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revision 1.14, Thu Jun 9 19:06:55 2005 UTC revision 1.30, Wed Sep 14 13:13:25 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$len";
627          }          }
628          # Return the list in the format indicated by the context.          # Return the list in the format indicated by the context.
629          return (wantarray ? @retVal : join(' ', @retVal));      return (wantarray ? @retVal : join(',', @retVal));
630  }  }
631    
632  =head3 ParseLocation  =head3 ParseLocation
# Line 752  Line 765 
765                  # the start point is the ending. Note that in the latter case we must reverse the DNA string                  # the start point is the ending. Note that in the latter case we must reverse the DNA string
766                  # before putting it in the return value.                  # before putting it in the return value.
767                  my ($start, $stop);                  my ($start, $stop);
768            Tracer("Parsed location is $beg$dir$len.") if T(SDNA => 4);
769                  if ($dir eq "+") {                  if ($dir eq "+") {
770                          $start = $beg;                          $start = $beg;
771                          $stop = $beg + $len - 1;                          $stop = $beg + $len - 1;
772                  } else {                  } else {
773                          $start = $beg + $len + 1;              $start = $beg - $len + 1;
774                          $stop = $beg;                          $stop = $beg;
775                  }                  }
776            Trace("Looking for sequences containing $start through $stop.") if T(SDNA => 4);
777                  my $query = $self->Get(['IsMadeUpOf','Sequence'],                  my $query = $self->Get(['IsMadeUpOf','Sequence'],
778                          "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .                          "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .
779                          " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",                          " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",
# Line 770  Line 785 
785                                  $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)',                                  $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)',
786                                                                     'IsMadeUpOf(len)']);                                                                     'IsMadeUpOf(len)']);
787                          my $stopPosition = $startPosition + $sequenceLength;                          my $stopPosition = $startPosition + $sequenceLength;
788                Trace("Sequence is from $startPosition to $stopPosition.") if T(SDNA => 4);
789                          # Figure out the start point and length of the relevant section.                          # Figure out the start point and length of the relevant section.
790                          my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);                          my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);
791                          my $len = ($stopPosition <= $stop ? $stopPosition : $stop) - $startPosition - $pos1;              my $len1 = ($stopPosition <= $stop ? $stopPosition : $stop) - $startPosition - $pos1;
792                Trace("Position is $pos1 for length $len1.") if T(SDNA => 4);
793                          # Add the relevant data to the location data.                          # Add the relevant data to the location data.
794                          $locationDNA .= substr($sequenceData, $pos1, $len);              $locationDNA .= substr($sequenceData, $pos1, $len1);
795                  }                  }
796                  # Add this location's data to the return string. Note that we may need to reverse it.                  # Add this location's data to the return string. Note that we may need to reverse it.
797                  if ($dir eq '+') {                  if ($dir eq '+') {
798                          $retVal .= $locationDNA;                          $retVal .= $locationDNA;
799                  } else {                  } else {
800                          $locationDNA = join('', reverse split //, $locationDNA);              $retVal .= FIG::reverse_comp($locationDNA);
                         $retVal .= $locationDNA;  
801                  }                  }
802          }          }
803          # Return the result.          # Return the result.
# Line 1230  Line 1246 
1246    
1247  =item RETURN  =item RETURN
1248    
1249  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
1250  their best hits.  on the target genome.
1251    
1252  =back  =back
1253    
# Line 1259  Line 1275 
1275          return \%retVal;          return \%retVal;
1276  }  }
1277    
1278    =head3 SimList
1279    
1280    C<< my %similarities = $sprout->SimList($featureID, $count); >>
1281    
1282    Return a list of the similarities to the specified feature.
1283    
1284    Sprout does not support real similarities, so this method just returns the bidirectional
1285    best hits.
1286    
1287    =over 4
1288    
1289    =item featureID
1290    
1291    ID of the feature whose similarities are desired.
1292    
1293    =item count
1294    
1295    Maximum number of similar features to be returned, or C<0> to return them all.
1296    
1297    =back
1298    
1299    =cut
1300    #: Return Type %;
1301    sub SimList {
1302        # Get the parameters.
