[Bio] / Sprout / SearchHelper.pm Repository:
ViewVC logotype

Diff of /Sprout/SearchHelper.pm

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.26, Sun Feb 4 13:07:24 2007 UTC revision 1.37, Mon Aug 20 23:22:42 2007 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.  
   
88  =back  =back
89    
90  =head2 Adding a new Search Tool  =head2 Adding a new Search Tool
# Line 103  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 113  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 149  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 201  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 225  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.
217  entirely in favor of your own custom filtering, you could include extra columns  
218  in the output, or you could search for something that's not a feature at all. The  In addition to the finding and filtering, it is necessary to send status messages
219  above code is just a loose framework.  to the output so that the user does not get bored waiting for results. The L</PrintLine>
220    method performs this function. The single parameter should be text to be
221    output to the browser. In general, you'll invoke it as follows.
222    
223  If you wish to add your own extra columns to the output, use the B<AddExtraColumns>      $self->PrintLine("...my message text...<br />");
 method of the feature query object.  
224    
225      $fq->AddExtraColumns(score => $sc);  The break tag is optional. When the Find method gets control, a paragraph will
226    have been started so that everything is XHTML-compliant.
227    
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
# Line 251  Line 241 
241    
242  =head3 new  =head3 new
243    
244  C<< my $shelp = SearchHelper->new($query); >>  C<< my $shelp = SearchHelper->new($cgi); >>
245    
246  Construct a new SearchHelper object.  Construct a new SearchHelper object.
247    
# Line 275  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 291  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 309  Line 303 
303                    scriptQueue => [],                    scriptQueue => [],
304                    genomeList => undef,                    genomeList => undef,
305                    genomeParms => [],                    genomeParms => [],
                   filtered => 0,  
306                   };                   };
307      # Bless and return it.      # Bless and return it.
308      bless $retVal, $class;      bless $retVal, $class;
# Line 475  Line 468 
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 564  Line 550 
550    
551  =head3 OpenSession  =head3 OpenSession
552    
553  C<< $shelp->OpenSession(); >>  C<< $shelp->OpenSession($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
# Line 619  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);  
         # Here we need to set up the column information. Start with the extras,  
         # sorted by column name.  
         my @colNames = ();  
         for my $col (sort keys %{$extraCols}) {  
             push @colNames, "X=$col";  
         }  
         # Add the default columns.  
         push @colNames, $self->DefaultFeatureColumns();  
         # Add any additional columns requested by the feature filter.  
         push @colNames, FeatureQuery::AdditionalColumns($self);  
         Trace("Full column list determined.") if T(3);  
         # Save the full list.  
         $self->{cols} = \@colNames;  
         # Write out the column headers. This also prepares the cache file to receive  
         # output.  
         Trace("Writing column headers.") if T(3);  
         $self->WriteColumnHeaders(map { $self->FeatureColumnTitle($_) } @{$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.  
     my @output = ();  
     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); >>  C<< $shelp->WriteColumnHeaders(@colNames); >>
# Line 717  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 729  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 739  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    C<< 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); >>  C<< $shelp->WriteColumnData($key, @colValues); >>
# Line 765  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
# Line 783  Line 743 
743          # We found one, so close it.          # We found one, so close it.
744          Trace("Closing session file.") if T(2);          Trace("Closing session file.") if T(2);
745          close $self->{fileHandle};          close $self->{fileHandle};
746            # Tell the user.
747            my $cgi = $self->Q();
748            $self->PrintLine("Output formatting complete.<br />");
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); >>  C<< my ($orgName, $group) = $shelp->Organism($genomeID); >>
# Line 825  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 837  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, $domain);
802  }  }
803    
804  =head3 Organism  =head3 Organism
# Line 882  Line 826 
826      # Get the parameters.      # Get the parameters.
827      my ($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); >>  C<< my $fasta = $shelp->ComputeFASTA($desiredType, $sequence, $flankingWidth); >>
837    
838  Parse a sequence input and convert it into a FASTA string of the desired type.  Parse a sequence input and convert it into a FASTA string of the desired type with
839    the desired flanking width.
840    
841  =over 4  =over 4
842    
843  =item desiredType  =item desiredType
844    
845  C<dna> to return a DNA sequence, C<prot> to return a protein sequence.  C<dna> to return a DNA sequence, C<prot> to return a protein sequence, C<dnaPattern>
846    to return a DNA search pattern, C<protPattern> to return a protein search pattern.
847    
848  =item sequence  =item sequence
849    
# Line 980  Line 853 
853  if the input does not begin with a greater-than sign (FASTA label line), a default label  if the input does not begin with a greater-than sign (FASTA label line), a default label
854  line will be provided.  line will be provided.
855    
856    =item flankingWidth
857    
858    If the DNA FASTA of a feature is desired, the number of base pairs to either side of the
859    feature that should be included. Currently we can't do this for Proteins because the
860    protein translation of a feature doesn't always match the DNA and is taken directly
