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revision 1.34, Mon Jul 16 20:04:51 2007 UTC revision 1.43, Mon Jan 19 21:56:19 2009 UTC
# Line 16  Line 16 
16      use FIGRules;      use FIGRules;
17      use HTML;      use HTML;
18      use BasicLocation;      use BasicLocation;
     use FeatureQuery;  
19      use URI::Escape;      use URI::Escape;
20      use PageBuilder;      use PageBuilder;
21      use AliasAnalysis;      use AliasAnalysis;
22        use CGI::Cookie;
23      use FreezeThaw qw(freeze thaw);      use FreezeThaw qw(freeze thaw);
24    
25  =head1 Search Helper Base Class  =head1 Search Helper Base Class
# Line 86  Line 86 
86    
87  List of the parameters that are used to select multiple genomes.  List of the parameters that are used to select multiple genomes.
88    
89    =item notices
90    
91    A list of messages to be put in the notice file.
92    
93  =back  =back
94    
95  =head2 Adding a new Search Tool  =head2 Adding a new Search Tool
# Line 242  Line 246 
246    
247  =head3 new  =head3 new
248    
249  C<< my $shelp = SearchHelper->new($cgi); >>      my $shelp = SearchHelper->new($cgi);
250    
251  Construct a new SearchHelper object.  Construct a new SearchHelper object.
252    
# Line 259  Line 263 
263  sub new {  sub new {
264      # Get the parameters.      # Get the parameters.
265      my ($class, $cgi) = @_;      my ($class, $cgi) = @_;
266      # Check for a session ID.      # Check for a session ID. First we look in the CGI parameters.
267      my $session_id = $cgi->param("SessionID");      my $session_id = $cgi->param("SessionID");
268      my $type = "old";      my $type = "old";
269      if (! $session_id) {      if (! $session_id) {
270            # We need a session ID. Try to get it from the cookies.
271            my %cookies = fetch CGI::Cookie;
272            my $session_cookie = $cookies{$class};
273            if (! $session_cookie) {
274          Trace("No session ID found.") if T(3);          Trace("No session ID found.") if T(3);
275          # Here we're starting a new session. We create the session ID and          # Here we're starting a new session. We create the session ID and
276          # store it in the query object.              # store it in a cookie.
277          $session_id = FIGRules::NewSessionID();          $session_id = FIGRules::NewSessionID();
278          Trace("New session ID is $session_id.") if T(3);          Trace("New session ID is $session_id.") if T(3);
279                $session_cookie = new CGI::Cookie(-name => $class,
280                                                  -value => $session_id,
281                                                  -expires => '+7d');
282                $session_cookie->bake();
283            } else {
284                # Here we're recovering an old session. The session ID is
285                # used to find any old search options lying around, but we're
286                # still considered a new session.
287                $session_id = $session_cookie->value();
288                Trace("Session $session_id recovered from cookie.") if T(3);
289            }
290            # Denote this is a new session.
291          $type = "new";          $type = "new";
292            # Put the session IS in the parameters.
293          $cgi->param(-name => 'SessionID', -value => $session_id);          $cgi->param(-name => 'SessionID', -value => $session_id);
294      } else {      } else {
295          Trace("Session ID is $session_id.") if T(3);          Trace("Session ID is $session_id.") if T(3);
# Line 304  Line 325 
325                    scriptQueue => [],                    scriptQueue => [],
326                    genomeList => undef,                    genomeList => undef,
327                    genomeParms => [],                    genomeParms => [],
328                      notices => [],
329                   };                   };
330      # Bless and return it.      # Bless and return it.
331      bless $retVal, $class;      bless $retVal, $class;
# Line 312  Line 334 
334    
335  =head3 Q  =head3 Q
336    
337  C<< my $query = $shelp->Q(); >>      my $query = $shelp->Q();
338    
339  Return the CGI query object.  Return the CGI query object.
340    
# Line 326  Line 348 
348  }  }
349    
350    
   
351  =head3 DB  =head3 DB
352    
353  C<< my $sprout = $shelp->DB(); >>      my $sprout = $shelp->DB();
354    
355  Return the Sprout database object.  Return the Sprout database object.
356    
# Line 350  Line 371 
371    
372  =head3 IsNew  =head3 IsNew
373    
374  C<< my $flag = $shelp->IsNew(); >>      my $flag = $shelp->IsNew();
375    
376  Return TRUE if this is a new session, FALSE if this is an old session. An old  Return TRUE if this is a new session, FALSE if this is an old session. An old
377  session already has search results ready to process.  session already has search results ready to process.
# Line 366  Line 387 
387    
388  =head3 ID  =head3 ID
389    
390  C<< my $sessionID = $shelp->ID(); >>      my $sessionID = $shelp->ID();
391    
392  Return the current session ID.  Return the current session ID.
393    
# Line 381  Line 402 
402    
403  =head3 FormName  =head3 FormName
404    
405  C<< my $name = $shelp->FormName(); >>      my $name = $shelp->FormName();
406    
407  Return the name of the form this helper object will generate.  Return the name of the form this helper object will generate.
408    
# Line 396  Line 417 
417    
418  =head3 QueueFormScript  =head3 QueueFormScript
419    
420  C<< $shelp->QueueFormScript($statement); >>      $shelp->QueueFormScript($statement);
421    
422  Add the specified statement to the queue of JavaScript statements that are to be  Add the specified statement to the queue of JavaScript statements that are to be
423  executed when the form has been fully defined. This is necessary because until  executed when the form has been fully defined. This is necessary because until
# Line 431  Line 452 
452    
453  =head3 FormStart  =head3 FormStart
454    
455  C<< my $html = $shelp->FormStart($title); >>      my $html = $shelp->FormStart($title);
456    
457  Return the initial section of a form designed to perform another search of the  Return the initial section of a form designed to perform another search of the
458  same type. The form header is included along with hidden fields to persist the  same type. The form header is included along with hidden fields to persist the
# Line 461  Line 482 
482      # Start the form. Note we use the override option on the Class value, in      # Start the form. Note we use the override option on the Class value, in
483      # case the Advanced button was used.      # case the Advanced button was used.
484      my $retVal = "<div class=\"search\">\n" .      my $retVal = "<div class=\"search\">\n" .
485                   $cgi->start_form(-method => 'POST',                   CGI::start_form(-method => 'POST',
486                                    -action => $cgi->url(-relative => 1),                                    -action => "$FIG_Config::cgi_url/wiki/rest.cgi/NmpdrPlugin/search",
487                                    -name => $self->FormName()) .                                    -name => $self->FormName()) .
488                   $cgi->hidden(-name => 'Class',                   CGI::hidden(-name => 'Class',
489                                -value => $self->{class},                                -value => $self->{class}) .
490                                -override => 1) .                   CGI::hidden(-name => 'SPROUT',
                  $cgi->hidden(-name => 'SPROUT',  
491                                -value => 1) .                                -value => 1) .
492                   $cgi->h3($title);                   CGI::h3("$title" . Hint($self->{class}, "Click here for more information."));
     # If tracing is on, add it to the form.  
     if ($cgi->param('Trace')) {  
         $retVal .= $cgi->hidden(-name => 'Trace',  
                                 -value => $cgi->param('Trace')) .  