1303        my ($self, $featureID, $count) = @_;
1304        # Ask for the best hits.
1305        my @lists = $self->GetAll(['IsBidirectionalBestHitOf'],
1306                                  "IsBidirectionalBestHitOf(from-link) = ? ORDER BY IsBidirectionalBestHitOf(score) DESC",
1307                                  [$featureID], ['IsBidirectionalBestHitOf(to-link)', 'IsBidirectionalBestHitOf(score)'],
1308                                  $count);
1309        # Create the return value.
1310        my %retVal = ();
1311        for my $tuple (@lists) {
1312            $retVal{$tuple->[0]} = $tuple->[1];
1313        }
1314        # Return the result.
1315        return %retVal;
1316    }
1317    
1318    
1319    
1320    =head3 IsComplete
1321    
1322    C<< my $flag = $sprout->IsComplete($genomeID); >>
1323    
1324    Return TRUE if the specified genome is complete, else FALSE.
1325    
1326    =over 4
1327    
1328    =item genomeID
1329    
1330    ID of the genome whose completeness status is desired.
1331    
1332    =item RETURN
1333    
1334    Returns TRUE if the genome is complete, FALSE if it is incomplete, and C<undef> if it is
1335    not found.
1336    
1337    =back
1338    
1339    =cut
1340    #: Return Type $;
1341    sub IsComplete {
1342        # Get the parameters.
1343        my ($self, $genomeID) = @_;
1344        # Declare the return variable.
1345        my $retVal;
1346        # Get the genome's data.
1347        my $genomeData = $self->GetEntity('Genome', $genomeID);
1348        if ($genomeData) {
1349            # The genome exists, so get the completeness flag.
1350            ($retVal) = $genomeData->Value('complete');
1351        }
1352        # Return the result.
1353        return $retVal;
1354    }
1355    
1356  =head3 FeatureAliases  =head3 FeatureAliases
1357    
1358  C<< my @aliasList = $sprout->FeatureAliases($featureID); >>  C<< my @aliasList = $sprout->FeatureAliases($featureID); >>
# Line 1378  Line 1472 
1472          return %retVal;          return %retVal;
1473  }  }
1474    
1475    =head3 CouplingEvidence
1476    
1477    C<< my @evidence = $sprout->CouplingEvidence($peg1, $peg2); >>
1478    
1479    Return the evidence for a functional coupling.
1480    
1481    A pair of features is considered evidence of a coupling between two other
1482    features if they occur close together on a contig and both are similar to
1483    the coupled features. So, if B<A1> and B<A2> are close together on a contig,
1484    B<B1> and B<B2> are considered evidence for the coupling if (1) B<B1> and
1485    B<B2> are close together, (2) B<B1> is similar to B<A1>, and (3) B<B2> is
1486    similar to B<A2>.
1487    
1488    The score of a coupling is determined by the number of pieces of evidence
1489    that are considered I<representative>. If several evidence items belong to
1490    a group of genomes that are close to each other, only one of those items
1491    is considered representative. The other evidence items are presumed to be
1492    there because of the relationship between the genomes rather than because
1493    the two proteins generated by the features have a related functionality.
1494    
1495    Each evidence item is returned as a three-tuple in the form C<[>I<$peg1a>C<,>
1496    I<$peg2a>C<,> I<$rep>C<]>, where I<$peg1a> is similar to I<$peg1>, I<$peg2a>
1497    is similar to I<$peg2>, and I<$rep> is TRUE if the evidence is representative
1498    and FALSE otherwise.
1499    
1500    =over 4
1501    
1502    =item peg1
1503    
1504    ID of the feature of interest.
1505    
1506    =item peg2
1507    
1508    ID of a feature functionally coupled to the feature of interest.
1509    
1510    =item RETURN
1511    
1512    Returns a list of 3-tuples. Each tuple consists of a feature similar to the feature
1513    of interest, a feature similar to the functionally coupled feature, and a flag
1514    that is TRUE for a representative piece of evidence and FALSE otherwise.