861    from the database.
862    
863  =item RETURN  =item RETURN
864    
865  Returns a string in FASTA format representing the content of the desired sequence with  Returns a string in FASTA format representing the content of the desired sequence with
# Line 992  Line 872 
872    
873  sub ComputeFASTA {  sub ComputeFASTA {
874      # Get the parameters.      # Get the parameters.
875      my ($self, $desiredType, $sequence) = @_;      my ($self, $desiredType, $sequence, $flankingWidth) = @_;
876      # Declare the return variable. If an error occurs, it will remain undefined.      # Declare the return variable. If an error occurs, it will remain undefined.
877      my $retVal;      my $retVal;
878      # This variable will be cleared if an error is detected.      # This variable will be cleared if an error is detected.
# Line 1000  Line 880 
880      # Create variables to hold the FASTA label and data.      # Create variables to hold the FASTA label and data.
881      my ($fastaLabel, $fastaData);      my ($fastaLabel, $fastaData);
882      Trace("FASTA desired type is $desiredType.") if T(4);      Trace("FASTA desired type is $desiredType.") if T(4);
883      # Check for a feature specification.      # Check for a feature specification. The smoking gun for that is a vertical bar.
884      if ($sequence =~ /^\s*(\w+\|\S+)\s*$/) {      if ($sequence =~ /^\s*(\w+\|\S+)\s*$/) {
885          # Here we have a feature ID in $1. We'll need the Sprout object to process          # Here we have a feature ID in $1. We'll need the Sprout object to process
886          # it.          # it.
# Line 1015  Line 895 
895              $self->SetMessage("No gene found with the ID \"$fid\".");              $self->SetMessage("No gene found with the ID \"$fid\".");
896              $okFlag = 0;              $okFlag = 0;
897          } else {          } else {
898              # Set the FASTA label.              # Set the FASTA label. The ID is the first favored alias.
899              my $fastaLabel = $fid;              my $favored = $self->Q()->param('FavoredAlias') || 'fig';
900                my $favorLen = length $favored;
901                ($fastaLabel) = grep { substr($_, 0, $favorLen) eq $favored } $sprout->FeatureAliases($fid);
902                if (! $fastaLabel) {
903                    # In an emergency, fall back to the original ID.
904                    $fastaLabel = $fid;
905                }
906              # Now proceed according to the sequence type.              # Now proceed according to the sequence type.
907              if ($desiredType eq 'prot') {              if ($desiredType =~ /prot/) {
908                  # We want protein, so get the translation.                  # We want protein, so get the translation.
909                  $fastaData = $sprout->FeatureTranslation($figID);                  $fastaData = $sprout->FeatureTranslation($figID);
910                  Trace(length $fastaData . " characters returned for translation of $fastaLabel.") if T(3);                  Trace(length $fastaData . " characters returned for translation of $fastaLabel.") if T(3);
911              } else {              } elsif ($desiredType =~ /dna/) {
912                  # 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
913                    # locations.
914                  my @locList = $sprout->FeatureLocation($figID);                  my @locList = $sprout->FeatureLocation($figID);
915                    if ($flankingWidth > 0) {
916                        # Here we need to add flanking data. Convert the locations to a list
917                        # of location objects.
918                        my @locObjects = map { BasicLocation->new($_) } @locList;
919                        # Initialize the return variable. We will put the DNA in here segment by segment.
920                        $fastaData = "";
921                        # Now we widen each location by the flanking width and stash the results. This
922                        # requires getting the contig length for each contig so we don't fall off the end.
923                        for my $locObject (@locObjects) {
924                            Trace("Current location is " . $locObject->String . ".") if T(4);
925                            # Remember the current start and length.
926                            my ($start, $len) = ($locObject->Left, $locObject->Length);
927                            # Get the contig length.
928                            my $contigLen = $sprout->ContigLength($locObject->Contig);
929                            # Widen the location and get its DNA.
930                            $locObject->Widen($flankingWidth, $contigLen);
931                            my $fastaSegment = $sprout->DNASeq([$locObject->String()]);
932                            # Now we need to do some case changing. The main DNA is upper case and
933                            # the flanking DNA is lower case.
934                            my $leftFlank = $start - $locObject->Left;
935                            my $rightFlank = $leftFlank + $len;
936                            Trace("Wide location is " . $locObject->String . ". Flanks are $leftFlank and $rightFlank. Contig len is $contigLen.") if T(4);
937                            my $fancyFastaSegment = lc(substr($fastaSegment, 0, $leftFlank)) .
938                                                    uc(substr($fastaSegment, $leftFlank, $rightFlank - $leftFlank)) .
939                                                    lc(substr($fastaSegment, $rightFlank));
940                            $fastaData .= $fancyFastaSegment;
941                        }
942                    } else {
943                        # Here we have just the raw sequence.
944                  $fastaData = $sprout->DNASeq(\@locList);                  $fastaData = $sprout->DNASeq(\@locList);
945                  Trace(length $fastaData . " characters returned for DNA of $fastaLabel.") if T(3);                  }
946                    Trace((length $fastaData) . " characters returned for DNA of $fastaLabel.") if T(3);
947              }              }
948          }          }
949      } else {      } else {
# Line 1041  Line 958 
958              Trace("No label found in match to sequence:\n$sequence") if T(4);              Trace("No label found in match to sequence:\n$sequence") if T(4);
