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revision 1.19, Sun Aug 14 23:32:08 2005 UTC revision 1.54, Thu Feb 16 04:10:07 2006 UTC
# Line 70  Line 70 
70    
71  * B<maxSequenceLength> maximum number of residues per sequence, (default C<8000>)  * B<maxSequenceLength> maximum number of residues per sequence, (default C<8000>)
72    
73    * B<noDBOpen> suppresses the connection to the database if TRUE, else FALSE
74    
75  =back  =back
76    
77  For example, the following constructor call specifies a database named I<Sprout> and a user name of  For example, the following constructor call specifies a database named I<Sprout> and a user name of
# Line 90  Line 92 
92                                                          # database type                                                          # database type
93                         dataDir      => $FIG_Config::sproutData,                         dataDir      => $FIG_Config::sproutData,
94                                                          # data file directory                                                          # data file directory
95                         xmlFileName  => "$FIG_Config::sproutData/SproutDBD.xml",                         xmlFileName  => "$FIG_Config::fig/SproutDBD.xml",
96                                                          # database definition file name                                                          # database definition file name
97                         userData     => "$FIG_Config::dbuser/$FIG_Config::dbpass",                         userData     => "$FIG_Config::dbuser/$FIG_Config::dbpass",
98                                                          # user name and password                                                          # user name and password
# Line 98  Line 100 
100                                                          # database connection port                                                          # 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 105  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 382  Line 389 
389    
390  =head3 LoadUpdate  =head3 LoadUpdate
391    
392  C<< my %stats = $sprout->LoadUpdate($truncateFlag, \@tableList); >>  C<< my $stats = $sprout->LoadUpdate($truncateFlag, \@tableList); >>
393    
394  Load updates to one or more database tables. This method enables the client to make changes to one  Load updates to one or more database tables. This method enables the client to make changes to one
395  or two tables without reloading the whole database. For each table, there must be a corresponding  or two tables without reloading the whole database. For each table, there must be a corresponding
# Line 576  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 603  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 += $prevLen;
624                  # Pop the old segment off. The new one will replace it later.                  # Pop the old segment off. The new one will replace it later.
# Line 615  Line 627 
627          }          }
628          # Remember this specifier for the adjacent-segment test the next time through.          # Remember this specifier for the adjacent-segment test the next time through.
629          ($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$len";
634      }      }
635      # Return the list in the format indicated by the context.      # Return the list in the format indicated by the context.
636      return (wantarray ? @retVal : join(' ', @retVal));      return (wantarray ? @retVal : join(',', @retVal));
637  }  }
638    
639  =head3 ParseLocation  =head3 ParseLocation
# Line 650  Line 664 
664      shift if UNIVERSAL::isa($_[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 ($dir eq "_") {
# Line 758  Line 772 
772          # the start point is the ending. Note that in the latter case we must reverse the DNA string          # the start point is the ending. Note that in the latter case we must reverse the DNA string
773          # before putting it in the return value.          # before putting it in the return value.
774          my ($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 776  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 .= $locationDNA;  
808          }          }
809      }      }
810      # Return the result.      # Return the result.
# Line 857  Line 874 
874      # Set it from the sequence data, if any.      # Set it from the sequence data, if any.
875      if ($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 1007  Line 1072 
1072    
1073  =head3 FeatureAnnotations  =head3 FeatureAnnotations
1074    
1075  C<< my @descriptors = $sprout->FeatureAnnotations($featureID); >>  C<< my @descriptors = $sprout->FeatureAnnotations($featureID, $rawFlag); >>
1076    
1077  Return the annotations of a feature.  Return the annotations of a feature.
1078    
# Line 1017  Line 1082 
1082    
1083  ID of the feature whose annotations are desired.  ID of the feature whose annotations are desired.
1084    
1085    =item rawFlag
1086    
1087    If TRUE, the annotation timestamps will be returned in raw form; otherwise, they
1088    will be returned in human-readable form.
1089    
1090  =item RETURN  =item RETURN
1091    
1092  Returns a list of annotation descriptors. Each descriptor is a hash with the following fields.  Returns a list of annotation descriptors. Each descriptor is a hash with the following fields.
1093    
1094  * B<featureID> ID of the relevant feature.  * B<featureID> ID of the relevant feature.