1515    
1516    =back
1517    
1518    =cut
1519    #: Return Type @@;
1520    sub CouplingEvidence {
1521        # Get the parameters.
1522        my ($self, $peg1, $peg2) = @_;
1523        # Declare the return variable.
1524        my @retVal = ();
1525        # Our first task is to find out the nature of the coupling: whether or not
1526        # it exists, its score, and whether the features are stored in the same
1527        # order as the ones coming in.
1528        my ($couplingID, $inverted, $score) = $self->GetCoupling($peg1, $peg2);
1529        # Only proceed if a coupling exists.
1530        if ($couplingID) {
1531            # Determine the ordering to place on the evidence items. If we're
1532            # inverted, we want to see feature 2 before feature 1 (descending); otherwise,
1533            # we want feature 1 before feature 2 (normal).
1534            Trace("Coupling evidence for ($peg1, $peg2) with inversion flag $inverted.") if T(Coupling => 4);
1535            my $ordering = ($inverted ? "DESC" : "");
1536            # Get the coupling evidence.
1537            my @evidenceList = $self->GetAll(['IsEvidencedBy', 'PCH', 'UsesAsEvidence'],
1538                                              "IsEvidencedBy(from-link) = ? ORDER BY PCH(id), UsesAsEvidence(pos) $ordering",
1539                                              [$couplingID],
1540                                              ['PCH(used)', 'UsesAsEvidence(to-link)']);
1541            # Loop through the evidence items. Each piece of evidence is represented by two
1542            # positions in the evidence list, one for each feature on the other side of the
1543            # evidence link. If at some point we want to generalize to couplings with
1544            # more than two positions, this section of code will need to be re-done.
1545            while (@evidenceList > 0) {
1546                my $peg1Data = shift @evidenceList;
1547                my $peg2Data = shift @evidenceList;
1548                Trace("Peg 1 is " . $peg1Data->[1] . " and Peg 2 is " . $peg2Data->[1] . ".") if T(Coupling => 4);
1549                push @retVal, [$peg1Data->[1], $peg2Data->[1], $peg1Data->[0]];
1550            }
1551            Trace("Last index in evidence result is is $#retVal.") if T(Coupling => 4);
1552        }
1553        # Return the result.
1554        return @retVal;
1555    }
1556    
1557    =head3 GetCoupling
1558    
1559    C<< my ($couplingID, $inverted, $score) = $sprout->GetCoupling($peg1, $peg2); >>
1560    
1561    Return the coupling (if any) for the specified pair of PEGs. If a coupling
1562    exists, we return the coupling ID along with an indicator of whether the
1563    coupling is stored as C<(>I<$peg1>C<, >I<$peg2>C<)> or C<(>I<$peg2>C<, >I<$peg1>C<)>.
1564    In the second case, we say the coupling is I<inverted>. The importance of an
1565    inverted coupling is that the PEGs in the evidence will appear in reverse order.
1566    
1567    =over 4
1568    
1569    =item peg1
1570    
1571    ID of the feature of interest.
1572    
1573    =item peg2
1574    
1575    ID of the potentially coupled feature.
1576    
1577    =item RETURN
1578    
1579    Returns a three-element list. The first element contains the database ID of
1580    the coupling. The second element is FALSE if the coupling is stored in the
1581    database in the caller specified order and TRUE if it is stored in the
1582    inverted order. The third element is the coupling's score. If the coupling
1583    does not exist, all three list elements will be C<undef>.
1584    
1585    =back
1586    
1587    =cut
1588    #: Return Type $%@;
1589    sub GetCoupling {
1590        # Get the parameters.
1591        my ($self, $peg1, $peg2) = @_;
1592        # Declare the return values. We'll start with the coupling ID and undefine the
1593        # flag and score until we have more information.
1594        my ($retVal, $inverted, $score) = (CouplingID($peg1, $peg2), undef, undef);
1595        # Find the coupling data.
1596        my @pegs = $self->GetAll(['Coupling', 'ParticipatesInCoupling'],
1597                                     "Coupling(id) = ? ORDER BY ParticipatesInCoupling(pos)",
1598                                     [$retVal], ["ParticipatesInCoupling(from-link)", "Coupling(score)"]);
1599        # Check to see if we found anything.