                    $cgi->hidden(-name => 'TF',  
                                 -value => ($cgi->param('TF') ? 1 : 0));  
     }  
493      # Put in an anchor tag in case there's a table of contents.      # Put in an anchor tag in case there's a table of contents.
494      my $anchorName = $self->FormName();      my $anchorName = $self->FormName();
495      $retVal .= "<a name=\"$anchorName\"></a>\n";      $retVal .= "<a name=\"$anchorName\"></a>\n";
# Line 486  Line 499 
499    
500  =head3 FormEnd  =head3 FormEnd
501    
502  C<< my $htmlText = $shelp->FormEnd(); >>      my $htmlText = $shelp->FormEnd();
503    
504  Return the HTML text for closing a search form. This closes both the C<form> and  Return the HTML text for closing a search form. This closes both the C<form> and
505  C<div> tags.  C<div> tags.
# Line 518  Line 531 
531    
532  =head3 SetMessage  =head3 SetMessage
533    
534  C<< $shelp->SetMessage($msg); >>      $shelp->SetMessage($msg);
535    
536  Store the specified text as the result message. The result message is displayed  Store the specified text as the result message. The result message is displayed
537  if an invalid parameter value is specified.  if an invalid parameter value is specified.
# Line 542  Line 555 
555    
556  =head3 Message  =head3 Message
557    
558  C<< my $text = $shelp->Message(); >>      my $text = $shelp->Message();
559    
560  Return the result message. The result message is displayed if an invalid parameter  Return the result message. The result message is displayed if an invalid parameter
561  value is specified.  value is specified.
# Line 558  Line 571 
571    
572  =head3 OpenSession  =head3 OpenSession
573    
574  C<< $shelp->OpenSession($rhelp); >>      $shelp->OpenSession($rhelp);
575    
576  Set up the session cache file and write out the column headers.  Set up the session cache file and write out the column headers.
577  This method should not be called until all the columns have  This method should not be called until all the columns have
# Line 593  Line 606 
606    
607  =head3 GetCacheFileName  =head3 GetCacheFileName
608    
609  C<< my $fileName = $shelp->GetCacheFileName(); >>      my $fileName = $shelp->GetCacheFileName();
610    
611  Return the name to be used for this session's cache file.  Return the name to be used for this session's cache file.
612    
# Line 608  Line 621 
621    
622  =head3 GetTempFileName  =head3 GetTempFileName
623    
624  C<< my $fileName = $shelp->GetTempFileName($type); >>      my $fileName = $shelp->GetTempFileName($type);
625    
626  Return the name to be used for a temporary file of the specified type. The  Return the name to be used for a temporary file of the specified type. The
627  name is computed from the session name with the type as a suffix.  name is computed from the session name with the type as a suffix.
# Line 639  Line 652 
652    
653  =head3 WriteColumnHeaders  =head3 WriteColumnHeaders
654    
655  C<< $shelp->WriteColumnHeaders(@colNames); >>      $shelp->WriteColumnHeaders(@colNames);
656    
657  Write out the column headers for the current search session. The column headers  Write out the column headers for the current search session. The column headers
658  are sent to the cache file, and then the cache is re-opened as a sort pipe and  are sent to the cache file, and then the cache is re-opened as a sort pipe and
# Line 674  Line 687 
687      $self->{fileHandle} = Open(undef, "| sort | cut --fields=2- >>$fileName");      $self->{fileHandle} = Open(undef, "| sort | cut --fields=2- >>$fileName");
688  }  }
689    
690    =head3 SetNotice
691    
692        $shelp->SetNotice($message);
693    
694    This method creates a notice that will be displayed on the search results
695    page. After the search is complete, notices are placed in a small temporary
696    file that is checked by the results display engine.
697    
698    =over 4
699    
700    =item message
701    
702    Message to write to the notice file.
703    
704    =back
705    
706    =cut
707    
708    sub SetNotice {
709        # Get the parameters.
710        my ($self, $message) = @_;
711        # Save the message.
712        push @{$self->{notices}}, $message;
713    }
714    
715    
716  =head3 ReadColumnHeaders  =head3 ReadColumnHeaders
717    
718  C<< my @colHdrs = $shelp->ReadColumnHeaders($fh); >>      my @colHdrs = $shelp->ReadColumnHeaders($fh);
719    
720  Read the column headers from the specified file handle. The column headers are  Read the column headers from the specified file handle. The column headers are
721  frozen strings intermixed with frozen hash references. The strings represent  frozen strings intermixed with frozen hash references. The strings represent
# Line 708  Line 747 
747    
748  =head3 WriteColumnData  =head3 WriteColumnData
749    
750  C<< $shelp->WriteColumnData($key, @colValues); >>      $shelp->WriteColumnData($key, @colValues);
751    
752  Write a row of column values to the current search session. It is assumed that  Write a row of column values to the current search session. It is assumed that
753  the session file is already open for output.  the session file is already open for output.
# Line 737  Line 776 
776    
777  =head3 CloseSession  =head3 CloseSession
778    
779  C<< $shelp->CloseSession(); >>      $shelp->CloseSession();
780    
781  Close the session file.  Close the session file.
782    
# Line 755  Line 794 
794          my $cgi = $self->Q();          my $cgi = $self->Q();
795          $self->PrintLine("Output formatting complete.<br />");          $self->PrintLine("Output formatting complete.<br />");
796      }      }
797        # Check for notices.
798        my @notices = @{$self->{notices}};
799        if (scalar @notices) {
800            # We have some, so put then in a notice file.
801            my $noticeFile = $self->GetTempFileName('notices');
802            my $nh = Open(undef, ">$noticeFile");
803            print $nh join("\n", @notices, "");
804            close $nh;
805            $self->PrintLine(scalar(@notices) . " notices saved.<br />");
806        }
807  }  }
808    
809  =head3 OrganismData  =head3 OrganismData
810    
811  C<< my ($orgName, $group) = $shelp->Organism($genomeID); >>      my ($orgName, $group) = $shelp->Organism($genomeID);
812    
813  Return the name and status of the organism corresponding to the specified genome ID.  Return the name and status of the organism corresponding to the specified genome ID.
814  For performance reasons, this information is cached in a special hash table, so we  For performance reasons, this information is cached in a special hash table, so we
# Line 790  Line 839 
839      my $cache = $self->{orgs};      my $cache = $self->{orgs};
840      if (exists $cache->{$genomeID}) {      if (exists $cache->{$genomeID}) {
841          ($orgName, $group, $domain) = @{$cache->{$genomeID}};          ($orgName, $group, $domain) = @{$cache->{$genomeID}};
842            Trace("Cached organism $genomeID has group \"$group\".") if T(4);
843      } else {      } else {
844          # Here we have to use the database.          # Here we have to use the database.
