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revision 1.17, Mon Jun 27 20:00:55 2005 UTC revision 1.41, Tue Oct 18 02:24:23 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 $retVal;
447  }  }
# Line 570  Line 583 
583  =item RETURN  =item RETURN
584    
585  Returns a list of the feature's contig segments. The locations are returned as a list in a list  Returns a list of the feature's contig segments. The locations are returned as a list in a list
586  context and as a space-delimited string in a scalar context.  context and as a comma-delimited string in a scalar context.
587    
588  =back  =back
589    
# Line 597  Line 610 
610          if ($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 ($dir eq "_") {
# Line 752  Line 772 
772          # the start point is the ending. Note that in the latter case we must reverse the DNA string          # the start point is the ending. Note that in the latter case we must reverse the DNA string
773          # before putting it in the return value.          # before putting it in the return value.
774          my ($start, $stop);          my ($start, $stop);
775            Trace("Parse of \"$location\" is $beg$dir$len.") if T(SDNA => 4);
776          if ($dir eq "+") {          if ($dir eq "+") {
777              $start = $beg;              $start = $beg;
778              $stop = $beg + $len - 1;              $stop = $beg + $len - 1;
779          } else {          } else {
780              $start = $beg + $len + 1;              $start = $beg - $len + 1;
781              $stop = $beg;              $stop = $beg;
782          }          }
783            Trace("Looking for sequences containing $start through $stop.") if T(SDNA => 4);
784          my $query = $self->Get(['IsMadeUpOf','Sequence'],          my $query = $self->Get(['IsMadeUpOf','Sequence'],
785              "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .              "IsMadeUpOf(from-link) = ? AND IsMadeUpOf(start-position) + IsMadeUpOf(len) > ? AND " .
786              " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",              " IsMadeUpOf(start-position) <= ? ORDER BY IsMadeUpOf(start-position)",
# Line 770  Line 792 
792                  $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)',                  $sequence->Values(['IsMadeUpOf(start-position)', 'Sequence(sequence)',
793                                     'IsMadeUpOf(len)']);                                     'IsMadeUpOf(len)']);
794              my $stopPosition = $startPosition + $sequenceLength;              my $stopPosition = $startPosition + $sequenceLength;
795                Trace("Sequence is from $startPosition to $stopPosition.") if T(SDNA => 4);
796              # Figure out the start point and length of the relevant section.              # Figure out the start point and length of the relevant section.
797              my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);              my $pos1 = ($start < $startPosition ? 0 : $start - $startPosition);
798              my $len = ($stopPosition <= $stop ? $stopPosition : $stop) - $startPosition - $pos1;              my $len1 = ($stopPosition < $stop ? $stopPosition : $stop) + 1 - $startPosition - $pos1;
799                Trace("Position is $pos1 for length $len1.") if T(SDNA => 4);
800              # Add the relevant data to the location data.              # Add the relevant data to the location data.
801              $locationDNA .= substr($sequenceData, $pos1, $len);              $locationDNA .= substr($sequenceData, $pos1, $len1);
802          }          }
803          # Add this location's data to the return string. Note that we may need to reverse it.          # Add this location's data to the return string. Note that we may need to reverse it.
804          if ($dir eq '+') {          if ($dir eq '+') {
805              $retVal .= $locationDNA;              $retVal .= $locationDNA;
806          } else {          } else {
807              $locationDNA = join('', reverse split //, $locationDNA);              $retVal .= FIG::reverse_comp($locationDNA);
             $retVal .= $locationDNA;  
808          }          }
809      }      }
810      # Return the result.      # Return the result.
# Line 851  Line 874 
874      # Set it from the sequence data, if any.      # Set it from the sequence data, if any.
875      if ($sequence) {      if ($sequence) {
876          my ($start, $len) = $sequence->Values(['IsMadeUpOf(start-position)', 'IsMadeUpOf(len)']);          my ($start, $len) = $sequence->Values(['IsMadeUpOf(start-position)', 'IsMadeUpOf(len)']);
877          $retVal = $start + $len;          $retVal = $start + $len - 1;
878        }
879        # Return the result.
