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revision 1.44, Thu Oct 20 09:32:18 2005 UTC revision 1.47, Thu Oct 20 12:02:43 2005 UTC
# Line 1153  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 1163  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 ($type, $function) = _ParseAssignment($text);
1180          if ($user && ! exists $timeHash{$user}) {          if ($type && ! exists $retVal{$user}) {
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;              $retVal{$user} = $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 1200  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 1291  Line 1288 
1288      return $retVal;      return $retVal;
1289  }  }
1290    
1291    =head3 FunctionsOf
1292    
1293    C<< my @functionList = $sprout->FunctionOf($featureID, $userID); >>
1294    
1295    Return the functional assignments of a particular feature.
1296    
1297    The functional assignment is handled differently depending on the type of feature. If
1298    the feature is identified by a FIG ID (begins with the string C<fig|>), then a functional
1299    assignment is a type of annotation. The format of an assignment is described in
1300    L</ParseAssignment>. Its worth noting that we cannot filter on the content of the
1301    annotation itself because it's a text field; however, this is not a big problem because
1302    most features only have a small number of annotations.
1303    
1304    If the feature is B<not> identified by a FIG ID, then the functional assignment
1305    information is taken from the B<ExternalAliasFunc> table. If the table does
1306    not contain an entry for the feature, an empty list is returned.
1307    
1308    =over 4
1309    
1310    =item featureID
1311    
1312    ID of the feature whose functional assignments are desired.
1313    
1314    =item RETURN
1315    
1316    Returns a list of 2-tuples, each consisting of a user ID and the text of an assignment by
1317    that user.
1318    
1319    =back
1320    
1321    =cut
1322    #: Return Type @@;
1323    sub FunctionsOf {
1324        # Get the parameters.
1325        my ($self, $featureID) = @_;
1326        # Declare the return value.
1327        my @retVal = ();
1328        # Determine the ID type.
1329        if ($featureID =~ m/^fig\|/) {
1330            # Here we have a FIG feature ID. We must build the list of trusted
1331            # users.
1332            my %trusteeTable = ();
1333            # Build a query for all of the feature's annotations, sorted by date.
1334            my $query = $self->Get(['IsTargetOfAnnotation', 'Annotation'],
1335                                   "IsTargetOfAnnotation(from-link) = ? ORDER BY Annotation(time) DESC",
1336                                   [$featureID]);
1337            my $timeSelected = 0;
1338            # Loop until we run out of annotations.
1339            while (my $annotation = $query->Fetch()) {
1340                # Get the annotation text.
1341                my ($text, $time) = $annotation->Values(['Annotation(annotation)','Annotation(time)']);
1342                # Check to see if this is a functional assignment for a trusted user.
1343                my ($user, $function) = _ParseAssignment($text);
1344                if ($user) {
1345                    # Here it is a functional assignment.
1346                    push @retVal, [$user, $function];
1347                }
1348            }
1349        } else {
1350            # Here we have a non-FIG feature ID. In this case the user ID does not
1351            # matter. We simply get the information from the External Alias Function
1352            # table.
1353            push @retVal, $self->GetEntityValues('ExternalAliasFunc', $featureID, ['ExternalAliasFunc(func)']);
1354        }
1355        # Return the assignments found.
1356        return @retVal;
1357    }
1358    
1359  =head3 BBHList  =head3 BBHList
1360    
1361  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>  C<< my $bbhHash = $sprout->BBHList($genomeID, \@featureList); >>

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