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revision 1.31, Fri May 11 06:28:21 2007 UTC revision 1.42, Fri Oct 17 16:41:47 2008 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 FreezeThaw qw(freeze thaw);
23    
24  =head1 Search Helper Base Class  =head1 Search Helper Base Class
25    
# Line 65  Line 66 
66    
67  =item orgs  =item orgs
68    
69  Reference to a hash mapping genome IDs to organism names.  Reference to a hash mapping genome IDs to organism data. (Used to
70    improve performance.)
71    
72  =item name  =item name
73    
# Line 83  Line 85 
85    
86  List of the parameters that are used to select multiple genomes.  List of the parameters that are used to select multiple genomes.
87    
 =item filtered  
   
 TRUE if this is a feature-filtered search, else FALSE. B<NOTE> that this  
 field is updated by the B<FeatureQuery> object.  
   
 =item extraPos  
   
 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.  
   
88  =back  =back
89    
90  =head2 Adding a new Search Tool  =head2 Adding a new Search Tool
# Line 109  Line 100 
100  =item 2  =item 2
101    
102  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
103  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
104    type of search.
105    
106  =item 3  =item 3
107    
# Line 119  Line 111 
111    
112  =item 4  =item 4
113    
114  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
115    must create a new subclass of B<ResultHelper>. Its name must be
116    C<RH>I<className>, where I<className> is the type of result.
117    
118  =back  =back
119    
# Line 155  Line 149 
149    
150  Several helper methods are provided for particular purposes.  Several helper methods are provided for particular purposes.
151    
 =over 4  
   
 =item 1  
   
152  L</NmpdrGenomeMenu> generates a control for selecting one or more genomes. Use  L</NmpdrGenomeMenu> generates a control for selecting one or more genomes. Use
153  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
154  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
155  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
156  be returned.  be returned.
157    
 =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  
   
158  L</QueueFormScript> allows you to queue JavaScript statements for execution  L</QueueFormScript> allows you to queue JavaScript statements for execution
159  after the form is fully generated. If you are using very complicated  after the form is fully generated. If you are using very complicated
160  form controls, the L</QueueFormScript> method allows you to perform  form controls, the L</QueueFormScript> method allows you to perform
161  JavaScript initialization. The L</NmpdrGenomeMenu> control uses this  JavaScript initialization. The L</NmpdrGenomeMenu> control uses this
162  facility to display a list of the pre-selected genomes.  facility to display a list of the pre-selected genomes.
163    
 =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>.  
   
164  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
165  query parameters as default values so that the search request is persistent.  query parameters as default values so that the search request is persistent.
166    
167  =head3 Finding Search Results  =head3 Finding Search Results
168    
169  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
170  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.  
171    
172      sub Find {      sub Find {
173          my ($self) = @_;          my ($self) = @_;
# Line 207  Line 180 
180          ... validate the parameters ...          ... validate the parameters ...
181          if (... invalid parameters...) {          if (... invalid parameters...) {
182              $self->SetMessage(...appropriate message...);              $self->SetMessage(...appropriate message...);
183          } elsif (FeatureQuery::Valid($self)) {          } else {
184                # Determine the result type.
185                my $rhelp = SearchHelper::GetHelper($self, RH => $resultType);
186                # Specify the columns.
187                $self->DefaultColumns($rhelp);
188                # You may want to add extra columns. $name is the column name and
189                # $loc is its location. The other parameters take their names from the
190                # corresponding column methods.
191                $rhelp->AddExtraColumn($name => $loc, style => $style, download => $flag,
192                    title => $title);
193                # Some searches require optional columns that are configured by the
194                # user or by the search query itself. There are some special methods
195                # for this in the result helpers, but there's also the direct approach
196                # shown below.
197                $rhelp->AddOptionalColumn($name => $loc);
198              # Initialize the session file.              # Initialize the session file.
199              $self->OpenSession();              $self->OpenSession($rhelp);
200              # Initialize the result counter.              # Initialize the result counter.
201              $retVal = 0;              $retVal = 0;
202              ... get a list of genomes ...              ... set up to loop through the results ...
203              for my $genomeID (... each genome ...) {              while (...more results...) {
204                  my $fq = FeatureQuery->new($self, $genomeID);                  ...compute extra columns and call PutExtraColumns...
205                  while (my $feature = $fq->Fetch()) {                  $rhelp->PutData($sortKey, $objectID, $record);
                     ... examine the feature ...  
                     if (... we want to keep it ...) {  
                         $self->PutFeature($fq);  
206                          $retVal++;                          $retVal++;
207                      }                      }
                 }  
             }  
208              # Close the session file.              # Close the session file.
209              $self->CloseSession();              $self->CloseSession();
210          }          }
# Line 231  Line 213 
213      }      }
214    
215  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
216  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.  
217    
218  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
219  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 225 
225  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
226  have been started so that everything is XHTML-compliant.  have been started so that everything is XHTML-compliant.
227    
 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);  
   
228  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
229  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
230  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 241 
241    
242  =head3 new  =head3 new
243    
244  C<< my $shelp = SearchHelper->new($cgi); >>      my $shelp = SearchHelper->new($cgi);
245    
246  Construct a new SearchHelper object.  Construct a new SearchHelper object.
247    
# Line 291  Line 265 
265          Trace("No session ID found.") if T(3);          Trace("No session ID found.") if T(3);
266          # 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
267          # store it in the query object.          # store it in the query object.
268          $session_id = NewSessionID();          $session_id = FIGRules::NewSessionID();
269            Trace("New session ID is $session_id.") if T(3);
270          $type = "new";          $type = "new";
271          $cgi->param(-name => 'SessionID', -value => $session_id);          $cgi->param(-name => 'SessionID', -value => $session_id);
272      } else {      } else {
273          Trace("Session ID is $session_id.") if T(3);          Trace("Session ID is $session_id.") if T(3);
274      }      }
275        Trace("Computing subclass.") if T(3);
276      # Compute the subclass name.      # Compute the subclass name.
277      my $subClass;      my $subClass;
278      if ($class =~ /SH(.+)$/) {      if ($class =~ /SH(.+)$/) {
# Line 307  Line 283 
283          # process search results.          # process search results.
284          $subClass = 'SearchHelper';          $subClass = 'SearchHelper';
285      }      }
286        Trace("Subclass name is $subClass.") if T(3);
287      # Insure everybody knows we're in Sprout mode.      # Insure everybody knows we're in Sprout mode.
288      $cgi->param(-name => 'SPROUT', -value => 1);      $cgi->param(-name => 'SPROUT', -value => 1);
289      # Generate the form name.      # Generate the form name.
290      my $formName = "$class$formCount";      my $formName = "$class$formCount";
291      $formCount++;      $formCount++;
292        Trace("Creating helper.") if T(3);
293      # 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)
294      # 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
295      # class name and a placeholder for the Sprout object.      # class name and a placeholder for the Sprout object.
# Line 325  Line 303 
303                    scriptQueue => [],                    scriptQueue => [],
304                    genomeList => undef,                    genomeList => undef,
305                    genomeParms => [],                    genomeParms => [],
                   filtered => 0,  
                   extraPos => {},  
306                   };                   };
307      # Bless and return it.      # Bless and return it.
308      bless $retVal, $class;      bless $retVal, $class;
# Line 335  Line 311 
311    
312  =head3 Q  =head3 Q
313    
314  C<< my $query = $shelp->Q(); >>      my $query = $shelp->Q();
315    
316  Return the CGI query object.  Return the CGI query object.
317    
# Line 352  Line 328 
328    
329  =head3 DB  =head3 DB
330    
331  C<< my $sprout = $shelp->DB(); >>      my $sprout = $shelp->DB();
332    
333  Return the Sprout database object.  Return the Sprout database object.
334    
# Line 373  Line 349 
349    
350  =head3 IsNew  =head3 IsNew
351    
352  C<< my $flag = $shelp->IsNew(); >>      my $flag = $shelp->IsNew();
353    
354  Return TRUE if this is a new session, FALSE if this is an old session. An old  Return TRUE if this is a new session, FALSE if this is an old session. An old
355  session already has search results ready to process.  session already has search results ready to process.
# Line 387  Line 363 
363      return ($self->{type} eq 'new');      return ($self->{type} eq 'new');
364  }  }
365    
 =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;  
 }  
   
