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revision 1.6, Mon Jul 16 20:04:51 2007 UTC revision 1.9, Tue Apr 29 20:53:35 2008 UTC
# Line 36  Line 36 
36    
37  =head3 Form  =head3 Form
38    
39  C<< my $html = $shelp->Form(); >>      my $html = $shelp->Form();
40    
41  Generate the HTML for a form to request a new search.  Generate the HTML for a form to request a new search.
42    
# Line 49  Line 49 
49      my $cgi = $self->Q();      my $cgi = $self->Q();
50      my $sprout = $self->DB();      my $sprout = $self->DB();
51      # Start the form.      # Start the form.
52      my $retVal = $self->FormStart("Open Subsystem OR Search for Genes by Subsystem or Class");      my $retVal = $self->FormStart("Search for Genes by Subsystem or Class");
53      # Create a subsystem tree.      # Create a subsystem tree.
54      my $tree = SearchHelper::SubsystemTree($sprout, radio => 1, links => 1);      my $tree = SearchHelper::SubsystemTree($sprout, radio => 1, links => 1);
55      # Build a form field out of it.      # Build a form field out of it.
# Line 79  Line 79 
79    
80  =head3 Find  =head3 Find
81    
82  C<< my $resultCount = $shelp->Find(); >>      my $resultCount = $shelp->Find();
83    
84  Conduct a search based on the current CGI query parameters. The search results will  Conduct a search based on the current CGI query parameters. The search results will
85  be written to the session cache file and the number of results will be  be written to the session cache file and the number of results will be
# Line 101  Line 101 
101      if (! $spec) {      if (! $spec) {
102          $self->SetMessage("No subsystem or class selected.");          $self->SetMessage("No subsystem or class selected.");
103      } else {      } else {
104          # Create a feature data object to store our results.          # We need to build a query to get our features. This involves building
105          my $fd = FeatureData->new($self);          # a filter clause and a parameter list.
         # We need to build a query to get our features. We need to remember  
         # the filter clause format and the parameter.  
106          my ($filterClause, $parameter);          my ($filterClause, $parameter);
107          if ($spec =~ /^id=(.+)$/) {          if ($spec =~ /^id=(.+)$/) {
108              # Here we're filtering for a single subsystem.              # Here we're filtering for a single subsystem.
# Line 140  Line 138 
138              $self->DefaultColumns($rhelp);              $self->DefaultColumns($rhelp);
139              # Initialize the session file.              # Initialize the session file.
140              $self->OpenSession($rhelp);              $self->OpenSession($rhelp);
141              # Initialize the result counter.              # Clear the result counter.
142              $retVal = 0;              $retVal = 0;
143              # Loop through the selected features.              # Process the query results.
144              while (my $record = $query->Fetch()) {              while (my $record = $query->Fetch()) {
145                  $fd->Store($record);                  # Compute the sort key.
146                  $self->PutFeature($fd);                  my $sort = $rhelp->SortKey($record);
147                    # Store this feature.
148                    $rhelp->PutData($sort, $record->PrimaryValue('Feature(id)'), $record);
149                    # Increment the result counter.
150                  $retVal++;                  $retVal++;
                 if ($retVal % 100 == 0) {  
                     $self->PrintLine("$retVal features processed.<br />");  
                 }  
151              }              }
152              # Close the session file.              # Close the session file.
153              $self->CloseSession();              $self->CloseSession();
# Line 161  Line 159 
159    
160  =head3 Description  =head3 Description
161    
162  C<< my $htmlText = $shelp->Description(); >>      my $htmlText = $shelp->Description();
163    
164  Return a description of this search. The description is used for the table of contents  Return a description of this search. The description is used for the table of contents
165  on the main search tools page. It may contain HTML, but it should be character-level,  on the main search tools page. It may contain HTML, but it should be character-level,

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