880        return $retVal;
881    }
882    
883    =head3 ClusterPEGs
884    
885    C<< my $clusteredList = $sprout->ClusterPEGs($sub, \@pegs); >>
886    
887    Cluster the PEGs in a list according to the cluster coding scheme of the specified
888    subsystem. In order for this to work properly, the subsystem object must have
889    been used recently to retrieve the PEGs using the B<get_pegs_from_cell> method.
890    This causes the cluster numbers to be pulled into the subsystem's color hash.
891    If a PEG is not found in the color hash, it will not appear in the output
892    sequence.
893    
894    =over 4
895    
896    =item sub
897    
898    Sprout subsystem object for the relevant subsystem, from the L</get_subsystem>
899    method.
900    
901    =item pegs
902    
903    Reference to the list of PEGs to be clustered.
904    
905    =item RETURN
906    
907    Returns a list of the PEGs, grouped into smaller lists by cluster number.
908    
909    =back
910    
911    =cut
912    #: Return Type $@@;
913    sub ClusterPEGs {
914        # Get the parameters.
915        my ($self, $sub, $pegs) = @_;
916        # Declare the return variable.
917        my $retVal = [];
918        # Loop through the PEGs, creating arrays for each cluster.
919        for my $pegID (@{$pegs}) {
920            my $clusterNumber = $sub->get_cluster_number($pegID);
921            # Only proceed if the PEG is in a cluster.
922            if ($clusterNumber >= 0) {
923                # Push this PEG onto the sub-list for the specified cluster number.
924                push @{$retVal->[$clusterNumber]}, $pegID;
925            }
926      }      }
927      # Return the result.      # Return the result.
928      return $retVal;      return $retVal;
# Line 1001  Line 1072 
1072    
1073  =head3 FeatureAnnotations  =head3 FeatureAnnotations
1074    
1075  C<< my @descriptors = $sprout->FeatureAnnotations($featureID); >>  C<< my @descriptors = $sprout->FeatureAnnotations($featureID, $rawFlag); >>
1076    
1077  Return the annotations of a feature.  Return the annotations of a feature.
1078    
# Line 1011  Line 1082 
1082    
1083  ID of the feature whose annotations are desired.  ID of the feature whose annotations are desired.
1084    
1085    =item rawFlag
1086    
1087    If TRUE, the annotation timestamps will be returned in raw form; otherwise, they
1088    will be returned in human-readable form.
1089    
1090  =item RETURN  =item RETURN
1091    
1092  Returns a list of annotation descriptors. Each descriptor is a hash with the following fields.  Returns a list of annotation descriptors. Each descriptor is a hash with the following fields.
1093    
1094  * B<featureID> ID of the relevant feature.  * B<featureID> ID of the relevant feature.
1095    
1096  * B<timeStamp> time the annotation was made, in user-friendly format.  * B<timeStamp> time the annotation was made.
1097    
1098  * B<user> ID of the user who made the annotation  * B<user> ID of the user who made the annotation
1099    
# Line 1029  Line 1105 
1105  #: Return Type @%;  #: Return Type @%;
1106  sub FeatureAnnotations {  sub FeatureAnnotations {
1107      # Get the parameters.      # Get the parameters.
1108      my ($self, $featureID) = @_;      my ($self, $featureID, $rawFlag) = @_;
1109      # 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.
1110      my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],      my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1111                             "IsTargetOfAnnotation(from-link) = ?", [$featureID]);                             "IsTargetOfAnnotation(from-link) = ?", [$featureID]);
# Line 1042  Line 1118 
1118              $annotation->Values(['IsTargetOfAnnotation(from-link)',              $annotation->Values(['IsTargetOfAnnotation(from-link)',
1119                                   'Annotation(time)', 'MadeAnnotation(from-link)',                                   'Annotation(time)', 'MadeAnnotation(from-link)',
1120                                   'Annotation(annotation)']);                                   'Annotation(annotation)']);
1121            # Convert the time, if necessary.