366  =head3 ID  =head3 ID
367    
368  C<< my $sessionID = $shelp->ID(); >>      my $sessionID = $shelp->ID();
369    
370  Return the current session ID.  Return the current session ID.
371    
# Line 429  Line 380 
380    
381  =head3 FormName  =head3 FormName
382    
383  C<< my $name = $shelp->FormName(); >>      my $name = $shelp->FormName();
384    
385  Return the name of the form this helper object will generate.  Return the name of the form this helper object will generate.
386    
# Line 444  Line 395 
395    
396  =head3 QueueFormScript  =head3 QueueFormScript
397    
398  C<< $shelp->QueueFormScript($statement); >>      $shelp->QueueFormScript($statement);
399    
400  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
401  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 430 
430    
431  =head3 FormStart  =head3 FormStart
432    
433  C<< my $html = $shelp->FormStart($title); >>      my $html = $shelp->FormStart($title);
434    
435  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
436  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 510  Line 461 
461      # case the Advanced button was used.      # case the Advanced button was used.
462      my $retVal = "<div class=\"search\">\n" .      my $retVal = "<div class=\"search\">\n" .
463                   $cgi->start_form(-method => 'POST',                   $cgi->start_form(-method => 'POST',
464                                    -action => $cgi->url(-relative => 1),                                    -action => "$FIG_Config::cgi_url/SearchSkeleton.cgi",
465                                    -name => $self->FormName()) .                                    -name => $self->FormName()) .
466                   $cgi->hidden(-name => 'Class',                   $cgi->hidden(-name => 'Class',
467                                -value => $self->{class},                                -value => $self->{class},
468                                -override => 1) .                                -override => 1) .
469                   $cgi->hidden(-name => 'SPROUT',                   $cgi->hidden(-name => 'SPROUT',
470                                -value => 1) .                                -value => 1) .
471                   $cgi->h3($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));  
     }  
472      # 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.
473      my $anchorName = $self->FormName();      my $anchorName = $self->FormName();
474      $retVal .= "<a name=\"$anchorName\"></a>\n";      $retVal .= "<a name=\"$anchorName\"></a>\n";
# Line 534  Line 478 
478    
479  =head3 FormEnd  =head3 FormEnd
480    
481  C<< my $htmlText = $shelp->FormEnd(); >>      my $htmlText = $shelp->FormEnd();
482    
483  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
484  C<div> tags.  C<div> tags.
# Line 566  Line 510 
510    
511  =head3 SetMessage  =head3 SetMessage
512    
513  C<< $shelp->SetMessage($msg); >>      $shelp->SetMessage($msg);
514    
515  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
516  if an invalid parameter value is specified.  if an invalid parameter value is specified.
# Line 590  Line 534 
534    
535  =head3 Message  =head3 Message
536    
537  C<< my $text = $shelp->Message(); >>      my $text = $shelp->Message();
538    
539  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
540  value is specified.  value is specified.
# Line 606  Line 550 
550    
551  =head3 OpenSession  =head3 OpenSession
552    
553  C<< $shelp->OpenSession(); >>      $shelp->OpenSession($rhelp);
554    
555  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.
556  open the file until after we know the column headers.  This method should not be called until all the columns have
557    been configured, including the extra columns.
558    
559    =over 4
560    
561    =item rhelp
562    
563    Result helper for formatting the output. This has the column
564    headers stored in it.
565    
566    =back
567    
568  =cut  =cut
569    
570  sub OpenSession {  sub OpenSession {
571      # Get the parameters.      # Get the parameters.
572      my ($self) = @_;      my ($self, $rhelp) = @_;
573      # Denote we have not yet written out the column headers.      # Insure the result helper is valid.
574      $self->{cols} = undef;      if (! defined($rhelp)) {
575            Confess("No result type specified for $self->{class}.");
576        } elsif(! $rhelp->isa('ResultHelper')) {
577            Confess("Invalid result type specified for $self->{class}.");
578        } else {
579            # Get the column headers and write them out.
580            my $colHdrs = $rhelp->GetColumnHeaders();
581            Trace(scalar(@{$colHdrs}) . " column headers written to output.") if T(3);
582            $self->WriteColumnHeaders(@{$colHdrs});
583        }
584  }  }
585    
586  =head3 GetCacheFileName  =head3 GetCacheFileName
587    
588  C<< my $fileName = $shelp->GetCacheFileName(); >>      my $fileName = $shelp->GetCacheFileName();
589    
590  Return the name to be used for this session's cache file.  Return the name to be used for this session's cache file.
591    
# Line 637  Line 600 
600    
601  =head3 GetTempFileName  =head3 GetTempFileName
602    
603  C<< my $fileName = $shelp->GetTempFileName($type); >>      my $fileName = $shelp->GetTempFileName($type);
604    
605  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
606  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 624 
624      my ($self, $type) = @_;      my ($self, $type) = @_;
625      # Compute the file name. Note it gets stuffed in the FIG temporary      # Compute the file name. Note it gets stuffed in the FIG temporary
626      # directory.      # directory.
627      my $retVal = "$FIG_Config::temp/tmp_" . $self->ID() . ".$type";      my $retVal = FIGRules::GetTempFileName(sessionID => $self->ID(), extension => $type);
628      # Return the result.      # Return the result.
629      return $retVal;      return $retVal;
630  }  }
631    
 =head3 PutFeature  
   
 C<< $shelp->PutFeature($fdata); >>  
   
 Store a feature in the result cache. This is the workhorse method for most  
 searches, since the primary data item in the database is features.  
   
 For each feature, there are certain columns that are standard: the feature name, the  
 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.  
   
