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revision 1.31, Fri May 11 06:28:21 2007 UTC revision 1.44, Thu Feb 5 07:17:03 2009 UTC
# Line 10  Line 10 
10      use File::Path;      use File::Path;
11      use File::stat;      use File::stat;
12      use LWP::UserAgent;      use LWP::UserAgent;
13      use Time::HiRes 'gettimeofday';      use FIGRules;
14      use Sprout;      use Sprout;
15      use SFXlate;      use SFXlate;
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;
22        use CGI::Cookie;
23        use FreezeThaw qw(freeze thaw);
24    
25  =head1 Search Helper Base Class  =head1 Search Helper Base Class
26    
# Line 65  Line 67 
67    
68  =item orgs  =item orgs
69    
70  Reference to a hash mapping genome IDs to organism names.  Reference to a hash mapping genome IDs to organism data. (Used to
71    improve performance.)
72    
73  =item name  =item name
74    
# Line 83  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 filtered  =item notices
   
 TRUE if this is a feature-filtered search, else FALSE. B<NOTE> that this  
 field is updated by the B<FeatureQuery> object.  
90    
91  =item extraPos  A list of messages to be put in the notice file.
   
 Hash indicating which extra columns should be put at the end. Extra columns  
 not mentioned in this hash are put at the beginning. Use the L</SetExtraPos>  
 method to change this option.  
92    
93  =back  =back
94    
# Line 109  Line 105 
105  =item 2  =item 2
106    
107  Create a new subclass of this object and implement each of the virtual methods. The  Create a new subclass of this object and implement each of the virtual methods. The
108  name of the subclass must be C<SH>I<className>.  name of the subclass must be C<SH>I<className>, where I<className> is the
109    type of search.
110    
111  =item 3  =item 3
112    
# Line 119  Line 116 
116    
117  =item 4  =item 4
118    
119  In the C<SearchSkeleton.cgi> script and add a C<use> statement for your search tool.  If your search produces a result for which a helper does not exist, you
120    must create a new subclass of B<ResultHelper>. Its name must be
121    C<RH>I<className>, where I<className> is the type of result.
122    
123  =back  =back
124    
# Line 155  Line 154 
154    
155  Several helper methods are provided for particular purposes.  Several helper methods are provided for particular purposes.
156    
 =over 4  
   
 =item 1  
   
157  L</NmpdrGenomeMenu> generates a control for selecting one or more genomes. Use  L</NmpdrGenomeMenu> generates a control for selecting one or more genomes. Use
158  L</GetGenomes> to retrieve all the genomes passed in for a specified parameter  L</GetGenomes> to retrieve all the genomes passed in for a specified parameter
159  name. Note that as an assist to people working with GET-style links, if no  name. Note that as an assist to people working with GET-style links, if no
160  genomes are specified and the incoming request style is GET, all genomes will  genomes are specified and the incoming request style is GET, all genomes will
161  be returned.  be returned.
162    
 =item 2  
   
 L</FeatureFilterRow> formats several rows of controls for filtering features.  
 When you start building the code for the L</Find> method, you can use a  
 B<FeatureQuery> object to automatically filter each genome's features using  
 the values from the filter controls.  
   
 =item 3  
   
163  L</QueueFormScript> allows you to queue JavaScript statements for execution  L</QueueFormScript> allows you to queue JavaScript statements for execution
164  after the form is fully generated. If you are using very complicated  after the form is fully generated. If you are using very complicated
165  form controls, the L</QueueFormScript> method allows you to perform  form controls, the L</QueueFormScript> method allows you to perform
166  JavaScript initialization. The L</NmpdrGenomeMenu> control uses this  JavaScript initialization. The L</NmpdrGenomeMenu> control uses this
167  facility to display a list of the pre-selected genomes.  facility to display a list of the pre-selected genomes.
168    
 =back  
   
 If you are doing a feature search, you can also change the list of feature  
 columns displayed and their display order by overriding  
 L</DefaultFeatureColumns>.  
   
169  Finally, when generating the code for your controls, be sure to use any incoming  Finally, when generating the code for your controls, be sure to use any incoming
170  query parameters as default values so that the search request is persistent.  query parameters as default values so that the search request is persistent.
171    
172  =head3 Finding Search Results  =head3 Finding Search Results
173    
174  The L</Find> method is used to create the search results. For a search that  The L</Find> method is used to create the search results. The basic code
175  wants to return features (which is most of them), the basic code structure  structure would work as follows.
 would work as follows. It is assumed that the L</FeatureFilterRows> method  
 has been used to create feature filtering parameters.  
176    
177      sub Find {      sub Find {
178          my ($self) = @_;          my ($self) = @_;
# Line 207  Line 185 
185          ... validate the parameters ...          ... validate the parameters ...
186          if (... invalid parameters...) {          if (... invalid parameters...) {
187              $self->SetMessage(...appropriate message...);              $self->SetMessage(...appropriate message...);
188          } elsif (FeatureQuery::Valid($self)) {          } else {
189                # Determine the result type.
190                my $rhelp = SearchHelper::GetHelper($self, RH => $resultType);
191                # Specify the columns.
192                $self->DefaultColumns($rhelp);
193                # You may want to add extra columns. $name is the column name and
194                # $loc is its location. The other parameters take their names from the
195                # corresponding column methods.
196                $rhelp->AddExtraColumn($name => $loc, style => $style, download => $flag,
197                    title => $title);
198                # Some searches require optional columns that are configured by the
199                # user or by the search query itself. There are some special methods
200                # for this in the result helpers, but there's also the direct approach
201                # shown below.
202                $rhelp->AddOptionalColumn($name => $loc);
203              # Initialize the session file.              # Initialize the session file.
204              $self->OpenSession();              $self->OpenSession($rhelp);
205              # Initialize the result counter.              # Initialize the result counter.
206              $retVal = 0;              $retVal = 0;
207              ... get a list of genomes ...              ... set up to loop through the results ...
208              for my $genomeID (... each genome ...) {              while (...more results...) {
209                  my $fq = FeatureQuery->new($self, $genomeID);                  ...compute extra columns and call PutExtraColumns...
210                  while (my $feature = $fq->Fetch()) {                  $rhelp->PutData($sortKey, $objectID, $record);
                     ... examine the feature ...  
                     if (... we want to keep it ...) {  
                         $self->PutFeature($fq);  
211                          $retVal++;                          $retVal++;
212                      }                      }
                 }  
             }  
213              # Close the session file.              # Close the session file.
214              $self->CloseSession();              $self->CloseSession();
215          }          }
# Line 231  Line 218 
218      }      }
219    
220  A Find method is of course much more complicated than generating a form, and there  A Find method is of course much more complicated than generating a form, and there
221  are variations on the above theme. For example, you could eschew feature filtering  are variations on the above theme.
 entirely in favor of your own custom filtering, you could include extra columns  
 in the output, or you could search for something that's not a feature at all. The  
 above code is just a loose framework.  
222    
223  In addition to the finding and filtering, it is necessary to send status messages  In addition to the finding and filtering, it is necessary to send status messages
224  to the output so that the user does not get bored waiting for results. The L</PrintLine>  to the output so that the user does not get bored waiting for results. The L</PrintLine>
# Line 246  Line 230 
230  The break tag is optional. When the Find method gets control, a paragraph will  The break tag is optional. When the Find method gets control, a paragraph will
231  have been started so that everything is XHTML-compliant.  have been started so that everything is XHTML-compliant.
232    
 If you wish to add your own extra columns to the output, use the B<AddExtraColumns>  
 method of the feature query object.  
   
     $fq->AddExtraColumns(score => $sc);  
   
233  The L</Find> method must return C<undef> if the search parameters are invalid. If this  The L</Find> method must return C<undef> if the search parameters are invalid. If this
234  is the case, then a message describing the problem should be passed to the framework  is the case, then a message describing the problem should be passed to the framework
235  by calling L</SetMessage>. If the parameters are valid, then the method must return  by calling L</SetMessage>. If the parameters are valid, then the method must return
# Line 267  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 284  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 = NewSessionID();              $session_id = FIGRules::NewSessionID();
278                Trace("New session ID is $session_id.") if T(3);
279                $session_cookie = new CGI::Cookie(-name => $class,
280                                                  -value => $session_id);
281                $session_cookie->bake();
282            } else {
283                # Here we're recovering an old session. The session ID is
284                # used to find any old search options lying around, but we're
285                # still considered a new session.
286                $session_id = $session_cookie->value();
287                Trace("Session $session_id recovered from cookie.") if T(3);
288            }
289            # Denote this is a new session.
290          $type = "new";          $type = "new";
291            # Put the session IS in the parameters.
292          $cgi->param(-name => 'SessionID', -value => $session_id);          $cgi->param(-name => 'SessionID', -value => $session_id);
293      } else {      } else {
294          Trace("Session ID is $session_id.") if T(3);          Trace("Session ID is $session_id.") if T(3);
295      }      }
296        Trace("Computing subclass.") if T(3);
297      # Compute the subclass name.      # Compute the subclass name.
298      my $subClass;      my $subClass;
299      if ($class =~ /SH(.+)$/) {      if ($class =~ /SH(.+)$/) {
# Line 307  Line 304 
304          # process search results.          # process search results.
305          $subClass = 'SearchHelper';          $subClass = 'SearchHelper';
306      }      }
307        Trace("Subclass name is $subClass.") if T(3);
308      # Insure everybody knows we're in Sprout mode.      # Insure everybody knows we're in Sprout mode.
309      $cgi->param(-name => 'SPROUT', -value => 1);      $cgi->param(-name => 'SPROUT', -value => 1);
310      # Generate the form name.      # Generate the form name.
311      my $formName = "$class$formCount";      my $formName = "$class$formCount";
312      $formCount++;      $formCount++;
313        Trace("Creating helper.") if T(3);
314      # Create the shelp object. It contains the query object (with the session ID)      # Create the shelp object. It contains the query object (with the session ID)
315      # as well as an indicator as to whether or not the session is new, plus the      # as well as an indicator as to whether or not the session is new, plus the
316      # class name and a placeholder for the Sprout object.      # class name and a placeholder for the Sprout object.
# Line 325  Line 324 
324                    scriptQueue => [],                    scriptQueue => [],
325                    genomeList => undef,                    genomeList => undef,
326                    genomeParms => [],                    genomeParms => [],
327                    filtered => 0,                    notices => [],
                   extraPos => {},  
328                   };                   };
329      # Bless and return it.      # Bless and return it.
330      bless $retVal, $class;      bless $retVal, $class;
# Line 335  Line 333 
333    
334  =head3 Q  =head3 Q
335    
336  C<< my $query = $shelp->Q(); >>      my $query = $shelp->Q();
337    
338  Return the CGI query object.  Return the CGI query object.
339    
# Line 349  Line 347 
347  }  }
348    
349    
   
350  =head3 DB  =head3 DB
351    
352  C<< my $sprout = $shelp->DB(); >>      my $sprout = $shelp->DB();
353    
354  Return the Sprout database object.  Return the Sprout database object.
355    
# Line 373  Line 370 
370    
371  =head3 IsNew  =head3 IsNew
372    
373  C<< my $flag = $shelp->IsNew(); >>      my $flag = $shelp->IsNew();
374    
375  Return TRUE if this is a new session, FALSE if this is an old session. An old  Return TRUE if this is a new session, FALSE if this is an old session. An old
376  session already has search results ready to process.  session already has search results ready to process.
# Line 387  Line 384 
384      return ($self->{type} eq 'new');      return ($self->{type} eq 'new');
385  }  }
386    
 =head3 SetExtraPos  
   
 C<< $shelp->SetExtraPos(@columnMap); >>  
   
 Indicate whether the extra columns should be in the front (C<0>) or end (C<1>) columns of the results.  
   
 =over 4  
   
 =item columnMap  
   
 A list of extra columns to display at the end.  
   