1600        if (!@pegs) {
1601            Trace("No coupling found.") if T(Coupling => 4);
1602            # No coupling, so undefine the return value.
1603            $retVal = undef;
1604        } else {
1605            # We have a coupling! Get the score and check for inversion.
1606            $score = $pegs[0]->[1];
1607            my $firstFound = $pegs[0]->[0];
1608            $inverted = ($firstFound ne $peg1);
1609            Trace("Coupling score is $score. First peg is $firstFound, peg 1 is $peg1.") if T(Coupling => 4);
1610        }
1611        # Return the result.
1612        return ($retVal, $inverted, $score);
1613    }
1614    
1615    =head3 CouplingID
1616    
1617    C<< my $couplingID = Sprout::CouplingID($peg1, $peg2); >>
1618    
1619    Return the coupling ID for a pair of feature IDs.
1620    
1621    The coupling ID is currently computed by joining the feature IDs in
1622    sorted order with a space. Client modules (that is, modules which
1623    use Sprout) should not, however, count on this always being the
1624    case. This method provides a way for abstracting the concept of a
1625    coupling ID. All that we know for sure about it is that it can be
1626    generated easily from the feature IDs and the order of the IDs
1627    in the parameter list does not matter (i.e. C<CouplingID("a1", "b1")>
1628    will have the same value as C<CouplingID("b1", "a1")>.
1629    
1630    =over 4
1631    
1632    =item peg1
1633    
1634    First feature of interest.
1635    
1636    =item peg2
1637    
1638    Second feature of interest.
1639    
1640    =item RETURN
1641    
1642    Returns the ID that would be used to represent a functional coupling of
1643    the two specified PEGs.
1644    
1645    =back
1646    
1647    =cut
1648    #: Return Type $;
1649    sub CouplingID {
1650        return join " ", sort @_;
1651    }
1652    
1653  =head3 GetEntityTypes  =head3 GetEntityTypes
1654    
1655  C<< my @entityList = $sprout->GetEntityTypes(); >>  C<< my @entityList = $sprout->GetEntityTypes(); >>
# Line 1439  Line 1711 
1711                  if ($line =~ m/^>\s*(.+?)(\s|\n)/) {                  if ($line =~ m/^>\s*(.+?)(\s|\n)/) {
1712                          # Here we have a new header. Store the current sequence if we have one.                          # Here we have a new header. Store the current sequence if we have one.
1713                          if ($id) {                          if ($id) {
1714                                  $retVal{$id} = uc $sequence;                  $retVal{$id} = lc $sequence;
1715                          }                          }
1716                          # Clear the sequence accumulator and save the new ID.                          # Clear the sequence accumulator and save the new ID.
1717                          ($id, $sequence) = ("$prefix$1", "");                          ($id, $sequence) = ("$prefix$1", "");
1718                  } else {                  } else {
1719                          # 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.
1720                          # 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
1721                          # case.                          # case.
1722                          $line =~ /^\s*(.*?)(\s|\n)/;                          $line =~ /^\s*(.*?)(\s|\n)/;
1723                          $sequence .= $1;                          $sequence .= $1;
# Line 1453  Line 1725 
1725          }          }
1726          # Flush out the last sequence (if any).          # Flush out the last sequence (if any).
1727          if ($sequence) {          if ($sequence) {
1728                  $retVal{$id} = uc $sequence;          $retVal{$id} = lc $sequence;
1729          }          }
1730          # Close the file.          # Close the file.
1731          close FASTAFILE;          close FASTAFILE;
# Line 1572  Line 1844 
1844  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
1845  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>.
1846    
1847  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<< $sprout->InsertObject('HasProperty', { 'from-link' => 'fig|158879.1.peg.1', 'to-link' => 4, evidence => 'http://seedu.uchicago.edu/query.cgi?article_id=142'}); >>
1848    
1849  =over 4  =over 4
1850    
# Line 1779  Line 2051 
2051          # Get the parameters.          # Get the parameters.