959              # 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
960              # as data.              # as data.
961              $fastaLabel = "User-specified $desiredType sequence";              $fastaLabel = "$desiredType sequence specified by user";
962              $fastaData = $sequence;              $fastaData = $sequence;
963          }          }
964          # The next step is to clean the junk out of the sequence.          # If we are not doing a pattern search, we need to clean the junk out of the sequence.
965            if ($desiredType !~ /pattern/i) {
966          $fastaData =~ s/\n//g;          $fastaData =~ s/\n//g;
967          $fastaData =~ s/\s+//g;          $fastaData =~ s/\s+//g;
968            }
969          # Finally, verify that it's DNA if we're doing DNA stuff.          # Finally, verify that it's DNA if we're doing DNA stuff.
970          if ($desiredType eq 'dna' && $fastaData =~ /[^agctxn]/i) {          if ($desiredType eq 'dna' && $fastaData =~ /[^agctxn-]/i) {
971              $self->SetMessage("Invalid characters detected. Is the input really a DNA sequence?");              $self->SetMessage("Invalid characters detected. Is the input really a DNA sequence?");
972              $okFlag = 0;              $okFlag = 0;
973          }          }
# Line 1056  Line 975 
975      Trace("FASTA data sequence: $fastaData") if T(4);      Trace("FASTA data sequence: $fastaData") if T(4);
976      # Only proceed if no error was detected.      # Only proceed if no error was detected.
977      if ($okFlag) {      if ($okFlag) {
978            if ($desiredType =~ /pattern/i) {
979                # For a scan, there is no label and no breakup.
980                $retVal = $fastaData;
981            } else {
982          # 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
983          # grep-split trick. The split, because of the presence of the parentheses,          # grep-split trick. The split, because of the presence of the parentheses,
984          # 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 1064  Line 987 
987          my @chunks = grep { $_ } split /(.{1,60})/, $fastaData;          my @chunks = grep { $_ } split /(.{1,60})/, $fastaData;
988          $retVal = join("\n", ">$fastaLabel", @chunks, "");          $retVal = join("\n", ">$fastaLabel", @chunks, "");
989      }      }
990        }
991      # Return the result.      # Return the result.
992      return $retVal;      return $retVal;
993  }  }
# Line 1202  Line 1126 
1126              if ($optionThing->{links}) {              if ($optionThing->{links}) {
1127                  # Compute the link value.                  # Compute the link value.
1128                  my $linkable = uri_escape($id);                  my $linkable = uri_escape($id);
1129                  $nodeContent->{link} = "../FIG/display_subsys.cgi?ssa_name=$linkable;request=show_ssa;sort=by_phylo;SPROUT=1";                  $nodeContent->{link} = "../FIG/display_subsys.cgi?ssa_name=$linkable;request=show_ssa;sort=by_phylo;show_clusters=1;SPROUT=1";
1130              }              }
1131              if ($optionThing->{radio}) {              if ($optionThing->{radio}) {
1132                  # Compute the radio value.                  # Compute the radio value.
# Line 1277  Line 1201 
1201      # Get the form name.      # Get the form name.
1202      my $formName = $self->FormName();      my $formName = $self->FormName();
1203      # Check to see if we already have a genome list in memory.      # Check to see if we already have a genome list in memory.
     my $genomes = $self->{genomeList};  
1204      my $groupHash;      my $groupHash;
1205        my @groups;
1206        my $nmpdrGroupCount;
1207        my $genomes = $self->{genomeList};
1208      if (defined $genomes) {      if (defined $genomes) {
1209          # We have a list ready to use.          # We have a list ready to use.
1210          $groupHash = $genomes;          $groupHash = $genomes;
1211            @groups = @{$self->{groupList}};
1212            $nmpdrGroupCount = $self->{groupCount};
1213      } else {      } else {
1214          # Get a list of all the genomes in group order. In fact, we only need them ordered          # Get a list of all the genomes in group order. In fact, we only need them ordered
1215          # by name (genus,species,strain), but putting primary-group in front enables us to          # by name (genus,species,strain), but putting primary-group in front enables us to
# Line 1290  Line 1218 
1218                                           "ORDER BY Genome(primary-group), Genome(genus), Genome(species), Genome(unique-characterization)",                                           "ORDER BY Genome(primary-group), Genome(genus), Genome(species), Genome(unique-characterization)",
1219                                           [], ['Genome(primary-group)', 'Genome(id)',                                           [], ['Genome(primary-group)', 'Genome(id)',
1220                                                'Genome(genus)', 'Genome(species)',                                                'Genome(genus)', 'Genome(species)',
1221                                                'Genome(unique-characterization)']);                                                'Genome(unique-characterization)',
1222                                                  'Genome(taxonomy)']);
1223          # Create a hash to organize the genomes by group. Each group will contain a list of          # Create a hash to organize the genomes by group. Each group will contain a list of
1224          # 2-tuples, the first element being the genome ID and the second being the genome          # 2-tuples, the first element being the genome ID and the second being the genome
1225          # name.          # name.
1226          my %gHash = ();          my %gHash = ();
1227          for my $genome (@genomeList) {          for my $genome (@genomeList) {
1228              # Get the genome data.              # Get the genome data.
1229              my ($group, $genomeID, $genus, $species, $strain) = @{$genome};              my ($group, $genomeID, $genus, $species, $strain, $taxonomy) = @{$genome};
1230              # Compute and cache its name and display group.              # Compute and cache its name and display group.