845          my $sprout = $self->DB();          my $sprout = $self->DB();
846          my ($genus, $species, $strain, $group, $taxonomy) = $sprout->GetEntityValues('Genome', $genomeID,          my ($genus, $species, $strain, $newGroup, $taxonomy) = $sprout->GetEntityValues('Genome', $genomeID,
847                                                                  ['Genome(genus)', 'Genome(species)',                                                                  ['Genome(genus)', 'Genome(species)',
848                                                                   'Genome(unique-characterization)',                                                                   'Genome(unique-characterization)',
849                                                                   'Genome(primary-group)',                                                                   'Genome(primary-group)',
850                                                                   'Genome(taxonomy)']);                                                                   'Genome(taxonomy)']);
851          # Format and cache the name and display group.          # Format and cache the name and display group.
852          ($orgName, $group, $domain) = $self->SaveOrganismData($group, $genomeID, $genus, $species,          Trace("Caching organism $genomeID with group \"$newGroup\".") if T(4);
853            ($orgName, $group, $domain) = $self->SaveOrganismData($newGroup, $genomeID, $genus, $species,
854                                                                $strain, $taxonomy);                                                                $strain, $taxonomy);
855            Trace("Returning group $group.") if T(4);
856      }      }
857      # Return the result.      # Return the result.
858      return ($orgName, $group, $domain);      return ($orgName, $group, $domain);
# Line 808  Line 860 
860    
861  =head3 Organism  =head3 Organism
862    
863  C<< my $orgName = $shelp->Organism($genomeID); >>      my $orgName = $shelp->Organism($genomeID);
864    
865  Return the name of the relevant organism. The name is computed from the genus,  Return the name of the relevant organism. The name is computed from the genus,
866  species, and unique characterization. A cache is used to improve performance.  species, and unique characterization. A cache is used to improve performance.
# Line 838  Line 890 
890    
891  =head3 ComputeFASTA  =head3 ComputeFASTA
892    
893  C<< my $fasta = $shelp->ComputeFASTA($desiredType, $sequence, $flankingWidth); >>      my $fasta = $shelp->ComputeFASTA($desiredType, $sequence, $flankingWidth, $comments);
894    
895  Parse a sequence input and convert it into a FASTA string of the desired type with  Parse a sequence input and convert it into a FASTA string of the desired type with
896  the desired flanking width.  the desired flanking width.
# Line 865  Line 917 
917  protein translation of a feature doesn't always match the DNA and is taken directly  protein translation of a feature doesn't always match the DNA and is taken directly
918  from the database.  from the database.
919    
920    =item comments
921    
922    Comment string to be added to the FASTA header.
923    
924  =item RETURN  =item RETURN
925    
926  Returns a string in FASTA format representing the content of the desired sequence with  Returns a string in FASTA format representing the content of the desired sequence with
# Line 877  Line 933 
933    
934  sub ComputeFASTA {  sub ComputeFASTA {
935      # Get the parameters.      # Get the parameters.
936      my ($self, $desiredType, $sequence, $flankingWidth) = @_;      my ($self, $desiredType, $sequence, $flankingWidth, $comment) = @_;
937      # Declare the return variable. If an error occurs, it will remain undefined.      # Declare the return variable. If an error occurs, it will remain undefined.
938      my $retVal;      my $retVal;
939      # This variable will be cleared if an error is detected.      # This variable will be cleared if an error is detected.
# Line 908  Line 964 
964                  # In an emergency, fall back to the original ID.                  # In an emergency, fall back to the original ID.
965                  $fastaLabel = $fid;                  $fastaLabel = $fid;
966              }              }
967                # Add any specified comments.
968                if ($comment) {
969                    $fastaLabel .= " $comment";
970                }
971              # Now proceed according to the sequence type.              # Now proceed according to the sequence type.
972              if ($desiredType =~ /prot/) {              if ($desiredType =~ /prot/) {
973                  # We want protein, so get the translation.                  # We want protein, so get the translation.
# Line 999  Line 1059 
1059    
1060  =head3 SubsystemTree  =head3 SubsystemTree
1061    
1062  C<< my $tree = SearchHelper::SubsystemTree($sprout, %options); >>      my $tree = SearchHelper::SubsystemTree($sprout, %options);
1063    
1064  This method creates a subsystem selection tree suitable for passing to  This method creates a subsystem selection tree suitable for passing to
1065  L</SelectionTree>. Each leaf node in the tree will have a link to the  L</SelectionTree>. Each leaf node in the tree will have a link to the
# Line 1057  Line 1117 
1117              push @subs, $classLess;              push @subs, $classLess;
1118          }          }
1119      }      }
1120        # Get the seedviewer URL.
1121        my $svURL = $FIG_Config::linkinSV || "$FIG_Config::cgi_url/seedviewer.cgi";
1122        Trace("Seed Viewer URL is $svURL.") if T(3);
1123      # Declare the return variable.      # Declare the return variable.
1124      my @retVal = ();      my @retVal = ();
1125      # Each element in @subs represents a leaf node, so as we loop through it we will be      # Each element in @subs represents a leaf node, so as we loop through it we will be
# Line 1131  Line 1194 
1194              if ($optionThing->{links}) {              if ($optionThing->{links}) {
1195                  # Compute the link value.                  # Compute the link value.
1196                  my $linkable = uri_escape($id);                  my $linkable = uri_escape($id);
1197                  $nodeContent->{link} = "../FIG/display_subsys.cgi?ssa_name=$linkable;request=show_ssa;sort=by_phylo;show_clusters=1;SPROUT=1";                  $nodeContent->{link} = "$svURL?page=Subsystems;subsystem=$linkable";
1198              }              }
1199              if ($optionThing->{radio}) {              if ($optionThing->{radio}) {
1200                  # Compute the radio value.                  # Compute the radio value.
# Line 1149  Line 1212 
1212    
1213  =head3 NmpdrGenomeMenu  =head3 NmpdrGenomeMenu
1214    
1215  C<< my $htmlText = $shelp->NmpdrGenomeMenu($menuName, $multiple, \@selected, $rows); >>      my $htmlText = $shelp->NmpdrGenomeMenu($menuName, $multiple, \@selected, $rows);
1216    
1217  This method creates a hierarchical HTML menu for NMPDR genomes organized by category. The  This method creates a hierarchical HTML menu for NMPDR genomes organized by category. The
1218  category indicates the low-level NMPDR group. Organizing the genomes in this way makes it  category indicates the low-level NMPDR group. Organizing the genomes in this way makes it
# Line 1178  Line 1241 
1241    
1242  =item crossMenu (optional)  =item crossMenu (optional)
1243    
1244  If specified, is presumed to be the name of another genome menu whose contents  This is currently not supported.
 are to be mutually exclusive with the contents of this menu. As a result, instead  
 of the standard onChange event, the onChange event will deselect any entries in  
 the other menu.  
1245    
1246  =item RETURN  =item RETURN
1247    
# Line 1201  Line 1261 
1261      if (! defined $rows) {      if (! defined $rows) {
1262          $rows = ($multiple ? 10 : 1);          $rows = ($multiple ? 10 : 1);
1263      }      }
1264      # Create the multiple tag.      # Get a comma-delimited list of the preselected genomes.
1265      my $multipleTag = ($multiple ? " multiple" : "");      my $preselected = "";
1266      # Get the form name.      if ($selected) {
1267      my $formName = $self->FormName();          $preselected = join(", ", @$selected);
1268      # Check to see if we already have a genome list in memory.      }
1269      my $groupHash;      # Ask Sprout for a genome menu.