 =back  
   
 =cut  
   
 sub SetExtraPos {  
     # Get the parameters.  
     my ($self, @columnMap) = @_;  
     # Convert the column map to a hash.  
     my %map = map { $_ => 1 } @columnMap;  
     # Save a reference to it.  
     $self->{extraPos} = \%map;  
 }  
   
387  =head3 ID  =head3 ID
388    
389  C<< my $sessionID = $shelp->ID(); >>      my $sessionID = $shelp->ID();
390    
391  Return the current session ID.  Return the current session ID.
392    
# Line 429  Line 401 
401    
402  =head3 FormName  =head3 FormName
403    
404  C<< my $name = $shelp->FormName(); >>      my $name = $shelp->FormName();
405    
406  Return the name of the form this helper object will generate.  Return the name of the form this helper object will generate.
407    
# Line 444  Line 416 
416    
417  =head3 QueueFormScript  =head3 QueueFormScript
418    
419  C<< $shelp->QueueFormScript($statement); >>      $shelp->QueueFormScript($statement);
420    
421  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
422  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 479  Line 451 
451    
452  =head3 FormStart  =head3 FormStart
453    
454  C<< my $html = $shelp->FormStart($title); >>      my $html = $shelp->FormStart($title);
455    
456  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
457  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 509  Line 481 
481      # 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
482      # case the Advanced button was used.      # case the Advanced button was used.
483      my $retVal = "<div class=\"search\">\n" .      my $retVal = "<div class=\"search\">\n" .
484                   $cgi->start_form(-method => 'POST',                   CGI::start_form(-method => 'POST',
485                                    -action => $cgi->url(-relative => 1),                                    -action => "$FIG_Config::cgi_url/wiki/rest.cgi/NmpdrPlugin/search",
486                                    -name => $self->FormName()) .                                    -name => $self->FormName()) .
487                   $cgi->hidden(-name => 'Class',                   CGI::hidden(-name => 'Class',
488                                -value => $self->{class},                                -value => $self->{class}) .
489                                -override => 1) .                   CGI::hidden(-name => 'SPROUT',
                  $cgi->hidden(-name => 'SPROUT',  
490                                -value => 1) .                                -value => 1) .
491                   $cgi->h3($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));  
     }  
492      # 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.
493      my $anchorName = $self->FormName();      my $anchorName = $self->FormName();
494      $retVal .= "<a name=\"$anchorName\"></a>\n";      $retVal .= "<a name=\"$anchorName\"></a>\n";
# Line 534  Line 498 
498    
499  =head3 FormEnd  =head3 FormEnd
500    
501  C<< my $htmlText = $shelp->FormEnd(); >>      my $htmlText = $shelp->FormEnd();
502    
503  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
504  C<div> tags.  C<div> tags.
# Line 566  Line 530 
530    
531  =head3 SetMessage  =head3 SetMessage
532    
533  C<< $shelp->SetMessage($msg); >>      $shelp->SetMessage($msg);
534    
535  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
536  if an invalid parameter value is specified.  if an invalid parameter value is specified.
# Line 590  Line 554 
554    
555  =head3 Message  =head3 Message
556    
557  C<< my $text = $shelp->Message(); >>      my $text = $shelp->Message();
558    
559  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
560  value is specified.  value is specified.
# Line 606  Line 570 
570    
571  =head3 OpenSession  =head3 OpenSession
572    
573  C<< $shelp->OpenSession(); >>      $shelp->OpenSession($rhelp);
574    
575  Set up to open the session cache file for writing. Note we don't actually  Set up the session cache file and write out the column headers.
576  open the file until after we know the column headers.  This method should not be called until all the columns have
577    been configured, including the extra columns.
578    
579    =over 4
580    
581    =item rhelp
582    
583    Result helper for formatting the output. This has the column
584    headers stored in it.
585    
586    =back
587    
588  =cut  =cut
589    
590  sub OpenSession {  sub OpenSession {
591      # Get the parameters.      # Get the parameters.
592      my ($self) = @_;      my ($self, $rhelp) = @_;
593      # Denote we have not yet written out the column headers.      # Insure the result helper is valid.
594      $self->{cols} = undef;      if (! defined($rhelp)) {
595            Confess("No result type specified for $self->{class}.");
596        } elsif(! $rhelp->isa('ResultHelper')) {
597            Confess("Invalid result type specified for $self->{class}.");
598        } else {
599            # Get the column headers and write them out.
600            my $colHdrs = $rhelp->GetColumnHeaders();
601            Trace(scalar(@{$colHdrs}) . " column headers written to output.") if T(3);
602            $self->WriteColumnHeaders(@{$colHdrs});
603        }
604  }  }
605    
606  =head3 GetCacheFileName  =head3 GetCacheFileName
607    
608  C<< my $fileName = $shelp->GetCacheFileName(); >>      my $fileName = $shelp->GetCacheFileName();
609    
610  Return the name to be used for this session's cache file.  Return the name to be used for this session's cache file.
611    
# Line 637  Line 620 
620    
621  =head3 GetTempFileName  =head3 GetTempFileName
622    
623  C<< my $fileName = $shelp->GetTempFileName($type); >>      my $fileName = $shelp->GetTempFileName($type);
624    
625  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
626  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 661  Line 644 
644      my ($self, $type) = @_;      my ($self, $type) = @_;
645      # Compute the file name. Note it gets stuffed in the FIG temporary      # Compute the file name. Note it gets stuffed in the FIG temporary
646      # directory.      # directory.
647      my $retVal = "$FIG_Config::temp/tmp_" . $self->ID() . ".$type";      my $retVal = FIGRules::GetTempFileName(sessionID => $self->ID(), extension => $type);
648      # Return the result.      # Return the result.
649      return $retVal;      return $retVal;
650  }  }
651    
652  =head3 PutFeature  =head3 WriteColumnHeaders
653    
654        $shelp->WriteColumnHeaders(@colNames);
655    
656  C<< $shelp->PutFeature($fdata); >>  Write out the column headers for the current search session. The column headers
657    are sent to the cache file, and then the cache is re-opened as a sort pipe and
658    the handle saved.
659    
660  Store a feature in the result cache. This is the workhorse method for most  =over 4
 searches, since the primary data item in the database is features.  
661    
662  For each feature, there are certain columns that are standard: the feature name, the  =item colNames
 GBrowse and protein page links, the functional assignment, and so forth. If additional  
 columns are required by a particular search subclass, they should be stored in  
 the feature query object using the B<AddExtraColumns> method. For example, the following  
 code adds columns for essentiality and virulence.  
663    
664      $fd->AddExtraColumns(essential => $essentialFlag, virulence => $vfactor);  A list of column names in the desired presentation order. For extra columns,
665      $shelp->PutFeature($fd);  the column name is the hash supplied as the column definition.
666    
667  For correct results, all values should be specified for all extra columns in all calls to  =back
 B<PutFeature>. (In particular, the column header names are computed on the first  
 call.) If a column is to be blank for the current feature, its value can be given  
 as C<undef>.  
668    
669      if (! $essentialFlag) {  =cut
670          $essentialFlag = undef;  
671    sub WriteColumnHeaders {
672        # Get the parameters.
673        my ($self, @colNames) = @_;
674        # Get the cache file name and open it for output.
675        my $fileName = $self->GetCacheFileName();
676        my $handle1 = Open(undef, ">$fileName");
677        # Freeze the column headers.
678        my @colHdrs = map { freeze($_) } @colNames;
679        # Write the column headers and close the file.
680        Tracer::PutLine($handle1, \@colHdrs);
681        close $handle1;
682        # Now open the sort pipe and save the file handle. Note how we append the
683        # sorted data to the column header row already in place. The output will
684        # contain a sort key followed by the real columns. The sort key is
685        # hacked off before going to the output file.
686        $self->{fileHandle} = Open(undef, "| sort | cut --fields=2- >>$fileName");
687      }      }
688      $fd->AddExtraColumns(essential => $essentialFlag, virulence => $vfactor);  
689      $shelp->PutFeature($fd);  =head3 SetNotice
690    
691        $shelp->SetNotice($message);
692    
693    This method creates a notice that will be displayed on the search results
694    page. After the search is complete, notices are placed in a small temporary
695    file that is checked by the results display engine.
696    
697  =over 4  =over 4
698    
699  =item fdata  =item message
700    
701  B<FeatureData> object containing the current feature data.  Message to write to the notice file.
702    
703  =back  =back
704    
705  =cut  =cut
706    
707  sub PutFeature {  sub SetNotice {
708      # Get the parameters.      # Get the parameters.
709      my ($self, $fd) = @_;      my ($self, $message) = @_;
710      # Get the CGI query object.      # Save the message.
711      my $cgi = $self->Q();      push @{$self->{notices}}, $message;
     # Get the feature data.  
     my $record = $fd->Feature();  
     my $extraCols = $fd->ExtraCols();  
     # Check for a first-call situation.  
     if (! defined $self->{cols}) {  
         Trace("Setting up the columns.") if T(3);  
         # Tell the user what's happening.  
         $self->PrintLine("Creating output columns.<br />");  
         # Here we need to set up the column information. First we accumulate the extras,  
         # sorted by column name and separate by whether they go in the beginning or the  
         # end.  
         my @xtraNamesFront = ();  
         my @xtraNamesEnd = ();  
         my $xtraPosMap = $self->{extraPos};  
         for my $col (sort keys %{$extraCols}) {  
             if ($xtraPosMap->{$col}) {  
                 push @xtraNamesEnd, "X=$col";  
             } else {  
                 push @xtraNamesFront, "X=$col";  
             }  
         }  
         # Set up the column name array.  
         my @colNames = ();  
         # Put in the extra columns that go in the beginning.  
         push @colNames, @xtraNamesFront;  
         # Add the default columns.  
         push @colNames, $self->DefaultFeatureColumns();  
         # Add any additional columns requested by the feature filter.  
         push @colNames, FeatureQuery::AdditionalColumns($self);  
         # If extras go at the end, put them in here.  
         push @colNames, @xtraNamesEnd;  
         Trace("Full column list determined.") if T(3);  
         # Save the full list.  
         $self->{cols} = \@colNames;  
         # Write out the column names. This also prepares the cache file to receive  
         # output.  
         Trace("Writing column headers.") if T(3);  
         $self->WriteColumnHeaders(@{$self->{cols}});  
         Trace("Column headers written.") if T(3);  
     }  
     # Get the feature ID.  
     my $fid = $fd->FID();  
     # Loop through the column headers, producing the desired data. The first column  
     # is the feature ID. The feature ID does not show up in the output: its purpose  
     # is to help the various output formatters.  
     my @output = ($fid);  
     for my $colName (@{$self->{cols}}) {  
         push @output, $self->FeatureColumnValue($colName, $record, $extraCols);  
     }  
     # Compute the sort key. The sort key usually floats NMPDR organism features to the  
     # top of the return list.  
     my $key = $self->SortKey($fd);  
     # Write the feature data.  
     $self->WriteColumnData($key, @output);  
712  }  }
713    
 =head3 WriteColumnHeaders  
714    
715  C<< $shelp->WriteColumnHeaders(@colNames); >>  =head3 ReadColumnHeaders
716    
717  Write out the column headers for the current search session. The column headers      my @colHdrs = $shelp->ReadColumnHeaders($fh);
718  are sent to the cache file, and then the cache is re-opened as a sort pipe and  
719  the handle saved.  Read the column headers from the specified file handle. The column headers are
720    frozen strings intermixed with frozen hash references. The strings represent
721    column names defined in the result helper. The hash references represent the
722    definitions of the extra columns.
723    
724  =over 4  =over 4
725    
726  =item colNames  =item fh
727    
728  A list of column names in the desired presentation order.  File handle from which the column headers are to be read.
729    
730    =item RETURN
731    
732    Returns a list of the column headers pulled from the specified file's first line.
733    
734  =back  =back
735    
736  =cut  =cut
737    
738  sub WriteColumnHeaders {  sub ReadColumnHeaders {
739      # Get the parameters.      # Get the parameters.
740      my ($self, @colNames) = @_;      my ($self, $fh) = @_;
741      # Get the cache file name and open it for output.      # Read and thaw the columns.
742      my $fileName = $self->GetCacheFileName();      my @retVal = map { thaw($_) } Tracer::GetLine($fh);
743      my $handle1 = Open(undef, ">$fileName");      # Return them to the caller.
744      # Write the column headers and close the file.      return @retVal;
     Tracer::PutLine($handle1, \@colNames);  
     close $handle1;  
     # Now open the sort pipe and save the file handle. Note how we append the  
     # sorted data to the column header row already in place. The output will  
     # contain a sort key followed by the real columns. The sort key is  
     # hacked off before going to the output file.  
     $self->{fileHandle} = Open(undef, "| sort | cut --fields=2- >>$fileName");  
745  }  }
746    
747  =head3 WriteColumnData  =head3 WriteColumnData
748    
749  C<< $shelp->WriteColumnData($key, @colValues); >>      $shelp->WriteColumnData($key, @colValues);
750    
751  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
752  the session file is already open for output.  the session file is already open for output.
# Line 824  Line 770 
770      my ($self, $key, @colValues) = @_;      my ($self, $key, @colValues) = @_;
771      # Write them to the cache file.      # Write them to the cache file.
772      Tracer::PutLine($self->{fileHandle}, [$key, @colValues]);      Tracer::PutLine($self->{fileHandle}, [$key, @colValues]);
773        Trace("Column data is " . join("; ", $key, @colValues) . ".") if T(4);
774  }  }
775    
776  =head3 CloseSession  =head3 CloseSession
777    
778  C<< $shelp->CloseSession(); >>      $shelp->CloseSession();
779    
780  Close the session file.  Close the session file.
781    
# Line 846  Line 793 
793          my $cgi = $self->Q();          my $cgi = $self->Q();
794          $self->PrintLine("Output formatting complete.<br />");          $self->PrintLine("Output formatting complete.<br />");
795      }      }
796        # Check for notices.
797        my @notices = @{$self->{notices}};
798        if (scalar @notices) {
799            # We have some, so put then in a notice file.
800            my $noticeFile = $self->GetTempFileName('notices');
801            my $nh = Open(undef, ">$noticeFile");
802            print $nh join("\n", @notices, "");
803            close $nh;
804            $self->PrintLine(scalar(@notices) . " notices saved.<br />");
805  }  }
   