1231              my ($name, $displayGroup) = $self->SaveOrganismData($group, $genomeID, $genus, $species,              my ($name, $displayGroup, $domain) = $self->SaveOrganismData($group, $genomeID, $genus, $species,
1232                                                                  $strain);                                                                           $strain, $taxonomy);
1233              # Push the genome into the group's list. Note that we use the real group              # Push the genome into the group's list. Note that we use the real group
1234              # name here, not the display group name.              # name here, not the display group name.
1235              push @{$gHash{$group}}, [$genomeID, $name];              push @{$gHash{$group}}, [$genomeID, $name, $domain];
1236            }
1237            # We are almost ready to unroll the menu out of the group hash. The final step is to separate
1238            # the supporting genomes by domain. First, we sort the NMPDR groups.
1239            @groups = sort grep { $_ ne $FIG_Config::otherGroup } keys %gHash;
1240            # Remember the number of NMPDR groups.
1241            $nmpdrGroupCount = scalar @groups;
1242            # Loop through the supporting genomes, classifying them by domain. We'll also keep a list
1243            # of the domains found.
1244            my @otherGenomes = @{$gHash{$FIG_Config::otherGroup}};
1245            my @domains = ();
1246            for my $genomeData (@otherGenomes) {
1247                my ($genomeID, $name, $domain) = @{$genomeData};
1248                if (exists $gHash{$domain}) {
1249                    push @{$gHash{$domain}}, $genomeData;
1250                } else {
1251                    $gHash{$domain} = [$genomeData];
1252                    push @domains, $domain;
1253          }          }
1254            }
1255            # Add the domain groups at the end of the main group list. The main group list will now
1256            # contain all the categories we need to display the genomes.
1257            push @groups, sort @domains;
1258            # Delete the supporting group.
1259            delete $gHash{$FIG_Config::otherGroup};
1260          # Save the genome list for future use.          # Save the genome list for future use.
1261          $self->{genomeList} = \%gHash;          $self->{genomeList} = \%gHash;
1262            $self->{groupList} = \@groups;
1263            $self->{groupCount} = $nmpdrGroupCount;
1264          $groupHash = \%gHash;          $groupHash = \%gHash;
1265      }      }
     # 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;  
1266      # Next, create a hash that specifies the pre-selected entries. Note that we need to deal      # Next, create a hash that specifies the pre-selected entries. Note that we need to deal
1267      # with the possibility of undefined values in the incoming list.      # with the possibility of undefined values in the incoming list.
1268      my %selectedHash = ();      my %selectedHash = ();
# Line 1349  Line 1299 
1299          # Get the genomes in the group.          # Get the genomes in the group.
1300          for my $genome (@{$groupHash->{$group}}) {          for my $genome (@{$groupHash->{$group}}) {
1301              # Count this organism if it's NMPDR.              # Count this organism if it's NMPDR.
1302              if ($group ne $FIG_Config::otherGroup) {              if ($nmpdrGroupCount > 0) {
1303                  $nmpdrCount++;                  $nmpdrCount++;
1304              }              }
1305              # Get the organism ID and name.              # Get the organism ID, name, and domain.
1306              my ($genomeID, $name) = @{$genome};              my ($genomeID, $name, $domain) = @{$genome};
1307              # See if it's selected.              # See if it's selected.
1308              my $select = ($selectedHash{$genomeID} ? " selected" : "");              my $select = ($selectedHash{$genomeID} ? " selected" : "");
1309              # Generate the option tag.              # Generate the option tag.
1310              my $optionTag = "<OPTION value=\"$genomeID\"$select>$name <em>($genomeID)</em></OPTION>";              my $optionTag = "<OPTION class=\"$domain\" value=\"$genomeID\"$select>$name <em>($genomeID)</em></OPTION>";
1311              push @lines, "    $optionTag";              push @lines, "    $optionTag";
1312          }          }
1313          # Close the option group.          # Close the option group.
1314          push @lines, "  </OPTGROUP>";          push @lines, "  </OPTGROUP>";
1315            # Record this group in the nmpdrGroup count. When that gets to 0, we've finished the NMPDR
1316            # groups.
1317            $nmpdrGroupCount--;
1318      }      }
1319      # Close the SELECT tag.      # Close the SELECT tag.
1320      push @lines, "</SELECT>";      push @lines, "</SELECT>";
# Line 1372  Line 1325 
1325          # the text selected automatically.          # the text selected automatically.
1326          my $searchThingName = "${menuName}_SearchThing";          my $searchThingName = "${menuName}_SearchThing";
1327          push @lines, "<br />" .          push @lines, "<br />" .
1328                       "<INPUT type=\"button\" name=\"Search\" class=\"button\" value=\"Select genomes containing\" onClick=\"selectViaSearch($menuName, $searchThingName); $showSelect\" />&nbsp;" .                       "<INPUT type=\"button\" name=\"MacroSearch\" class=\"button\" value=\"Select genomes containing\" onClick=\"selectViaSearch($menuName, $searchThingName); $showSelect\" />&nbsp;" .
1329                       "<INPUT type=\"text\" name=\"$searchThingName\" size=\"30\" />";                       "<INPUT type=\"text\" name=\"$searchThingName\" size=\"30\" />" . Hint("Genome Control",
1330                                                                                                "Enter a genome number, then click the button to the left " .
1331                                                                                                "in order to select the genome with that number. " .
1332                                                                                                "Enter a genus, species, or strain and click the " .
1333                                                                                                "button to select all genomes with that genus, species, " .