1095    
1096  * B<timeStamp> time the annotation was made, in user-friendly format.  * B<timeStamp> time the annotation was made.
1097    
1098  * B<user> ID of the user who made the annotation  * B<user> ID of the user who made the annotation
1099    
# Line 1035  Line 1105 
1105  #: Return Type @%;  #: Return Type @%;
1106  sub FeatureAnnotations {  sub FeatureAnnotations {
1107      # Get the parameters.      # Get the parameters.
1108      my ($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 1048  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, $annotationHash;
# Line 1079  Line 1153 
1153    
1154  =item RETURN  =item RETURN
1155    
1156  Returns a hash mapping the functional assignment IDs to user IDs.  Returns a hash mapping the user IDs to functional assignment IDs.
1157    
1158  =back  =back
1159    
# Line 1089  Line 1163 
1163      # Get the parameters.      # Get the parameters.
1164      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
1165      # Get all of the feature's annotations.      # Get all of the feature's annotations.
1166      my @query = $self->GetAll(['IsTargetOfAnnotation', 'Annotation'],      my @query = $self->GetAll(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1167                              "IsTargetOfAnnotation(from-link) = ?",                              "IsTargetOfAnnotation(from-link) = ?",
1168                              [$featureID], ['Annotation(time)', 'Annotation(annotation)']);                              [$featureID], ['Annotation(time)', 'Annotation(annotation)',
1169                                               'MadeAnnotation(from-link)']);
1170      # Declare the return hash.      # Declare the return hash.
1171      my %retVal;      my %retVal;
     # Declare a hash for insuring we only make one assignment per user.  
     my %timeHash = ();  
1172      # Now we sort the assignments by timestamp in reverse.      # Now we sort the assignments by timestamp in reverse.
1173      my @sortedQuery = sort { -($a->[0] <=> $b->[0]) } @query;      my @sortedQuery = sort { -($a->[0] <=> $b->[0]) } @query;
1174      # Loop until we run out of annotations.      # Loop until we run out of annotations.
1175      for my $annotation (@sortedQuery) {      for my $annotation (@sortedQuery) {
1176          # Get the annotation fields.          # Get the annotation fields.
1177          my ($timeStamp, $text) = @{$annotation};          my ($timeStamp, $text, $user) = @{$annotation};
1178          # Check to see if this is a functional assignment.          # Check to see if this is a functional assignment.
1179          my ($user, $function) = _ParseAssignment($text);          my ($actualUser, $function) = _ParseAssignment($user, $text);
1180          if ($user && ! exists $timeHash{$user}) {          if ($actualUser && ! exists $retVal{$actualUser}) {
1181              # Here it is a functional assignment and there has been no              # Here it is a functional assignment and there has been no
1182              # previous assignment for this user, so we stuff it in the              # previous assignment for this user, so we stuff it in the
1183              # return hash.              # return hash.
1184              $retVal{$function} = $user;              $retVal{$actualUser} = $function;
             # Insure we don't assign to this user again.  
             $timeHash{$user} = 1;  
1185          }          }
1186      }      }
1187      # Return the hash of assignments found.      # Return the hash of assignments found.
# Line 1126  Line 1197 
1197  The functional assignment is handled differently depending on the type of feature. If  The functional assignment is handled differently depending on the type of feature. If
1198  the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional  the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional
1199  assignment is a type of annotation. The format of an assignment is described in  assignment is a type of annotation. The format of an assignment is described in
1200  L</ParseLocation>. Its worth noting that we cannot filter on the content of the  L</ParseAssignment>. Its worth noting that we cannot filter on the content of the
1201  annotation itself because it's a text field; however, this is not a big problem because  annotation itself because it's a text field; however, this is not a big problem because
1202  most features only have a small number of annotations.  most features only have a small number of annotations.
1203    
# Line 1188  Line 1259 
1259              }              }
1260          }          }
1261          # Build a query for all of the feature's annotations, sorted by date.          # Build a query for all of the feature's annotations, sorted by date.
1262          my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation'],          my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1263                                 "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",                                 "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1264                                 [$featureID]);                                 [$featureID]);
1265          my $timeSelected = 0;          my $timeSelected = 0;
1266          # Loop until we run out of annotations.          # Loop until we run out of annotations.