1270      my @groups;      my $retVal = $sprout->GenomeMenu(name => $menuName,
1271      my $nmpdrGroupCount;                                       multiSelect => $multiple,
1272      my $genomes = $self->{genomeList};                                       selected => $preselected,
1273      if (defined $genomes) {                                       size => $rows);
         # We have a list ready to use.  
         $groupHash = $genomes;  
         @groups = @{$self->{groupList}};  
         $nmpdrGroupCount = $self->{groupCount};  
     } else {  
         # Get a list of all the genomes in group order. In fact, we only need them ordered  
         # by name (genus,species,strain), but putting primary-group in front enables us to  
         # take advantage of an existing index.  
         my @genomeList = $sprout->GetAll(['Genome'],  
                                          "ORDER BY Genome(primary-group), Genome(genus), Genome(species), Genome(unique-characterization)",  
                                          [], ['Genome(primary-group)', 'Genome(id)',  
                                               'Genome(genus)', 'Genome(species)',  
                                               'Genome(unique-characterization)',  
                                               'Genome(taxonomy)']);  
         # Create a hash to organize the genomes by group. Each group will contain a list of  
         # 2-tuples, the first element being the genome ID and the second being the genome  
         # name.  
         my %gHash = ();  
         for my $genome (@genomeList) {  
             # Get the genome data.  
             my ($group, $genomeID, $genus, $species, $strain, $taxonomy) = @{$genome};  
             # Compute and cache its name and display group.  
             my ($name, $displayGroup, $domain) = $self->SaveOrganismData($group, $genomeID, $genus, $species,  
                                                                          $strain, $taxonomy);  
             # Push the genome into the group's list. Note that we use the real group  
             # name here, not the display group name.  
             push @{$gHash{$group}}, [$genomeID, $name, $domain];  
         }  
         # We are almost ready to unroll the menu out of the group hash. The final step is to separate  
         # the supporting genomes by domain. First, we sort the NMPDR groups.  
         @groups = sort grep { $_ ne $FIG_Config::otherGroup } keys %gHash;  
         # Remember the number of NMPDR groups.  
         $nmpdrGroupCount = scalar @groups;  
         # Loop through the supporting genomes, classifying them by domain. We'll also keep a list  
         # of the domains found.  
         my @otherGenomes = @{$gHash{$FIG_Config::otherGroup}};  
         my @domains = ();  
         for my $genomeData (@otherGenomes) {  
             my ($genomeID, $name, $domain) = @{$genomeData};  
             if (exists $gHash{$domain}) {  
                 push @{$gHash{$domain}}, $genomeData;  
             } else {  
                 $gHash{$domain} = [$genomeData];  
                 push @domains, $domain;  
             }  
         }  
         # Add the domain groups at the end of the main group list. The main group list will now  
         # contain all the categories we need to display the genomes.  
         push @groups, sort @domains;  
         # Delete the supporting group.  
         delete $gHash{$FIG_Config::otherGroup};  
         # Save the genome list for future use.  
         $self->{genomeList} = \%gHash;  
         $self->{groupList} = \@groups;  
         $self->{groupCount} = $nmpdrGroupCount;  
         $groupHash = \%gHash;  
     }  
     # Next, create a hash that specifies the pre-selected entries. Note that we need to deal  
     # with the possibility of undefined values in the incoming list.  
     my %selectedHash = ();  
     if (defined $selected) {  
         %selectedHash = map { $_ => 1 } grep { defined($_) } @{$selected};  
     }  
     # Now it gets complicated. We need a way to mark all the NMPDR genomes. We take advantage  
     # of the fact they come first in the list. We'll accumulate a count of the NMPDR genomes  
     # and use that to make the selections.  
     my $nmpdrCount = 0;  
     # Create the type counters.  
     my $groupCount = 1;  
     # Compute the ID for the status display.  
     my $divID = "${formName}_${menuName}_status";  
     # Compute the JavaScript call for updating the status.  
     my $showSelect = "showSelected($menuName, '$divID', 1000);";  
     # If multiple selection is supported, create an onChange event.  
     my $onChange = "";  
     if ($cross) {  
         # Here we have a paired menu. Selecting something in our menu unselects it in the  
         # other and redisplays the status of both.  
         $onChange = " onChange=\"crossUnSelect($menuName, '$divID', $cross, '${formName}_${cross}_status', 1000)\"";  
     } elsif ($multiple) {  
         # This is an unpaired menu, so all we do is redisplay our status.  
         $onChange = " onChange=\"$showSelect\"";  
     }  
     # Create the SELECT tag and stuff it into the output array.  
     my @lines = ("<SELECT name=\"$menuName\"$onChange$multipleTag size=\"$rows\">");  
     # Loop through the groups.  
     for my $group (@groups) {  
         # Create the option group tag.  
         my $tag = "<OPTGROUP label=\"$group\">";  
         push @lines, "  $tag";  
         # Get the genomes in the group.  
         for my $genome (@{$groupHash->{$group}}) {  
             # Count this organism if it's NMPDR.  
             if ($nmpdrGroupCount > 0) {  
                 $nmpdrCount++;  
             }  
             # Get the organism ID, name, and domain.  
             my ($genomeID, $name, $domain) = @{$genome};  
             # See if it's selected.  
             my $select = ($selectedHash{$genomeID} ? " selected" : "");  
             # Generate the option tag.  
             my $optionTag = "<OPTION class=\"$domain\" value=\"$genomeID\"$select>$name <em>($genomeID)</em></OPTION>";  
             push @lines, "    $optionTag";  
         }  
         # Close the option group.  
         push @lines, "  </OPTGROUP>";  
         # Record this group in the nmpdrGroup count. When that gets to 0, we've finished the NMPDR  
         # groups.  
         $nmpdrGroupCount--;  
     }  
     # Close the SELECT tag.  
     push @lines, "</SELECT>";  
     # Check for multiple selection.  
     if ($multiple) {  
         # Multi-select is on, so we need to add some selection helpers. First is  
         # the search box. This allows the user to type text and have all genomes containing  
         # the text selected automatically.  
         my $searchThingName = "${menuName}_SearchThing";  
         push @lines, "<br />" .  
                      "<INPUT type=\"button\" name=\"MacroSearch\" class=\"button\" value=\"Select genomes containing\" onClick=\"selectViaSearch($menuName, $searchThingName); $showSelect\" />&nbsp;" .  
                      "<INPUT type=\"text\" name=\"$searchThingName\" size=\"30\" />" . Hint("Enter a genome number click the button to the left " .  
                                                                                             "in order to select the genome with that number. " .  
                                                                                             "Enter a genus, species, or strain and click the " .  
                                                                                             "button to select all genomes with that genus, species, " .  