 =head3 NewSessionID  
   
 C<< my $id = SearchHelpers::NewSessionID(); >>  
   
 Generate a new session ID for the current user.  
   
 =cut  
   
 sub NewSessionID {  
     # Declare the return variable.  
     my $retVal;  
     # Get a digest encoder.  
     my $md5 = Digest::MD5->new();  
     # Add the PID, the IP, and the time stamp. Note that the time stamp is  
     # actually two numbers, and we get them both because we're in list  
     # context.  
     $md5->add($$, $ENV{REMOTE_ADDR}, $ENV{REMOTE_PORT}, gettimeofday());  
     # Hash up all this identifying data.  
     $retVal = $md5->hexdigest();  
     # Return the result.  
     return $retVal;  
806  }  }
807    
808  =head3 OrganismData  =head3 OrganismData
809    
810  C<< my ($orgName, $group) = $shelp->Organism($genomeID); >>      my ($orgName, $group) = $shelp->Organism($genomeID);
811    
812  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.
813  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 887  Line 821 
821    
822  =item RETURN  =item RETURN
823    
824  Returns a list of two items. The first item in the list is the organism name,  Returns a list of three items. The first item in the list is the organism name,
825  and the second is the name of the NMPDR group, or an empty string if the  and the second is the name of the NMPDR group, or an empty string if the
826  organism is not in an NMPDR group.  organism is not in an NMPDR group. The third item is the organism's domain.
827    
828  =back  =back
829    
# Line 899  Line 833 
833      # Get the parameters.      # Get the parameters.
834      my ($self, $genomeID) = @_;      my ($self, $genomeID) = @_;
835      # Declare the return variables.      # Declare the return variables.
836      my ($orgName, $group);      my ($orgName, $group, $domain);
837      # Check the cache.      # Check the cache.
838      my $cache = $self->{orgs};      my $cache = $self->{orgs};
839      if (exists $cache->{$genomeID}) {      if (exists $cache->{$genomeID}) {
840          ($orgName, $group) = @{$cache->{$genomeID}};          ($orgName, $group, $domain) = @{$cache->{$genomeID}};
841            Trace("Cached organism $genomeID has group \"$group\".") if T(4);
842      } else {      } else {
843          # Here we have to use the database.          # Here we have to use the database.
844          my $sprout = $self->DB();          my $sprout = $self->DB();
845          my ($genus, $species, $strain, $group) = $sprout->GetEntityValues('Genome', $genomeID,          my ($genus, $species, $strain, $newGroup, $taxonomy) = $sprout->GetEntityValues('Genome', $genomeID,
846                                                      ['Genome(genus)', 'Genome(species)',                                                      ['Genome(genus)', 'Genome(species)',
847                                                       'Genome(unique-characterization)',                                                       'Genome(unique-characterization)',
848                                                       'Genome(primary-group)']);                                                                   'Genome(primary-group)',
849                                                                     'Genome(taxonomy)']);
850          # Format and cache the name and display group.          # Format and cache the name and display group.
851          ($orgName, $group) = $self->SaveOrganismData($group, $genomeID, $genus, $species,          Trace("Caching organism $genomeID with group \"$newGroup\".") if T(4);
852                                                              $strain);          ($orgName, $group, $domain) = $self->SaveOrganismData($newGroup, $genomeID, $genus, $species,
853                                                                  $strain, $taxonomy);
854            Trace("Returning group $group.") if T(4);
855      }      }
856      # Return the result.      # Return the result.
857      return ($orgName, $group);      return ($orgName, $group, $domain);
858  }  }
859    
860  =head3 Organism  =head3 Organism
861    
862  C<< my $orgName = $shelp->Organism($genomeID); >>      my $orgName = $shelp->Organism($genomeID);
863    
864  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,
865  species, and unique characterization. A cache is used to improve performance.  species, and unique characterization. A cache is used to improve performance.
# Line 944  Line 882 
882      # Get the parameters.      # Get the parameters.
883      my ($self, $genomeID) = @_;      my ($self, $genomeID) = @_;
884      # Get the organism data.      # Get the organism data.
885      my ($retVal, $group) = $self->OrganismData($genomeID);      my ($retVal) = $self->OrganismData($genomeID);
     # Return the result.  
     return $retVal;  
 }  
   
 =head3 FeatureGroup  
   
 C<< my $groupName = $shelp->FeatureGroup($fid); >>  
   
 Return the group name for the specified feature.  
   
 =over 4  
   
 =item fid  
   
 ID of the relevant feature.  
   
 =item RETURN  
   
 Returns the name of the NMPDR group to which the feature belongs, or an empty  
 string if it is not part of an NMPDR group.  
   
 =back  
   
 =cut  
   
 sub FeatureGroup {  
     # Get the parameters.  
     my ($self, $fid) = @_;  
     # Parse the feature ID to get the genome ID.  
     my ($genomeID) = FIGRules::ParseFeatureID($fid);  
     # Get the organism data.  
     my (undef, $retVal) = $self->OrganismData($genomeID);  
     # Return the result.  
     return $retVal;  
 }  
   
 =head3 FeatureName  
   
 C<< my $fidName = $shelp->FeatureName($fid); >>  
   
 Return the display name of the specified feature.  
   
 =over 4  
   
 =item fid  
   
 ID of the feature whose name is desired.  
   
 =item RETURN  
   
 A displayable feature name, consisting of the organism name plus some feature  
 type and location information.  
   