     $fd->AddExtraColumns(essential => $essentialFlag, virulence => $vfactor);  
     $shelp->PutFeature($fd);  
   
 For correct results, all values should be specified for all extra columns in all calls to  
 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>.  
   
     if (! $essentialFlag) {  
         $essentialFlag = undef;  
     }  
     $fd->AddExtraColumns(essential => $essentialFlag, virulence => $vfactor);  
     $shelp->PutFeature($fd);  
   
 =over 4  
   
 =item fdata  
   
 B<FeatureData> object containing the current feature data.  
   
 =back  
   
 =cut  
   
 sub PutFeature {  
     # Get the parameters.  
     my ($self, $fd) = @_;  
     # Get the CGI query object.  
     my $cgi = $self->Q();  
     # 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);  
 }  
   
632  =head3 WriteColumnHeaders  =head3 WriteColumnHeaders
633    
634  C<< $shelp->WriteColumnHeaders(@colNames); >>      $shelp->WriteColumnHeaders(@colNames);
635    
636  Write out the column headers for the current search session. The column headers  Write out the column headers for the current search session. The column headers
637  are sent to the cache file, and then the cache is re-opened as a sort pipe and  are sent to the cache file, and then the cache is re-opened as a sort pipe and
# Line 776  Line 641 
641    
642  =item colNames  =item colNames
643    
644  A list of column names in the desired presentation order.  A list of column names in the desired presentation order. For extra columns,
645    the column name is the hash supplied as the column definition.
646    
647  =back  =back
648    
# Line 788  Line 654 
654      # Get the cache file name and open it for output.      # Get the cache file name and open it for output.
655      my $fileName = $self->GetCacheFileName();      my $fileName = $self->GetCacheFileName();
656      my $handle1 = Open(undef, ">$fileName");      my $handle1 = Open(undef, ">$fileName");
657        # Freeze the column headers.
658        my @colHdrs = map { freeze($_) } @colNames;
659      # Write the column headers and close the file.      # Write the column headers and close the file.
660      Tracer::PutLine($handle1, \@colNames);      Tracer::PutLine($handle1, \@colHdrs);
661      close $handle1;      close $handle1;
662      # Now open the sort pipe and save the file handle. Note how we append the      # Now open the sort pipe and save the file handle. Note how we append the
663      # sorted data to the column header row already in place. The output will      # sorted data to the column header row already in place. The output will
# Line 798  Line 666 
666      $self->{fileHandle} = Open(undef, "| sort | cut --fields=2- >>$fileName");      $self->{fileHandle} = Open(undef, "| sort | cut --fields=2- >>$fileName");
667  }  }
668    
669    =head3 ReadColumnHeaders
670    
671        my @colHdrs = $shelp->ReadColumnHeaders($fh);
672    
673    Read the column headers from the specified file handle. The column headers are
674    frozen strings intermixed with frozen hash references. The strings represent
675    column names defined in the result helper. The hash references represent the
676    definitions of the extra columns.
677    
678    =over 4
679    
680    =item fh
681    
682    File handle from which the column headers are to be read.
683    
684    =item RETURN
685    
686    Returns a list of the column headers pulled from the specified file's first line.
687    
688    =back
689    
690    =cut
691    
692    sub ReadColumnHeaders {
693        # Get the parameters.
694        my ($self, $fh) = @_;
695        # Read and thaw the columns.
696        my @retVal = map { thaw($_) } Tracer::GetLine($fh);
697        # Return them to the caller.
698        return @retVal;
699    }
700    
701  =head3 WriteColumnData  =head3 WriteColumnData
702    
703  C<< $shelp->WriteColumnData($key, @colValues); >>      $shelp->WriteColumnData($key, @colValues);
704    
705  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
706  the session file is already open for output.  the session file is already open for output.
# Line 824  Line 724 
724      my ($self, $key, @colValues) = @_;      my ($self, $key, @colValues) = @_;
725      # Write them to the cache file.      # Write them to the cache file.
726      Tracer::PutLine($self->{fileHandle}, [$key, @colValues]);      Tracer::PutLine($self->{fileHandle}, [$key, @colValues]);
727        Trace("Column data is " . join("; ", $key, @colValues) . ".") if T(4);
728  }  }
729    
730  =head3 CloseSession  =head3 CloseSession
731    
732  C<< $shelp->CloseSession(); >>      $shelp->CloseSession();
733    
734  Close the session file.  Close the session file.
735    
# Line 848  Line 749 
749      }      }
750  }  }
751    
 =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;  
 }  
   