                                                                                             "or strain name.");  
         # Next are the buttons to set and clear selections.  
         push @lines, "<br />";  
         push @lines, "<INPUT type=\"button\" name=\"ClearAll\" class=\"bigButton\"  value=\"Clear All\" onClick=\"clearAll($menuName); $showSelect\" />";  
         push @lines, "<INPUT type=\"button\" name=\"SelectAll\" class=\"bigButton\" value=\"Select All\" onClick=\"selectAll($menuName); $showSelect\" />";  
         push @lines, "<INPUT type=\"button\" name=\"NMPDROnly\" class=\"bigButton\"  value=\"Select NMPDR\" onClick=\"selectSome($menuName, $nmpdrCount, true); $showSelect\" />";  
         push @lines, "<INPUT type=\"button\" name=\"OtherOnly\" class=\"bigButton\" value=\"Select Supporting\" onClick=\"selectSome($menuName, $nmpdrCount, false); $showSelect\" />";  
         # Add the status display, too.  
         push @lines, "<DIV id=\"$divID\" class=\"selectStatus\"></DIV>";  
         # Queue to update the status display when the form loads. We need to modify the show statement  
         # slightly because the queued statements are executed outside the form. This may seem like a lot of  
         # trouble, but we want all of the show statement calls to be generated from a single line of code,  
         # in case we decide to twiddle the parameters.  
         $showSelect =~ s/showSelected\(/showSelected\(thisForm\./;  
         $self->QueueFormScript($showSelect);  
         # Finally, add this parameter to the list of genome parameters. This enables us to  
         # easily find all the parameters used to select one or more genomes.  
         push @{$self->{genomeParms}}, $menuName;  
     }  
     # Assemble all the lines into a string.  
     my $retVal = join("\n", @lines, "");  
1274      # Return the result.      # Return the result.
1275      return $retVal;      return $retVal;
1276  }  }
1277    
1278  =head3 PropertyMenu  =head3 PropertyMenu
1279    
1280  C<< my $htmlText = $shelp->PropertyMenu($menuName, $selected, $force); >>      my $htmlText = $shelp->PropertyMenu($menuName, $selected, $force);
1281    
1282  Generate a property name dropdown menu.  Generate a property name dropdown menu.
1283    
# Line 1404  Line 1319 
1319      # Get all the property names, putting them after the null choice if one exists.      # Get all the property names, putting them after the null choice if one exists.
1320      push @propNames, $sprout->GetChoices('Property', 'property-name');      push @propNames, $sprout->GetChoices('Property', 'property-name');
1321      # Create a menu from them.      # Create a menu from them.
1322      my $retVal = $cgi->popup_menu(-name=> $menuName, -values => \@propNames,      my $retVal = CGI::popup_menu(-name=> $menuName, -values => \@propNames,
1323                                    -default => $selected);                                    -default => $selected);
1324      # Return the result.      # Return the result.
1325      return $retVal;      return $retVal;
# Line 1412  Line 1327 
1327    
1328  =head3 MakeTable  =head3 MakeTable
1329    
1330  C<< my $htmlText = $shelp->MakeTable(\@rows); >>      my $htmlText = $shelp->MakeTable(\@rows);
1331    
1332  Create a table from a group of table rows. The table rows must be fully pre-formatted: in  Create a table from a group of table rows. The table rows must be fully pre-formatted: in
1333  other words, each must have the TR and TD tags included.  other words, each must have the TR and TD tags included.
# Line 1466  Line 1381 
1381          }          }
1382      }      }
1383      # Create the table.      # Create the table.
1384      my $retVal = $cgi->table({border => 2, cellspacing => 2,      my $retVal = CGI::table({border => 2, cellspacing => 2,
1385                                width => 700, class => 'search'},                                width => 700, class => 'search'},
1386                               @{$rows});                               @{$rows});
1387      # Return the result.      # Return the result.
# Line 1475  Line 1390 
1390    
1391  =head3 SubmitRow  =head3 SubmitRow
1392    
1393  C<< my $htmlText = $shelp->SubmitRow($caption); >>      my $htmlText = $shelp->SubmitRow($caption);
1394    
1395  Returns the HTML text for the row containing the page size control  Returns the HTML text for the row containing the page size control
1396  and the submit button. All searches should have this row somewhere  and the submit button. All searches should have this row somewhere
# Line 1507  Line 1422 
1422      # Get the current feature ID type.      # Get the current feature ID type.
1423      my $aliasType = $self->GetPreferredAliasType();      my $aliasType = $self->GetPreferredAliasType();
1424      # Create the rows.      # Create the rows.
1425      my $retVal = $cgi->Tr($cgi->td("ID Type"), $cgi->td({ colspan => 2 },      my $retVal = CGI::Tr(CGI::td("Identifier Type "),
1426                                                          $cgi->popup_menu(-name => 'AliasType',                            CGI::td({ colspan => 2 },
1427                                       CGI::popup_menu(-name => 'AliasType',
1428                                                                           -values => ['FIG', AliasAnalysis::AliasTypes() ],                                                                           -values => ['FIG', AliasAnalysis::AliasTypes() ],
1429                                                                           -default => $aliasType) .                                                                           -default => $aliasType) .
1430                                                          Hint("Specify how you want gene names to be displayed."))) .                                     Hint("Identifier Type", "Specify how you want gene names to be displayed."))) .
1431                   "\n" .                   "\n" .
1432                   $cgi->Tr($cgi->td("Results/Page"),                   CGI::Tr(CGI::td("Results/Page"),
1433                            $cgi->td($cgi->popup_menu(-name => 'PageSize',                            CGI::td(CGI::popup_menu(-name => 'PageSize',
1434                                                      -values => [10, 25, 50, 100, 1000],                                                      -values => [10, 25, 50, 100, 1000],
1435                                                      -default => $pageSize)),                                                      -default => $pageSize)),
1436                            $cgi->td($cgi->submit(-class => 'goButton',                            CGI::td(CGI::submit(-class => 'goButton',
1437                                                  -name => 'Search',                                                  -name => 'Search',
1438                                                  -value => $realCaption)));                                                  -value => $realCaption)));
1439      # Return the result.      # Return the result.
# Line 1526  Line 1442 
1442    
1443  =head3 GetGenomes  =head3 GetGenomes
1444    
1445  C<< my @genomeList = $shelp->GetGenomes($parmName); >>      my @genomeList = $shelp->GetGenomes($parmName);
1446    
1447  Return the list of genomes specified by the specified CGI query parameter.  Return the list of genomes specified by the specified CGI query parameter.
1448  If the request method is POST, then the list of genome IDs is returned  If the request method is POST, then the list of genome IDs is returned
# Line 1568  Line 1484 
1484      return @retVal;      return @retVal;
1485  }  }
1486    
 =head3 GetHelpText  
   
 C<< my $htmlText = $shelp->GetHelpText(); >>  
   
 Get the help text for this search. The help text is stored in files on the template  
 server. The help text for a specific search is taken from a file named  
 C<SearchHelp_>I<class>C<.inc> in the template directory C<$FIG_Config::template_url>.  
 There are also three standard help files: C<SearchHelp1_Filtering.inc> describes the  
 feature filtering performed by the B<FeatureQuery> object, C<SearchHelp1_GenomeControl.inc>  
 describes how to use a multiple-selection genome control, and C<SearchHelp1_Standard.inc>  
 describes the standard controls for a search, such as page size, URL display, and  
 external alias display.  