2052          my ($self, $entityName, $entityID) = @_;          my ($self, $entityName, $entityID) = @_;
2053          # Check for the entity instance.          # Check for the entity instance.
2054        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
2055          my $testInstance = $self->GetEntity($entityName, $entityID);          my $testInstance = $self->GetEntity($entityName, $entityID);
2056          # Return an existence indicator.          # Return an existence indicator.
2057          my $retVal = ($testInstance ? 1 : 0);          my $retVal = ($testInstance ? 1 : 0);
# Line 1970  Line 2243 
2243          return @retVal;          return @retVal;
2244  }  }
2245    
2246    =head3 GetProperties
2247    
2248    C<< my @list = $sprout->GetProperties($fid, $key, $value, $url); >>
2249    
2250    Return a list of the properties with the specified characteristics.
2251    
2252    Properties are arbitrary key-value pairs associated with a feature. (At some point they
2253    will also be associated with genomes.) A property value is represented by a 4-tuple of
2254    the form B<($fid, $key, $value, $url)>. These exactly correspond to the parameter
2255    
2256    =over 4
2257    
2258    =item fid
2259    
2260    ID of the feature possessing the property.
2261    
2262    =item key
2263    
2264    Name or key of the property.
2265    
2266    =item value
2267    
2268    Value of the property.
2269    
2270    =item url
2271    
2272    URL of the document that indicated the property should have this particular value, or an
2273    empty string if no such document exists.
2274    
2275    =back
2276    
2277    The parameters act as a filter for the desired data. Any non-null parameter will
2278    automatically match all the tuples returned. So, specifying just the I<$fid> will
2279    return all the properties of the specified feature; similarly, specifying the I<$key>
2280    and I<$value> parameters will return all the features having the specified property
2281    value.
2282    
2283    A single property key can have many values, representing different ideas about the
2284    feature in question. For example, one paper may declare that a feature C<fig|83333.1.peg.10> is
2285    virulent, and another may declare that it is not virulent. A query about the virulence of
2286    C<fig|83333.1.peg.10> would be coded as
2287    
2288        my @list = $sprout->GetProperties('fig|83333.1.peg.10', 'virulence', '', '');
2289    
2290    Here the I<$value> and I<$url> fields are left blank, indicating that those fields are
2291    not to be filtered. The tuples returned would be
2292    
2293        ('fig|83333.1.peg.10', 'virulence', 'yes', 'http://www.somewhere.edu/first.paper.pdf')
2294        ('fig|83333.1.peg.10', 'virulence', 'no', 'http://www.somewhere.edu/second.paper.pdf')
2295    
2296    =cut
2297    #: Return Type @@;
2298    sub GetProperties {
2299        # Get the parameters.
2300        my ($self, @parms) = @_;
2301        # Declare the return variable.
2302        my @retVal = ();
2303        # Now we need to create a WHERE clause that will get us the data we want. First,
2304        # we create a list of the columns containing the data for each parameter.
2305        my @colNames = ('HasProperty(from-link)', 'Property(property-name)',
2306                        'Property(property-value)', 'HasProperty(evidence)');
2307        # Now we build the WHERE clause and the list of parameter values.
2308        my @where = ();
2309        my @values = ();
2310        for (my $i = 0; $i <= $#colNames; $i++) {
2311            my $parm = $parms[$i];
2312            if (defined $parm && ($parm ne '')) {
2313                push @where, "$colNames[$i] = ?";
2314                push @values, $parm;
2315            }
2316        }
2317        # Format the WHERE clause.
2318        my $filter = (@values > 0 ? (join " AND ", @where) : undef);
2319        # Ask for all the propertie values with the desired characteristics.
2320        my $query = $self->Get(['HasProperty', 'Property'], $filter, \@values);
2321        while (my $valueObject = $query->Fetch()) {
2322            my @tuple = $valueObject->Values(\@colNames);
2323            push @retVal, \@tuple;
2324        }
2325        # Return the result.