752  =head3 OrganismData  =head3 OrganismData
753    
754  C<< my ($orgName, $group) = $shelp->Organism($genomeID); >>      my ($orgName, $group) = $shelp->Organism($genomeID);
755    
756  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.
757  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 765 
765    
766  =item RETURN  =item RETURN
767    
768  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,
769  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
770  organism is not in an NMPDR group.  organism is not in an NMPDR group. The third item is the organism's domain.
771    
772  =back  =back
773    
# Line 899  Line 777 
777      # Get the parameters.      # Get the parameters.
778      my ($self, $genomeID) = @_;      my ($self, $genomeID) = @_;
779      # Declare the return variables.      # Declare the return variables.
780      my ($orgName, $group);      my ($orgName, $group, $domain);
781      # Check the cache.      # Check the cache.
782      my $cache = $self->{orgs};      my $cache = $self->{orgs};
783      if (exists $cache->{$genomeID}) {      if (exists $cache->{$genomeID}) {
784          ($orgName, $group) = @{$cache->{$genomeID}};          ($orgName, $group, $domain) = @{$cache->{$genomeID}};
785            Trace("Cached organism $genomeID has group \"$group\".") if T(4);
786      } else {      } else {
787          # Here we have to use the database.          # Here we have to use the database.
788          my $sprout = $self->DB();          my $sprout = $self->DB();
789          my ($genus, $species, $strain, $group) = $sprout->GetEntityValues('Genome', $genomeID,          my ($genus, $species, $strain, $newGroup, $taxonomy) = $sprout->GetEntityValues('Genome', $genomeID,
790                                                      ['Genome(genus)', 'Genome(species)',                                                      ['Genome(genus)', 'Genome(species)',
791                                                       'Genome(unique-characterization)',                                                       'Genome(unique-characterization)',
792                                                       'Genome(primary-group)']);                                                                   'Genome(primary-group)',
793                                                                     'Genome(taxonomy)']);
794          # Format and cache the name and display group.          # Format and cache the name and display group.
795          ($orgName, $group) = $self->SaveOrganismData($group, $genomeID, $genus, $species,          Trace("Caching organism $genomeID with group \"$newGroup\".") if T(4);
796                                                              $strain);          ($orgName, $group, $domain) = $self->SaveOrganismData($newGroup, $genomeID, $genus, $species,
797                                                                  $strain, $taxonomy);
798            Trace("Returning group $group.") if T(4);
799      }      }
800      # Return the result.      # Return the result.
801      return ($orgName, $group);      return ($orgName, $group, $domain);
802  }  }
803    
804  =head3 Organism  =head3 Organism
805    
806  C<< my $orgName = $shelp->Organism($genomeID); >>      my $orgName = $shelp->Organism($genomeID);
807    
808  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,
809  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 826 
826      # Get the parameters.      # Get the parameters.
827      my ($self, $genomeID) = @_;      my ($self, $genomeID) = @_;
828      # Get the organism data.      # Get the organism data.
829      my ($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]";  
     }  
830      # Return the result.      # Return the result.
831      return $retVal;      return $retVal;
832  }  }
833    
834  =head3 ComputeFASTA  =head3 ComputeFASTA
835    
836  C<< my $fasta = $shelp->ComputeFASTA($desiredType, $sequence); >>      my $fasta = $shelp->ComputeFASTA($desiredType, $sequence, $flankingWidth, $comments);
837    
838  Parse a sequence input and convert it into a FASTA string of the desired type.  Parse a sequence input and convert it into a FASTA string of the desired type with
839    the desired flanking width.
840    
841  =over 4  =over 4
842    
843  =item desiredType  =item desiredType
844    
845  C<dna> to return a DNA sequence, C<prot> to return a protein sequence.  C<dna> to return a DNA sequence, C<prot> to return a protein sequence, C<dnaPattern>
846    to return a DNA search pattern, C<protPattern> to return a protein search pattern.
847    
848  =item sequence  =item sequence
849    
# Line 1042  Line 853 
853  if the input does not begin with a greater-than sign (FASTA label line), a default label  if the input does not begin with a greater-than sign (FASTA label line), a default label
854  line will be provided.  line will be provided.
855    
856    =item flankingWidth
857    
858    If the DNA FASTA of a feature is desired, the number of base pairs to either side of the
859    feature that should be included. Currently we can't do this for Proteins because the
860    protein translation of a feature doesn't always match the DNA and is taken directly
861    from the database.
862    
863    =item comments
864    
865    Comment string to be added to the FASTA header.
866    
867  =item RETURN  =item RETURN
868    
869  Returns a string in FASTA format representing the content of the desired sequence with  Returns a string in FASTA format representing the content of the desired sequence with
# Line 1054  Line 876 
876    
877  sub ComputeFASTA {  sub ComputeFASTA {
878      # Get the parameters.      # Get the parameters.
879      my ($self, $desiredType, $sequence) = @_;      my ($self, $desiredType, $sequence, $flankingWidth, $comment) = @_;
880      # Declare the return variable. If an error occurs, it will remain undefined.      # Declare the return variable. If an error occurs, it will remain undefined.
881      my $retVal;      my $retVal;
882      # This variable will be cleared if an error is detected.      # This variable will be cleared if an error is detected.
# Line 1085  Line 907 
907                  # In an emergency, fall back to the original ID.                  # In an emergency, fall back to the original ID.
908                  $fastaLabel = $fid;                  $fastaLabel = $fid;
909              }              }
910                # Add any specified comments.
911                if ($comment) {
912                    $fastaLabel .= " $comment";
913                }
914              # Now proceed according to the sequence type.              # Now proceed according to the sequence type.
915              if ($desiredType eq 'prot') {              if ($desiredType =~ /prot/) {
916                  # We want protein, so get the translation.                  # We want protein, so get the translation.
917                  $fastaData = $sprout->FeatureTranslation($figID);                  $fastaData = $sprout->FeatureTranslation($figID);
918                  Trace(length $fastaData . " characters returned for translation of $fastaLabel.") if T(3);                  Trace(length $fastaData . " characters returned for translation of $fastaLabel.") if T(3);
919              } else {              } elsif ($desiredType =~ /dna/) {
920                  # 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
921                    # locations.
922                  my @locList = $sprout->FeatureLocation($figID);                  my @locList = $sprout->FeatureLocation($figID);
923                    if ($flankingWidth > 0) {
924                        # Here we need to add flanking data. Convert the locations to a list
925                        # of location objects.
926                        my @locObjects = map { BasicLocation->new($_) } @locList;
927                        # Initialize the return variable. We will put the DNA in here segment by segment.
928                        $fastaData = "";
929                        # Now we widen each location by the flanking width and stash the results. This
930                        # requires getting the contig length for each contig so we don't fall off the end.
931                        for my $locObject (@locObjects) {
932                            Trace("Current location is " . $locObject->String . ".") if T(4);
933                            # Remember the current start and length.
934                            my ($start, $len) = ($locObject->Left, $locObject->Length);
935                            # Get the contig length.
936                            my $contigLen = $sprout->ContigLength($locObject->Contig);
937                            # Widen the location and get its DNA.
938                            $locObject->Widen($flankingWidth, $contigLen);
939                            my $fastaSegment = $sprout->DNASeq([$locObject->String()]);
940                            # Now we need to do some case changing. The main DNA is upper case and
941                            # the flanking DNA is lower case.
942                            my $leftFlank = $start - $locObject->Left;
943                            my $rightFlank = $leftFlank + $len;
944                            Trace("Wide location is " . $locObject->String . ". Flanks are $leftFlank and $rightFlank. Contig len is $contigLen.") if T(4);
945                            my $fancyFastaSegment = lc(substr($fastaSegment, 0, $leftFlank)) .
946                                                    uc(substr($fastaSegment, $leftFlank, $rightFlank - $leftFlank)) .
947                                                    lc(substr($fastaSegment, $rightFlank));
948                            $fastaData .= $fancyFastaSegment;