   
 =cut  
   
 sub GetHelpText {  
     # Get the parameters.  
     my ($self) = @_;  
     # Create a list to hold the pieces of the help.  
     my @helps = ();  
     # Get the template directory URL.  
     my $urlBase = $FIG_Config::template_url;  
     # Start with the specific help.  
     my $class = $self->{class};  
     push @helps, PageBuilder::GetPage("$urlBase/SearchHelp_$class.inc");  
     # Add the genome control help if needed.  
     if (scalar @{$self->{genomeParms}}) {  
         push @helps, PageBuilder::GetPage("$urlBase/SearchHelp1_GenomeControl.inc");  
     }  
     # Next the filter help.  
     if ($self->{filtered}) {  
         push @helps, PageBuilder::GetPage("$urlBase/SearchHelp1_Filtering.inc");  
     }  
     # Finally, the standard help.  
     push @helps, PageBuilder::GetPage("$urlBase/SearchHelp1_Standard.inc");  
     # Assemble the pieces.  
     my $retVal = join("\n<p>&nbsp;</p>\n", @helps);  
     # Return the result.  
     return $retVal;  
 }  
   
1487  =head3 ComputeSearchURL  =head3 ComputeSearchURL
1488    
1489  C<< my $url = $shelp->ComputeSearchURL(%overrides); >>      my $url = $shelp->ComputeSearchURL(%overrides);
1490    
1491  Compute the GET-style URL for the current search. In order for this to work, there  Compute the GET-style URL for the current search. In order for this to work, there
1492  must be a copy of the search form on the current page. This will always be the  must be a copy of the search form on the current page. This will always be the
# Line 1644  Line 1519 
1519      my $cgi = $self->Q();      my $cgi = $self->Q();
1520      my $sprout = $self->DB();      my $sprout = $self->DB();
1521      # Start with the full URL.      # Start with the full URL.
1522      my $retVal = $cgi->url(-full => 1);      my $retVal = "$FIG_Config::cgi_url/SearchSkeleton.cgi";
1523      # Get all the query parameters in a hash.      # Get all the query parameters in a hash.
1524      my %parms = $cgi->Vars();      my %parms = $cgi->Vars();
1525      # Now we need to do some fixing. Each multi-valued parameter is encoded as a string with null      # Now we need to do some fixing. Each multi-valued parameter is encoded as a string with null
# Line 1704  Line 1579 
1579    
1580  =head3 AdvancedClassList  =head3 AdvancedClassList
1581    
1582  C<< my @classes = SearchHelper::AdvancedClassList(); >>      my @classes = SearchHelper::AdvancedClassList();
1583    
1584  Return a list of advanced class names. This list is used to generate the directory  Return a list of advanced class names. This list is used to generate the directory
1585  of available searches on the search page.  of available searches on the search page.
# Line 1727  Line 1602 
1602    
1603  =head3 SelectionTree  =head3 SelectionTree
1604    
1605  C<< my $htmlText = SearchHelper::SelectionTree($cgi, \%tree, %options); >>      my $htmlText = SearchHelper::SelectionTree($cgi, \%tree, %options);
1606    
1607  Display a selection tree.  Display a selection tree.
1608    
# Line 1836  Line 1711 
1711  =item nodeImageClosed  =item nodeImageClosed
1712    
1713  URL of the image to display next to the tree nodes when they are collapsed. Clicking  URL of the image to display next to the tree nodes when they are collapsed. Clicking
1714  on the image will expand a section of the tree. The default is C<../FIG/Html/plus.gif>.  on the image will expand a section of the tree. The default is C<plus.gif>.
1715    
1716  =item nodeImageOpen  =item nodeImageOpen
1717    
1718  URL of the image to display next to the tree nodes when they are expanded. Clicking  URL of the image to display next to the tree nodes when they are expanded. Clicking
1719  on the image will collapse a section of the tree. The default is C<../FIG/Html/minus.gif>.  on the image will collapse a section of the tree. The default is C<minus.gif>.
1720    
1721  =item style  =item style
1722    
# Line 1881  Line 1756 
1756      my ($cgi, $tree, %options) = @_;      my ($cgi, $tree, %options) = @_;
1757      # Get the options.      # Get the options.
1758      my $optionThing = Tracer::GetOptions({ name => 'selection',      my $optionThing = Tracer::GetOptions({ name => 'selection',
1759                                             nodeImageClosed => '../FIG/Html/plus.gif',                                             nodeImageClosed => "$FIG_Config::cgi_url/Html/plus.gif",
1760                                             nodeImageOpen => '../FIG/Html/minus.gif',                                             nodeImageOpen => "$FIG_Config::cgi_url/Html/minus.gif",
1761                                             style => 'tree',                                             style => 'tree',
1762                                             target => '_self',                                             target => '_self',
1763                                             selected => undef},                                             selected => undef},
# Line 1901  Line 1776 
1776              Confess("Hash reference found at start of selection tree. The tree as a whole cannot have attributes, only tree nodes.");              Confess("Hash reference found at start of selection tree. The tree as a whole cannot have attributes, only tree nodes.");
1777          } else {          } else {
1778              # Here we have a real tree. Apply the tree style.              # Here we have a real tree. Apply the tree style.
1779              push @retVal, $cgi->start_div({ class => $optionThing->{style} });              push @retVal, CGI::start_div({ class => $optionThing->{style} });
1780              # Give us a DIV ID.              # Give us a DIV ID.
1781              my $divID = GetDivID($optionThing->{name});              my $divID = GetDivID($optionThing->{name});
1782              # Show the tree.              # Show the tree.
1783              push @retVal, ShowBranch($cgi, "(root)", $divID, $tree, $optionThing, 'block');              push @retVal, ShowBranch($cgi, "(root)", $divID, $tree, $optionThing, 'block');
1784              # Close the DIV block.              # Close the DIV block.
1785              push @retVal, $cgi->end_div();              push @retVal, CGI::end_div();
1786          }          }
1787      }      }
1788      # Return the result.      # Return the result.
# Line 1916  Line 1791 
1791    
1792  =head3 ShowBranch  =head3 ShowBranch
1793    
1794  C<< my @htmlLines = SearchHelper::ShowBranch($cgi, $label, $id, $branch, $options, $displayType); >>      my @htmlLines = SearchHelper::ShowBranch($cgi, $label, $id, $branch, $options, $displayType);
1795    
1796  This is a recursive method that displays a branch of the tree.  This is a recursive method that displays a branch of the tree.
1797    
# Line 1965  Line 1840 
1840      # Declare the return variable.      # Declare the return variable.
1841      my @retVal = ();      my @retVal = ();
1842      # Start the branch.      # Start the branch.
1843      push @retVal, $cgi->start_ul({ id => $id, style => "display:$displayType" });      push @retVal, CGI::start_ul({ id => $id, style => "display:$displayType" });
1844      # Check for the hash and choose the start location accordingly.      # Check for the hash and choose the start location accordingly.
1845      my $i0 = (ref $branch->[0] eq 'HASH' ? 1 : 0);      my $i0 = (ref $branch->[0] eq 'HASH' ? 1 : 0);
1846      # Get the list length.      # Get the list length.
# Line 2011  Line 1886 
1886                      # If we have children, create the child list with a recursive call.                      # If we have children, create the child list with a recursive call.
