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revision 1.2, Mon Jul 16 20:04:51 2007 UTC revision 1.4, Thu Dec 6 14:58:03 2007 UTC
# Line 60  Line 60 
60    
61  =head3 Form  =head3 Form
62    
63  C<< my $html = $shelp->Form(); >>      my $html = $shelp->Form();
64    
65  Generate the HTML for a form to request a new search.  Generate the HTML for a form to request a new search.
66    
# Line 89  Line 89 
89                           $cgi->td($cgi->textfield(-name => 'nearDistance',                           $cgi->td($cgi->textfield(-name => 'nearDistance',
90                                                    -value => $options->{nearDistance},                                                    -value => $options->{nearDistance},
91                                                    -size => 5) .                                                    -size => 5) .
92                                    SearchHelper::Hint("If the distance between two genes " .                                    SearchHelper::Hint("OpSearch",
93                                                         "If the distance between two genes " .
94                                                       "is greater than this number of base " .                                                       "is greater than this number of base " .
95                                                       "pairs, they will be treated as " .                                                       "pairs, they will be treated as " .
96                                                       "belonging to different operons."))),                                                       "belonging to different operons."))),
# Line 97  Line 98 
98                           $cgi->td($cgi->textfield(-name => 'upstream',                           $cgi->td($cgi->textfield(-name => 'upstream',
99                                                    -value => $options->{upstream},                                                    -value => $options->{upstream},
100                                                    -size => 5) .                                                    -size => 5) .
101                           SearchHelper::Hint("When displaying the upstream DNA, this is " .                           SearchHelper::Hint("OpSearch",
102                                                "When displaying the upstream DNA, this is " .
103                                              "the number of base pairs preceding the gene " .                                              "the number of base pairs preceding the gene " .
104                                              "that will be shown."))),                                              "that will be shown."))),
105                  $cgi->Tr($cgi->td("Instream base pairs to display"),                  $cgi->Tr($cgi->td("Instream base pairs to display"),
106                           $cgi->td($cgi->textfield(-name => 'instream',                           $cgi->td($cgi->textfield(-name => 'instream',
107                                                    -value => $options->{instream},                                                    -value => $options->{instream},
108                                                    -size => 5) .                                                    -size => 5) .
109                                    SearchHelper::Hint("When displaying the upstream DNA, this is " .                                    SearchHelper::Hint("OpSearch",
110                                                         "When displaying the upstream DNA, this is " .
111                                                       "the number of base pairs from inside the " .                                                       "the number of base pairs from inside the " .
112                                                       "gene that will be shown."))),                                                       "gene that will be shown."))),
113                  $cgi->Tr($cgi->td("Maximum lint size"),                  $cgi->Tr($cgi->td("Maximum lint size"),
114                           $cgi->td($cgi->textfield(-name => 'lintSize',                           $cgi->td($cgi->textfield(-name => 'lintSize',
115                                                    -value => $options->{lintSize},                                                    -value => $options->{lintSize},
116                                                    -size => 5) .                                                    -size => 5) .
117                                    SearchHelper::Hint("Genes whose size in base pairs are equal to " .                                    SearchHelper::Hint("OpSearch",
118                                                         "Genes whose size in base pairs are equal to " .
119                                                       "or less than this amount will; be ignored.")));                                                       "or less than this amount will; be ignored.")));
120      # Add the special feature options.      # Add the special feature options.
121      push @rows, RHFeatures::FeatureFilterFormRows($self, 'options');      push @rows, RHFeatures::FeatureFilterFormRows($self, 'options');
# Line 127  Line 131 
131    
132  =head3 Find  =head3 Find
133    
134  C<< my $resultCount = $shelp->Find(); >>      my $resultCount = $shelp->Find();
135    
136  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
137  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 266  Line 270 
270    
271  =head3 Description  =head3 Description
272    
273  C<< my $htmlText = $shelp->Description(); >>      my $htmlText = $shelp->Description();
274    
275  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
276  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 283  Line 287 
287    
288  =head3 SortKey  =head3 SortKey
289    
290  C<< my $key = $shelp->SortKey($rhelp, $record); >>      my $key = $shelp->SortKey($rhelp, $record);
291    
292  Return the sort key for the current feature. The features are  Return the sort key for the current feature. The features are
293  sorted by sequence within operon, which is determined entirely  sorted by sequence within operon, which is determined entirely
# Line 328  Line 332 
332    
333  =head3 OutputFeature  =head3 OutputFeature
334    
335  C<< $shelp->OutputFeature($rhelp, $feature, $location, $options); >>      $shelp->OutputFeature($rhelp, $feature, $location, $options);
336    
337  Output the current feature. We use the location to compute an upstream location for the feature,  Output the current feature. We use the location to compute an upstream location for the feature,
338  and this is added to the feature data object as an extra column named C<Upstream DNA>. The operon ID  and this is added to the feature data object as an extra column named C<Upstream DNA>. The operon ID
# Line 400  Line 404 
404    
405  =head3 SearchTitle  =head3 SearchTitle
406    
407  C<< my $titleHtml = $shelp->SearchTitle(); >>      my $titleHtml = $shelp->SearchTitle();
408    
409  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.
410  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

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