1122            if (! $rawFlag) {
1123                $timeStamp = FriendlyTimestamp($timeStamp);
1124            }
1125          # Assemble them into a hash.          # Assemble them into a hash.
1126          my $annotationHash = { featureID => $featureID,          my $annotationHash = { featureID => $featureID,
1127                                 timeStamp => FriendlyTimestamp($timeStamp),                                 timeStamp => $timeStamp,
1128                                 user => $user, text => $text };                                 user => $user, text => $text };
1129          # Add it to the return list.          # Add it to the return list.
1130          push @retVal, $annotationHash;          push @retVal, $annotationHash;
# Line 1248  Line 1328 
1328          my $query = $self->Get(['IsBidirectionalBestHitOf'],          my $query = $self->Get(['IsBidirectionalBestHitOf'],
1329                                 "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",                                 "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",
1330                                 [$featureID, $genomeID]);                                 [$featureID, $genomeID]);
1331          # Look for the best hit.          # Peel off the BBHs found.
1332          my $bbh = $query->Fetch;          my @found = ();
1333          if ($bbh) {          while (my $bbh = $query->Fetch) {
1334              my ($targetFeature) = $bbh->Value('IsBidirectionalBestHitOf(to-link)');              push @found, $bbh->Value('IsBidirectionalBestHitOf(to-link)');
             $retVal{$featureID} = $targetFeature;  
1335          }          }
1336            $retVal{$featureID} = \@found;
1337      }      }
1338      # Return the mapping.      # Return the mapping.
1339      return \%retVal;      return \%retVal;
# Line 1506  Line 1586 
1586      my ($self, $peg1, $peg2) = @_;      my ($self, $peg1, $peg2) = @_;
1587      # Declare the return variable.      # Declare the return variable.
1588      my @retVal = ();      my @retVal = ();
1589      # Our first task is to find out the nature of the coupling.      # Our first task is to find out the nature of the coupling: whether or not
1590        # it exists, its score, and whether the features are stored in the same
1591        # order as the ones coming in.
1592      my ($couplingID, $inverted, $score) = $self->GetCoupling($peg1, $peg2);      my ($couplingID, $inverted, $score) = $self->GetCoupling($peg1, $peg2);
1593      # Only proceed if a coupling exists.      # Only proceed if a coupling exists.
1594      if ($couplingID) {      if ($couplingID) {
1595          # Determine the ordering to place on the evidence items. If we're          # Determine the ordering to place on the evidence items. If we're
1596          # inverted, we want to see feature 2 before feature 1; otherwise,          # inverted, we want to see feature 2 before feature 1 (descending); otherwise,
1597          # we want the reverse.          # we want feature 1 before feature 2 (normal).
1598            Trace("Coupling evidence for ($peg1, $peg2) with inversion flag $inverted.") if T(Coupling => 4);
1599          my $ordering = ($inverted ? "DESC" : "");          my $ordering = ($inverted ? "DESC" : "");
1600          # Get the coupling evidence.          # Get the coupling evidence.
1601          my @evidenceList = $self->GetAll(['IsEvidencedBy', 'PCH', 'UsesAsEvidence'],          my @evidenceList = $self->GetAll(['IsEvidencedBy', 'PCH', 'UsesAsEvidence'],
# Line 1526  Line 1609 
1609          while (@evidenceList > 0) {          while (@evidenceList > 0) {
1610              my $peg1Data = shift @evidenceList;              my $peg1Data = shift @evidenceList;
1611              my $peg2Data = shift @evidenceList;              my $peg2Data = shift @evidenceList;
1612                Trace("Peg 1 is " . $peg1Data->[1] . " and Peg 2 is " . $peg2Data->[1] . ".") if T(Coupling => 4);
1613              push @retVal, [$peg1Data->[1], $peg2Data->[1], $peg1Data->[0]];              push @retVal, [$peg1Data->[1], $peg2Data->[1], $peg1Data->[0]];
1614          }          }
1615            Trace("Last index in evidence result is is $#retVal.") if T(Coupling => 4);
1616      }      }
     # TODO: code  
1617      # Return the result.      # Return the result.