1334                                                                                                "or strain name.");
1335          # Next are the buttons to set and clear selections.          # Next are the buttons to set and clear selections.
1336          push @lines, "<br />";          push @lines, "<br />";
1337          push @lines, "<INPUT type=\"button\" name=\"ClearAll\" class=\"bigButton\"  value=\"Clear All\" onClick=\"clearAll($menuName); $showSelect\" />";          push @lines, "<INPUT type=\"button\" name=\"ClearAll\" class=\"bigButton\"  value=\"Clear All\" onClick=\"clearAll($menuName); $showSelect\" />";
1338          push @lines, "<INPUT type=\"button\" name=\"SelectAll\" class=\"bigButton\" value=\"Select All\" onClick=\"selectAll($menuName); $showSelect\" />";          push @lines, "<INPUT type=\"button\" name=\"SelectAll\" class=\"bigButton\" value=\"Select All\" onClick=\"selectAll($menuName); $showSelect\" />";
1339          push @lines, "<INPUT type=\"button\" name=\"NMPDROnly\" class=\"bigButton\"  value=\"Select NMPDR\" onClick=\"selectSome($menuName, $nmpdrCount, true); $showSelect\" />";          push @lines, "<INPUT type=\"button\" name=\"NMPDROnly\" class=\"bigButton\"  value=\"Select NMPDR\" onClick=\"selectSome($menuName, $nmpdrCount, true); $showSelect\" />";
1340          push @lines, "<INPUT type=\"button\" name=\"OtherOnly\" class=\"bigButton\" value=\"Select Supporting\" onClick=\"selectSome($menuName, $nmpdrCount, false); $showSelect\" />";          # push @lines, "<INPUT type=\"button\" name=\"OtherOnly\" class=\"bigButton\" value=\"Select Supporting\" onClick=\"selectSome($menuName, $nmpdrCount, false); $showSelect\" />";
1341          # Add the status display, too.          # Add the status display, too.
1342          push @lines, "<DIV id=\"$divID\" class=\"selectStatus\"></DIV>";          push @lines, "<DIV id=\"$divID\" class=\"selectStatus\"></DIV>";
1343          # Queue to update the status display when the form loads. We need to modify the show statement          # Queue to update the status display when the form loads. We need to modify the show statement
# Line 1466  Line 1424 
1424  =item rows  =item rows
1425    
1426  Reference to a list of table rows. Each table row must be in HTML form with all  Reference to a list of table rows. Each table row must be in HTML form with all
1427  the TR and TD tags set up. The first TD or TH tag in each row will be modified to  the TR and TD tags set up. The first TD or TH tag in the first non-colspanned row
1428  set the width. Everything else will be left as is.  will be modified to set the width. Everything else will be left as is.
1429    
1430  =item RETURN  =item RETURN
1431    
# Line 1482  Line 1440 
1440      my ($self, $rows) = @_;      my ($self, $rows) = @_;
1441      # Get the CGI object.      # Get the CGI object.
1442      my $cgi = $self->Q();      my $cgi = $self->Q();
1443      # Fix the widths on the first column. Note that we eschew the use of the "g"      # The first column of the first row must have its width fixed.
1444        # This flag will be set to FALSE when that happens.
1445        my $needWidth = 1;
1446      # modifier becase we only want to change the first tag. Also, if a width      # modifier becase we only want to change the first tag. Also, if a width
1447      # is already specified on the first column bad things will happen.      # is already specified on the first column bad things will happen.
1448      for my $row (@{$rows}) {      for my $row (@{$rows}) {
1449          $row =~ s/(<td|th)/$1 width="150"/i;          # See if this row needs a width.
1450            if ($needWidth && $row =~ /<(td|th) ([^>]+)>/i) {
1451                # Here we have a first cell and its tag parameters are in $2.
1452                my $elements = $2;
1453                if ($elements !~ /colspan/i) {
1454                    Trace("No colspan tag found in element \'$elements\'.") if T(3);
1455                    # Here there's no colspan, so we plug in the width. We
1456                    # eschew the "g" modifier on the substitution because we
1457                    # only want to update the first cell.
1458                    $row =~ s/(<(td|th))/$1 width="150"/i;
1459                    # Denote we don't need this any more.
1460                    $needWidth = 0;
1461                }
1462            }
1463      }      }
1464      # Create the table.      # Create the table.
1465      my $retVal = $cgi->table({border => 2, cellspacing => 2,      my $retVal = $cgi->table({border => 2, cellspacing => 2,
# Line 1527  Line 1500 
1500      my $realCaption = (defined $caption ? $caption : 'Go');      my $realCaption = (defined $caption ? $caption : 'Go');
1501      # Get the current page size.      # Get the current page size.
1502      my $pageSize = $cgi->param('PageSize');      my $pageSize = $cgi->param('PageSize');
1503      # Get the incoming external-link flag.      # Get the current feature ID type.
1504      my $aliases = ($cgi->param('ShowAliases') ? 1 : 0);      my $aliasType = $self->GetPreferredAliasType();
1505      # Create the row.      # Create the rows.
1506      my $retVal = $cgi->Tr($cgi->td("Results/Page"),      my $retVal = $cgi->Tr($cgi->td("Identifier Type "),
1507                              $cgi->td({ colspan => 2 },
1508                                       $cgi->popup_menu(-name => 'AliasType',
1509                                                        -values => ['FIG', AliasAnalysis::AliasTypes() ],
1510                                                        -default => $aliasType) .
1511                                       Hint("Identifier type", "Specify how you want gene names to be displayed."))) .
1512                     "\n" .
1513                     $cgi->Tr($cgi->td("Results/Page"),
1514                            $cgi->td($cgi->popup_menu(-name => 'PageSize',                            $cgi->td($cgi->popup_menu(-name => 'PageSize',
1515                                                      -values => [10, 25, 50, 100, 1000],                                                      -values => [10, 25, 50, 100, 1000],
1516                                                      -default => $pageSize)),                                                      -default => $pageSize)),
# Line 1541  Line 1521 
1521      return $retVal;      return $retVal;
1522  }  }
1523    
 =head3 FeatureFilterRows  
   
