list.
2542      my @subsystems = $self->GetAll(['ContainsFeature', 'HasSSCell', 'IsRoleOf'],      my @subsystems = $self->GetAll(['ContainsFeature', 'HasSSCell', 'IsRoleOf'],
2543                                      "ContainsFeature(to-link) = ?", [$featureID],                                      "ContainsFeature(to-link) = ?", [$featureID],
2544                                      ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);                                      ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);
# Line 2440  Line 2546 
2546      my %retVal = ();      my %retVal = ();
2547      # Loop through the results, adding them to the hash.      # Loop through the results, adding them to the hash.
2548      for my $record (@subsystems) {      for my $record (@subsystems) {
2549          $retVal{$record->[0]} = $record->[1];          my ($subsys, $role) = @{$record};
2550            if (exists $retVal{$subsys}) {
2551                push @{$retVal{$subsys}}, $role;
2552            } else {
2553                $retVal{$subsys} = [$role];
2554            }
2555      }      }
2556      # Return the hash.      # Return the hash.
2557      return %retVal;      return %retVal;
2558  }  }
2559    
2560    =head3 SubsystemList
2561    
2562    C<< my @subsystems = $sprout->SubsystemList($featureID); >>
2563    
2564    Return a list containing the names of the subsystems in which the specified
2565    feature participates. Unlike L</SubsystemsOf>, this method only returns the
2566    subsystem names, not the roles.
2567    
2568    =over 4
2569    
2570    =item featureID
2571    
2572    ID of the feature whose subsystem names are desired.
2573    
2574    =item RETURN
2575    
2576    Returns a list of the names of the subsystems in which the feature participates.
2577    
2578    =back
2579    
2580    =cut
2581    #: Return Type @;
2582    sub SubsystemList {
2583        # Get the parameters.
2584        my ($self, $featureID) = @_;
2585        # Get the list of names.
2586        my @retVal = $self->GetFlat(['ContainsFeature', 'HasSSCell'], "ContainsFeature(to-link) = ?",
2587                                    [$featureID], 'HasSSCell(from-link)');
2588        # Return the result.
2589        return @retVal;
2590    }
2591    
2592  =head3 RelatedFeatures  =head3 RelatedFeatures
2593    
2594  C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>  C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>
# Line 2864  Line 3007 
3007      return %retVal;      return %retVal;
3008  }  }
3009    
3010    =head3 MyGenomes
3011    
3012    C<< my @genomes = Sprout::MyGenomes($dataDir); >>
3013    
3014    Return a list of the genomes to be included in the Sprout.
3015    
3016    This method is provided for use during the Sprout load. It presumes the Genome load file has
3017    already been created. (It will be in the Sprout data directory and called either C<Genome>
3018    or C<Genome.dtx>.) Essentially, it reads in the Genome load file and strips out the genome
3019    IDs.
3020    
3021    =over 4
3022    
3023    =item dataDir
3024    
3025    Directory containing the Sprout load files.
3026    
3027    =back
3028    
3029    =cut
3030    #: Return Type @;
3031    sub MyGenomes {
3032        # Get the parameters.
3033        my ($dataDir) = @_;
3034        # Compute the genome file name.
3035        my $genomeFileName = LoadFileName($dataDir, "Genome");
3036        # Extract the genome IDs from the files.
3037        my @retVal = map { $_ =~ /^(\S+)/; $1 } Tracer::GetFile($genomeFileName);
3038        # Return the result.
3039        return @retVal;
3040    }
3041    
3042    =head3 LoadFileName
3043    
3044    C<< my $fileName = Sprout::LoadFileName($dataDir, $tableName); >>
3045    
3046    Return the name of the load file for the specified table in the specified data
3047    directory.
3048    
3049    =over 4
3050    
3051    =item dataDir
3052    
3053    Directory containing the Sprout load files.
3054    
3055    =item tableName
3056    
3057    Name of the table whose load file is desired.
3058    
3059    =item RETURN
3060    
3061    Returns the name of the file containing the load data for the specified table, or
3062    C<undef> if no load file is present.
3063    
3064    =back
3065    
3066    =cut
3067    #: Return Type $;
3068    sub LoadFileName {
3069        # Get the parameters.
3070        my ($dataDir, $tableName) = @_;
3071        # Declare the return variable.
3072        my $retVal;
3073        # Check for the various file names.
3074        if (-e "$dataDir/$tableName") {
3075            $retVal = "$dataDir/$tableName";
3076        } elsif (-e "$dataDir/$tableName.dtx") {
3077            $retVal = "$dataDir/$tableName.dtx";
3078        }
3079        # Return the result.
3080        return $retVal;
3081    }
3082    
3083  =head2 Internal Utility Methods  =head2 Internal Utility Methods
3084    
3085  =head3 ParseAssignment  =head3 ParseAssignment
# Line 2996  Line 3212 
3212      $self->Insert('HasProperty', { 'from-link' => $featureID, 'to-link' => $propID, evidence => $url });      $self->Insert('HasProperty', { 'from-link' => $featureID, 'to-link' => $propID, evidence => $url });
3213  }  }
3214    
3215    
3216    
3217  1;  1;

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