 =back  
   
 =cut  
   
 sub FeatureName {  
     # Get the parameters.  
     my ($self, $fid) = @_;  
     # Declare the return variable  
     my $retVal;  
     # Parse the feature ID.  
     my ($genomeID, $type, $num) = FIGRules::ParseFeatureID($fid);  
     if (! defined $genomeID) {  
         # Here the feature ID has an invalid format.  
         $retVal = "External: $fid";  
     } else {  
         # Here we can get its genome data.  
         $retVal = $self->Organism($genomeID);  
         # Append the FIG ID.  
         $retVal .= " [$fid]";  
     }  
886      # Return the result.      # Return the result.
887      return $retVal;      return $retVal;
888  }  }
889    
890  =head3 ComputeFASTA  =head3 ComputeFASTA
891    
892  C<< my $fasta = $shelp->ComputeFASTA($desiredType, $sequence); >>      my $fasta = $shelp->ComputeFASTA($desiredType, $sequence, $flankingWidth, $comments);
893    
894  Parse a sequence input and convert it into a FASTA string of the desired type.  Parse a sequence input and convert it into a FASTA string of the desired type with
895    the desired flanking width.
896    
897  =over 4  =over 4
898    
899  =item desiredType  =item desiredType
900    
901  C<dna> to return a DNA sequence, C<prot> to return a protein sequence.  C<dna> to return a DNA sequence, C<prot> to return a protein sequence, C<dnaPattern>
902    to return a DNA search pattern, C<protPattern> to return a protein search pattern.
903    
904  =item sequence  =item sequence
905    
# Line 1042  Line 909 
909  if the input does not begin with a greater-than sign (FASTA label line), a default label  if the input does not begin with a greater-than sign (FASTA label line), a default label
910  line will be provided.  line will be provided.
911    
912    =item flankingWidth
913    
914    If the DNA FASTA of a feature is desired, the number of base pairs to either side of the
915    feature that should be included. Currently we can't do this for Proteins because the
916    protein translation of a feature doesn't always match the DNA and is taken directly
917    from the database.
918    
919    =item comments
920    
921    Comment string to be added to the FASTA header.
922    
923  =item RETURN  =item RETURN
924    
925  Returns a string in FASTA format representing the content of the desired sequence with  Returns a string in FASTA format representing the content of the desired sequence with
# Line 1054  Line 932 
932    
933  sub ComputeFASTA {  sub ComputeFASTA {
934      # Get the parameters.      # Get the parameters.
935      my ($self, $desiredType, $sequence) = @_;      my ($self, $desiredType, $sequence, $flankingWidth, $comment) = @_;
936      # Declare the return variable. If an error occurs, it will remain undefined.      # Declare the return variable. If an error occurs, it will remain undefined.
937      my $retVal;      my $retVal;
938      # This variable will be cleared if an error is detected.      # This variable will be cleared if an error is detected.
# Line 1085  Line 963 
963                  # In an emergency, fall back to the original ID.                  # In an emergency, fall back to the original ID.
964                  $fastaLabel = $fid;                  $fastaLabel = $fid;
965              }              }
966                # Add any specified comments.
967                if ($comment) {
968                    $fastaLabel .= " $comment";
969                }
970              # Now proceed according to the sequence type.              # Now proceed according to the sequence type.
971              if ($desiredType eq 'prot') {              if ($desiredType =~ /prot/) {
972                  # We want protein, so get the translation.                  # We want protein, so get the translation.
973                  $fastaData = $sprout->FeatureTranslation($figID);                  $fastaData = $sprout->FeatureTranslation($figID);
974                  Trace(length $fastaData . " characters returned for translation of $fastaLabel.") if T(3);                  Trace(length $fastaData . " characters returned for translation of $fastaLabel.") if T(3);
975              } else {              } elsif ($desiredType =~ /dna/) {
976                  # We want DNA, so get the DNA sequence. This is a two-step process.                  # We want DNA, so get the DNA sequence. This is a two-step process. First, we get the
977                    # locations.
978                  my @locList = $sprout->FeatureLocation($figID);                  my @locList = $sprout->FeatureLocation($figID);
979                    if ($flankingWidth > 0) {
980                        # Here we need to add flanking data. Convert the locations to a list
981                        # of location objects.
982                        my @locObjects = map { BasicLocation->new($_) } @locList;
983                        # Initialize the return variable. We will put the DNA in here segment by segment.
984                        $fastaData = "";
985                        # Now we widen each location by the flanking width and stash the results. This
986                        # requires getting the contig length for each contig so we don't fall off the end.
987                        for my $locObject (@locObjects) {
988                            Trace("Current location is " . $locObject->String . ".") if T(4);
989                            # Remember the current start and length.
990                            my ($start, $len) = ($locObject->Left, $locObject->Length);
991                            # Get the contig length.
992                            my $contigLen = $sprout->ContigLength($locObject->Contig);
993                            # Widen the location and get its DNA.
994                            $locObject->Widen($flankingWidth, $contigLen);
995                            my $fastaSegment = $sprout->DNASeq([$locObject->String()]);
996                            # Now we need to do some case changing. The main DNA is upper case and
997                            # the flanking DNA is lower case.
998                            my $leftFlank = $start - $locObject->Left;
999                            my $rightFlank = $leftFlank + $len;
1000                            Trace("Wide location is " . $locObject->String . ". Flanks are $leftFlank and $rightFlank. Contig len is $contigLen.") if T(4);
1001                            my $fancyFastaSegment = lc(substr($fastaSegment, 0, $leftFlank)) .
1002                                                    uc(substr($fastaSegment, $leftFlank, $rightFlank - $leftFlank)) .
1003                                                    lc(substr($fastaSegment, $rightFlank));
1004                            $fastaData .= $fancyFastaSegment;
1005                        }
1006                    } else {
1007                        # Here we have just the raw sequence.
1008                  $fastaData = $sprout->DNASeq(\@locList);                  $fastaData = $sprout->DNASeq(\@locList);
1009                  Trace(length $fastaData . " characters returned for DNA of $fastaLabel.") if T(3);                  }
1010                    Trace((length $fastaData) . " characters returned for DNA of $fastaLabel.") if T(3);
1011              }              }
1012          }          }
1013      } else {      } else {
# Line 1109  Line 1022 
1022              Trace("No label found in match to sequence:\n$sequence") if T(4);              Trace("No label found in match to sequence:\n$sequence") if T(4);
1023              # Here we have no label, so we create one and use the entire sequence              # Here we have no label, so we create one and use the entire sequence
1024              # as data.              # as data.
1025              $fastaLabel = "User-specified $desiredType sequence";              $fastaLabel = "$desiredType sequence specified by user";
1026              $fastaData = $sequence;              $fastaData = $sequence;
1027          }          }
1028          # The next step is to clean the junk out of the sequence.          # If we are not doing a pattern search, we need to clean the junk out of the sequence.
1029            if ($desiredType !~ /pattern/i) {
1030          $fastaData =~ s/\n//g;          $fastaData =~ s/\n//g;
1031          $fastaData =~ s/\s+//g;          $fastaData =~ s/\s+//g;
1032            }
1033          # Finally, verify that it's DNA if we're doing DNA stuff.          # Finally, verify that it's DNA if we're doing DNA stuff.
1034          if ($desiredType eq 'dna' && $fastaData =~ /[^agctxn]/i) {          if ($desiredType eq 'dna' && $fastaData =~ /[^agctxn-]/i) {
1035              $self->SetMessage("Invalid characters detected. Is the input really a DNA sequence?");              $self->SetMessage("Invalid characters detected. Is the input really a DNA sequence?");
1036              $okFlag = 0;              $okFlag = 0;
1037          }          }
# Line 1124  Line 1039 
1039      Trace("FASTA data sequence: $fastaData") if T(4);      Trace("FASTA data sequence: $fastaData") if T(4);
1040      # Only proceed if no error was detected.      # Only proceed if no error was detected.
1041      if ($okFlag) {      if ($okFlag) {
1042            if ($desiredType =~ /pattern/i) {
1043                # For a scan, there is no label and no breakup.
1044                $retVal = $fastaData;
1045            } else {
1046          # We need to format the sequence into 60-byte chunks. We use the infamous          # We need to format the sequence into 60-byte chunks. We use the infamous
1047          # grep-split trick. The split, because of the presence of the parentheses,          # grep-split trick. The split, because of the presence of the parentheses,
1048          # includes the matched delimiters in the output list. The grep strips out          # includes the matched delimiters in the output list. The grep strips out
# Line 1132  Line 1051 
1051          my @chunks = grep { $_ } split /(.{1,60})/, $fastaData;          my @chunks = grep { $_ } split /(.{1,60})/, $fastaData;
1052          $retVal = join("\n", ">$fastaLabel", @chunks, "");          $retVal = join("\n", ">$fastaLabel", @chunks, "");
1053      }      }
1054        }
1055      # Return the result.      # Return the result.
1056      return $retVal;      return $retVal;
1057  }  }
1058    
1059  =head3 SubsystemTree  =head3 SubsystemTree
1060    
1061  C<< my $tree = SearchHelper::SubsystemTree($sprout, %options); >>      my $tree = SearchHelper::SubsystemTree($sprout, %options);
1062    
1063  This method creates a subsystem selection tree suitable for passing to  This method creates a subsystem selection tree suitable for passing to
1064  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 1196  Line 1116 
1116              push @subs, $classLess;              push @subs, $classLess;
1117          }          }
1118      }      }
1119        # Get the seedviewer URL.
1120        my $svURL = $FIG_Config::linkinSV || "$FIG_Config::cgi_url/seedviewer.cgi";
1121        Trace("Seed Viewer URL is $svURL.") if T(3);
1122      # Declare the return variable.      # Declare the return variable.
1123      my @retVal = ();      my @retVal = ();
1124      # Each element in @subs represents a leaf node, so as we loop through it we will be      # Each element in @subs represents a leaf node, so as we loop through it we will be
# Line 1270  Line 1193 
1193              if ($optionThing->{links}) {              if ($optionThing->{links}) {
1194                  # Compute the link value.                  # Compute the link value.
1195                  my $linkable = uri_escape($id);                  my $linkable = uri_escape($id);
1196                  $nodeContent->{link} = "../FIG/display_subsys.cgi?ssa_name=$linkable;request=show_ssa;sort=by_phylo;show_clusters=1;SPROUT=1";                  $nodeContent->{link} = "$svURL?page=Subsystems;subsystem=$linkable";
1197              }              }
1198              if ($optionThing->{radio}) {              if ($optionThing->{radio}) {
1199                  # Compute the radio value.                  # Compute the radio value.
# Line 1288  Line 1211 
1211    
1212  =head3 NmpdrGenomeMenu  =head3 NmpdrGenomeMenu
1213    
1214  C<< my $htmlText = $shelp->NmpdrGenomeMenu($menuName, $multiple, \@selected, $rows); >>      my $htmlText = $shelp->NmpdrGenomeMenu($menuName, $multiple, \@selected, $rows);
1215    
1216  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
1217  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 1317  Line 1240 
1240    
1241  =item crossMenu (optional)  =item crossMenu (optional)
1242    
1243  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.  
1244    
1245  =item RETURN  =item RETURN
1246    
# Line 1340  Line 1260 
1260      if (! defined $rows) {      if (! defined $rows) {
1261          $rows = ($multiple ? 10 : 1);          $rows = ($multiple ? 10 : 1);
1262      }      }
1263      # Create the multiple tag.      # Get a comma-delimited list of the preselected genomes.
1264      my $multipleTag = ($multiple ? " multiple" : "");      my $preselected = "";
1265      # Get the form name.      if ($selected) {
1266      my $formName = $self->FormName();          $preselected = join(", ", @$selected);
1267      # Check to see if we already have a genome list in memory.      }
1268      my $genomes = $self->{genomeList};      # Ask Sprout for a genome menu.
1269      my $groupHash;      my $retVal = $sprout->GenomeMenu(name => $menuName,
1270      if (defined $genomes) {                                       multiSelect => $multiple,
1271          # We have a list ready to use.                                       selected => $preselected,
1272          $groupHash = $genomes;                                       size => $rows);
     } 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)']);  
         # 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, $strain) = @{$genome};  
             # Compute and cache its name and display group.  
             my ($name, $displayGroup) = $self->SaveOrganismData($group, $genomeID, $genus, $species,  
                                                                 $strain);  
             # Push the genome into the group's list. Note that we use the real group  
             # name here, not the display group name.  
             push @{$gHash{$group}}, [$genomeID, $name];  
         }  
         # Save the genome list for future use.  
         $self->{genomeList} = \%gHash;  
         $groupHash = \%gHash;  
     }  
     # Now we are ready to unroll the menu out of the group hash. First, we sort the groups, putting  
     # the supporting-genome group last.  
     my @groups = sort grep { $_ ne $FIG_Config::otherGroup } keys %{$groupHash};  
     push @groups, $FIG_Config::otherGroup;  
     # 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->{$group}}) {  
             # Count this organism if it's NMPDR.  
             if ($group ne $FIG_Config::otherGroup) {  
                 $nmpdrCount++;  
             }  
             # Get the organism ID and name.  
             my ($genomeID, $name) = @{$genome};  
             # See if it's selected.  
             my $select = ($selectedHash{$genomeID} ? " selected" : "");  
             # Generate the option tag.  
             my $optionTag = "<OPTION value=\"$genomeID\"$select>$name <em>($genomeID)</em></OPTION>";  
             push @lines, "    $optionTag";  
         }  
         # Close the option group.  
         push @lines, "  </OPTGROUP>";  
     }  
     # Close the SELECT tag.  
     push @lines, "</SELECT>";  
     # Check for multiple selection.  
     if ($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=\"Search\" class=\"button\" value=\"Select genomes containing\" onClick=\"selectViaSearch($menuName, $searchThingName); $showSelect\" />&nbsp;" .  
                      "<INPUT type=\"text\" name=\"$searchThingName\" size=\"30\" />";  
         # 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, "");  
1273      # Return the result.      # Return the result.
1274      return $retVal;      return $retVal;
1275  }  }
1276    
1277  =head3 PropertyMenu  =head3 PropertyMenu
1278    
1279  C<< my $htmlText = $shelp->PropertyMenu($menuName, $selected, $force); >>      my $htmlText = $shelp->PropertyMenu($menuName, $selected, $force);
1280    
1281  Generate a property name dropdown menu.  Generate a property name dropdown menu.
1282    
# Line 1510  Line 1318 
1318      # 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.
1319      push @propNames, $sprout->GetChoices('Property', 'property-name');      push @propNames, $sprout->GetChoices('Property', 'property-name');
1320      # Create a menu from them.      # Create a menu from them.
1321      my $retVal = $cgi->popup_menu(-name=> $menuName, -values => \@propNames,      my $retVal = CGI::popup_menu(-name=> $menuName, -values => \@propNames,
1322                                    -default => $selected);                                    -default => $selected);
1323      # Return the result.      # Return the result.
1324      return $retVal;      return $retVal;
# Line 1518  Line 1326 
1326    
1327  =head3 MakeTable  =head3 MakeTable
1328    
1329  C<< my $htmlText = $shelp->MakeTable(\@rows); >>      my $htmlText = $shelp->MakeTable(\@rows);
1330    
1331  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
1332  other words, each must have the TR and TD tags included.  other words, each must have the TR and TD tags included.
# Line 1572  Line 1380 
1380          }          }
1381      }      }
1382      # Create the table.      # Create the table.
1383      my $retVal = $cgi->table({border => 2, cellspacing => 2,      my $retVal = CGI::table({border => 2, cellspacing => 2,
1384                                width => 700, class => 'search'},                                width => 700, class => 'search'},
1385                               @{$rows});                               @{$rows});
1386      # Return the result.      # Return the result.
# Line 1581  Line 1389 
1389    
1390  =head3 SubmitRow  =head3 SubmitRow
1391    
1392  C<< my $htmlText = $shelp->SubmitRow($caption); >>      my $htmlText = $shelp->SubmitRow($caption);
1393    
1394  Returns the HTML text for the row containing the page size control  Returns the HTML text for the row containing the page size control
1395  and the submit button. All searches should have this row somewhere  and the submit button. All searches should have this row somewhere
# Line 1610  Line 1418 
1418      my $realCaption = (defined $caption ? $caption : 'Go');      my $realCaption = (defined $caption ? $caption : 'Go');
1419      # Get the current page size.      # Get the current page size.
1420      my $pageSize = $cgi->param('PageSize');      my $pageSize = $cgi->param('PageSize');
1421      # Get the incoming external-link flag.      # Get the current feature ID type.
1422      my $aliases = ($cgi->param('ShowAliases') ? 1 : 0);      my $aliasType = $self->GetPreferredAliasType();
1423      # Create the row.      # Create the rows.
1424      my $retVal = $cgi->Tr($cgi->td("Results/Page"),      my $retVal = CGI::Tr(CGI::td("Identifier Type "),
1425                            $cgi->td($cgi->popup_menu(-name => 'PageSize',                            CGI::td({ colspan => 2 },
1426                                       CGI::popup_menu(-name => 'AliasType',
1427                                                        -values => ['FIG', AliasAnalysis::AliasTypes() ],
1428                                                        -default => $aliasType) .
1429                                       Hint("Identifier Type", "Specify how you want gene names to be displayed."))) .
1430                     "\n" .
1431                     CGI::Tr(CGI::td("Results/Page"),
1432                              CGI::td(CGI::popup_menu(-name => 'PageSize',
1433                                                      -values => [10, 25, 50, 100, 1000],                                                      -values => [10, 25, 50, 100, 1000],
1434                                                      -default => $pageSize)),                                                      -default => $pageSize)),
1435                            $cgi->td($cgi->submit(-class => 'goButton',                            CGI::td(CGI::submit(-class => 'goButton',
1436                                                  -name => 'Search',                                                  -name => 'Search',
1437                                                  -value => $realCaption)));                                                  -value => $realCaption)));
1438      # Return the result.      # Return the result.
1439      return $retVal;      return $retVal;
1440  }  }
1441    
 =head3 FeatureFilterRows  
   
 C<< my $htmlText = $shelp->FeatureFilterRows(@subset); >>  
   
 This method creates table rows that can be used to filter features. The form  
 values can be used to select features by genome using the B<FeatureQuery>  
 object.  
   