 C<< my $htmlText = $shelp->FeatureFilterRows(); >>  
   
 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.  
   
 =cut  
   
 sub FeatureFilterRows {  
     # Get the parameters.  
     my ($self) = @_;  
     # Return the result.  
     return FeatureQuery::FilterRows($self);  
 }  
   
 =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;  
 }  
   
1524  =head3 GetGenomes  =head3 GetGenomes
1525    
1526  C<< my @genomeList = $shelp->GetGenomes($parmName); >>  C<< my @genomeList = $shelp->GetGenomes($parmName); >>
# Line 1688  Line 1573 
1573  server. The help text for a specific search is taken from a file named  server. The help text for a specific search is taken from a file named
1574  C<SearchHelp_>I<class>C<.inc> in the template directory C<$FIG_Config::template_url>.  C<SearchHelp_>I<class>C<.inc> in the template directory C<$FIG_Config::template_url>.
1575  There are also three standard help files: C<SearchHelp1_Filtering.inc> describes the  There are also three standard help files: C<SearchHelp1_Filtering.inc> describes the
1576  feature filtering performed by the B<FeatureQuery> object, C<SearchHelp1_GenomeControl.inc>  feature filtering performed by the B<RHFeatures> object, C<SearchHelp1_GenomeControl.inc>
1577  describes how to use a multiple-selection genome control, and C<SearchHelp1_Standard.inc>  describes how to use a multiple-selection genome control, and C<SearchHelp1_Standard.inc>
1578  describes the standard controls for a search, such as page size, URL display, and  describes the standard controls for a search, such as page size, URL display, and
1579  external alias display.  external alias display.
# Line 1814  Line 1699 
1699      return $retVal;      return $retVal;
1700  }  }
1701    
 =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;  
 }  
   
1702  =head3 AdvancedClassList  =head3 AdvancedClassList
1703    
1704  C<< my @classes = SearchHelper::AdvancedClassList(); >>  C<< my @classes = SearchHelper::AdvancedClassList(); >>
# Line 1857  Line 1706 
1706  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
1707  of available searches on the search page.  of available searches on the search page.
1708    
1709  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.
1710    
1711  =cut  =cut
1712    
1713  sub AdvancedClassList {  sub AdvancedClassList {
1714      my @retVal = map { $_ =~ /^SH(\w+)\.pm/; $1 } grep { $_ =~ /^SH/ } keys %INC;      # Determine the search helper module directory.
1715      return @retVal;      my $libDirectory = $INC{'SearchHelper.pm'};
1716        $libDirectory =~ s/SearchHelper\.pm//;
1717        # Read it, keeping only the helper modules.
1718        my @modules = grep { /^SH\w+\.pm/ } Tracer::OpenDir($libDirectory, 0);
1719        # Convert the file names to search types.
1720        my @retVal = map { $_ =~ /^SH(\w+)\.pm/; $1 } @modules;
1721        # Return the result in alphabetical order.
1722        return sort @retVal;
1723  }  }
1724    
1725  =head3 SelectionTree  =head3 SelectionTree
# Line 2153  Line 2009 
2009                      if ($hasChildren) {                      if ($hasChildren) {
2010                          Trace("Processing children of $myLabel.") if T(4);                          Trace("Processing children of $myLabel.") if T(4);
2011                          push @childHtml, ShowBranch($cgi, $myLabel, $myID, $myContent, $options, 'none');                          push @childHtml, ShowBranch($cgi, $myLabel, $myID, $myContent, $options, 'none');
2012                            Trace("Children of $myLabel finished.") if T(4);
2013                      }                      }
2014                  }                  }
2015              }              }
# Line 2187  Line 2044 
2044              }              }
2045              # Next, we format the label.              # Next, we format the label.
2046              my $labelHtml = $myLabel;              my $labelHtml = $myLabel;
2047              Trace("Formatting tree node for $myLabel.") if T(4);              Trace("Formatting tree node for \"$myLabel\".") if T(4);
2048              # Apply a hyperlink if necessary.              # Apply a hyperlink if necessary.
2049              if (defined $attrHash->{link}) {              if (defined $attrHash->{link}) {
2050                  $labelHtml = $cgi->a({ href => $attrHash->{link}, target => $options->{target} },                  $labelHtml = $cgi->a({ href => $attrHash->{link}, target => $options->{target} },
# Line 2237  Line 2094 
2094      return $retVal;      return $retVal;
2095  }  }
2096    
2097  =head2 Feature Column Methods  =head3 PrintLine
   
 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>, and  
 everything else will happen automatically.  
   
 There is one 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.  
2098    
2099  =head3 DefaultFeatureColumns  C<< $shelp->PrintLine($message); >>
2100    
2101  C<< my @colNames = $shelp->DefaultFeatureColumns(); >>  Print a line of CGI output. This is used during the operation of the B<Find> method while
2102    searching, so the user sees progress in real-time.
 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.  
2103    
2104  =over 4  =over 4
2105    
2106  =item name  =item message
   
 Name of the desired feature column.  
   
 =item RETURN  
2107    
2108  Returns the title to be used as the column header for the named feature column.  HTML text to display.
2109    
2110  =back  =back
2111    
2112  =cut  =cut
2113    
2114  sub FeatureColumnTitle {  sub PrintLine {
2115      # Get the parameters.      # Get the parameters.
2116      my ($self, $colName) = @_;      my ($self, $message) = @_;
2117      # Declare the return variable. We default to a blank column name.      # Send them to the output.
2118      my $retVal = "&nbsp;";      print "$message\n";
     # 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 'subsystem') {  
         $retVal = "Subsystems";  
     }  
     # Return the result.  
     return $retVal;  
2119  }  }
2120    
2121    =head3 GetHelper
2122    
2123  =head3 FeatureColumnValue  C<< my $shelp = SearchHelper::GetHelper($parm, $type => $className); >>
2124    
2125  C<< my $value = $shelp->FeatureColumnValue($colName, $fid, \%extraCols); >>  Return a helper object with the given class name. If no such class exists, an
2126    error will be thrown.
 Return the value to be displayed in the specified feature column.  
2127    
2128  =over 4  =over 4
2129    
2130  =item colName  =item parm
   
 Name of the column to be displayed.  
   