1887                      if ($hasChildren) {                      if ($hasChildren) {
1888                          Trace("Processing children of $myLabel.") if T(4);                          Trace("Processing children of $myLabel.") if T(4);
1889                          push @childHtml, ShowBranch($cgi, $myLabel, $myID, $myContent, $options, 'none');                          push @childHtml, ShowBranch($cgi, $myLabel, $myID, $myContent, $options, 'block');
1890                          Trace("Children of $myLabel finished.") if T(4);                          Trace("Children of $myLabel finished.") if T(4);
1891                      }                      }
1892                  }                  }
# Line 2023  Line 1898 
1898              # closed images.              # closed images.
1899              my @images = ($options->{nodeImageOpen}, $options->{nodeImageClosed});              my @images = ($options->{nodeImageOpen}, $options->{nodeImageClosed});
1900              my $image = $images[$hasChildren];              my $image = $images[$hasChildren];
1901              my $prefixHtml = $cgi->img({src => $image, id => "${myID}img"});              my $prefixHtml = CGI::img({src => $image, id => "${myID}img"});
1902              if ($hasChildren) {              if ($hasChildren) {
1903                  # If there are children, we wrap the image in a toggle hyperlink.                  # If there are children, we wrap the image in a toggle hyperlink.
1904                  $prefixHtml = $cgi->a({ onClick => "javascript:treeToggle('$myID','$images[0]', '$images[1]')" },                  $prefixHtml = CGI::a({ onClick => "javascript:treeToggle('$myID','$images[0]', '$images[1]')" },
1905                                        $prefixHtml);                                        $prefixHtml);
1906              }              }
1907              # Now the radio button, if any. Note we use "defined" in case the user wants the              # Now the radio button, if any. Note we use "defined" in case the user wants the
# Line 2043  Line 1918 
1918                  if (defined $options->{selected} && $options->{selected} eq $attrHash->{value}) {                  if (defined $options->{selected} && $options->{selected} eq $attrHash->{value}) {
1919                      $radioParms->{checked} = undef;                      $radioParms->{checked} = undef;
1920                  }                  }
1921                  $prefixHtml .= $cgi->input($radioParms);                  $prefixHtml .= CGI::input($radioParms);
1922              }              }
1923              # Next, we format the label.              # Next, we format the label.
1924              my $labelHtml = $myLabel;              my $labelHtml = $myLabel;
1925              Trace("Formatting tree node for \"$myLabel\".") if T(4);              Trace("Formatting tree node for \"$myLabel\".") if T(4);
1926              # Apply a hyperlink if necessary.              # Apply a hyperlink if necessary.
1927              if (defined $attrHash->{link}) {              if (defined $attrHash->{link}) {
1928                  $labelHtml = $cgi->a({ href => $attrHash->{link}, target => $options->{target} },                  $labelHtml = CGI::a({ href => $attrHash->{link}, target => $options->{target} },
1929                                       $labelHtml);                                       $labelHtml);
1930              }              }
1931              # Finally, roll up the child HTML. If there are no children, we'll get a null string              # Finally, roll up the child HTML. If there are no children, we'll get a null string
1932              # here.              # here.
1933              my $childHtml = join("\n", @childHtml);              my $childHtml = join("\n", @childHtml);
1934              # Now we have all the pieces, so we can put them together.              # Now we have all the pieces, so we can put them together.
1935              push @retVal, $cgi->li("$prefixHtml$labelHtml$childHtml");              push @retVal, CGI::li("$prefixHtml$labelHtml$childHtml");
1936          }          }
1937      }      }
1938      # Close the tree branch.      # Close the tree branch.
1939      push @retVal, $cgi->end_ul();      push @retVal, CGI::end_ul();
1940      # Return the result.      # Return the result.
1941      return @retVal;      return @retVal;
1942  }  }
1943    
1944  =head3 GetDivID  =head3 GetDivID
1945    
1946  C<< my $idString = SearchHelper::GetDivID($name); >>      my $idString = SearchHelper::GetDivID($name);
1947    
1948  Return a new HTML ID string.  Return a new HTML ID string.
1949    
# Line 2099  Line 1974 
1974    
1975  =head3 PrintLine  =head3 PrintLine
1976    
1977  C<< $shelp->PrintLine($message); >>      $shelp->PrintLine($message);
1978    
1979  Print a line of CGI output. This is used during the operation of the B<Find> method while  Print a line of CGI output. This is used during the operation of the B<Find> method while
1980  searching, so the user sees progress in real-time.  searching, so the user sees progress in real-time.
# Line 2117  Line 1992 
1992  sub PrintLine {  sub PrintLine {
1993      # Get the parameters.      # Get the parameters.
1994      my ($self, $message) = @_;      my ($self, $message) = @_;
1995      # Send them to the output.      # Send the message to the output.
1996      print "$message\n";      print "$message\n";
1997  }  }
1998    
1999  =head3 GetHelper  =head3 GetHelper
2000    
2001  C<< my $shelp = SearchHelper::GetHelper($parm, $type => $className); >>      my $shelp = SearchHelper::GetHelper($parm, $type => $className);
2002    
2003  Return a helper object with the given class name. If no such class exists, an  Return a helper object with the given class name. If no such class exists, an
2004  error will be thrown.  error will be thrown.
# Line 2169  Line 2044 
2044          # Commit suicide if it didn't work.          # Commit suicide if it didn't work.
2045          if (! defined $retVal) {          if (! defined $retVal) {
2046              die "Could not find a $type handler of type $className.";              die "Could not find a $type handler of type $className.";
2047            } else {
2048                # Perform any necessary subclass initialization.
2049                $retVal->Initialize();
2050          }          }
2051      };      };
2052      # Check for errors.      # Check for errors.
# Line 2181  Line 2059 
2059    
2060  =head3 SaveOrganismData  =head3 SaveOrganismData
2061    
2062  C<< my ($name, $displayGroup) = $shelp->SaveOrganismData($group, $genomeID, $genus, $species, $strain, $taxonomy); >>      my ($name, $displayGroup, $domain) = $shelp->SaveOrganismData($group, $genomeID, $genus, $species, $strain, $taxonomy);
2063    
2064  Format the name of an organism and the display version of its group name. The incoming  Format the name of an organism and the display version of its group name. The incoming
2065  data should be the relevant fields from the B<Genome> record in the database. The  data should be the relevant fields from the B<Genome> record in the database. The
# Line 2242  Line 2120 
2120          # Compute the display group. This is currently the same as the incoming group          # Compute the display group. This is currently the same as the incoming group
2121          # name unless it's the supporting group, which is nulled out.          # name unless it's the supporting group, which is nulled out.
2122          $displayGroup = ($group eq $FIG_Config::otherGroup ? "" : $group);          $displayGroup = ($group eq $FIG_Config::otherGroup ? "" : $group);
2123            Trace("Group = $displayGroup, translated from \"$group\".") if T(4);
2124      }      }
2125      # Compute the domain from the taxonomy.      # Compute the domain from the taxonomy.