1267          while (my $annotation = $query->Fetch()) {          while (my $annotation = $query->Fetch()) {
1268              # Get the annotation text.              # Get the annotation text.
1269              my ($text, $time) = $annotation->Values(['Annotation(annotation)','Annotation(time)']);              my ($text, $time, $user) = $annotation->Values(['Annotation(annotation)',
1270                                                         'Annotation(time)', 'MadeAnnotation(from-link)']);
1271              # Check to see if this is a functional assignment for a trusted user.              # Check to see if this is a functional assignment for a trusted user.
1272              my ($user, $function) = _ParseAssignment($text);              my ($actualUser, $function) = _ParseAssignment($user, $text);
1273              if ($user) {              Trace("Assignment user is $actualUser, text is $function.") if T(4);
1274                if ($actualUser) {
1275                  # Here it is a functional assignment. Check the time and the user                  # Here it is a functional assignment. Check the time and the user
1276                  # name. The time must be recent and the user must be trusted.                  # name. The time must be recent and the user must be trusted.
1277                  if ((exists $trusteeTable{$user}) && ($time > $timeSelected)) {                  if ((exists $trusteeTable{$actualUser}) && ($time > $timeSelected)) {
1278                      $retVal = $function;                      $retVal = $function;
1279                      $timeSelected = $time;                      $timeSelected = $time;
1280                  }                  }
# Line 1217  Line 1290 
1290      return $retVal;      return $retVal;
1291  }  }
1292    
1293    =head3 FunctionsOf
1294    
1295    C<< my @functionList = $sprout->FunctionOf($featureID, $userID); >>
1296    
1297    Return the functional assignments of a particular feature.
1298    
1299    The functional assignment is handled differently depending on the type of feature. If
1300    the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional
1301    assignment is a type of annotation. The format of an assignment is described in
1302    L</ParseAssignment>. Its worth noting that we cannot filter on the content of the
1303    annotation itself because it's a text field; however, this is not a big problem because
1304    most features only have a small number of annotations.
1305    
1306    If the feature is B<not> identified by a FIG ID, then the functional assignment
1307    information is taken from the B<ExternalAliasFunc> table. If the table does
1308    not contain an entry for the feature, an empty list is returned.
1309    
1310    =over 4
1311    
1312    =item featureID
1313    
1314    ID of the feature whose functional assignments are desired.
1315    
1316    =item RETURN
1317    
1318    Returns a list of 2-tuples, each consisting of a user ID and the text of an assignment by
1319    that user.
1320    
1321    =back
1322    
1323    =cut
1324    #: Return Type @@;
1325    sub FunctionsOf {
1326        # Get the parameters.
1327        my ($self, $featureID) = @_;
1328        # Declare the return value.
1329        my @retVal = ();
1330        # Determine the ID type.
1331        if ($featureID =~ m/^fig\|/) {
1332            # Here we have a FIG feature ID. We must build the list of trusted
1333            # users.
1334            my %trusteeTable = ();
1335            # Build a query for all of the feature's annotations, sorted by date.
1336            my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1337                                   "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1338                                   [$featureID]);
1339            my $timeSelected = 0;
1340            # Loop until we run out of annotations.
1341            while (my $annotation = $query->Fetch()) {
1342                # Get the annotation text.
1343                my ($text, $time, $user) = $annotation->Values(['Annotation(annotation)',
1344                                                                'Annotation(time)',
1345                                                                'MadeAnnotation(user)']);
1346                # Check to see if this is a functional assignment for a trusted user.
1347                my ($actualUser, $function) = _ParseAssignment($user, $text);
1348                if ($actualUser) {
1349                    # Here it is a functional assignment.
1350                    push @retVal, [$actualUser, $function];
1351                }
1352            }
1353        } else {
1354            # Here we have a non-FIG feature ID. In this case the user ID does not
1355            # matter. We simply get the information from the External Alias Function
1356            # table.
1357            my @assignments = $self->GetEntityValues('ExternalAliasFunc', $featureID,
1358                                                     ['ExternalAliasFunc(func)']);
1359            push @retVal, map { ['master', $_] } @assignments;
1360        }
1361        # Return the assignments found.