949                        }
950                    } else {
951                        # Here we have just the raw sequence.
952                  $fastaData = $sprout->DNASeq(\@locList);                  $fastaData = $sprout->DNASeq(\@locList);
953                  Trace(length $fastaData . " characters returned for DNA of $fastaLabel.") if T(3);                  }
954                    Trace((length $fastaData) . " characters returned for DNA of $fastaLabel.") if T(3);
955              }              }
956          }          }
957      } else {      } else {
# Line 1109  Line 966 
966              Trace("No label found in match to sequence:\n$sequence") if T(4);              Trace("No label found in match to sequence:\n$sequence") if T(4);
967              # 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
968              # as data.              # as data.
969              $fastaLabel = "User-specified $desiredType sequence";              $fastaLabel = "$desiredType sequence specified by user";
970              $fastaData = $sequence;              $fastaData = $sequence;
971          }          }
972          # The next step is to clean the junk out of the sequence.          # If we are not doing a pattern search, we need to clean the junk out of the sequence.
973            if ($desiredType !~ /pattern/i) {
974          $fastaData =~ s/\n//g;          $fastaData =~ s/\n//g;
975          $fastaData =~ s/\s+//g;          $fastaData =~ s/\s+//g;
976            }
977          # Finally, verify that it's DNA if we're doing DNA stuff.          # Finally, verify that it's DNA if we're doing DNA stuff.
978          if ($desiredType eq 'dna' && $fastaData =~ /[^agctxn]/i) {          if ($desiredType eq 'dna' && $fastaData =~ /[^agctxn-]/i) {
979              $self->SetMessage("Invalid characters detected. Is the input really a DNA sequence?");              $self->SetMessage("Invalid characters detected. Is the input really a DNA sequence?");
980              $okFlag = 0;              $okFlag = 0;
981          }          }
# Line 1124  Line 983 
983      Trace("FASTA data sequence: $fastaData") if T(4);      Trace("FASTA data sequence: $fastaData") if T(4);
984      # Only proceed if no error was detected.      # Only proceed if no error was detected.
985      if ($okFlag) {      if ($okFlag) {
986            if ($desiredType =~ /pattern/i) {
987                # For a scan, there is no label and no breakup.
988                $retVal = $fastaData;
989            } else {
990          # 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
991          # grep-split trick. The split, because of the presence of the parentheses,          # grep-split trick. The split, because of the presence of the parentheses,
992          # 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 995 
995          my @chunks = grep { $_ } split /(.{1,60})/, $fastaData;          my @chunks = grep { $_ } split /(.{1,60})/, $fastaData;
996          $retVal = join("\n", ">$fastaLabel", @chunks, "");          $retVal = join("\n", ">$fastaLabel", @chunks, "");
997      }      }
998        }
999      # Return the result.      # Return the result.
1000      return $retVal;      return $retVal;
1001  }  }
1002    
1003  =head3 SubsystemTree  =head3 SubsystemTree
1004    
1005  C<< my $tree = SearchHelper::SubsystemTree($sprout, %options); >>      my $tree = SearchHelper::SubsystemTree($sprout, %options);
1006    
1007  This method creates a subsystem selection tree suitable for passing to  This method creates a subsystem selection tree suitable for passing to
1008  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 1060 
1060              push @subs, $classLess;              push @subs, $classLess;
1061          }          }
1062      }      }
1063        # Get the seedviewer URL.
1064        my $svURL = $FIG_Config::linkinSV || "$FIG_Config::cgi_url/seedviewer.cgi";
1065        Trace("Seed Viewer URL is $svURL.") if T(3);
1066      # Declare the return variable.      # Declare the return variable.
1067      my @retVal = ();      my @retVal = ();
1068      # Each element in @subs represents a leaf node, so as we loop through it we will be      # Each element in @subs represents a leaf node, so as we loop through it we will be
# Line 1270  Line 1137 
1137              if ($optionThing->{links}) {              if ($optionThing->{links}) {
1138                  # Compute the link value.                  # Compute the link value.
1139                  my $linkable = uri_escape($id);                  my $linkable = uri_escape($id);
1140                  $nodeContent->{link} = "../FIG/display_subsys.cgi?ssa_name=$linkable;request=show_ssa;sort=by_phylo;show_clusters=1;SPROUT=1";                  $nodeContent->{link} = "$svURL?page=Subsystems;subsystem=$linkable";
1141              }              }
1142              if ($optionThing->{radio}) {              if ($optionThing->{radio}) {
1143                  # Compute the radio value.                  # Compute the radio value.
# Line 1288  Line 1155 
1155    
1156  =head3 NmpdrGenomeMenu  =head3 NmpdrGenomeMenu
1157    
1158  C<< my $htmlText = $shelp->NmpdrGenomeMenu($menuName, $multiple, \@selected, $rows); >>      my $htmlText = $shelp->NmpdrGenomeMenu($menuName, $multiple, \@selected, $rows);
1159    
1160  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
1161  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 1184 
1184    
1185  =item crossMenu (optional)  =item crossMenu (optional)
1186    
1187  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.  
1188    
1189  =item RETURN  =item RETURN
1190    
# Line 1340  Line 1204 
1204      if (! defined $rows) {      if (! defined $rows) {
1205          $rows = ($multiple ? 10 : 1);          $rows = ($multiple ? 10 : 1);
1206      }      }
1207      # Create the multiple tag.      # Get a comma-delimited list of the preselected genomes.
1208      my $multipleTag = ($multiple ? " multiple" : "");      my $preselected = "";
1209      # Get the form name.      if ($selected) {
1210      my $formName = $self->FormName();          $preselected = join(", ", @$selected);
1211      # Check to see if we already have a genome list in memory.      }
1212      my $genomes = $self->{genomeList};      # Ask Sprout for a genome menu.
1213      my $groupHash;      my $retVal = $sprout->GenomeMenu(name => $menuName,
1214      if (defined $genomes) {                                       multiSelect => $multiple,
1215          # We have a list ready to use.                                       selected => $preselected,
1216          $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, "");  
1217      # Return the result.      # Return the result.
1218      return $retVal;      return $retVal;
1219  }  }
1220    
1221  =head3 PropertyMenu  =head3 PropertyMenu
1222    
1223  C<< my $htmlText = $shelp->PropertyMenu($menuName, $selected, $force); >>      my $htmlText = $shelp->PropertyMenu($menuName, $selected, $force);
1224    
1225  Generate a property name dropdown menu.  Generate a property name dropdown menu.
1226    
# Line 1518  Line 1270 
1270    
1271  =head3 MakeTable  =head3 MakeTable
1272    
1273  C<< my $htmlText = $shelp->MakeTable(\@rows); >>      my $htmlText = $shelp->MakeTable(\@rows);
1274    
1275  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
1276  other words, each must have the TR and TD tags included.  other words, each must have the TR and TD tags included.
# Line 1581  Line 1333 
1333    
1334  =head3 SubmitRow  =head3 SubmitRow
1335    
1336  C<< my $htmlText = $shelp->SubmitRow($caption); >>      my $htmlText = $shelp->SubmitRow($caption);
1337    
1338  Returns the HTML text for the row containing the page size control  Returns the HTML text for the row containing the page size control
1339  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 1362 
1362      my $realCaption = (defined $caption ? $caption : 'Go');      my $realCaption = (defined $caption ? $caption : 'Go');
1363      # Get the current page size.      # Get the current page size.
1364      my $pageSize = $cgi->param('PageSize');      my $pageSize = $cgi->param('PageSize');
1365      # Get the incoming external-link flag.      # Get the current feature ID type.
1366      my $aliases = ($cgi->param('ShowAliases') ? 1 : 0);      my $aliasType = $self->GetPreferredAliasType();
1367      # Create the row.      # Create the rows.
1368      my $retVal = $cgi->Tr($cgi->td("Results/Page"),      my $retVal = $cgi->Tr($cgi->td("Identifier Type "),
1369                              $cgi->td({ colspan => 2 },
1370                                       $cgi->popup_menu(-name => 'AliasType',
1371                                                        -values => ['FIG', AliasAnalysis::AliasTypes() ],
1372                                                        -default => $aliasType) .
1373                                       Hint("Identifier Type", "Specify how you want gene names to be displayed."))) .
1374                     "\n" .
1375                     $cgi->Tr($cgi->td("Results/Page"),
1376                            $cgi->td($cgi->popup_menu(-name => 'PageSize',                            $cgi->td($cgi->popup_menu(-name => 'PageSize',
1377                                                      -values => [10, 25, 50, 100, 1000],                                                      -values => [10, 25, 50, 100, 1000],
1378                                                      -default => $pageSize)),                                                      -default => $pageSize)),
# Line 1624  Line 1383 
1383      return $retVal;      return $retVal;
1384  }  }
1385    
 =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;  
 }  
   
