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revision 1.5, Sat Oct 7 13:20:35 2006 UTC revision 1.9, Sat Dec 2 09:46:01 2006 UTC
# Line 61  Line 61 
61    
62  =head3 Form  =head3 Form
63    
64  C<< my $html = $shelp->Include(); >>  C<< my $html = $shelp->Form(); >>
65    
66  Generate the HTML for a form to request a new search.  Generate the HTML for a form to request a new search.
67    
# Line 86  Line 86 
86      # Get the default values to use for the commonality and cutoff controls.      # Get the default values to use for the commonality and cutoff controls.
87      my $commonality = $cgi->param('commonality') || "0.8";      my $commonality = $cgi->param('commonality') || "0.8";
88      my $cutoff = $cgi->param('cutoff') || "1e-10";      my $cutoff = $cgi->param('cutoff') || "1e-10";
89      my $statistical = $cgi->param('statistical') || 0;      my $statistical = $cgi->param('statistical') || 1;
90      # Now we build the table rows. The top contains the two numeric parameters and      # Now we build the table rows.
     # the submit button.  
91      my @rows = ();      my @rows = ();
92        # First we have the given genome.
93        push @rows, $cgi->Tr($cgi->td({valign => "top"}, "Reference Genome"),
94                             $cgi->td({colspan => 2}, $givenMenu));
95        # Now show the target and exclusion menus.
96        push @rows, $cgi->Tr($cgi->td({valign => "top"}, "Inclusion Genomes (Set 1)"),
97                             $cgi->td({colspan => 2}, $targetMenu));
98        push @rows, $cgi->Tr($cgi->td({valign => "top"}, "Exclusion Genomes (Set 2)"),
99                             $cgi->td({colspan => 2}, $excludeMenu));
100        # Next, the numeric parameters.
101      push @rows, $cgi->Tr($cgi->td("Commonality"),      push @rows, $cgi->Tr($cgi->td("Commonality"),
102                           $cgi->td($cgi->textfield(-name => 'commonality',                           $cgi->td($cgi->textfield(-name => 'commonality',
103                                                    -value => $commonality,                                                    -value => $commonality,
104                                                    -size => 5) . "&nbsp;" .                                                    -size => 5))),
105                    $cgi->Tr($cgi->td(), $cgi->td(
106                                    $cgi->checkbox(-name => 'statistical',                                    $cgi->checkbox(-name => 'statistical',
107                                                   -checked => $statistical,                                                   -checked => $statistical,
108                                                   -value => 1,                                                   -value => 1,
# Line 102  Line 111 
111                           $cgi->td($cgi->textfield(-name => 'cutoff',                           $cgi->td($cgi->textfield(-name => 'cutoff',
112                                                    -value => $cutoff,                                                    -value => $cutoff,
113                                                    -size => 5)));                                                    -size => 5)));
114      push @rows, $self->SubmitRow();      # Next, the feature filter rows.
     # The next rows have the given genome and a feature filter.  
     push @rows, $cgi->Tr($cgi->td({valign => "top"}, "Given Genome"),  
                          $cgi->td({colspan => 2}, $givenMenu));  
115      push @rows, $self->FeatureFilterRows();      push @rows, $self->FeatureFilterRows();
116      # Now show the target and exclusion menus.      # Finally, the submit button.
117      push @rows, $cgi->Tr($cgi->td({valign => "top"}, "Target Genomes (Set 1)"),      push @rows, $self->SubmitRow();
                          $cgi->td({colspan => 2}, $targetMenu));  
     push @rows, $cgi->Tr($cgi->td({valign => "top"}, "Exclusion Genomes (Set 2)"),  
                          $cgi->td({colspan => 2}, $excludeMenu));  
118      # Create the table.      # Create the table.
119      $retVal .= $self->MakeTable(\@rows);      $retVal .= $self->MakeTable(\@rows);
120      # Close the form.      # Close the form.
# Line 253  Line 256 
256      # Get the parameters.      # Get the parameters.
257      my ($self) = @_;      my ($self) = @_;
258      # Return the result.      # Return the result.
259      return "Search for features that are common to a group of organisms or that discriminate between two groups of organisms.";      return "Search for genes that are common to a group of organisms or that discriminate between two groups of organisms.";
260  }  }
261    
262  =head2 Internal Utilities  =head2 Internal Utilities

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