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revision 1.16, Mon Jul 16 20:04:51 2007 UTC revision 1.19, Tue Apr 29 20:52:45 2008 UTC
# Line 67  Line 67 
67    
68  =head3 Form  =head3 Form
69    
70  C<< my $html = $shelp->Form(); >>      my $html = $shelp->Form();
71    
72  Generate the HTML for a form to request a new search.  Generate the HTML for a form to request a new search.
73    
# Line 116  Line 116 
116                                                   -checked => $statistical,                                                   -checked => $statistical,
117                                                   -value => 1,                                                   -value => 1,
118                                                   -label => 'Use Statistical Algorithm') .                                                   -label => 'Use Statistical Algorithm') .
119                                    SearchHelper::Hint("When two sets of genomees are specified, check this " .                                    SearchHelper::Hint("SigGenes",
120                                                         "When two sets of genomes are specified, check this " .
121                                                       "box to use a statistical algorithm designed " .                                                       "box to use a statistical algorithm designed " .
122                                                       "specifically to choose differentiating genes. " .                                                       "specifically to choose differentiating genes. " .
123                                                       "This box has no effect when looking for genes " .                                                       "This box has no effect when looking for genes " .
# Line 125  Line 126 
126                                                   -checked => $useSims,                                                   -checked => $useSims,
127                                                   -value => 1,                                                   -value => 1,
128                                                   -label => 'Use Similarities') .                                                   -label => 'Use Similarities') .
129                                    SearchHelper::Hint("Normally, Bidirectional Best Hits are used to " .                                    SearchHelper::Hint("SigGenes",
130                                                         "Normally, Bidirectional Best Hits are used to " .
131                                                       "find matching genes. Check this box to use " .                                                       "find matching genes. Check this box to use " .
132                                                       "similarities instead.")))),                                                       "similarities instead.")))),
133                  $cgi->Tr($cgi->td(), $cgi->td(join(" ",                  $cgi->Tr($cgi->td(), $cgi->td(join(" ",
# Line 133  Line 135 
135                                                   -checked => $showMatch,                                                   -checked => $showMatch,
136                                                   -value => 1,                                                   -value => 1,
137                                                   -label => 'Show Matching Genes') .                                                   -label => 'Show Matching Genes') .
138                                    SearchHelper::Hint("Check this button to display the genes matching " .                                    SearchHelper::Hint("SigGenes",
139                                                         "Check this button to display the genes matching " .
140                                                       "each gene displayed in the results.")))),                                                       "each gene displayed in the results.")))),
141                  $cgi->Tr($cgi->td("Cutoff"),                  $cgi->Tr($cgi->td("Cutoff"),
142                           $cgi->td($cgi->textfield(-name => 'cutoff',                           $cgi->td($cgi->textfield(-name => 'cutoff',
# Line 154  Line 157 
157    
158  =head3 Find  =head3 Find
159    
160  C<< my $resultCount = $shelp->Find(); >>      my $resultCount = $shelp->Find();
161    
162  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
163  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 398  Line 401 
401    
402  =head3 Description  =head3 Description
403    
404  C<< my $htmlText = $shelp->Description(); >>      my $htmlText = $shelp->Description();
405    
406  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
407  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,
# Line 415  Line 418 
418    
419  =head3 SearchTitle  =head3 SearchTitle
420    
421  C<< my $titleHtml = $shelp->SearchTitle(); >>      my $titleHtml = $shelp->SearchTitle();
422    
423  Return the display title for this search. The display title appears above the search results.  Return the display title for this search. The display title appears above the search results.
424  If no result is returned, no title will be displayed. The result should be an html string  If no result is returned, no title will be displayed. The result should be an html string
# Line 439  Line 442 
442    
443  =head3 IsCommon  =head3 IsCommon
444    
445  C<< my $score = SHSigGenes::IsCommon($count, $size, $commonality); >>      my $score = SHSigGenes::IsCommon($count, $size, $commonality);
446    
447  Return the match score if a specified count indicates a gene is common in a specified set  Return the match score if a specified count indicates a gene is common in a specified set
448  and 0 otherwise. Commonality is computed by dividing the count by the size of the set and  and 0 otherwise. Commonality is computed by dividing the count by the size of the set and

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