1362        return @retVal;
1363    }
1364    
1365  =head3 BBHList  =head3 BBHList
1366    
1367  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>
# Line 1254  Line 1399 
1399          my $query = $self->Get(['IsBidirectionalBestHitOf'],          my $query = $self->Get(['IsBidirectionalBestHitOf'],
1400                                 "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",                                 "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",
1401                                 [$featureID, $genomeID]);                                 [$featureID, $genomeID]);
1402          # Look for the best hit.          # Peel off the BBHs found.
1403          my $bbh = $query->Fetch;          my @found = ();
1404          if ($bbh) {          while (my $bbh = $query->Fetch) {
1405              my ($targetFeature) = $bbh->Value('IsBidirectionalBestHitOf(to-link)');              push @found, $bbh->Value('IsBidirectionalBestHitOf(to-link)');
             $retVal{$featureID} = $targetFeature;  
1406          }          }
1407            $retVal{$featureID} = \@found;
1408      }      }
1409      # Return the mapping.      # Return the mapping.
1410      return \%retVal;      return \%retVal;
# Line 1337  Line 1482 
1482      my $genomeData = $self->GetEntity('Genome', $genomeID);      my $genomeData = $self->GetEntity('Genome', $genomeID);
1483      if ($genomeData) {      if ($genomeData) {
1484          # The genome exists, so get the completeness flag.          # The genome exists, so get the completeness flag.
1485          ($retVal) = $genomeData->Value('complete');          ($retVal) = $genomeData->Value('Genome(complete)');
1486      }      }
1487      # Return the result.      # Return the result.
1488      return $retVal;      return $retVal;
# Line 1521  Line 1666 
1666          # Determine the ordering to place on the evidence items. If we're          # Determine the ordering to place on the evidence items. If we're
1667          # inverted, we want to see feature 2 before feature 1 (descending); otherwise,          # inverted, we want to see feature 2 before feature 1 (descending); otherwise,
1668          # we want feature 1 before feature 2 (normal).          # we want feature 1 before feature 2 (normal).
1669            Trace("Coupling evidence for ($peg1, $peg2) with inversion flag $inverted.") if T(Coupling => 4);
1670          my $ordering = ($inverted ? "DESC" : "");          my $ordering = ($inverted ? "DESC" : "");
1671          # Get the coupling evidence.          # Get the coupling evidence.
1672          my @evidenceList = $self->GetAll(['IsEvidencedBy', 'PCH', 'UsesAsEvidence'],          my @evidenceList = $self->GetAll(['IsEvidencedBy', 'PCH', 'UsesAsEvidence'],
# Line 1534  Line 1680 
1680          while (@evidenceList > 0) {          while (@evidenceList > 0) {
1681              my $peg1Data = shift @evidenceList;              my $peg1Data = shift @evidenceList;
1682              my $peg2Data = shift @evidenceList;              my $peg2Data = shift @evidenceList;
1683                Trace("Peg 1 is " . $peg1Data->[1] . " and Peg 2 is " . $peg2Data->[1] . ".") if T(Coupling => 4);
1684              push @retVal, [$peg1Data->[1], $peg2Data->[1], $peg1Data->[0]];              push @retVal, [$peg1Data->[1], $peg2Data->[1], $peg1Data->[0]];
1685          }          }
1686            Trace("Last index in evidence result is is $#retVal.") if T(Coupling => 4);
1687      }      }
1688      # Return the result.      # Return the result.
1689      return @retVal;      return @retVal;
# Line 1585  Line 1733 
1733                                   [$retVal], ["ParticipatesInCoupling(from-link)", "Coupling(score)"]);                                   [$retVal], ["ParticipatesInCoupling(from-link)", "Coupling(score)"]);
1734      # Check to see if we found anything.      # Check to see if we found anything.
1735      if (!@pegs) {      if (!@pegs) {
1736            Trace("No coupling found.") if T(Coupling => 4);
1737          # No coupling, so undefine the return value.          # No coupling, so undefine the return value.
1738          $retVal = undef;          $retVal = undef;
1739      } else {      } else {
1740          # We have a coupling! Get the score and check for inversion.          # We have a coupling! Get the score and check for inversion.
1741          $score = $pegs[0]->[1];          $score = $pegs[0]->[1];
1742          $inverted = ($pegs[0]->[0] eq $peg1);          my $firstFound = $pegs[0]->[0];
1743            $inverted = ($firstFound ne $peg1);
1744            Trace("Coupling score is $score. First peg is $firstFound, peg 1 is $peg1.") if T(Coupling => 4);
1745      }      }
1746      # Return the result.      # Return the result.