1386  =head3 GetGenomes  =head3 GetGenomes
1387    
1388  C<< my @genomeList = $shelp->GetGenomes($parmName); >>      my @genomeList = $shelp->GetGenomes($parmName);
1389    
1390  Return the list of genomes specified by the specified CGI query parameter.  Return the list of genomes specified by the specified CGI query parameter.
1391  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 1427 
1427      return @retVal;      return @retVal;
1428  }  }
1429    
 =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;  
 }  
   
1430  =head3 ComputeSearchURL  =head3 ComputeSearchURL
1431    
1432  C<< my $url = $shelp->ComputeSearchURL(%overrides); >>      my $url = $shelp->ComputeSearchURL(%overrides);
1433    
1434  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
1435  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 1462 
1462      my $cgi = $self->Q();      my $cgi = $self->Q();
1463      my $sprout = $self->DB();      my $sprout = $self->DB();
1464      # Start with the full URL.      # Start with the full URL.
1465      my $retVal = $cgi->url(-full => 1);      my $retVal = "$FIG_Config::cgi_url/SearchSkeleton.cgi";
1466      # Get all the query parameters in a hash.      # Get all the query parameters in a hash.
1467      my %parms = $cgi->Vars();      my %parms = $cgi->Vars();
1468      # 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 1520 
1520      return $retVal;      return $retVal;
1521  }  }
1522    
 =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;  
 }  
   
1523  =head3 AdvancedClassList  =head3 AdvancedClassList
1524    
1525  C<< my @classes = SearchHelper::AdvancedClassList(); >>      my @classes = SearchHelper::AdvancedClassList();
1526    
1527  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
1528  of available searches on the search page.  of available searches on the search page.
1529    
1530  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.
1531    
1532  =cut  =cut
1533    
1534  sub AdvancedClassList {  sub AdvancedClassList {
1535      my @retVal = map { $_ =~ /^SH(\w+)\.pm/; $1 } grep { $_ =~ /^SH/ } keys %INC;      # Determine the search helper module directory.
1536        my $libDirectory = $INC{'SearchHelper.pm'};
1537        $libDirectory =~ s/SearchHelper\.pm//;
1538        # Read it, keeping only the helper modules.
1539        my @modules = grep { /^SH\w+\.pm/ } Tracer::OpenDir($libDirectory, 0);
1540        # Convert the file names to search types.
1541        my @retVal = map { $_ =~ /^SH(\w+)\.pm/; $1 } @modules;
1542        # Return the result in alphabetical order.
1543      return sort @retVal;      return sort @retVal;
1544  }  }
1545    
1546  =head3 SelectionTree  =head3 SelectionTree
1547    
1548  C<< my $htmlText = SearchHelper::SelectionTree($cgi, \%tree, %options); >>      my $htmlText = SearchHelper::SelectionTree($cgi, \%tree, %options);
1549    
1550  Display a selection tree.  Display a selection tree.
1551    
# Line 2077  Line 1654 
1654  =item nodeImageClosed  =item nodeImageClosed
1655    
1656  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
1657  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>.
1658    
1659  =item nodeImageOpen  =item nodeImageOpen
1660    
1661  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
1662  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>.
1663    
1664  =item style  =item style
1665    
# Line 2122  Line 1699 
1699      my ($cgi, $tree, %options) = @_;      my ($cgi, $tree, %options) = @_;
1700      # Get the options.      # Get the options.
1701      my $optionThing = Tracer::GetOptions({ name => 'selection',      my $optionThing = Tracer::GetOptions({ name => 'selection',
1702                                             nodeImageClosed => '../FIG/Html/plus.gif',                                             nodeImageClosed => "$FIG_Config::cgi_url/Html/plus.gif",
1703                                             nodeImageOpen => '../FIG/Html/minus.gif',                                             nodeImageOpen => "$FIG_Config::cgi_url/Html/minus.gif",
1704                                             style => 'tree',                                             style => 'tree',
1705                                             target => '_self',                                             target => '_self',
1706                                             selected => undef},                                             selected => undef},
# Line 2157  Line 1734 
1734    
1735  =head3 ShowBranch  =head3 ShowBranch
1736    
1737  C<< my @htmlLines = SearchHelper::ShowBranch($cgi, $label, $id, $branch, $options, $displayType); >>      my @htmlLines = SearchHelper::ShowBranch($cgi, $label, $id, $branch, $options, $displayType);
1738    
1739  This is a recursive method that displays a branch of the tree.  This is a recursive method that displays a branch of the tree.
1740    
# Line 2252  Line 1829 
1829                      # If we have children, create the child list with a recursive call.                      # If we have children, create the child list with a recursive call.
1830                      if ($hasChildren) {                      if ($hasChildren) {
1831                          Trace("Processing children of $myLabel.") if T(4);                          Trace("Processing children of $myLabel.") if T(4);
1832                          push @childHtml, ShowBranch($cgi, $myLabel, $myID, $myContent, $options, 'none');                          push @childHtml, ShowBranch($cgi, $myLabel, $myID, $myContent, $options, 'block');
1833                          Trace("Children of $myLabel finished.") if T(4);                          Trace("Children of $myLabel finished.") if T(4);
1834                      }                      }
1835                  }                  }
# Line 2309  Line 1886 
1886    
1887  =head3 GetDivID  =head3 GetDivID
1888    
1889  C<< my $idString = SearchHelper::GetDivID($name); >>      my $idString = SearchHelper::GetDivID($name);
1890    
1891  Return a new HTML ID string.  Return a new HTML ID string.
1892    
# Line 2338  Line 1915 
1915      return $retVal;      return $retVal;
1916  }  }
1917    
   
1918  =head3 PrintLine  =head3 PrintLine
1919    
1920  C<< $shelp->PrintLine($message); >>      $shelp->PrintLine($message);
1921    
1922  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
1923  searching, so the user sees progress in real-time.  searching, so the user sees progress in real-time.
# Line 2363  Line 1939 
1939      print "$message\n";      print "$message\n";
1940  }  }
1941    
1942  =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  
   
 C<< my @colNames = $shelp->DefaultFeatureColumns(); >>  
   
 Return a list of the default feature column identifiers. These identifiers can  
 be passed to L</FeatureColumnTitle> and L</FeatureColumnValue> in order to  
 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.  
   
