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revision 1.39, Wed Sep 14 14:04:13 2005 UTC revision 1.48, Thu Oct 20 12:33:00 2005 UTC
# Line 389  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 610  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 += $prevLen;
624                  # Pop the old segment off. The new one will replace it later.                  # Pop the old segment off. The new one will replace it later.
# Line 659  Line 664 
664      shift if UNIVERSAL::isa($_[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 ($dir eq "_") {
# Line 869  Line 874 
874      # Set it from the sequence data, if any.      # Set it from the sequence data, if any.
875      if ($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 1019  Line 1072 
1072    
1073  =head3 FeatureAnnotations  =head3 FeatureAnnotations
1074    
1075  C<< my @descriptors = $sprout->FeatureAnnotations($featureID); >>  C<< my @descriptors = $sprout->FeatureAnnotations($featureID, $rawFlag); >>
1076    
1077  Return the annotations of a feature.  Return the annotations of a feature.
1078    
# Line 1029  Line 1082 
1082    
1083  ID of the feature whose annotations are desired.  ID of the feature whose annotations are desired.
1084    
1085    =item rawFlag
1086    
1087    If TRUE, the annotation timestamps will be returned in raw form; otherwise, they
1088    will be returned in human-readable form.
1089    
1090  =item RETURN  =item RETURN
1091    
1092  Returns a list of annotation descriptors. Each descriptor is a hash with the following fields.  Returns a list of annotation descriptors. Each descriptor is a hash with the following fields.
1093    
1094  * B<featureID> ID of the relevant feature.  * B<featureID> ID of the relevant feature.
1095    
1096  * B<timeStamp> time the annotation was made, in user-friendly format.  * B<timeStamp> time the annotation was made.
1097    
1098  * B<user> ID of the user who made the annotation  * B<user> ID of the user who made the annotation
1099    
# Line 1047  Line 1105 
1105  #: Return Type @%;  #: Return Type @%;
1106  sub FeatureAnnotations {  sub FeatureAnnotations {
1107      # Get the parameters.      # Get the parameters.
1108      my ($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 1060  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, $annotationHash;
# Line 1091  Line 1153 
1153    
1154  =item RETURN  =item RETURN
1155    
1156  Returns a hash mapping the functional assignment IDs to user IDs.  Returns a hash mapping the user IDs to functional assignment IDs.
1157    
1158  =back  =back
1159    
# Line 1101  Line 1163 
1163      # Get the parameters.      # Get the parameters.
1164      my ($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 1138  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 1200  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) {              if ($actualUser) {
1274                  # Here it is a functional assignment. Check the time and the user                  # Here it is a functional assignment. Check the time and the user
1275                  # name. The time must be recent and the user must be trusted.                  # name. The time must be recent and the user must be trusted.
1276                  if ((exists $trusteeTable{$user}) && ($time > $timeSelected)) {                  if ((exists $trusteeTable{$user}) && ($time > $timeSelected)) {
# Line 1229  Line 1289 
1289      return $retVal;      return $retVal;
1290  }  }
1291    
1292    =head3 FunctionsOf
1293    
1294    C<< my @functionList = $sprout->FunctionOf($featureID, $userID); >>
1295    
1296    Return the functional assignments of a particular feature.
1297    
1298    The functional assignment is handled differently depending on the type of feature. If
1299    the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional
1300    assignment is a type of annotation. The format of an assignment is described in
1301    L</ParseAssignment>. Its worth noting that we cannot filter on the content of the
1302    annotation itself because it's a text field; however, this is not a big problem because
1303    most features only have a small number of annotations.
1304    
1305    If the feature is B<not> identified by a FIG ID, then the functional assignment
1306    information is taken from the B<ExternalAliasFunc> table. If the table does
1307    not contain an entry for the feature, an empty list is returned.
1308    
1309    =over 4
1310    
1311    =item featureID
1312    
1313    ID of the feature whose functional assignments are desired.
1314    
1315    =item RETURN
1316    
1317    Returns a list of 2-tuples, each consisting of a user ID and the text of an assignment by
1318    that user.
1319    
1320    =back
1321    
1322    =cut
1323    #: Return Type @@;
1324    sub FunctionsOf {
1325        # Get the parameters.
1326        my ($self, $featureID) = @_;
1327        # Declare the return value.
1328        my @retVal = ();
1329        # Determine the ID type.
1330        if ($featureID =~ m/^fig\|/) {
1331            # Here we have a FIG feature ID. We must build the list of trusted
1332            # users.
1333            my %trusteeTable = ();
1334            # Build a query for all of the feature's annotations, sorted by date.
1335            my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation', 'MadeAnnotation'],
1336                                   "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1337                                   [$featureID]);
1338            my $timeSelected = 0;
1339            # Loop until we run out of annotations.
1340            while (my $annotation = $query->Fetch()) {
1341                # Get the annotation text.
1342                my ($text, $time, $user) = $annotation->Values(['Annotation(annotation)',
1343                                                                'Annotation(time)',
1344                                                                'MadeAnnotation(user)']);
1345                # Check to see if this is a functional assignment for a trusted user.
1346                my ($actualUser, $function) = _ParseAssignment($user, $text);
1347                if ($actualUser) {
1348                    # Here it is a functional assignment.
1349                    push @retVal, [$actualUser, $function];
1350                }
1351            }
1352        } else {
1353            # Here we have a non-FIG feature ID. In this case the user ID does not
1354            # matter. We simply get the information from the External Alias Function
1355            # table.