 =over 4  
   
 =item subset  
   
 List of rows to display. The default (C<all>) is to display all rows.  
 C<words> displays the word search box, C<subsys> displays the subsystem  
 selector, and C<options> displays the options row.  
   
 =item RETURN  
   
 Returns the html text for table rows containing the desired feature filtering controls.  
   
 =back  
   
 =cut  
   
 sub FeatureFilterRows {  
     # Get the parameters.  
     my ($self, @subset) = @_;  
     if (@subset == 0 || $subset[0] eq 'all') {  
         @subset = qw(words subsys options);  
     }  
     # Return the result.  
     return FeatureQuery::FilterRows($self, @subset);  
 }  
   
 =head3 GBrowseFeatureURL  
   
 C<< my $url = SearchHelper::GBrowseFeatureURL($sprout, $feat); >>  
   
 Compute the URL required to pull up a Gbrowse page for the the specified feature.  
 In order to do this, we need to pull out the ID of the feature's Genome, its  
 contig ID, and some rough starting and stopping offsets.  
   
 =over 4  
   
 =item sprout  
   
 Sprout object for accessing the database.  
   
 =item feat  
   
 ID of the feature whose Gbrowse URL is desired.  
   
 =item RETURN  
   
 Returns a GET-style URL for the Gbrowse CGI, with parameters specifying the genome  
 ID, contig ID, starting offset, and stopping offset.  
   
 =back  
   
 =cut  
   
 sub GBrowseFeatureURL {  
     # Get the parameters.  
     my ($sprout, $feat) = @_;  
     # Declare the return variable.  
     my $retVal;  
     # Compute the genome ID.  
     my ($genomeID) = FIGRules::ParseFeatureID($feat);  
     # Only proceed if the feature ID produces a valid genome.  
     if ($genomeID) {  
         # Get the feature location string.  
         my $loc = $sprout->FeatureLocation($feat);  
         # Compute the contig, start, and stop points.  
         my($contig, $start, $stop) = BasicLocation::Parse($loc);  
         Trace("Start and stop are ($start,$stop) on contig $contig.") if T(3);  
         # Now we need to do some goofiness to insure that the location is not too  
         # big and that we get some surrounding stuff.  
         my $mid = int(($start + $stop) / 2);  
         my $chunk_len = 20000;  
         my $max_feature = 40000;  
         my $feat_len = abs($stop - $start);  
         if ($feat_len > $chunk_len) {  
             if ($feat_len > $max_feature) {  
                 $chunk_len = $max_feature;  
             } else {  
                 $chunk_len = $feat_len + 100;  
             }  
         }  
         my($show_start, $show_stop);  
         if ($chunk_len == $max_feature) {  
             $show_start = $start - 300;  
         } else {  
             $show_start = $mid - int($chunk_len / 2);  
         }  
         if ($show_start < 1) {  
             $show_start = 1;  
         }  
         $show_stop = $show_start + $chunk_len - 1;  
         my $clen = $sprout->ContigLength($contig);  
         if ($show_stop > $clen) {  
             $show_stop = $clen;  
         }  
         my $seg_id = $contig;  
         $seg_id =~ s/:/--/g;  
         Trace("Show limits are ($show_start,$show_stop) in genome $genomeID with ref $seg_id.") if T(3);  
         # Assemble all the pieces.  
         $retVal = "gbrowse.cgi/GB_$genomeID?ref=$seg_id;start=$show_start;stop=$show_stop";  
     }  
     # Return the result.  
     return $retVal;  
 }  
   
1442  =head3 GetGenomes  =head3 GetGenomes
1443    
1444  C<< my @genomeList = $shelp->GetGenomes($parmName); >>      my @genomeList = $shelp->GetGenomes($parmName);
1445    
1446  Return the list of genomes specified by the specified CGI query parameter.  Return the list of genomes specified by the specified CGI query parameter.
1447  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 1780  Line 1483 
1483      return @retVal;      return @retVal;
1484  }  }
1485    
 =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;  
 }  
   
1486  =head3 ComputeSearchURL  =head3 ComputeSearchURL
1487    
1488  C<< my $url = $shelp->ComputeSearchURL(%overrides); >>      my $url = $shelp->ComputeSearchURL(%overrides);
1489    
1490  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
1491  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 1856  Line 1518 
1518      my $cgi = $self->Q();      my $cgi = $self->Q();
1519      my $sprout = $self->DB();      my $sprout = $self->DB();
1520      # Start with the full URL.      # Start with the full URL.
1521      my $retVal = $cgi->url(-full => 1);      my $retVal = "$FIG_Config::cgi_url/SearchSkeleton.cgi";
1522      # Get all the query parameters in a hash.      # Get all the query parameters in a hash.
1523      my %parms = $cgi->Vars();      my %parms = $cgi->Vars();
1524      # 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 1914  Line 1576 
1576      return $retVal;      return $retVal;
1577  }  }
1578    
 =head3 GetRunTimeValue  
   
 C<< my $htmlText = $shelp->GetRunTimeValue($text); >>  
   
 Compute a run-time column value.  
   
 =over 4  
   
 =item text  
   
 The run-time column text. It consists of 2 percent signs, a column type, an equal  
 sign, and the data for the current row.  
   
 =item RETURN  
   
 Returns the fully-formatted HTML text to go into the current column of the current row.  
   
 =back  
   
 =cut  
   
 sub GetRunTimeValue {  
     # Get the parameters.  
     my ($self, $text) = @_;  
     # Declare the return variable.  
     my $retVal;  
     # Parse the incoming text.  
     if ($text =~ /^%%([^=]+)=(.*)$/) {  
         $retVal = $self->RunTimeColumns($1, $2);  
     } else {  
         Confess("Invalid run-time column string \"$text\" encountered in session file.");  
     }  
     # Return the result.  
     return $retVal;  
 }  
   
1579  =head3 AdvancedClassList  =head3 AdvancedClassList
1580    
1581  C<< my @classes = SearchHelper::AdvancedClassList(); >>      my @classes = SearchHelper::AdvancedClassList();
1582    
1583  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
1584  of available searches on the search page.  of available searches on the search page.
1585    
1586  We use the %INC variable to accomplish this.  We do a file search to accomplish this, but to pull it off we need to look at %INC.
1587    
1588  =cut  =cut
1589    
1590  sub AdvancedClassList {  sub AdvancedClassList {
1591      my @retVal = map { $_ =~ /^SH(\w+)\.pm/; $1 } grep { $_ =~ /^SH/ } keys %INC;      # Determine the search helper module directory.
1592        my $libDirectory = $INC{'SearchHelper.pm'};
1593        $libDirectory =~ s/SearchHelper\.pm//;
1594        # Read it, keeping only the helper modules.
1595        my @modules = grep { /^SH\w+\.pm/ } Tracer::OpenDir($libDirectory, 0);
1596        # Convert the file names to search types.
1597        my @retVal = map { $_ =~ /^SH(\w+)\.pm/; $1 } @modules;
1598        # Return the result in alphabetical order.
1599      return sort @retVal;      return sort @retVal;
1600  }  }
1601    
1602  =head3 SelectionTree  =head3 SelectionTree
1603    
1604  C<< my $htmlText = SearchHelper::SelectionTree($cgi, \%tree, %options); >>      my $htmlText = SearchHelper::SelectionTree($cgi, \%tree, %options);
1605    
1606  Display a selection tree.  Display a selection tree.
1607    
# Line 2077  Line 1710 
1710  =item nodeImageClosed  =item nodeImageClosed
1711    
1712  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
1713  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>.
1714    
1715  =item nodeImageOpen  =item nodeImageOpen
1716    
1717  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
1718  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>.
1719    
1720  =item style  =item style
1721    
# Line 2122  Line 1755 
1755      my ($cgi, $tree, %options) = @_;      my ($cgi, $tree, %options) = @_;
1756      # Get the options.      # Get the options.
1757      my $optionThing = Tracer::GetOptions({ name => 'selection',      my $optionThing = Tracer::GetOptions({ name => 'selection',
1758                                             nodeImageClosed => '../FIG/Html/plus.gif',                                             nodeImageClosed => "$FIG_Config::cgi_url/Html/plus.gif",
1759                                             nodeImageOpen => '../FIG/Html/minus.gif',                                             nodeImageOpen => "$FIG_Config::cgi_url/Html/minus.gif",
1760                                             style => 'tree',                                             style => 'tree',
1761                                             target => '_self',                                             target => '_self',
1762                                             selected => undef},                                             selected => undef},
# Line 2142  Line 1775 
1775              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.");
1776          } else {          } else {
1777              # Here we have a real tree. Apply the tree style.              # Here we have a real tree. Apply the tree style.
1778              push @retVal, $cgi->start_div({ class => $optionThing->{style} });              push @retVal, CGI::start_div({ class => $optionThing->{style} });
1779              # Give us a DIV ID.              # Give us a DIV ID.
1780              my $divID = GetDivID($optionThing->{name});              my $divID = GetDivID($optionThing->{name});
1781              # Show the tree.              # Show the tree.
1782              push @retVal, ShowBranch($cgi, "(root)", $divID, $tree, $optionThing, 'block');              push @retVal, ShowBranch($cgi, "(root)", $divID, $tree, $optionThing, 'block');
1783              # Close the DIV block.              # Close the DIV block.
1784              push @retVal, $cgi->end_div();              push @retVal, CGI::end_div();
1785          }          }
1786      }      }
1787      # Return the result.      # Return the result.
# Line 2157  Line 1790 
1790    
1791  =head3 ShowBranch  =head3 ShowBranch
1792    
1793  C<< my @htmlLines = SearchHelper::ShowBranch($cgi, $label, $id, $branch, $options, $displayType); >>      my @htmlLines = SearchHelper::ShowBranch($cgi, $label, $id, $branch, $options, $displayType);
1794    
1795  This is a recursive method that displays a branch of the tree.  This is a recursive method that displays a branch of the tree.
1796    
# Line 2206  Line 1839 
1839      # Declare the return variable.      # Declare the return variable.
1840      my @retVal = ();      my @retVal = ();
1841      # Start the branch.      # Start the branch.
1842      push @retVal, $cgi->start_ul({ id => $id, style => "display:$displayType" });      push @retVal, CGI::start_ul({ id => $id, style => "display:$displayType" });
1843      # Check for the hash and choose the start location accordingly.      # Check for the hash and choose the start location accordingly.
1844      my $i0 = (ref $branch->[0] eq 'HASH' ? 1 : 0);      my $i0 = (ref $branch->[0] eq 'HASH' ? 1 : 0);
1845      # Get the list length.      # Get the list length.
# Line 2252  Line 1885 
1885                      # If we have children, create the child list with a recursive call.                      # If we have children, create the child list with a recursive call.
1886                      if ($hasChildren) {                      if ($hasChildren) {
1887                          Trace("Processing children of $myLabel.") if T(4);                          Trace("Processing children of $myLabel.") if T(4);
1888                          push @childHtml, ShowBranch($cgi, $myLabel, $myID, $myContent, $options, 'none');                          push @childHtml, ShowBranch($cgi, $myLabel, $myID, $myContent, $options, 'block');
1889                          Trace("Children of $myLabel finished.") if T(4);                          Trace("Children of $myLabel finished.") if T(4);
1890                      }                      }
1891                  }                  }
# Line 2264  Line 1897 
1897              # closed images.              # closed images.
1898              my @images = ($options->{nodeImageOpen}, $options->{nodeImageClosed});              my @images = ($options->{nodeImageOpen}, $options->{nodeImageClosed});
1899              my $image = $images[$hasChildren];              my $image = $images[$hasChildren];
1900              my $prefixHtml = $cgi->img({src => $image, id => "${myID}img"});              my $prefixHtml = CGI::img({src => $image, id => "${myID}img"});
1901              if ($hasChildren) {              if ($hasChildren) {
1902                  # If there are children, we wrap the image in a toggle hyperlink.                  # If there are children, we wrap the image in a toggle hyperlink.
1903                  $prefixHtml = $cgi->a({ onClick => "javascript:treeToggle('$myID','$images[0]', '$images[1]')" },                  $prefixHtml = CGI::a({ onClick => "javascript:treeToggle('$myID','$images[0]', '$images[1]')" },
1904                                        $prefixHtml);                                        $prefixHtml);
1905              }              }
1906              # 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 2284  Line 1917 
1917                  if (defined $options->{selected} && $options->{selected} eq $attrHash->{value}) {                  if (defined $options->{selected} && $options->{selected} eq $attrHash->{value}) {
1918                      $radioParms->{checked} = undef;                      $radioParms->{checked} = undef;
1919                  }                  }
1920                  $prefixHtml .= $cgi->input($radioParms);                  $prefixHtml .= CGI::input($radioParms);
1921              }              }
1922              # Next, we format the label.              # Next, we format the label.
1923              my $labelHtml = $myLabel;              my $labelHtml = $myLabel;
1924              Trace("Formatting tree node for \"$myLabel\".") if T(4);              Trace("Formatting tree node for \"$myLabel\".") if T(4);
1925              # Apply a hyperlink if necessary.              # Apply a hyperlink if necessary.
1926              if (defined $attrHash->{link}) {              if (defined $attrHash->{link}) {
1927                  $labelHtml = $cgi->a({ href => $attrHash->{link}, target => $options->{target} },                  $labelHtml = CGI::a({ href => $attrHash->{link}, target => $options->{target} },
1928                                       $labelHtml);                                       $labelHtml);
1929              }              }
1930              # 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
1931              # here.              # here.
1932              my $childHtml = join("\n", @childHtml);              my $childHtml = join("\n", @childHtml);
1933              # Now we have all the pieces, so we can put them together.              # Now we have all the pieces, so we can put them together.
1934              push @retVal, $cgi->li("$prefixHtml$labelHtml$childHtml");              push @retVal, CGI::li("$prefixHtml$labelHtml$childHtml");
1935          }          }
1936      }      }
1937      # Close the tree branch.      # Close the tree branch.
1938      push @retVal, $cgi->end_ul();      push @retVal, CGI::end_ul();
1939      # Return the result.      # Return the result.
1940      return @retVal;      return @retVal;
1941  }  }
1942    
1943  =head3 GetDivID  =head3 GetDivID
1944    
1945  C<< my $idString = SearchHelper::GetDivID($name); >>      my $idString = SearchHelper::GetDivID($name);
1946    
1947  Return a new HTML ID string.  Return a new HTML ID string.
1948    
# Line 2338  Line 1971 
1971      return $retVal;      return $retVal;
1972  }  }
1973    
   