 =item record  
   
 DBObject 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  
2131    
2132  =cut  Parameter to pass to the constructor. This is a CGI object for a search helper
2133    and a search helper object for the result helper.
 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.  
         $retVal = "%%alias=$fid";  
     } 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 'subsystem') {  
         # Another run-time column: subsystem list.  
         $retVal = "%%subsystem=$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  
2134    
2135  =item type  =item type
2136    
2137  Type of column.  Type of helper: C<RH> for a result helper and C<SH> for a search helper.
2138    
2139  =item text  =item className
2140    
2141  Data relevant to this row of the column.  Class name for the helper object, without the preceding C<SH> or C<RH>. This is
2142    identical to what the script expects for the C<Class> or C<ResultType> parameter.
2143    
2144  =item RETURN  =item RETURN
2145    
2146  Returns the fully-formatted HTML text to go in the specified column.  Returns a helper object for the specified class.
2147    
2148  =back  =back
2149    
2150  =cut  =cut
2151    
2152  sub RunTimeColumns {  sub GetHelper {
2153      # Get the parameters.      # Get the parameters.
2154      my ($self, $type, $text) = @_;      my ($parm, $type, $className) = @_;
2155      # Declare the return variable.      # Declare the return variable.
2156      my $retVal = "";      my $retVal;
2157      # Get the Sprout and CGI objects.      # Try to create the helper.
2158      my $sprout = $self->DB();      eval {
2159      my $cgi = $self->Q();          # Load it into memory. If it's already there nothing will happen here.
2160      Trace("Runtime column $type with text \"$text\" found.") if T(4);          my $realName = "$type$className";
2161      # Separate the text into a type and data.          Trace("Requiring helper $realName.") if T(3);
2162      if ($type eq 'alias') {          require "$realName.pm";
2163          # Here the caller wants external alias links for a feature. The text          Trace("Constructing helper object.") if T(3);
2164          # is the feature ID.          # Construct the object.
2165          my $fid = $text;          $retVal = eval("$realName->new(\$parm)");
2166          # The complicated part is we have to hyperlink them. First, get the          # Commit suicide if it didn't work.
2167          # aliases.          if (! defined $retVal) {
2168          Trace("Generating aliases for feature $fid.") if T(4);              die "Could not find a $type handler of type $className.";
2169          my @aliases = $sprout->FeatureAliases($fid);          }
2170          # Only proceed if we found some.      };
2171          if (@aliases) {      # Check for errors.
2172              # Join the aliases into a comma-delimited list.      if ($@) {
2173              my $aliasList = join(", ", @aliases);          Confess("Error retrieving $type$className: $@");
             # 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);  
2174      }      }
2175      # Return the result.      # Return the result.
2176      return $retVal;      return $retVal;
# Line 2496  Line 2178 
2178    
2179  =head3 SaveOrganismData  =head3 SaveOrganismData
2180    
2181  C<< my ($name, $displayGroup) = $shelp->SaveOrganismData($group, $genomeID, $genus, $species, $strain); >>  C<< my ($name, $displayGroup, $domain) = $shelp->SaveOrganismData($group, $genomeID, $genus, $species, $strain, $taxonomy); >>
2182    
2183  Format the name of an organism and the display version of its group name. The incoming  Format the name of an organism and the display version of its group name. The incoming
2184  data should be the relevant fields from the B<Genome> record in the database. The  data should be the relevant fields from the B<Genome> record in the database. The
# Line 2526  Line 2208 
2208    
2209  Strain of the species represented by the genome.  Strain of the species represented by the genome.
2210    
2211    =item taxonomy
2212    
2213    Taxonomy of the species represented by the genome.
2214    
2215  =item RETURN  =item RETURN
2216    
2217  Returns a two-element list. The first element is the formatted genome name. The second  Returns a three-element list. The first element is the formatted genome name. The second
2218  element is the display name of the genome's group.  element is the display name of the genome's group. The third is the genome's domain.
2219    
2220  =back  =back
2221    
# Line 2537  Line 2223 
2223    
2224  sub SaveOrganismData {  sub SaveOrganismData {
2225      # Get the parameters.      # Get the parameters.
2226      my ($self, $group, $genomeID, $genus, $species, $strain) = @_;      my ($self, $group, $genomeID, $genus, $species, $strain, $taxonomy) = @_;
2227      # Declare the return values.      # Declare the return values.
2228      my ($name, $displayGroup);      my ($name, $displayGroup);
2229      # 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 2553  Line 2239 
2239          # 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
2240          # name unless it's the supporting group, which is nulled out.          # name unless it's the supporting group, which is nulled out.
2241          $displayGroup = ($group eq $FIG_Config::otherGroup ? "" : $group);          $displayGroup = ($group eq $FIG_Config::otherGroup ? "" : $group);
2242            Trace("Group = $displayGroup, translated from \"$group\".") if T(4);
2243      }      }
2244        # Compute the domain from the taxonomy.
2245        my ($domain) = split /\s*;\s*/, $taxonomy, 2;
2246      # Cache the group and organism data.      # Cache the group and organism data.
2247      my $cache = $self->{orgs};      my $cache = $self->{orgs};
2248      $cache->{$genomeID} = [$name, $displayGroup];      $cache->{$genomeID} = [$name, $displayGroup, $domain];
2249      # Return the result.      # Return the result.
2250      return ($name, $displayGroup);      return ($name, $displayGroup, $domain);
2251  }  }
2252    
2253  =head3 ValidateKeywords  =head3 ValidateKeywords
# Line 2611  Line 2300 
2300      return $retVal;      return $retVal;
2301  }  }
2302    
2303  =head3 FakeButton  =head3 TuningParameters
   