1356            my @assignments = $self->GetEntityValues('ExternalAliasFunc', $featureID,
1357                                                     ['ExternalAliasFunc(func)']);
1358            push @retVal, map { ['master', $_] } @assignments;
1359        }
1360        # Return the assignments found.
1361        return @retVal;
1362    }
1363    
1364  =head3 BBHList  =head3 BBHList
1365    
1366  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>
# Line 1266  Line 1398 
1398          my $query = $self->Get(['IsBidirectionalBestHitOf'],          my $query = $self->Get(['IsBidirectionalBestHitOf'],
1399                                 "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",                                 "IsBidirectionalBestHitOf(from-link) = ? AND IsBidirectionalBestHitOf(genome) = ?",
1400                                 [$featureID, $genomeID]);                                 [$featureID, $genomeID]);
1401          # Look for the best hit.          # Peel off the BBHs found.
1402          my $bbh = $query->Fetch;          my @found = ();
1403          if ($bbh) {          while (my $bbh = $query->Fetch) {
1404              my ($targetFeature) = $bbh->Value('IsBidirectionalBestHitOf(to-link)');              push @found, $bbh->Value('IsBidirectionalBestHitOf(to-link)');
             $retVal{$featureID} = $targetFeature;  
1405          }          }
1406            $retVal{$featureID} = \@found;
1407      }      }
1408      # Return the mapping.      # Return the mapping.
1409      return \%retVal;      return \%retVal;
# Line 2547  Line 2679 
2679                                      ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);                                      ['HasSSCell(from-link)', 'IsRoleOf(from-link)']);
2680      # Create the return value.      # Create the return value.
2681      my %retVal = ();      my %retVal = ();
2682        # Build a hash to weed out duplicates. Sometimes the same PEG and role appears
2683        # in two spreadsheet cells.
2684        my %dupHash = ();
2685      # Loop through the results, adding them to the hash.      # Loop through the results, adding them to the hash.
2686      for my $record (@subsystems) {      for my $record (@subsystems) {
2687            # Get this subsystem and role.
2688          my ($subsys, $role) = @{$record};          my ($subsys, $role) = @{$record};
2689          if (exists $retVal{$subsys}) {          # Insure it's the first time for both.
2690            my $dupKey = "$subsys\n$role";
2691            if (! exists $dupHash{"$subsys\n$role"}) {
2692                $dupHash{$dupKey} = 1;
2693              push @{$retVal{$subsys}}, $role;              push @{$retVal{$subsys}}, $role;
         } else {  
             $retVal{$subsys} = [$role];  
2694          }          }
2695      }      }
2696      # Return the hash.      # Return the hash.
# Line 3093  Line 3230 
3230    
3231  A functional assignment is always of the form  A functional assignment is always of the form
3232    
3233      I<XXXX>C<\nset >I<YYYY>C< function to\n>I<ZZZZZ>      C<set >I<YYYY>C< function to\n>I<ZZZZZ>
3234    
3235  where I<XXXX> is the B<assigning user>, I<YYYY> is the B<user>, and I<ZZZZ> is the  where I<YYYY> is the B<user>, and I<ZZZZ> is the actual functional role. In most cases,
3236  actual functional role. In most cases, the user and the assigning user will be the  the user and the assigning user (from MadeAnnotation) will be the same, but that is
3237  same, but that is not always the case.  not always the case.
3238    
3239  This is a static method.  This is a static method.
3240    
3241  =over 4  =over 4
3242    
3243    =item user
3244    
3245    Name of the assigning user.
3246    
3247  =item text  =item text
3248    
3249  Text of the annotation.  Text of the annotation.
# Line 3118  Line 3259 
3259    
3260  sub _ParseAssignment {  sub _ParseAssignment {
3261      # Get the parameters.      # Get the parameters.
3262      my ($text) = @_;      my ($user, $text) = @_;
3263      # Declare the return value.      # Declare the return value.
3264      my @retVal = ();      my @retVal = ();
3265      # Check to see if this is a functional assignment.      # Check to see if this is a functional assignment.
3266      my ($user, $type, $function) = split(/\n/, $text);      my ($type, $function) = split(/\n/, $text);
3267      if ($type =~ m/^set ([^ ]+) function to$/i) {      if ($type =~ m/^set function to$/i) {
3268          # Here it is, so we return the user name (which is in $1), the functional role text,          # Here we have an assignment without a user, so we use the incoming user ID.
3269          # and the assigning user.          @retVal = ($user, $function);
3270          @retVal = ($1, $function, $user);      } elsif ($type =~ m/^set (\S+) function to$/i) {
3271            # Here we have an assignment with a user, that is passed back to the caller.
3272            @retVal = ($1, $function);
3273      }      }
3274      # Return the result list.      # Return the result list.
3275      return @retVal;      return @retVal;
# Line 3154  Line 3297 
3297    
3298  sub FriendlyTimestamp {  sub FriendlyTimestamp {
3299      my ($timeValue) = @_;      my ($timeValue) = @_;
3300      my $retVal = strftime("%a %b %e %H:%M:%S %Y", localtime($timeValue));      my $retVal = localtime($timeValue);
3301      return $retVal;      return $retVal;
3302  }  }
3303    
# Line 3215  Line 3358 
3358      $self->Insert('HasProperty', { 'from-link' => $featureID, 'to-link' => $propID, evidence => $url });      $self->Insert('HasProperty', { 'from-link' => $featureID, 'to-link' => $propID, evidence => $url });
3359  }  }
3360    
   
   
3361  1;  1;

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