1618      return @retVal;      return @retVal;
1619  }  }
# Line 1578  Line 1662 
1662                                   [$retVal], ["ParticipatesInCoupling(from-link)", "Coupling(score)"]);                                   [$retVal], ["ParticipatesInCoupling(from-link)", "Coupling(score)"]);
1663      # Check to see if we found anything.      # Check to see if we found anything.
1664      if (!@pegs) {      if (!@pegs) {
1665            Trace("No coupling found.") if T(Coupling => 4);
1666          # No coupling, so undefine the return value.          # No coupling, so undefine the return value.
1667          $retVal = undef;          $retVal = undef;
1668      } else {      } else {
1669          # We have a coupling! Get the score and check for inversion.          # We have a coupling! Get the score and check for inversion.
1670          $score = $pegs[0]->[1];          $score = $pegs[0]->[1];
1671          $inverted = ($pegs[0]->[0] eq $peg1);          my $firstFound = $pegs[0]->[0];
1672            $inverted = ($firstFound ne $peg1);
1673            Trace("Coupling score is $score. First peg is $firstFound, peg 1 is $peg1.") if T(Coupling => 4);
1674      }      }
1675      # Return the result.      # Return the result.
1676      return ($retVal, $inverted, $score);      return ($retVal, $inverted, $score);
# Line 1688  Line 1775 
1775          if ($line =~ m/^>\s*(.+?)(\s|\n)/) {          if ($line =~ m/^>\s*(.+?)(\s|\n)/) {
1776              # Here we have a new header. Store the current sequence if we have one.              # Here we have a new header. Store the current sequence if we have one.
1777              if ($id) {              if ($id) {
1778                  $retVal{$id} = uc $sequence;                  $retVal{$id} = lc $sequence;
1779              }              }
1780              # Clear the sequence accumulator and save the new ID.              # Clear the sequence accumulator and save the new ID.
1781              ($id, $sequence) = ("$prefix$1", "");              ($id, $sequence) = ("$prefix$1", "");
1782          } else {          } else {
1783              # 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.
1784              # 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
1785              # case.              # case.
1786              $line =~ /^\s*(.*?)(\s|\n)/;              $line =~ /^\s*(.*?)(\s|\n)/;
1787              $sequence .= $1;              $sequence .= $1;
# Line 1702  Line 1789 
1789      }      }
1790      # Flush out the last sequence (if any).      # Flush out the last sequence (if any).
1791      if ($sequence) {      if ($sequence) {
1792          $retVal{$id} = uc $sequence;          $retVal{$id} = lc $sequence;
1793      }      }
1794      # Close the file.      # Close the file.
1795      close FASTAFILE;      close FASTAFILE;
# Line 2028  Line 2115 
2115      # Get the parameters.      # Get the parameters.
2116      my ($self, $entityName, $entityID) = @_;      my ($self, $entityName, $entityID) = @_;
2117      # Check for the entity instance.      # Check for the entity instance.
2118        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
2119      my $testInstance = $self->GetEntity($entityName, $entityID);      my $testInstance = $self->GetEntity($entityName, $entityID);
2120      # Return an existence indicator.      # Return an existence indicator.
2121      my $retVal = ($testInstance ? 1 : 0);      my $retVal = ($testInstance ? 1 : 0);
# Line 2219  Line 2307 
2307      return @retVal;      return @retVal;
2308  }  }
2309    
2310    =head3 GetProperties
2311    
2312    C<< my @list = $sprout->GetProperties($fid, $key, $value, $url); >>
2313    
2314    Return a list of the properties with the specified characteristics.
2315    
2316    Properties are arbitrary key-value pairs associated with a feature. (At some point they
2317    will also be associated with genomes.) A property value is represented by a 4-tuple of
2318    the form B<($fid, $key, $value, $url)>. These exactly correspond to the parameter
2319    
2320    =over 4
2321    
2322    =item fid
2323    
2324    ID of the feature possessing the property.
2325    
2326    =item key
2327    
2328    Name or key of the property.
2329    
2330    =item value
2331    
2332    Value of the property.
2333    
2334    =item url
2335    
2336    URL of the document that indicated the property should have this particular value, or an
2337    empty string if no such document exists.
