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revision 1.40, Mon Jun 28 19:14:22 2004 UTC revision 1.41, Mon Jun 28 19:36:33 2004 UTC
# Line 237  Line 237 
237    
238      push(@$html,      push(@$html,
239                  $cgi->start_form(-action => "index.cgi"),                  $cgi->start_form(-action => "index.cgi"),
240                  $cgi->h1('Searching for Genes or Functional Roles Using Text'),                  $cgi->h2('Searching for Genes or Functional Roles Using Text'),
241                  "<table><tr>",                  "<table><tr>",
242                  "<td>Search Pattern: </td><td>",                  "<td>Search Pattern: </td><td>",
243                  $cgi->textfield(-name => "pattern", -size => 65),                  $cgi->textfield(-name => "pattern", -size => 65),
# Line 251  Line 251 
251                  $cgi->textfield(-name => "maxrole", -size => 6, -value => 100),                  $cgi->textfield(-name => "maxrole", -size => 6, -value => 100),
252                  "</td></td></table>",                  "</td></td></table>",
253                  $cgi->submit('Search'),                  $cgi->submit('Search'),
254                  $cgi->reset('Clear'),                  $cgi->reset('Clear'));
255    
256        push(@$html,
257                  $cgi->hr,                  $cgi->hr,
258             #$cgi->h2('Work on Subsystems'),
259             #$cgi->start_form(-action => "ssa.cgi"),
260             #"Enter user: ",
261             #$cgi->textfield(-name => "user", -size => 20),
262             #$cgi->submit('Work on Subsystems'),
263             #$cgi->end_form,
264             $cgi->h2('Work on Subsystems'),
265             $cgi->start_form(-action => "ssa2.cgi"),
266             "Enter user: ",
267             $cgi->textfield(-name => "user", -size => 20),
268             $cgi->submit('Work on Subsystems'),
269             $cgi->end_form,
270            );
271    
272                  $cgi->h1('If You Need to Pick an Organism for Options Below'),      push(@$html, $cgi->hr,
273                    $cgi->h2('If You Need to Pick an Organism for Options Below'),
274                  $cgi->scrolling_list(-name => 'korgs',                  $cgi->scrolling_list(-name => 'korgs',
275                                       -values => [@orgs],                                       -values => [@orgs],
276                                       -size => 10                                       -size => 10
277                                      ),                                      ),
278                  $cgi->hr,                  $cgi->hr,
279    
280                  $cgi->h1('Finding Candidates for a Functional Role'),                  $cgi->h2('Finding Candidates for a Functional Role'),
281                  "Make sure that you type the functional role you want to search for in the Search Pattern above",                  "Make sure that you type the functional role you want to search for in the Search Pattern above",
282                  $cgi->br,                  $cgi->br,
283                  $cgi->submit('Find Genes in Org that Might Play the Role'),                  $cgi->submit('Find Genes in Org that Might Play the Role'),
284                  $cgi->hr,                  $cgi->hr,
285    
286                  $cgi->h1('Metabolic Overviews (via KEGG) - Choose KEGG Map'),                  $cgi->h2('Metabolic Overviews (via KEGG) - Choose KEGG Map'),
287                  $cgi->submit('Metabolic Overview'),                  $cgi->submit('Metabolic Overview'),
288                  $cgi->br,                  $cgi->br,
289                  $cgi->br,                  $cgi->br,
# Line 277  Line 293 
293                                      ),                                      ),
294                  $cgi->hr,                  $cgi->hr,
295    
296                  $cgi->h1('Searching DNA or Protein Sequences (in a selected organism)'),                  $cgi->h2('Searching DNA or Protein Sequences (in a selected organism)'),
297                  "<TABLE>\n",                  "<TABLE>\n",
298                  "    <TR>\n",                  "    <TR>\n",
299                  "        <TD>Sequence/Pattern: </TD>",                  "        <TD>Sequence/Pattern: </TD>",
# Line 289  Line 305 
305                  "    </TR>\n",                  "    </TR>\n",
306                  "</TABLE>\n",                  "</TABLE>\n",
307                  $cgi->submit('Search for Matches'),                  $cgi->submit('Search for Matches'),
308                  $cgi->hr,                  $cgi->hr);
309    
310                  $cgi->h1('Exporting Assignments'),      #
311                  "Extract assignments made by ",      # Make assignment export tbl.