1747      return ($retVal, $inverted, $score);      return ($retVal, $inverted, $score);
# Line 1695  Line 1846 
1846          if ($line =~ m/^>\s*(.+?)(\s|\n)/) {          if ($line =~ m/^>\s*(.+?)(\s|\n)/) {
1847              # Here we have a new header. Store the current sequence if we have one.              # Here we have a new header. Store the current sequence if we have one.
1848              if ($id) {              if ($id) {
1849                  $retVal{$id} = uc $sequence;                  $retVal{$id} = lc $sequence;
1850              }              }
1851              # Clear the sequence accumulator and save the new ID.              # Clear the sequence accumulator and save the new ID.
1852              ($id, $sequence) = ("$prefix$1", "");              ($id, $sequence) = ("$prefix$1", "");
1853          } else {          } else {
1854              # 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.
1855              # 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
1856              # case.              # case.
1857              $line =~ /^\s*(.*?)(\s|\n)/;              $line =~ /^\s*(.*?)(\s|\n)/;
1858              $sequence .= $1;              $sequence .= $1;
# Line 1709  Line 1860 
1860      }      }
1861      # Flush out the last sequence (if any).      # Flush out the last sequence (if any).
1862      if ($sequence) {      if ($sequence) {
1863          $retVal{$id} = uc $sequence;          $retVal{$id} = lc $sequence;
1864      }      }
1865      # Close the file.      # Close the file.
1866      close FASTAFILE;      close FASTAFILE;
# Line 2035  Line 2186 
2186      # Get the parameters.      # Get the parameters.
2187      my ($self, $entityName, $entityID) = @_;      my ($self, $entityName, $entityID) = @_;
2188      # Check for the entity instance.      # Check for the entity instance.
2189        Trace("Checking existence of $entityName with ID=$entityID.") if T(4);
2190      my $testInstance = $self->GetEntity($entityName, $entityID);      my $testInstance = $self->GetEntity($entityName, $entityID);
2191      # Return an existence indicator.      # Return an existence indicator.
2192      my $retVal = ($testInstance ? 1 : 0);      my $retVal = ($testInstance ? 1 : 0);
# Line 2503  Line 2655 
2655  C<< my %subsystems = $sprout->SubsystemsOf($featureID); >>  C<< my %subsystems = $sprout->SubsystemsOf($featureID); >>
2656    
2657  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
2658  to the role the feature performs.  to the roles the feature performs.
2659    
2660  =over 4  =over 4
2661    
# Line 2513  Line 2665 
2665    
2666  =item RETURN  =item RETURN
2667    
2668  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.
2669    
2670  =back  =back
2671    
2672  =cut  =cut
2673  #: Return Type %;  #: Return Type %@;
2674  sub SubsystemsOf {  sub SubsystemsOf {
2675      # Get the parameters.      # Get the parameters.
2676      my ($self, $featureID) = @_;      my ($self, $featureID) = @_;
# Line 2528  Line 2680 
2680                                      ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);                                      ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);
2681      # Create the return value.      # Create the return value.
2682      my %retVal = ();      my %retVal = ();
2683        # Build a hash to weed out duplicates. Sometimes the same PEG and role appears
2684        # in two spreadsheet cells.
2685        my %dupHash = ();
2686      # Loop through the results, adding them to the hash.      # Loop through the results, adding them to the hash.
2687      for my $record (@subsystems) {      for my $record (@subsystems) {
2688          $retVal{$record->[0]} = $record->[1];          # Get this subsystem and role.
2689            my ($subsys, $role) = @{$record};
2690            # Insure it's the first time for both.
2691            my $dupKey = "$subsys\n$role";
2692            if (! exists $dupHash{"$subsys\n$role"}) {
2693                $dupHash{$dupKey} = 1;
2694                push @{$retVal{$subsys}}, $role;
2695            }
2696      }      }
2697      # Return the hash.      # Return the hash.