2326        return @retVal;
2327    }
2328    
2329  =head3 FeatureProperties  =head3 FeatureProperties
2330    
2331  C<< my @properties = $sprout->FeatureProperties($featureID); >>  C<< my @properties = $sprout->FeatureProperties($featureID); >>
# Line 2164  Line 2520 
2520  C<< my %subsystems = $sprout->SubsystemsOf($featureID); >>  C<< my %subsystems = $sprout->SubsystemsOf($featureID); >>
2521    
2522  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
2523  to the role the feature performs.  to the roles the feature performs.
2524    
2525  =over 4  =over 4
2526    
# Line 2174  Line 2530 
2530    
2531  =item RETURN  =item RETURN
2532    
2533  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.
2534    
2535  =back  =back
2536    
2537  =cut  =cut
2538  #: Return Type %;  #: Return Type %@;
2539  sub SubsystemsOf {  sub SubsystemsOf {
2540          # Get the parameters.          # Get the parameters.
2541          my ($self, $featureID) = @_;          my ($self, $featureID) = @_;
2542          # Use the SSCell to connect features to subsystems.      # Get the subsystem list.
2543          my @subsystems = $self->GetAll(['ContainsFeature', 'HasSSCell', 'IsRoleOf'],          my @subsystems = $self->GetAll(['ContainsFeature', 'HasSSCell', 'IsRoleOf'],
2544                                                                          "ContainsFeature(to-link) = ?", [$featureID],                                                                          "ContainsFeature(to-link) = ?", [$featureID],
2545                                                                          ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);                                                                          ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);
# Line 2191  Line 2547 
2547          my %retVal = ();          my %retVal = ();
2548          # Loop through the results, adding them to the hash.          # Loop through the results, adding them to the hash.
2549          for my $record (@subsystems) {          for my $record (@subsystems) {
2550                  $retVal{$record->[0]} = $record->[1];          my ($subsys, $role) = @{$record};
2551            if (exists $retVal{$subsys}) {
2552                push @{$retVal{$subsys}}, $role;
2553            } else {
2554                $retVal{$subsys} = [$role];
2555            }
2556          }          }
2557          # Return the hash.          # Return the hash.
2558          return %retVal;          return %retVal;
2559  }  }
2560    
2561    =head3 SubsystemList
2562    
2563    C<< my @subsystems = $sprout->SubsystemList($featureID); >>
2564    
2565    Return a list containing the names of the subsystems in which the specified
2566    feature participates. Unlike L</SubsystemsOf>, this method only returns the
2567    subsystem names, not the roles.
2568    
2569    =over 4
2570    
2571    =item featureID
2572    
2573    ID of the feature whose subsystem names are desired.
2574    
2575    =item RETURN
2576    
2577    Returns a list of the names of the subsystems in which the feature participates.
2578    
2579    =back
2580    
2581    =cut
2582    #: Return Type @;
2583    sub SubsystemList {
2584        # Get the parameters.
2585        my ($self, $featureID) = @_;
2586        # Get the list of names.
2587        my @retVal = $self->GetFlat(['ContainsFeature', 'HasSSCell'], "ContainsFeature(to-link) = ?",
2588                                    [$featureID], 'HasSSCell(from-link)');
2589        # Return the result.
2590        return @retVal;
2591    }
2592    
2593  =head3 RelatedFeatures  =head3 RelatedFeatures
2594    
2595  C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>  C<< my @relatedList = $sprout->RelatedFeatures($featureID, $function, $userID); >>
# Line 2615  Line 3008 
3008      return %retVal;      return %retVal;
3009  }  }
3010    
3011    =head3 MyGenomes
3012    
3013    C<< my @genomes = Sprout::MyGenomes($dataDir); >>
3014    
3015    Return a list of the genomes to be included in the Sprout.
3016    
3017    This method is provided for use during the Sprout load. It presumes the Genome load file has
3018    already been created. (It will be in the Sprout data directory and called either C<Genome>
3019    or C<Genome.dtx>.) Essentially, it reads in the Genome load file and strips out the genome
3020    IDs.
3021    
3022    =over 4
3023    
3024    =item dataDir
3025    
3026    Directory containing the Sprout load files.
3027    
3028    =back
3029    
3030    =cut
3031    #: Return Type @;
3032    sub MyGenomes {
3033        # Get the parameters.