1974  =head3 PrintLine  =head3 PrintLine
1975    
1976  C<< $shelp->PrintLine($message); >>      $shelp->PrintLine($message);
1977    
1978  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
1979  searching, so the user sees progress in real-time.  searching, so the user sees progress in real-time.
# Line 2359  Line 1991 
1991  sub PrintLine {  sub PrintLine {
1992      # Get the parameters.      # Get the parameters.
1993      my ($self, $message) = @_;      my ($self, $message) = @_;
1994      # Send them to the output.      # Send the message to the output.
1995      print "$message\n";      print "$message\n";
1996  }  }
1997    
1998  =head2 Feature Column Methods  =head3 GetHelper
   
 The methods in this section manage feature column data. If you want to provide the  
 capability to include new types of data in feature columns, then all the changes  
 are made to this section of the source file. Technically, this should be implemented  
 using object-oriented methods, but this is simpler for non-programmers to maintain.  
 To add a new column of feature data, you must first give it a name. For example,  
 the name for the protein page link column is C<protlink>. If the column is to appear  
 in the default list of feature columns, add it to the list returned by  
 L</DefaultFeatureColumns>. Then add code to produce the column title to  
 L</FeatureColumnTitle> and code to produce its value to L</FeatureColumnValue>. If the  
 feature column should be excluded from downloads, add it to the C<FeatureColumnSkip>  
 hash. Everything else will happen automatically.  
   
 There is a special column name syntax for extra columns (that is, nonstandard  
 feature columns). If the column name begins with C<X=>, then it is presumed to be  
 an extra column. The column title is the text after the C<X=>, and its value is  
 pulled from the extra column hash.  
   
 =cut  
   
 # This hash is used to determine which columns should not be included in downloads.  
 my %FeatureColumnSkip = map { $_ => 1 } qw(gblink viewerlink protlink);  
   
 =head3 DefaultFeatureColumns  
1999    
2000  C<< my @colNames = $shelp->DefaultFeatureColumns(); >>      my $shelp = SearchHelper::GetHelper($parm, $type => $className);
2001    
2002  Return a list of the default feature column identifiers. These identifiers can  Return a helper object with the given class name. If no such class exists, an
2003  be passed to L</FeatureColumnTitle> and L</FeatureColumnValue> in order to  error will be thrown.
 produce the column titles and row values.  
   
 =cut  
   
 sub DefaultFeatureColumns {  
     # Get the parameters.  
     my ($self) = @_;  
     # Return the result.  
     return qw(orgName function gblink protlink);  
 }  
   
 =head3 FeatureColumnTitle  
   
 C<< my $title = $shelp->FeatureColumnTitle($colName); >>  
   
 Return the column heading title to be used for the specified feature column.  
2004    
2005  =over 4  =over 4
2006    
2007  =item name  =item parm
   
 Name of the desired feature column.  
   
 =item RETURN  
   
 Returns the title to be used as the column header for the named feature column.  
   
 =back  
   
 =cut  
   
 sub FeatureColumnTitle {  
     # Get the parameters.  
     my ($self, $colName) = @_;  
     # Declare the return variable. We default to a blank column name.  
     my $retVal = "&nbsp;";  
     # Process the column name.  
     if ($colName =~ /^X=(.+)$/) {  
         # Here we have an extra column.  
         $retVal = $1;  
     } elsif ($colName eq 'alias') {  
         $retVal = "External Aliases";  
     } elsif ($colName eq 'fid') {  
         $retVal = "FIG ID";  
     } elsif ($colName eq 'function') {  
         $retVal = "Functional Assignment";  
     } elsif ($colName eq 'gblink') {  
         $retVal = "GBrowse";  
     } elsif ($colName eq 'group') {  
         $retVal = "NMDPR Group";  
     } elsif ($colName =~ /^keyword:(.+)$/) {  
         $retVal = ucfirst $1;  
     } elsif ($colName eq 'orgName') {  
         $retVal = "Organism and Gene ID";  
     } elsif ($colName eq 'protlink') {  
         $retVal = "NMPDR Protein Page";  
     } elsif ($colName eq 'viewerlink') {  
         $retVal = "Annotation Page";  
     } elsif ($colName eq 'subsystem') {  
         $retVal = "Subsystems";  
     } elsif ($colName eq 'pdb') {  
         $retVal = "Best PDB Match";  
     }  
     # Return the result.  
     return $retVal;  
 }  
   
 =head3 FeatureColumnDownload  
   
 C<< my $keep = $shelp->FeatureColumnDownload($colName); >>  
   
 Return TRUE if the named feature column is to be kept when downloading, else FALSE.  
   
 =over 4  
   
 =item colName  
   
 Name of the relevant feature column.  
   
 =item RETURN  
   
 Return TRUE if the named column should be kept while downloading, else FALSE. In general,  
 FALSE is returned if the column generates a button, image, or other purely-HTML value.  
   
 =back  
   
 =cut  
   
 sub FeatureColumnDownload {  
     # Get the parameters.  
     my ($self, $colName) = @_;  
     # Return the determination. We download the column if it's not in the skip-hash.  
     # Note we return 0 and 1 instead of 1 and undef because it simplifies some tracing.  
     return (exists $FeatureColumnSkip{$colName} ? 0 : 1);  
 }  
   
   
 =head3 FeatureColumnValue  
   
 C<< my $value = $shelp->FeatureColumnValue($colName, $fid, \%extraCols); >>  
2008    
2009  Return the value to be displayed in the specified feature column.  Parameter to pass to the constructor. This is a CGI object for a search helper
2010    and a search helper object for the result helper.
 =over 4  
   
 =item colName  
   
 Name of the column to be displayed.  
   
 =item record  
   
 ERDBObject record for the feature being displayed in the current row.  
   
 =item extraCols  
   
 Reference to a hash of extra column names to values. If the incoming column name  
 begins with C<X=>, its value will be taken from this hash.  
   
 =item RETURN  
   
 Returns the HTML to be displayed in the named column for the specified feature.  
   
 =back  
   
 =cut  
   
 sub FeatureColumnValue {  
     # Get the parameters.  
     my ($self, $colName, $record, $extraCols) = @_;  
     # Get the sprout and CGI objects.  
     my $cgi = $self->Q();  
     my $sprout = $self->DB();  
     # Get the feature ID.  
     my ($fid) = $record->Value('Feature(id)');  
     # Declare the return variable. Denote that we default to a non-breaking space,  
     # which will translate to an empty table cell (rather than a table cell with no  
     # interior, which is what you get for a null string).  
     my $retVal = "&nbsp;";  
     # Process according to the column name.  
     if ($colName =~ /^X=(.+)$/) {  
         # Here we have an extra column. Only update if the value exists. Note that  
         # a value of C<undef> is treated as a non-existent value, because the  
         # caller may have put "colName => undef" in the "PutFeature" call in order  
         # to insure we know the extra column exists.  
         if (defined $extraCols->{$1}) {  
             $retVal = $extraCols->{$1};  
         }  
     } elsif ($colName eq 'alias') {  
         # In this case, the user wants a list of external aliases for the feature.  
         # These are very expensive, so we compute them when the row is displayed.  
         # To do the computation, we need to know the favored alias type and the  
         # feature ID.  
         my $favored = $cgi->param("FavoredAlias") || "fig";  
         $retVal = "%%alias=$fid,$favored";  
     } elsif ($colName eq 'fid') {  
         # Here we have the raw feature ID. We hyperlink it to the protein page.  
         $retVal = HTML::set_prot_links($fid);  
     } elsif ($colName eq 'function') {  
         # The functional assignment is just a matter of getting some text.  
         ($retVal) = $record->Value('Feature(assignment)');  
     } elsif ($colName eq 'gblink') {  
         # Here we want a link to the GBrowse page using the official GBrowse button.  
         $retVal = FakeButton('GBrowse', "GetGBrowse.cgi", undef,  
                           fid => $fid);  
     } elsif ($colName eq 'group') {  
         # Get the NMPDR group name.  
         my (undef, $group) = $self->OrganismData($fid);  
         # Dress it with a URL to the group's main page.  
         my $nurl = $sprout->GroupPageName($group);  
         $retVal = $cgi->a({ href => $nurl, title => "$group summary" },  
                           $group);  
     } elsif ($colName =~ /^keyword:(.+)$/) {  
         # Here we want keyword-related values. This is also expensive, so  
         # we compute them when the row is displayed.  
         $retVal = "%%$colName=$fid";  
     } elsif ($colName eq 'orgName') {  
         # Here we want the formatted organism name and feature number.  
         $retVal = $self->FeatureName($fid);  
     } elsif ($colName eq 'protlink') {  
         # Here we want a link to the protein page using the official NMPDR button.  
         $retVal = FakeButton('NMPDR', "protein.cgi", undef,  
                           prot => $fid, SPROUT => 1, new_framework => 0,  
                           user => '');  
     } elsif ($colName eq 'viewerlink') {  
         # Here we want a link to the SEED viewer page using the official viewer button.  
         $retVal = FakeButton('Annotation', "index.cgi", undef,  
                              action => 'ShowAnnotation', prot => $fid);  
     } elsif ($colName eq 'subsystem') {  
         # Another run-time column: subsystem list.  
         $retVal = "%%subsystem=$fid";  
     } elsif ($colName eq 'pdb') {  
         $retVal = "%%pdb=$fid";  
     }  
     # Return the result.  
     return $retVal;  
 }  
   