2338    
2339    =back
2340    
2341    The parameters act as a filter for the desired data. Any non-null parameter will
2342    automatically match all the tuples returned. So, specifying just the I<$fid> will
2343    return all the properties of the specified feature; similarly, specifying the I<$key>
2344    and I<$value> parameters will return all the features having the specified property
2345    value.
2346    
2347    A single property key can have many values, representing different ideas about the
2348    feature in question. For example, one paper may declare that a feature C<fig|83333.1.peg.10> is
2349    virulent, and another may declare that it is not virulent. A query about the virulence of
2350    C<fig|83333.1.peg.10> would be coded as
2351    
2352        my @list = $sprout->GetProperties('fig|83333.1.peg.10', 'virulence', '', '');
2353    
2354    Here the I<$value> and I<$url> fields are left blank, indicating that those fields are
2355    not to be filtered. The tuples returned would be
2356    
2357        ('fig|83333.1.peg.10', 'virulence', 'yes', 'http://www.somewhere.edu/first.paper.pdf')
2358        ('fig|83333.1.peg.10', 'virulence', 'no', 'http://www.somewhere.edu/second.paper.pdf')
2359    
2360    =cut
2361    #: Return Type @@;
2362    sub GetProperties {
2363        # Get the parameters.
2364        my ($self, @parms) = @_;
2365        # Declare the return variable.
2366        my @retVal = ();
2367        # Now we need to create a WHERE clause that will get us the data we want. First,
2368        # we create a list of the columns containing the data for each parameter.
2369        my @colNames = ('HasProperty(from-link)', 'Property(property-name)',
2370                        'Property(property-value)', 'HasProperty(evidence)');
2371        # Now we build the WHERE clause and the list of parameter values.
2372        my @where = ();
2373        my @values = ();
2374        for (my $i = 0; $i <= $#colNames; $i++) {
2375            my $parm = $parms[$i];
2376            if (defined $parm && ($parm ne '')) {
2377                push @where, "$colNames[$i] = ?";
2378                push @values, $parm;
2379            }
2380        }
2381        # Format the WHERE clause.
2382        my $filter = (@values > 0 ? (join " AND ", @where) : undef);
2383        # Ask for all the propertie values with the desired characteristics.
2384        my $query = $self->Get(['HasProperty', 'Property'], $filter, \@values);
2385        while (my $valueObject = $query->Fetch()) {
2386            my @tuple = $valueObject->Values(\@colNames);
2387            push @retVal, \@tuple;
2388        }
2389        # Return the result.
2390        return @retVal;
2391    }
2392    
2393  =head3 FeatureProperties  =head3 FeatureProperties
2394    
2395  C<< my @properties = $sprout->FeatureProperties($featureID); >>  C<< my @properties = $sprout->FeatureProperties($featureID); >>
# Line 2413  Line 2584 
2584  C<< my %subsystems = $sprout->SubsystemsOf($featureID); >>  C<< my %subsystems = $sprout->SubsystemsOf($featureID); >>
2585    
2586  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
2587  to the role the feature performs.  to the roles the feature performs.
2588    
2589  =over 4  =over 4
2590    
# Line 2423  Line 2594 
2594    
2595  =item RETURN  =item RETURN
2596    
2597  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.
2598    
2599  =back  =back
2600    
2601  =cut  =cut
2602  #: Return Type %;  #: Return Type %@;
2603  sub SubsystemsOf {  sub SubsystemsOf {
2604      # Get the parameters.      # Get the parameters.
