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revision 1.4, Wed Nov 15 12:14:40 2006 UTC revision 1.8, Tue Apr 10 06:11:43 2007 UTC
# Line 95  Line 95 
95                                                 -value => 'Advanced',                                                 -value => 'Advanced',
96                                                 -class => 'button')),                                                 -class => 'button')),
97                          );                          );
98      # The other row is for the submit button.      # The second row is for special options.
99        push @rows, FeatureQuery::SpecialOptions($self);
100        # The last row is for the submit button.
101      push @rows, $self->SubmitRow();      push @rows, $self->SubmitRow();
102      # Finally, if groups are specified, we include them as hidden fields and display      # Finally, if groups are specified, we include them as hidden fields and display
103      # an explanation.      # an explanation.
# Line 154  Line 156 
156          if (@groups) {          if (@groups) {
157              # Here we do the search a group at a time.              # Here we do the search a group at a time.
158              for my $group (@groups) {              for my $group (@groups) {
159                    Trace("Starting the search.") if T(3);
160                    $self->PrintLine("Submitting search query for $group.<br />");
161                  my $query = $sprout->Search($keywords, 0, ['Feature', 'HasFeature', 'Genome'],                  my $query = $sprout->Search($keywords, 0, ['Feature', 'HasFeature', 'Genome'],
162                                              "Genome(primary-group) = ?", [$group]);                                              "Genome(primary-group) = ?", [$group]);
163                    Trace("Processing results.") if T(3);
164                  $retVal += $self->ProcessQuery($query);                  $retVal += $self->ProcessQuery($query);
165                    Trace("Results processed.") if T(3);
166              }              }
167          } else {          } else {
168              # Here we do one search just for features.              # Here we do one search just for features.
169                Trace("Starting the search.") if T(3);
170                $self->PrintLine("Submitting search query for all genomes.<br />");
171              my $query = $sprout->Search($keywords, 0, ['Feature']);              my $query = $sprout->Search($keywords, 0, ['Feature']);
172                Trace("Processing results.") if T(3);
173              $retVal += $self->ProcessQuery($query);              $retVal += $self->ProcessQuery($query);
174                Trace("Results processed.") if T(3);
175          }          }
176          # Close the session file.          # Close the session file.
177          $self->CloseSession();          $self->CloseSession();
178            Trace("Session closed.") if T(3);
179      }      }
180      # Return the result count.      # Return the result count.
181      return $retVal;      return $retVal;
# Line 184  Line 195 
195      # Get the parameters.      # Get the parameters.
196      my ($self) = @_;      my ($self) = @_;
197      # Return the result.      # Return the result.
198      return "Search for features based on keywords.";      return "Search for genes based on keywords.";
199  }  }
200    
201  =head3 ProcessQuery  =head3 ProcessQuery
# Line 211  Line 222 
222  sub ProcessQuery {  sub ProcessQuery {
223      # Get the parameters.      # Get the parameters.
224      my ($self, $query) = @_;      my ($self, $query) = @_;
225        my $cgi = $self->Q();
226      # Clear the result counter.      # Clear the result counter.
227      my $retVal = 0;      my $retVal = 0;
228        $self->PrintLine("Processing query results.<br />");
229      # Create a feature data object for storing each result.      # Create a feature data object for storing each result.
230      my $fd = FeatureData->new($self);      my $fd = FeatureData->new($self);
231      Trace("Starting feature loop.") if T(3);      Trace("Starting feature loop.") if T(3);
# Line 224  Line 237 
237          $self->PutFeature($fd);          $self->PutFeature($fd);
238          # Increment the result counter.          # Increment the result counter.
239          $retVal++;          $retVal++;
240            if ($retVal % 100 == 0) {
241                $self->PrintLine("$retVal results processed.<br />");
242            }
243      }      }
244        $self->PrintLine("Results found: $retVal.<br />");
245      # Return the counter.      # Return the counter.
246      return $retVal;      return $retVal;
247  }  }

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