2698      return %retVal;      return %retVal;
# Line 3059  Line 3221 
3221      return $retVal;      return $retVal;
3222  }  }
3223    
3224    =head3 DeleteGenome
3225    
3226    C<< my $stats = $sprout->DeleteGenome($genomeID, $testFlag); >>
3227    
3228    Delete a genome from the database.
3229    
3230    =over 4
3231    
3232    =item genomeID
3233    
3234    ID of the genome to delete
3235    
3236    =item testFlag
3237    
3238    If TRUE, then the DELETE statements will be traced, but no deletions will occur.
3239    
3240    =item RETURN
3241    
3242    Returns a statistics object describing the rows deleted.
3243    
3244    =back
3245    
3246    =cut
3247    #: Return Type $%;
3248    sub DeleteGenome {
3249        # Get the parameters.
3250        my ($self, $genomeID, $testFlag) = @_;
3251        # Perform the delete for the genome's features.
3252        my $retVal = $self->{_erdb}->Delete('Feature', "fig|$genomeID.%", $testFlag);
3253        # Perform the delete for the primary genome data.
3254        my $stats = $self->{_erdb}->Delete('Genome', $genomeID, $testFlag);
3255        $retVal->Accumulate($stats);
3256        # Return the result.
3257        return $retVal;
3258    }
3259    
3260  =head2 Internal Utility Methods  =head2 Internal Utility Methods
3261    
3262  =head3 ParseAssignment  =head3 ParseAssignment
# Line 3069  Line 3267 
3267    
3268  A functional assignment is always of the form  A functional assignment is always of the form
3269    
3270      I<XXXX>C<\nset >I<YYYY>C< function to\n>I<ZZZZZ>      C<set >I<YYYY>C< function to\n>I<ZZZZZ>
3271    
3272  where I<XXXX> is the B<assigning user>, I<YYYY> is the B<user>, and I<ZZZZ> is the  where I<YYYY> is the B<user>, and I<ZZZZ> is the actual functional role. In most cases,
3273  actual functional role. In most cases, the user and the assigning user will be the  the user and the assigning user (from MadeAnnotation) will be the same, but that is
3274  same, but that is not always the case.  not always the case.
3275    
3276    In addition, the functional role may contain extra data that is stripped, such as
3277    terminating spaces or a comment separated from the rest of the text by a tab.
3278    
3279  This is a static method.  This is a static method.
3280    
3281  =over 4  =over 4
3282    
3283    =item user
3284    
3285    Name of the assigning user.
3286    
3287  =item text  =item text
3288    
3289  Text of the annotation.  Text of the annotation.
# Line 3094  Line 3299 
3299    
3300  sub _ParseAssignment {  sub _ParseAssignment {
3301      # Get the parameters.      # Get the parameters.
3302      my ($text) = @_;      my ($user, $text) = @_;
3303      # Declare the return value.      # Declare the return value.
3304      my @retVal = ();      my @retVal = ();
3305      # Check to see if this is a functional assignment.      # Check to see if this is a functional assignment.
3306      my ($user, $type, $function) = split(/\n/, $text);      my ($type, $function) = split(/\n/, $text);
3307      if ($type =~ m/^set ([^ ]+) function to$/i) {      if ($type =~ m/^set function to$/i) {
3308          # Here it is, so we return the user name (which is in $1), the functional role text,          # Here we have an assignment without a user, so we use the incoming user ID.
3309          # and the assigning user.          @retVal = ($user, $function);
3310          @retVal = ($1, $function, $user);      } elsif ($type =~ m/^set (\S+) function to$/i) {
3311            # Here we have an assignment with a user that is passed back to the caller.
3312            @retVal = ($1, $function);
3313        }
3314        # If we have an assignment, we need to clean the function text. There may be
3315        # extra junk at the end added as a note from the user.
3316        if (@retVal) {
3317            $retVal[1] =~ s/(\t\S)?\s*$//;
3318      }      }
3319      # Return the result list.      # Return the result list.
3320      return @retVal;      return @retVal;
# Line 3130  Line 3342 
3342    
3343  sub FriendlyTimestamp {  sub FriendlyTimestamp {
3344      my ($timeValue) = @_;      my ($timeValue) = @_;
3345      my $retVal = strftime("%a %b %e %H:%M:%S %Y", localtime($timeValue));      my $retVal = localtime($timeValue);
3346      return $retVal;      return $retVal;
3347  }  }
3348    
# Line 3192  Line 3404 
3404  }  }
3405    
3406    
   
3407  1;  1;

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