2605      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
# Line 2440  Line 2611 
2611      my %retVal = ();      my %retVal = ();
2612      # Loop through the results, adding them to the hash.      # Loop through the results, adding them to the hash.
2613      for my $record (@subsystems) {      for my $record (@subsystems) {
2614          $retVal{$record->[0]} = $record->[1];          my ($subsys, $role) = @{$record};
2615            if (exists $retVal{$subsys}) {
2616                push @{$retVal{$subsys}}, $role;
2617            } else {
2618                $retVal{$subsys} = [$role];
2619            }
2620      }      }
2621      # Return the hash.      # Return the hash.
2622      return %retVal;      return %retVal;
# Line 2896  Line 3072 
3072      return %retVal;      return %retVal;
3073  }  }
3074    
3075    =head3 MyGenomes
3076    
3077    C<< my @genomes = Sprout::MyGenomes($dataDir); >>
3078    
3079    Return a list of the genomes to be included in the Sprout.
3080    
3081    This method is provided for use during the Sprout load. It presumes the Genome load file has
3082    already been created. (It will be in the Sprout data directory and called either C<Genome>
3083    or C<Genome.dtx>.) Essentially, it reads in the Genome load file and strips out the genome
3084    IDs.
3085    
3086    =over 4
3087    
3088    =item dataDir
3089    
3090    Directory containing the Sprout load files.
3091    
3092    =back
3093    
3094    =cut
3095    #: Return Type @;
3096    sub MyGenomes {
3097        # Get the parameters.
3098        my ($dataDir) = @_;
3099        # Compute the genome file name.
3100        my $genomeFileName = LoadFileName($dataDir, "Genome");
3101        # Extract the genome IDs from the files.
3102        my @retVal = map { $_ =~ /^(\S+)/; $1 } Tracer::GetFile($genomeFileName);
3103        # Return the result.
3104        return @retVal;
3105    }
3106    
3107    =head3 LoadFileName
3108    
3109    C<< my $fileName = Sprout::LoadFileName($dataDir, $tableName); >>
3110    
3111    Return the name of the load file for the specified table in the specified data
3112    directory.
3113    
3114    =over 4
3115    
3116    =item dataDir
3117    
3118    Directory containing the Sprout load files.
3119    
3120    =item tableName
3121    
3122    Name of the table whose load file is desired.
3123    
3124    =item RETURN
3125    
3126    Returns the name of the file containing the load data for the specified table, or
3127    C<undef> if no load file is present.
3128    
3129    =back
3130    
3131    =cut
3132    #: Return Type $;
3133    sub LoadFileName {
3134        # Get the parameters.
3135        my ($dataDir, $tableName) = @_;
3136        # Declare the return variable.
3137        my $retVal;
3138        # Check for the various file names.
3139        if (-e "$dataDir/$tableName") {
3140            $retVal = "$dataDir/$tableName";
3141        } elsif (-e "$dataDir/$tableName.dtx") {
3142            $retVal = "$dataDir/$tableName.dtx";
3143        }
3144        # Return the result.
3145        return $retVal;
3146    }
3147    
3148  =head2 Internal Utility Methods  =head2 Internal Utility Methods
3149    
3150  =head3 ParseAssignment  =head3 ParseAssignment
# Line 2967  Line 3216 
3216    
3217  sub FriendlyTimestamp {  sub FriendlyTimestamp {
3218      my ($timeValue) = @_;      my ($timeValue) = @_;
3219      my $retVal = strftime("%a %b %e %H:%M:%S %Y", localtime($timeValue));      my $retVal = localtime($timeValue);
3220      return $retVal;      return $retVal;
3221  }  }
3222    
# Line 3028  Line 3277 
3277      $self->Insert('HasProperty', { 'from-link' => $featureID, 'to-link' => $propID, evidence => $url });      $self->Insert('HasProperty', { 'from-link' => $featureID, 'to-link' => $propID, evidence => $url });
3278  }  }
3279    
3280    
3281    
3282  1;  1;

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