3034        my ($dataDir) = @_;
3035        # Compute the genome file name.
3036        my $genomeFileName = LoadFileName($dataDir, "Genome");
3037        # Extract the genome IDs from the files.
3038        my @retVal = map { $_ =~ /^(\S+)/; $1 } Tracer::GetFile($genomeFileName);
3039        # Return the result.
3040        return @retVal;
3041    }
3042    
3043    =head3 LoadFileName
3044    
3045    C<< my $fileName = Sprout::LoadFileName($dataDir, $tableName); >>
3046    
3047    Return the name of the load file for the specified table in the specified data
3048    directory.
3049    
3050    =over 4
3051    
3052    =item dataDir
3053    
3054    Directory containing the Sprout load files.
3055    
3056    =item tableName
3057    
3058    Name of the table whose load file is desired.
3059    
3060    =item RETURN
3061    
3062    Returns the name of the file containing the load data for the specified table, or
3063    C<undef> if no load file is present.
3064    
3065    =back
3066    
3067    =cut
3068    #: Return Type $;
3069    sub LoadFileName {
3070        # Get the parameters.
3071        my ($dataDir, $tableName) = @_;
3072        # Declare the return variable.
3073        my $retVal;
3074        # Check for the various file names.
3075        if (-e "$dataDir/$tableName") {
3076            $retVal = "$dataDir/$tableName";
3077        } elsif (-e "$dataDir/$tableName.dtx") {
3078            $retVal = "$dataDir/$tableName.dtx";
3079        }
3080        # Return the result.
3081        return $retVal;
3082    }
3083    
3084  =head2 Internal Utility Methods  =head2 Internal Utility Methods
3085    
3086  =head3 ParseAssignment  =head3 ParseAssignment
# Line 2690  Line 3156 
3156      return $retVal;      return $retVal;
3157  }  }
3158    
3159    =head3 AddProperty
3160    
3161    C<< my  = $sprout->AddProperty($featureID, $key, $value, $url); >>
3162    
3163    Add a new attribute value (Property) to a feature. In the SEED system, attributes can
3164    be added to almost any object. In Sprout, they can only be added to features. In
3165    Sprout, attributes are implemented using I<properties>. A property represents a key/value
3166    pair. If the particular key/value pair coming in is not already in the database, a new
3167    B<Property> record is created to hold it.
3168    
3169    =over 4
3170    
3171    =item peg
3172    
3173    ID of the feature to which the attribute is to be replied.
3174    
3175    =item key
3176    
3177    Name of the attribute (key).
3178    
3179    =item value
3180    
3181    Value of the attribute.
3182    
3183    =item url
3184    
3185    URL or text citation from which the property was obtained.
3186    
3187    =back
3188    
3189    =cut
3190    #: Return Type ;
3191    sub AddProperty {
3192        # Get the parameters.
3193        my ($self, $featureID, $key, $value, $url) = @_;
3194        # Declare the variable to hold the desired property ID.
3195        my $propID;
3196        # Attempt to find a property record for this key/value pair.
3197        my @properties = $self->GetFlat(['Property'],
3198                                       "Property(property-name) = ? AND Property(property-value) = ?",
3199                                       [$key, $value], 'Property(id)');
3200        if (@properties) {
3201            # Here the property is already in the database. We save its ID.
3202            $propID = $properties[0];
3203            # Here the property value does not exist. We need to generate an ID. It will be set
3204            # to a number one greater than the maximum value in the database. This call to
3205            # GetAll will stop after one record.
3206            my @maxProperty = $self->GetAll(['Property'], "ORDER BY Property(id) DESC", [], ['Property(id)'],
3207                                            1);
3208            $propID = $maxProperty[0]->[0] + 1;
3209            # Insert the new property value.
3210            $self->Insert('Property', { 'property-name' => $key, 'property-value' => $value, id => $propID });
3211        }
3212        # Now we connect the incoming feature to the property.
3213        $self->Insert('HasProperty', { 'from-link' => $featureID, 'to-link' => $propID, evidence => $url });
3214    }
3215    
3216    
3217    
3218  1;  1;

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