2126      my ($domain) = split /\s*;\s*/, $taxonomy, 2;      my ($domain) = split /\s*;\s*/, $taxonomy, 2;
# Line 2254  Line 2133 
2133    
2134  =head3 ValidateKeywords  =head3 ValidateKeywords
2135    
2136  C<< my $okFlag = $shelp->ValidateKeywords($keywordString, $required); >>      my $okFlag = $shelp->ValidateKeywords($keywordString, $required);
2137    
2138  Insure that a keyword string is reasonably valid. If it is invalid, a message will be  Insure that a keyword string is reasonably valid. If it is invalid, a message will be
2139  set.  set.
# Line 2304  Line 2183 
2183    
2184  =head3 TuningParameters  =head3 TuningParameters
2185    
2186  C<< my $options = $shelp->TuningParameters(%parmHash); >>      my $options = $shelp->TuningParameters(%parmHash);
2187    
2188  Retrieve tuning parameters from the CGI query object. The parameter is a hash that maps parameter names  Retrieve tuning parameters from the CGI query object. The parameter is a hash that maps parameter names
2189  to their default values. The parameters and their values will be returned as a hash reference.  to their default values. The parameters and their values will be returned as a hash reference.
# Line 2347  Line 2226 
2226    
2227  =head3 GetPreferredAliasType  =head3 GetPreferredAliasType
2228    
2229  C<< my $type = $shelp->GetPreferredAliasType(); >>      my $type = $shelp->GetPreferredAliasType();
2230    
2231  Return the preferred alias type for the current session. This information is stored  Return the preferred alias type for the current session. This information is stored
2232  in the C<AliasType> parameter of the CGI query object, and the default is C<FIG>  in the C<AliasType> parameter of the CGI query object, and the default is C<FIG>
# Line 2365  Line 2244 
2244      return $retVal;      return $retVal;
2245  }  }
2246    
2247    =head3 Hint
2248    
2249        my $htmlText = SearchHelper::Hint($wikiPage, $hintText);
2250    
2251    Return the HTML for a small question mark that displays the specified hint text when it is clicked.
2252    This HTML can be put in forms to provide a useful hinting mechanism.
2253    
2254    =over 4
2255    
2256    =item wikiPage
2257    
2258    Name of the wiki page to be popped up when the hint mark is clicked.
2259    
2260    =item hintText
2261    
2262    Text to display for the hint. It is raw html, but may not contain any double quotes.
2263    
2264    =item RETURN
2265    
2266    Returns the html for the hint facility. The resulting html shows a small button-like thing that
2267    uses the standard FIG popup technology.
2268    
2269    =back
2270    
2271    =cut
2272    
2273    sub Hint {
2274        # Get the parameters.
2275        my ($wikiPage, $hintText) = @_;
2276        # Ask Sprout to draw the hint button for us.
2277        return Sprout::Hint($wikiPage, $hintText);
2278    }
2279    
2280    
2281    
2282  =head2 Virtual Methods  =head2 Virtual Methods
2283    
2284    =head3 HeaderHtml
2285    
2286        my $html = $shelp->HeaderHtml();
2287    
2288    Generate HTML for the HTML header. If extra styles or javascript are required,
2289    they should go in here.
2290    
2291    =cut
2292    
2293    sub HeaderHtml {
2294        return "";
2295    }
2296    
2297  =head3 Form  =head3 Form
2298    
2299  C<< my $html = $shelp->Form(); >>      my $html = $shelp->Form($mode);
2300    
2301    Generate the HTML for a form to request a new search. If the subclass does not
2302    override this method, then the search is formless, and must be started from an
2303    external page.
2304    
2305    =cut
2306    
2307  Generate the HTML for a form to request a new search.  sub Form {
2308        # Get the parameters.
2309        my ($self) = @_;
2310        return "";
2311    }
2312    
2313  =head3 Find  =head3 Find
2314    
2315  C<< my $resultCount = $shelp->Find(); >>      my $resultCount = $shelp->Find();
2316    
2317  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
2318  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 2393  Line 2330 
2330    
2331  =head3 Description  =head3 Description
2332    
2333  C<< my $htmlText = $shelp->Description(); >>      my $htmlText = $shelp->Description();
2334    
2335  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
2336  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 2410  Line 2347 
2347    
2348  =head3 SearchTitle  =head3 SearchTitle
2349    
2350  C<< my $titleHtml = $shelp->SearchTitle(); >>      my $titleHtml = $shelp->SearchTitle();
2351    
2352  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.
2353  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 2429  Line 2366 
2366    
2367  =head3 DefaultColumns  =head3 DefaultColumns
2368    
2369  C<< $shelp->DefaultColumns($rhelp); >>      $shelp->DefaultColumns($rhelp);
2370    
2371  Store the default columns in the result helper. The default action is just to ask  Store the default columns in the result helper. The default action is just to ask
2372  the result helper for its default columns, but this may be changed by overriding  the result helper for its default columns, but this may be changed by overriding
# Line 2454  Line 2391 
2391      $rhelp->SetColumns(@cols);      $rhelp->SetColumns(@cols);
2392  }  }
2393    
 =head3 Hint  
2394    
2395  C<< my $htmlText = SearchHelper::Hint($hintText); >>  =head3 Initialize
2396    
2397  Return the HTML for a small question mark that displays the specified hint text when it is clicked.      $shelp->Initialize();
2398  This HTML can be put in forms to provide a useful hinting mechanism.  
2399    Perform any initialization required after construction of the helper.
2400    
2401    =cut
2402    
2403    sub Initialize {
2404        # The default is to do nothing.
2405    }
2406    
2407    =head3 GetResultHelper
2408    
2409        my $rhelp = $shelp->GetResultHelper($className);
2410    
2411    Return a result helper for this search helper. The default action is to create
2412    a result helper from scratch; however, if the subclass has an internal result
2413    helper it can override this method to return it without having to create a new
2414    one.
2415    
2416  =over 4  =over 4
2417    
2418  =item hintText  =item className
2419    
2420  Text to display for the hint. It is raw html, but may not contain any double quotes.  Result helper class name.
2421    
2422  =item RETURN  =item RETURN
2423    
2424  Returns the html for the hint facility. The resulting html shows a small button-like thing that  Returns a result helper of the specified class connected to this search helper.
 uses the standard FIG popup technology.  
2425    
2426  =back  =back
2427    
2428  =cut  =cut
2429    
2430  sub Hint {  sub GetResultHelper {
2431      # Get the parameters.      # Get the parameters.
2432      my ($hintText) = @_;      my ($self, $className) = @_;
2433      # Escape the single quotes.      # Create the helper.
2434      my $quotedText = $hintText;      my $retVal = GetHelper($self, RH => $className);
2435      $quotedText =~ s/'/\\'/g;      # return it.
     # Create the html.  
     my $retVal = "&nbsp;<input type=\"button\" class=\"hintbutton\" onMouseOver=\"javascript:if (!this.tooltip) { " .  
                  "this.tooltip = new Popup_Tooltip(this, 'Search Hint', '$quotedText', '', 1); this.tooltip.addHandler(); } " .  
                  "return false;\" value=\"?\" />";  
     # Return it.  
2436      return $retVal;      return $retVal;
2437  }  }
2438    
   
2439  1;  1;

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