312                  $cgi->textfield(-name => "made_by", -size => 50),      #
313                  $cgi->br,  
314                  "Save as user: ",      my @atbl;
315                  $cgi->textfield(-name => "save_user", -size => 50),      push(@atbl, ["Extract assignments made by ",
316                  $cgi->br,                   $cgi->textfield(-name => "made_by", -size => 50)]);
317                  "After date (MM/DD/YYYY) ",      push(@atbl, ["Save as user: ",
318                  $cgi->textfield(-name => "after_date", -size => 15),                  $cgi->textfield(-name => "save_user", -size => 50)]);
319                  $cgi->br,      push(@atbl, ["After date (MM/DD/YYYY) ",
320                    $cgi->textfield(-name => "after_date", -size => 15)]);
321    
322        push(@$html,
323             $cgi->h2('Exporting Assignments'),
324             &HTML::make_table(undef, \@atbl, '', border => 0),
325                  $cgi->checkbox(-label => 'tab-delimited Spreadsheet: ', -name => 'tabs', -value => 1),                  $cgi->checkbox(-label => 'tab-delimited Spreadsheet: ', -name => 'tabs', -value => 1),
326                  $cgi->br,                  $cgi->br,
327                  $cgi->checkbox(-label => 'Save Assignments: ', -name => 'save_assignments', -value => 1),                  $cgi->checkbox(-label => 'Save Assignments: ', -name => 'save_assignments', -value => 1),
# Line 315  Line 336 
336                  $cgi->br,                  $cgi->br,
337                  $cgi->submit('Generate Assignments via Translation'),                  $cgi->submit('Generate Assignments via Translation'),
338                  $cgi->hr,                  $cgi->hr,
339                  $cgi->h1('Searching for Interesting Genes'),                  $cgi->h2('Searching for Interesting Genes'),
340                  $cgi->submit('Search for Genes Matching an Occurrence Profile or Common to a Set of Organisms'),                  $cgi->submit('Search for Genes Matching an Occurrence Profile or Common to a Set of Organisms'),
341                  $cgi->end_form                  $cgi->end_form
342           );           );
343    
344      push(@$html,      push(@$html,
345                  $cgi->hr,                  $cgi->hr,
346                  $cgi->h1('Process Saved Assignments Sets'),                  $cgi->h2('Process Saved Assignments Sets'),
347                  $cgi->start_form(-action => "assignments.cgi"),                  $cgi->start_form(-action => "assignments.cgi"),
348                  "Enter user: ",                  "Enter user: ",
349                  $cgi->textfield(-name => "user", -size => 20),                  $cgi->textfield(-name => "user", -size => 20),
# Line 332  Line 353 
353    
354      push(@$html,      push(@$html,
355                  $cgi->hr,                  $cgi->hr,
356                  #$cgi->h1('Work on Subsystems'),                  $cgi->h2('Align Sequences'),
                 #$cgi->start_form(-action => "ssa.cgi"),  
                 #"Enter user: ",  
                 #$cgi->textfield(-name => "user", -size => 20),  
                 #$cgi->submit('Work on Subsystems'),  
                 #$cgi->end_form,  
                 $cgi->h2('Work on Subsystems with the New, Somewhat Experimental, Version'),  
                 $cgi->start_form(-action => "ssa2.cgi"),  
                 "Enter user: ",  
                 $cgi->textfield(-name => "user", -size => 20),  
                 $cgi->submit('Work on Subsystems'),  
                 $cgi->end_form,  
          );  
   
     push(@$html,  
                 $cgi->hr,  
                 $cgi->h1('Align Sequences'),  
357                  $cgi->start_form(-action => "index.cgi"),                  $cgi->start_form(-action => "index.cgi"),
358                  "Enter user: ",                  "Enter user: ",
359                  $cgi->textfield(-name => "user", -size => 20), $cgi->br,                  $cgi->textfield(-name => "user", -size => 20), $cgi->br,

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