 =over 4  
   
 =item name  
   
 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  
1943    
1944  C<< my $value = $shelp->FeatureColumnValue($colName, $fid, \%extraCols); >>      my $shelp = SearchHelper::GetHelper($parm, $type => $className);
1945    
1946  Return the value to be displayed in the specified feature column.  Return a helper object with the given class name. If no such class exists, an
1947    error will be thrown.
1948    
1949  =over 4  =over 4
1950    
1951  =item colName  =item parm
   
 Name of the column to be displayed.  
1952    
1953  =item record  Parameter to pass to the constructor. This is a CGI object for a search helper
1954    and a search helper object for the result helper.
 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  
1955    
1956  =item type  =item type
1957    
1958  Type of column.  Type of helper: C<RH> for a result helper and C<SH> for a search helper.
1959    
1960  =item text  =item className
1961    
1962  Data relevant to this row of the column.  Class name for the helper object, without the preceding C<SH> or C<RH>. This is
1963    identical to what the script expects for the C<Class> or C<ResultType> parameter.
1964    
1965  =item RETURN  =item RETURN
1966    
1967  Returns the fully-formatted HTML text to go in the specified column.  Returns a helper object for the specified class.
1968    
1969  =back  =back
1970    
1971  =cut  =cut
1972    
1973  sub RunTimeColumns {  sub GetHelper {
1974      # Get the parameters.      # Get the parameters.
1975      my ($self, $type, $text) = @_;      my ($parm, $type, $className) = @_;
1976      # Declare the return variable.      # Declare the return variable.
1977      my $retVal = "";      my $retVal;
1978      # Get the Sprout and CGI objects.      # Try to create the helper.
1979      my $sprout = $self->DB();      eval {
1980      my $cgi = $self->Q();          # Load it into memory. If it's already there nothing will happen here.
1981      Trace("Runtime column $type with text \"$text\" found.") if T(4);          my $realName = "$type$className";
1982      # Separate the text into a type and data.          Trace("Requiring helper $realName.") if T(3);
1983      if ($type eq 'alias') {          require "$realName.pm";
1984          # Here the caller wants external alias links for a feature. The text          Trace("Constructing helper object.") if T(3);
1985          # parameter for computing the alias is the feature ID followed by          # Construct the object.
1986          # the favored alias type.          $retVal = eval("$realName->new(\$parm)");
1987          my ($fid, $favored) = split /\s*,\s*/, $text;          # Commit suicide if it didn't work.
1988          # The complicated part is we have to hyperlink them and handle the          if (! defined $retVal) {
1989          # 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;  
                 } else {  
                     push @unfavored, $alias;  
                 }  
             }  
             # 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"},  
                                        $dockString);  
             }  
1990          }          }
1991        };
1992        # Check for errors.
1993        if ($@) {
1994            Confess("Error retrieving $type$className: $@");
1995      }      }
1996      # Return the result.      # Return the result.
1997      return $retVal;      return $retVal;
# Line 2710  Line 1999 
1999    
2000  =head3 SaveOrganismData  =head3 SaveOrganismData
2001    
2002  C<< my ($name, $displayGroup) = $shelp->SaveOrganismData($group, $genomeID, $genus, $species, $strain); >>      my ($name, $displayGroup, $domain) = $shelp->SaveOrganismData($group, $genomeID, $genus, $species, $strain, $taxonomy);
2003    
2004  Format the name of an organism and the display version of its group name. The incoming  Format the name of an organism and the display version of its group name. The incoming
2005  data should be the relevant fields from the B<Genome> record in the database. The  data should be the relevant fields from the B<Genome> record in the database. The
# Line 2740  Line 2029 
2029    
2030  Strain of the species represented by the genome.  Strain of the species represented by the genome.
2031    
2032    =item taxonomy
2033    
2034    Taxonomy of the species represented by the genome.
2035    
2036  =item RETURN  =item RETURN
2037    
2038  Returns a two-element list. The first element is the formatted genome name. The second  Returns a three-element list. The first element is the formatted genome name. The second
2039  element is the display name of the genome's group.  element is the display name of the genome's group. The third is the genome's domain.
2040    
2041  =back  =back
2042    
# Line 2751  Line 2044 
2044    
2045  sub SaveOrganismData {  sub SaveOrganismData {
2046      # Get the parameters.      # Get the parameters.
2047      my ($self, $group, $genomeID, $genus, $species, $strain) = @_;      my ($self, $group, $genomeID, $genus, $species, $strain, $taxonomy) = @_;
2048      # Declare the return values.      # Declare the return values.
2049      my ($name, $displayGroup);      my ($name, $displayGroup);
2050      # 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 2060 
2060          # 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
2061          # name unless it's the supporting group, which is nulled out.          # name unless it's the supporting group, which is nulled out.
2062          $displayGroup = ($group eq $FIG_Config::otherGroup ? "" : $group);          $displayGroup = ($group eq $FIG_Config::otherGroup ? "" : $group);
2063            Trace("Group = $displayGroup, translated from \"$group\".") if T(4);
2064      }      }
2065        # Compute the domain from the taxonomy.
2066        my ($domain) = split /\s*;\s*/, $taxonomy, 2;
2067      # Cache the group and organism data.      # Cache the group and organism data.
2068      my $cache = $self->{orgs};      my $cache = $self->{orgs};
2069      $cache->{$genomeID} = [$name, $displayGroup];      $cache->{$genomeID} = [$name, $displayGroup, $domain];
2070      # Return the result.      # Return the result.
2071      return ($name, $displayGroup);      return ($name, $displayGroup, $domain);
2072  }  }
2073    
2074  =head3 ValidateKeywords  =head3 ValidateKeywords
2075    
2076  C<< my $okFlag = $shelp->ValidateKeywords($keywordString, $required); >>      my $okFlag = $shelp->ValidateKeywords($keywordString, $required);
2077    
2078  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
2079  set.  set.
# Line 2825  Line 2121 
2121      return $retVal;      return $retVal;
2122  }  }
2123    
 =head3 FakeButton  
   
 C<< my $html = SearchHelper::FakeButton($caption, $url, $target, %parms); >>  
   
 Create a fake button that hyperlinks to the specified URL with the specified parameters.  
 Unlike a real button, this one won't visibly click, but it will take the user to the  
 correct place.  
   
 The parameters of this method are deliberately identical to L</Formlet> so that we  
 can switch easily from real buttons to fake ones in the code.  
   
 =over 4  
   
 =item caption  
   
 Caption to be put on the button.  
   
 =item url  
   
 URL for the target page or script.  
   
 =item target  
   
 Frame or target in which the new page should appear. If C<undef> is specified,  
 the default target will be used.  
   
 =item parms  
   
 Hash containing the parameter names as keys and the parameter values as values.  
 These will be appended to the URL.  
   
 =back  
   
 =cut  
   
 sub FakeButton {  
     # Get the parameters.  
     my ($caption, $url, $target, %parms) = @_;  
     # Declare the return variable.  
     my $retVal;  
     # Compute the target URL.  
     my $targetUrl = "$url?" . join(";", map { "$_=" . uri_escape($parms{$_}) } keys %parms);  
     # Compute the target-frame HTML.  
     my $targetHtml = ($target ? " target=\"$target\"" : "");  
     # Assemble the result.  
     return "<a href=\"$targetUrl\" $targetHtml><div class=\"button2 button\">$caption</div></a>";  
 }  
   
 =head3 Formlet  
   
 C<< my $html = SearchHelper::Formlet($caption, $url, $target, %parms); >>  
   
 Create a mini-form that posts to the specified URL with the specified parameters. The  
 parameters will be stored in hidden fields, and the form's only visible control will  
 be a submit button with the specified caption.  
   