 =head3 RunTimeColumns  
   
 C<< my $htmlText = $shelp->RunTimeColumns($type, $text); >>  
   
 Return the HTML text for a run-time column. Run-time columns are evaluated when the  
 list is displayed, rather than when it is generated.  
   
 =over 4  
2011    
2012  =item type  =item type
2013    
2014  Type of column.  Type of helper: C<RH> for a result helper and C<SH> for a search helper.
2015    
2016  =item text  =item className
2017    
2018  Data relevant to this row of the column.  Class name for the helper object, without the preceding C<SH> or C<RH>. This is
2019    identical to what the script expects for the C<Class> or C<ResultType> parameter.
2020    
2021  =item RETURN  =item RETURN
2022    
2023  Returns the fully-formatted HTML text to go in the specified column.  Returns a helper object for the specified class.
2024    
2025  =back  =back
2026    
2027  =cut  =cut
2028    
2029  sub RunTimeColumns {  sub GetHelper {
2030      # Get the parameters.      # Get the parameters.
2031      my ($self, $type, $text) = @_;      my ($parm, $type, $className) = @_;
2032      # Declare the return variable.      # Declare the return variable.
2033      my $retVal = "";      my $retVal;
2034      # Get the Sprout and CGI objects.      # Try to create the helper.
2035      my $sprout = $self->DB();      eval {
2036      my $cgi = $self->Q();          # Load it into memory. If it's already there nothing will happen here.
2037      Trace("Runtime column $type with text \"$text\" found.") if T(4);          my $realName = "$type$className";
2038      # Separate the text into a type and data.          Trace("Requiring helper $realName.") if T(3);
2039      if ($type eq 'alias') {          require "$realName.pm";
2040          # Here the caller wants external alias links for a feature. The text          Trace("Constructing helper object.") if T(3);
2041          # parameter for computing the alias is the feature ID followed by          # Construct the object.
2042          # the favored alias type.          $retVal = eval("$realName->new(\$parm)");
2043          my ($fid, $favored) = split /\s*,\s*/, $text;          # Commit suicide if it didn't work.
2044          # The complicated part is we have to hyperlink them and handle the          if (! defined $retVal) {
2045          # favorites. First, get the aliases.              die "Could not find a $type handler of type $className.";
         Trace("Generating aliases for feature $fid.") if T(4);  
         my @aliases = sort $sprout->FeatureAliases($fid);  
         # Only proceed if we found some.  
         if (@aliases) {  
             # Split the aliases into favored and unfavored.  
             my @favored = ();  
             my @unfavored = ();  
             for my $alias (@aliases) {  
                 # Use substr instead of pattern match because $favored is specified by the user  
                 # and we don't want him to put funny meta-characters in there.  
                 if (substr($alias, 0, length($favored)) eq $favored) {  
                     push @favored, $alias;  
2046                  } else {                  } else {
2047                      push @unfavored, $alias;              # Perform any necessary subclass initialization.
2048                  }              $retVal->Initialize();
             }  
             # Rejoin the aliases into a comma-delimited list, with the favored ones first.  
             my $aliasList = join(", ", @favored, @unfavored);  
             # Ask the HTML processor to hyperlink them.  
             $retVal = HTML::set_prot_links($cgi, $aliasList);  
         }  
     } elsif ($type eq 'subsystem') {  
         # Here the caller wants the subsystems in which this feature participates.  
         # The text is the feature ID. We will list the subsystem names with links  
         # to the subsystem's summary page.  
         my $fid = $text;  
         # Get the subsystems.  
         Trace("Generating subsystems for feature $fid.") if T(4);  
         my %subs = $sprout->SubsystemsOf($fid);  
         # Extract the subsystem names.  
         my @names = map { HTML::sub_link($cgi, $_) } sort keys %subs;  
         # String them into a list.  
         $retVal = join(", ", @names);  
     } elsif ($type =~ /^keyword:(.+)$/) {  
         # Here the caller wants the value of the named keyword. The text is the  
         # feature ID.  
         my $keywordName = $1;  
         my $fid = $text;  
         # Get the attribute values.  
         Trace("Getting $keywordName values for feature $fid.") if T(4);  
         my @values = $sprout->GetFlat(['Feature'], "Feature(id) = ?", [$fid],  
                                       "Feature($keywordName)");  
         # String them into a list.  
         $retVal = join(", ", @values);  
     } elsif ($type eq 'pdb') {  
         # Here the caller wants the best PDB match to this feature. The text  
         # is the feature ID. We will display the PDB with a link to the  
         # PDB page along with the match score. If there are docking results we  
         # will display a link to the docking result search.  
         my $fid = $text;  
         # Ask for the best PDB.  
         my ($bestPDB) = $sprout->GetAll(['IsProteinForFeature', 'PDB'],  
                                         "IsProteinForFeature(from-link) = ? ORDER BY IsProteinForFeature(score) LIMIT 1",  
                                         [$fid], ['PDB(id)', 'PDB(docking-count)', 'IsProteinForFeature(score)']);  
         # Only proceed if there is a PDB.  
         if ($bestPDB) {  
             my ($pdbID, $dockingCount, $score) = @{$bestPDB};  
             # Convert the PDB ID to a hyperlink.  
             my $pdbLink = SHDrugSearch::PDBLink($cgi, $pdbID);  
             # Append the score.  
             $retVal = "$pdbLink ($score)";  
             # If there are docking results, append a docking results link.  
             if ($dockingCount > 0) {  
                 my $dockString = "$dockingCount docking results";  
                 my $dockLink = $cgi->a({ href =>  $cgi->url() . "?Class=DrugSearch;PDB=$pdbID;NoForm=1",  
                                          alt =>   "View computed docking results for $pdbID",  
                                          title => "View computed docking results for $pdbID",  
                                          target => "_blank"},  
                                        $dockString);  
             }  
2049          }          }
2050        };
2051        # Check for errors.
2052        if ($@) {
2053            Confess("Error retrieving $type$className: $@");
2054      }      }
2055      # Return the result.      # Return the result.
2056      return $retVal;      return $retVal;
# Line 2710  Line 2058 
2058    
2059  =head3 SaveOrganismData  =head3 SaveOrganismData
2060    
2061  C<< my ($name, $displayGroup) = $shelp->SaveOrganismData($group, $genomeID, $genus, $species, $strain); >>      my ($name, $displayGroup, $domain) = $shelp->SaveOrganismData($group, $genomeID, $genus, $species, $strain, $taxonomy);
2062    
2063  Format the name of an organism and the display version of its group name. The incoming  Format the name of an organism and the display version of its group name. The incoming
2064  data should be the relevant fields from the B<Genome> record in the database. The  data should be the relevant fields from the B<Genome> record in the database. The
# Line 2740  Line 2088 
2088    
2089  Strain of the species represented by the genome.  Strain of the species represented by the genome.
2090    
2091    =item taxonomy
2092    
2093    Taxonomy of the species represented by the genome.
2094    
2095  =item RETURN  =item RETURN
2096    
2097  Returns a two-element list. The first element is the formatted genome name. The second  Returns a three-element list. The first element is the formatted genome name. The second
2098  element is the display name of the genome's group.  element is the display name of the genome's group. The third is the genome's domain.
2099    
2100  =back  =back
2101    
# Line 2751  Line 2103 
2103    
2104  sub SaveOrganismData {  sub SaveOrganismData {
2105      # Get the parameters.      # Get the parameters.
2106      my ($self, $group, $genomeID, $genus, $species, $strain) = @_;      my ($self, $group, $genomeID, $genus, $species, $strain, $taxonomy) = @_;
2107      # Declare the return values.      # Declare the return values.
2108      my ($name, $displayGroup);      my ($name, $displayGroup);
2109      # If the organism does not exist, format an unknown name and a blank group.      # If the organism does not exist, format an unknown name and a blank group.
# Line 2767  Line 2119 
2119          # 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
2120          # name unless it's the supporting group, which is nulled out.          # name unless it's the supporting group, which is nulled out.
2121          $displayGroup = ($group eq $FIG_Config::otherGroup ? "" : $group);          $displayGroup = ($group eq $FIG_Config::otherGroup ? "" : $group);
2122            Trace("Group = $displayGroup, translated from \"$group\".") if T(4);
2123      }      }
2124        # Compute the domain from the taxonomy.
2125        my ($domain) = split /\s*;\s*/, $taxonomy, 2;
2126      # Cache the group and organism data.      # Cache the group and organism data.
2127      my $cache = $self->{orgs};      my $cache = $self->{orgs};
2128      $cache->{$genomeID} = [$name, $displayGroup];      $cache->{$genomeID} = [$name, $displayGroup, $domain];
2129      # Return the result.      # Return the result.
2130      return ($name, $displayGroup);      return ($name, $displayGroup, $domain);
2131  }  }
2132    
2133  =head3 ValidateKeywords  =head3 ValidateKeywords
2134    
2135  C<< my $okFlag = $shelp->ValidateKeywords($keywordString, $required); >>      my $okFlag = $shelp->ValidateKeywords($keywordString, $required);
2136    
2137  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
2138  set.  set.
# Line 2825  Line 2180 
2180      return $retVal;      return $retVal;
2181  }  }
2182    
2183  =head3 FakeButton  =head3 TuningParameters
   
 C<< my $html = SearchHelper::FakeButton($caption, $url, $target, %parms); >>  
2184    
2185  Create a fake button that hyperlinks to the specified URL with the specified parameters.      my $options = $shelp->TuningParameters(%parmHash);
 Unlike a real button, this one won't visibly click, but it will take the user to the  
 correct place.  
2186    
2187  The parameters of this method are deliberately identical to L</Formlet> so that we  Retrieve tuning parameters from the CGI query object. The parameter is a hash that maps parameter names
2188  can switch easily from real buttons to fake ones in the code.  to their default values. The parameters and their values will be returned as a hash reference.
2189    
2190  =over 4  =over 4
2191    
2192  =item caption  =item parmHash
   
 Caption to be put on the button.  
   
 =item url  
   
 URL for the target page or script.  
   
