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revision 1.1, Wed Nov 15 12:14:14 2006 UTC revision 1.6, Mon Jul 16 20:04:51 2007 UTC
# Line 4  Line 4 
4    
5      use strict;      use strict;
6      use Tracer;      use Tracer;
     use SearchHelper;  
7      use CGI;      use CGI;
8      use HTML;      use HTML;
9      use Sprout;      use Sprout;
10      use FeatureData;      use RHFeatures;
11      use FeatureQuery;      use base 'SearchHelper';
   
     our @ISA = qw(SearchHelper);  
12    
13  =head1 Subsystem Feature Search Helper  =head1 Subsystem Feature Search Helper
14    
# Line 52  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("Search for Genes by Subsystem or Class");      my $retVal = $self->FormStart("Open Subsystem OR 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 62  Line 59 
59                                                  selected => $cgi->param("specification"));                                                  selected => $cgi->param("specification"));
60      # We'll accumulate the form table in here.      # We'll accumulate the form table in here.
61      my @rows = ();      my @rows = ();
62      # Start with a keyword search box.      # Start with the subsystem tree.
     my $expressionString = $cgi->param('keywords') || "";  
     push @rows, $cgi->Tr($cgi->th("Search Words"),  
                          $cgi->td({ colspan => 2 },  
                                   $cgi->textfield(-name => 'keywords',  
                                                   -value => $expressionString,  
                                                   -size => 60)));  
     # Add the subsystem tree.  
63      push @rows, $cgi->Tr($cgi->th({ colspan => 3, align => "center" }, "Subsystem Tree")),      push @rows, $cgi->Tr($cgi->th({ colspan => 3, align => "center" }, "Subsystem Tree")),
64                  $cgi->Tr($cgi->td({ colspan => 3 }, $treeField));                  $cgi->Tr($cgi->td({ colspan => 3 }, $treeField));
65        # Put in the keyword search box.
66        my $expressionString = $cgi->param('keywords') || "";
67        push @rows, RHFeatures::WordSearchRow($self);
68      # Add the special options.      # Add the special options.
69      push @rows, FeatureQuery::SpecialOptions($self);      push @rows, RHFeatures::FeatureFilterFormRows($self, 'options');
70      # Finish it off with the submit row.      # Finish it off with the submit row.
71      push @rows, $self->SubmitRow();      push @rows, $self->SubmitRow();
72      # Convert the form rows into a table.      # Convert the form rows into a table.
# Line 134  Line 127 
127              # any keywords were specified.              # any keywords were specified.
128              my $query;              my $query;
129              if ($keywords) {              if ($keywords) {
130                    $self->PrintLine("Word search query submitted.<br />");
131                  $query = $sprout->Search($keywords, 2, @majorParms);                  $query = $sprout->Search($keywords, 2, @majorParms);
132              } else {              } else {
133                    $self->PrintLine("Standard search query submitted.<br />");
134                  $query = $sprout->Get(@majorParms);                  $query = $sprout->Get(@majorParms);
135              }              }
136                # Get the result helper for a feature search.
137                my $rhelp = RHFeatures->new($self);
138                # Compute the default columns. This is a very simple search which
139                # has no extra columns.
140                $self->DefaultColumns($rhelp);
141              # Initialize the session file.              # Initialize the session file.
142              $self->OpenSession();              $self->OpenSession($rhelp);
143              # Initialize the result counter.              # Initialize the result counter.
144              $retVal = 0;              $retVal = 0;
145              # Loop through the selected features.              # Loop through the selected features.
# Line 147  Line 147 
147                  $fd->Store($record);                  $fd->Store($record);
148                  $self->PutFeature($fd);                  $self->PutFeature($fd);
149                  $retVal++;                  $retVal++;
150                    if ($retVal % 100 == 0) {
151                        $self->PrintLine("$retVal features processed.<br />");
152                    }
153              }              }
154              # Close the session file.              # Close the session file.
155              $self->CloseSession();              $self->CloseSession();

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