 Note that we don't use B<CGI.pm> services here because they generate forms with extra characters  
 and tags that we don't want to deal with.  
   
 =over 4  
   
 =item caption  
   
 Caption to be put on the form button.  
   
 =item url  
   
 URL to be put in the form's action parameter.  
   
 =item target  
   
 Frame or target in which the form results should appear. If C<undef> is specified,  
 the default target will be used.  
   
 =item parms  
   
 Hash containing the parameter names as keys and the parameter values as values.  
   
 =back  
   
 =cut  
   
 sub Formlet {  
     # Get the parameters.  
     my ($caption, $url, $target, %parms) = @_;  
     # Compute the target HTML.  
     my $targetHtml = ($target ? " target=\"$target\"" : "");  
     # 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;  
 }  
   
2124  =head3 TuningParameters  =head3 TuningParameters
2125    
2126  C<< my $options = $shelp->TuningParameters(%parmHash); >>      my $options = $shelp->TuningParameters(%parmHash);
2127    
2128  Retrieve tuning parameters from the CGI query object. The parameter is a hash that maps parameter names  Retrieve tuning parameters from the CGI query object. The parameter is a hash that maps parameter names
2129  to their default values. The parameters and their values will be returned as a hash reference.  to their default values. The parameters and their values will be returned as a hash reference.
# Line 2969  Line 2164 
2164      return $retVal;      return $retVal;
2165  }  }
2166    
2167    =head3 GetPreferredAliasType
2168    
2169        my $type = $shelp->GetPreferredAliasType();
2170    
2171    Return the preferred alias type for the current session. This information is stored
2172    in the C<AliasType> parameter of the CGI query object, and the default is C<FIG>
2173    (which indicates the FIG ID).
2174    
2175    =cut
2176    
2177    sub GetPreferredAliasType {
2178        # Get the parameters.
2179        my ($self) = @_;
2180        # Determine the preferred type.
2181        my $cgi = $self->Q();
2182        my $retVal = $cgi->param('AliasType') || 'FIG';
2183        # Return it.
2184        return $retVal;
2185    }
2186    
2187  =head2 Virtual Methods  =head2 Virtual Methods
2188    
2189  =head3 Form  =head3 Form
2190    
2191  C<< my $html = $shelp->Form(); >>      my $html = $shelp->Form();
2192    
2193  Generate the HTML for a form to request a new search.  Generate the HTML for a form to request a new search.
2194    
2195  =head3 Find  =head3 Find
2196    
2197  C<< my $resultCount = $shelp->Find(); >>      my $resultCount = $shelp->Find();
2198    
2199  Conduct a search based on the current CGI query parameters. The search results will  Conduct a search based on the current CGI query parameters. The search results will
2200  be written to the session cache file and the number of results will be  be written to the session cache file and the number of results will be
2201  returned. If the search parameters are invalid, a result count of C<undef> will be  returned. If the search parameters are invalid, a result count of C<undef> will be
2202  returned and a result message will be stored in this object describing the problem.  returned and a result message will be stored in this object describing the problem.
2203    
2204    =cut
2205    
2206    sub Find {
2207        # Get the parameters.
2208        my ($self) = @_;
2209        $self->Message("Call to pure virtual Find method in helper of type " . ref($self) . ".");
2210        return undef;
2211    }
2212    
2213  =head3 Description  =head3 Description
2214    
2215  C<< my $htmlText = $shelp->Description(); >>      my $htmlText = $shelp->Description();
2216    
2217  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
2218  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,
2219  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.
2220    
 =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  
   
2221  =cut  =cut
2222    
2223  sub SortKey {  sub Description {
2224      # Get the parameters.      # Get the parameters.
2225      my ($self, $fdata) = @_;      my ($self) = @_;
2226      # Get the feature ID from the record.      $self->Message("Call to pure virtual Description method in helper of type " . ref($self) . ".");
2227      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;  
2228  }  }
2229    
2230  =head3 SearchTitle  =head3 SearchTitle
2231    
2232  C<< my $titleHtml = $shelp->SearchTitle(); >>      my $titleHtml = $shelp->SearchTitle();
2233    
2234  Return the display title for this search. The display title appears above the search results.  Return the display title for this search. The display title appears above the search results.
2235  If no result is returned, no title will be displayed. The result should be an html string  If no result is returned, no title will be displayed. The result should be an html string
# Line 3046  Line 2241 
2241      # Get the parameters.      # Get the parameters.
2242      my ($self) = @_;      my ($self) = @_;
2243      # Declare the return variable.      # Declare the return variable.
2244      my $retVal;      my $retVal = "";
2245      # Return it.      # Return it.
2246      return $retVal;      return $retVal;
2247  }  }
2248    
2249  =head3 DownloadFormatAvailable  =head3 DefaultColumns
2250    
2251  C<< my $okFlag = $shelp->DownloadFormatAvailable($format); >>      $shelp->DefaultColumns($rhelp);
2252    
2253  This method returns TRUE if a specified download format is legal for this type of search  Store the default columns in the result helper. The default action is just to ask
2254  and FALSE otherwise. For any feature-based search, there is no need to override this  the result helper for its default columns, but this may be changed by overriding
2255  method.  this method.
2256    
2257  =over 4  =over 4
2258    
2259  =item format  =item rhelp
2260    
2261  Download format type code.  Result helper object in which the column list should be stored.
2262    
2263    =back
2264    
2265    =cut
2266    
2267    sub DefaultColumns {
2268        # Get the parameters.
2269        my ($self, $rhelp) = @_;
2270        # Get the default columns from the result helper.
2271        my @cols = $rhelp->DefaultResultColumns();
2272        # Store them back.
2273        $rhelp->SetColumns(@cols);
2274    }
2275    
2276    =head3 Hint
2277    
2278        my $htmlText = SearchHelper::Hint($wikiPage, $hintText);
2279    
2280    Return the HTML for a small question mark that displays the specified hint text when it is clicked.
2281    This HTML can be put in forms to provide a useful hinting mechanism.
2282    
2283    =over 4
2284    
2285    =item wikiPage
2286    
2287    Name of the wiki page to be popped up when the hint mark is clicked.
2288    
2289    =item hintText
2290    
2291    Text to display for the hint. It is raw html, but may not contain any double quotes.
2292    
2293  =item RETURN  =item RETURN
2294    
2295  Returns TRUE if the download format is legal for this search and FALSE otherwise.  Returns the html for the hint facility. The resulting html shows a small button-like thing that
2296    uses the standard FIG popup technology.
2297    
2298  =back  =back
2299    
2300  =cut  =cut
2301    
2302  sub DownloadFormatAvailable {  sub Hint {
2303      # Get the parameters.      # Get the parameters.
2304      my ($self, $format) = @_;      my ($wikiPage, $hintText) = @_;
2305      # Declare the return variable.      # Ask Sprout to draw the hint button for us.
2306      my $retVal = 1;      return Sprout::Hint($wikiPage, $hintText);
     # Return the result.  
     return $retVal;  
2307  }  }
2308    
2309    
2310  1;  1;

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