 =item target  
2193    
2194  Frame or target in which the new page should appear. If C<undef> is specified,  Hash mapping parameter names to their default values.
 the default target will be used.  
2195    
2196  =item parms  =item RETURN
2197    
2198  Hash containing the parameter names as keys and the parameter values as values.  Returns a reference to a hash containing the parameter names mapped to their actual values.
 These will be appended to the URL.  
2199    
2200  =back  =back
2201    
2202  =cut  =cut
2203    
2204  sub FakeButton {  sub TuningParameters {
2205      # Get the parameters.      # Get the parameters.
2206      my ($caption, $url, $target, %parms) = @_;      my ($self, %parmHash) = @_;
2207      # Declare the return variable.      # Declare the return variable.
2208      my $retVal;      my $retVal = {};
2209      # Compute the target URL.      # Get the CGI Query Object.
2210      my $targetUrl = "$url?" . join(";", map { "$_=" . uri_escape($parms{$_}) } keys %parms);      my $cgi = $self->Q();
2211      # Compute the target-frame HTML.      # Loop through the parameter names.
2212      my $targetHtml = ($target ? " target=\"$target\"" : "");      for my $parm (keys %parmHash) {
2213      # Assemble the result.          # Get the incoming value for this parameter.
2214      return "<a href=\"$targetUrl\" $targetHtml><div class=\"button2 button\">$caption</div></a>";          my $value = $cgi->param($parm);
2215            # Zero might be a valid value, so we do an is-defined check rather than an OR.
2216            if (defined($value)) {
2217                $retVal->{$parm} = $value;
2218            } else {
2219                $retVal->{$parm} = $parmHash{$parm};
2220            }
2221        }
2222        # Return the result.
2223        return $retVal;
2224  }  }
2225    
2226  =head3 Formlet  =head3 GetPreferredAliasType
2227    
2228  C<< my $html = SearchHelper::Formlet($caption, $url, $target, %parms); >>      my $type = $shelp->GetPreferredAliasType();
2229    
2230  Create a mini-form that posts to the specified URL with the specified parameters. The  Return the preferred alias type for the current session. This information is stored
2231  parameters will be stored in hidden fields, and the form's only visible control will  in the C<AliasType> parameter of the CGI query object, and the default is C<FIG>
2232  be a submit button with the specified caption.  (which indicates the FIG ID).
2233    
2234  Note that we don't use B<CGI.pm> services here because they generate forms with extra characters  =cut
 and tags that we don't want to deal with.  
2235    
2236  =over 4  sub GetPreferredAliasType {
2237        # Get the parameters.
2238        my ($self) = @_;
2239        # Determine the preferred type.
2240        my $cgi = $self->Q();
2241        my $retVal = $cgi->param('AliasType') || 'FIG';
2242        # Return it.
2243        return $retVal;
2244    }
2245    
2246  =item caption  =head3 Hint
2247    
2248  Caption to be put on the form button.      my $htmlText = SearchHelper::Hint($wikiPage, $hintText);
2249    
2250  =item url  Return the HTML for a small question mark that displays the specified hint text when it is clicked.
2251    This HTML can be put in forms to provide a useful hinting mechanism.
2252    
2253  URL to be put in the form's action parameter.  =over 4
2254    
2255  =item target  =item wikiPage
2256    
2257  Frame or target in which the form results should appear. If C<undef> is specified,  Name of the wiki page to be popped up when the hint mark is clicked.
 the default target will be used.  
2258    
2259  =item parms  =item hintText
2260    
2261  Hash containing the parameter names as keys and the parameter values as values.  Text to display for the hint. It is raw html, but may not contain any double quotes.
2262    
2263    =item RETURN
2264    
2265    Returns the html for the hint facility. The resulting html shows a small button-like thing that
2266    uses the standard FIG popup technology.
2267    
2268  =back  =back
2269    
2270  =cut  =cut
2271    
2272  sub Formlet {  sub Hint {
2273      # Get the parameters.      # Get the parameters.
2274      my ($caption, $url, $target, %parms) = @_;      my ($wikiPage, $hintText) = @_;
2275      # Compute the target HTML.      # Ask Sprout to draw the hint button for us.
2276      my $targetHtml = ($target ? " target=\"$target\"" : "");      return Sprout::Hint($wikiPage, $hintText);
     # Start the form.  
     my $retVal = "<form method=\"POST\" action=\"$url\"$target>";  
     # Add the parameters.  
     for my $parm (keys %parms) {  
         $retVal .= "<input type=\"hidden\" name=\"$parm\" value=\"$parms{$parm}\" />";  
     }  
     # Put in the button.  
     $retVal .= "<input type=\"submit\" name=\"submit\" value=\"$caption\" class=\"button\" />";  
     # Close the form.  
     $retVal .= "</form>";  
     # Return the result.  
     return $retVal;  
2277  }  }
2278    
 =head3 TuningParameters  
   
 C<< my $options = $shelp->TuningParameters(%parmHash); >>  
   
 Retrieve tuning parameters from the CGI query object. The parameter is a hash that maps parameter names  
 to their default values. The parameters and their values will be returned as a hash reference.  
   
 =over 4  
2279    
 =item parmHash  
2280    
2281  Hash mapping parameter names to their default values.  =head2 Virtual Methods
2282    
2283  =item RETURN  =head3 HeaderHtml
2284    
2285  Returns a reference to a hash containing the parameter names mapped to their actual values.      my $html = $shelp->HeaderHtml();
2286    
2287  =back  Generate HTML for the HTML header. If extra styles or javascript are required,
2288    they should go in here.
2289    
2290  =cut  =cut
2291    
2292  sub TuningParameters {  sub HeaderHtml {
2293      # Get the parameters.      return "";
     my ($self, %parmHash) = @_;  
     # Declare the return variable.  
     my $retVal = {};  
     # Get the CGI Query Object.  
     my $cgi = $self->Q();  
     # Loop through the parameter names.  
     for my $parm (keys %parmHash) {  
         # Get the incoming value for this parameter.  
         my $value = $cgi->param($parm);  
         # Zero might be a valid value, so we do an is-defined check rather than an OR.  
         if (defined($value)) {  
             $retVal->{$parm} = $value;  
         } else {  
             $retVal->{$parm} = $parmHash{$parm};  
         }  
2294      }      }
     # Return the result.  
     return $retVal;  
 }  
   
 =head2 Virtual Methods  
2295    
2296  =head3 Form  =head3 Form
2297    
2298  C<< my $html = $shelp->Form(); >>      my $html = $shelp->Form($mode);
2299    
2300    Generate the HTML for a form to request a new search. If the subclass does not
2301    override this method, then the search is formless, and must be started from an
2302    external page.
2303    
2304  Generate the HTML for a form to request a new search.  =cut
2305    
2306    sub Form {
2307        # Get the parameters.
2308        my ($self) = @_;
2309        return "";
2310    }
2311    
2312  =head3 Find  =head3 Find
2313    
2314  C<< my $resultCount = $shelp->Find(); >>      my $resultCount = $shelp->Find();
2315    
2316  Conduct a search based on the current CGI query parameters. The search results will  Conduct a search based on the current CGI query parameters. The search results will
2317  be written to the session cache file and the number of results will be  be written to the session cache file and the number of results will be
2318  returned. If the search parameters are invalid, a result count of C<undef> will be  returned. If the search parameters are invalid, a result count of C<undef> will be
2319  returned and a result message will be stored in this object describing the problem.  returned and a result message will be stored in this object describing the problem.
2320    
2321    =cut
2322    
2323    sub Find {
2324        # Get the parameters.
2325        my ($self) = @_;
2326        $self->Message("Call to pure virtual Find method in helper of type " . ref($self) . ".");
2327        return undef;
2328    }
2329    
2330  =head3 Description  =head3 Description
2331    
2332  C<< my $htmlText = $shelp->Description(); >>      my $htmlText = $shelp->Description();
2333    
2334  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
2335  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,
2336  not block-level, since the description is going to appear in a list.  not block-level, since the description is going to appear in a list.
2337    
 =head3 SortKey  
   
 C<< my $key = $shelp->SortKey($fdata); >>  
   
 Return the sort key for the specified feature data. The default is to sort by feature name,  
 floating NMPDR organisms to the top. If a full-text search is used, then the default  
 sort is by relevance followed by feature name. This sort may be overridden by the  
 search class to provide fancier functionality. This method is called by  
 B<PutFeature>, so it is only used for feature searches. A non-feature search  
 would presumably have its own sort logic.  
   
 =over 4  
   
 =item record  
   
 The C<FeatureData> containing the current feature.  
   
 =item RETURN  
   
 Returns a key field that can be used to sort this row in among the results.  
   
 =back  
   
2338  =cut  =cut
2339    
2340  sub SortKey {  sub Description {
2341      # Get the parameters.      # Get the parameters.
2342      my ($self, $fdata) = @_;      my ($self) = @_;
2343      # Get the feature ID from the record.      $self->Message("Call to pure virtual Description method in helper of type " . ref($self) . ".");
2344      my $fid = $fdata->FID();      return "Unknown search type";
     # Get the group from the feature ID.  
     my $group = $self->FeatureGroup($fid);  
     # Ask the feature query object to form the sort key.  
     my $retVal = $fdata->SortKey($self, $group);  
     # Return the result.  
     return $retVal;  
2345  }  }
2346    
2347  =head3 SearchTitle  =head3 SearchTitle
2348    
2349  C<< my $titleHtml = $shelp->SearchTitle(); >>      my $titleHtml = $shelp->SearchTitle();
2350    
2351  Return the display title for this search. The display title appears above the search results.  Return the display title for this search. The display title appears above the search results.
2352  If no result is returned, no title will be displayed. The result should be an html string  If no result is returned, no title will be displayed. The result should be an html string
# Line 3046  Line 2358 
2358      # Get the parameters.      # Get the parameters.
2359      my ($self) = @_;      my ($self) = @_;
2360      # Declare the return variable.      # Declare the return variable.
2361      my $retVal;      my $retVal = "";
2362      # Return it.      # Return it.
2363      return $retVal;      return $retVal;
2364  }  }
2365    
2366  =head3 DownloadFormatAvailable  =head3 DefaultColumns
2367    
2368        $shelp->DefaultColumns($rhelp);
2369    
2370    Store the default columns in the result helper. The default action is just to ask
2371    the result helper for its default columns, but this may be changed by overriding
2372    this method.
2373    
2374    =over 4
2375    
2376    =item rhelp
2377    
2378    Result helper object in which the column list should be stored.
2379    
2380    =back
2381    
2382    =cut
2383    
2384    sub DefaultColumns {
2385        # Get the parameters.
2386        my ($self, $rhelp) = @_;
2387        # Get the default columns from the result helper.
2388        my @cols = $rhelp->DefaultResultColumns();
2389        # Store them back.
2390        $rhelp->SetColumns(@cols);
2391    }
2392    
2393    
2394    =head3 Initialize
2395    
2396  C<< my $okFlag = $shelp->DownloadFormatAvailable($format); >>      $shelp->Initialize();
2397    
2398  This method returns TRUE if a specified download format is legal for this type of search  Perform any initialization required after construction of the helper.
2399  and FALSE otherwise. For any feature-based search, there is no need to override this  
2400  method.  =cut
2401    
2402    sub Initialize {
2403        # The default is to do nothing.
2404    }
2405    
2406    =head3 GetResultHelper
2407    
2408        my $rhelp = $shelp->GetResultHelper($className);
2409    
2410    Return a result helper for this search helper. The default action is to create
2411    a result helper from scratch; however, if the subclass has an internal result
2412    helper it can override this method to return it without having to create a new
2413    one.
2414    
2415  =over 4  =over 4
2416    
2417  =item format  =item className
2418    
2419  Download format type code.  Result helper class name.
2420    
2421  =item RETURN  =item RETURN
2422    
2423  Returns TRUE if the download format is legal for this search and FALSE otherwise.  Returns a result helper of the specified class connected to this search helper.
2424    
2425  =back  =back
2426    
2427  =cut  =cut
2428    
2429  sub DownloadFormatAvailable {  sub GetResultHelper {
2430      # Get the parameters.      # Get the parameters.
2431      my ($self, $format) = @_;      my ($self, $className) = @_;
2432      # Declare the return variable.      # Create the helper.
2433      my $retVal = 1;      my $retVal = GetHelper($self, RH => $className);
2434      # Return the result.      # return it.
2435      return $retVal;      return $retVal;
2436  }  }
2437    

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