 C<< my $html = SearchHelper::FakeButton($caption, $url, $target, %parms); >>  
2304    
2305  Create a fake button that hyperlinks to the specified URL with the specified parameters.  C<< my $options = $shelp->TuningParameters(%parmHash); >>
 Unlike a real button, this one won't visibly click, but it will take the user to the  
 correct place.  
2306    
2307  The parameters of this method are deliberately identical to L</Formlet> so that we  Retrieve tuning parameters from the CGI query object. The parameter is a hash that maps parameter names
2308  can switch easily from real buttons to fake ones in the code.  to their default values. The parameters and their values will be returned as a hash reference.
2309    
2310  =over 4  =over 4
2311    
2312  =item caption  =item parmHash
   
 Caption to be put on the button.  
2313    
2314  =item url  Hash mapping parameter names to their default values.
2315    
2316  URL for the target page or script.  =item RETURN
   
 =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  
2317    
2318  Hash containing the parameter names as keys and the parameter values as values.  Returns a reference to a hash containing the parameter names mapped to their actual values.
 These will be appended to the URL.  
2319    
2320  =back  =back
2321    
2322  =cut  =cut
2323    
2324  sub FakeButton {  sub TuningParameters {
2325      # Get the parameters.      # Get the parameters.
2326      my ($caption, $url, $target, %parms) = @_;      my ($self, %parmHash) = @_;
2327      # Declare the return variable.      # Declare the return variable.
2328      my $retVal;      my $retVal = {};
2329      # Compute the target URL.      # Get the CGI Query Object.
2330      my $targetUrl = "$url?" . join(";", map { "$_=" . uri_escape($parms{$_}) } keys %parms);      my $cgi = $self->Q();
2331      # Compute the target-frame HTML.      # Loop through the parameter names.
2332      my $targetHtml = ($target ? " target=\"$target\"" : "");      for my $parm (keys %parmHash) {
2333      # Assemble the result.          # Get the incoming value for this parameter.
2334      return "<a href=\"$targetUrl\" $targetHtml><div class=\"button2 button\">$caption</div></a>";          my $value = $cgi->param($parm);
2335            # Zero might be a valid value, so we do an is-defined check rather than an OR.
2336            if (defined($value)) {
2337                $retVal->{$parm} = $value;
2338            } else {
2339                $retVal->{$parm} = $parmHash{$parm};
2340            }
2341        }
2342        # Return the result.
2343        return $retVal;
2344  }  }
2345    
2346  =head3 Formlet  =head3 GetPreferredAliasType
   
 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  
2347    
2348  Hash containing the parameter names as keys and the parameter values as values.  C<< my $type = $shelp->GetPreferredAliasType(); >>
2349    
2350  =back  Return the preferred alias type for the current session. This information is stored
2351    in the C<AliasType> parameter of the CGI query object, and the default is C<FIG>
2352    (which indicates the FIG ID).
2353    
2354  =cut  =cut
2355    
2356  sub Formlet {  sub GetPreferredAliasType {
2357      # Get the parameters.      # Get the parameters.
2358      my ($caption, $url, $target, %parms) = @_;      my ($self) = @_;
2359      # Compute the target HTML.      # Determine the preferred type.
2360      my $targetHtml = ($target ? " target=\"$target\"" : "");      my $cgi = $self->Q();
2361      # Start the form.      my $retVal = $cgi->param('AliasType') || 'FIG';
2362      my $retVal = "<form method=\"POST\" action=\"$url\"$target>";      # Return it.
     # 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.  
2363      return $retVal;      return $retVal;
2364  }  }
2365    
# Line 2729  Line 2380 
2380  returned. If the search parameters are invalid, a result count of C<undef> will be  returned. If the search parameters are invalid, a result count of C<undef> will be
2381  returned and a result message will be stored in this object describing the problem.  returned and a result message will be stored in this object describing the problem.
2382    
2383    =cut
2384    
2385    sub Find {
2386        # Get the parameters.
2387        my ($self) = @_;
2388        $self->Message("Call to pure virtual Find method in helper of type " . ref($self) . ".");
2389        return undef;
2390    }
2391    
2392  =head3 Description  =head3 Description
2393    
2394  C<< my $htmlText = $shelp->Description(); >>  C<< my $htmlText = $shelp->Description(); >>
# Line 2737  Line 2397 
2397  on the main search tools page. It may contain HTML, but it should be character-level,  on the main search tools page. It may contain HTML, but it should be character-level,
2398  not block-level, since the description is going to appear in a list.  not block-level, since the description is going to appear in a list.
2399    
2400  =head3 SortKey  =cut
2401    
2402    sub Description {
2403        # Get the parameters.
2404        my ($self) = @_;
2405        $self->Message("Call to pure virtual Description method in helper of type " . ref($self) . ".");
2406        return "Unknown search type";
2407    }
2408    
2409    =head3 SearchTitle
2410    
2411    C<< my $titleHtml = $shelp->SearchTitle(); >>
2412    
2413    Return the display title for this search. The display title appears above the search results.
2414    If no result is returned, no title will be displayed. The result should be an html string
2415    that can be legally put inside a block tag such as C<h3> or C<p>.
2416    
2417    =cut
2418    
2419    sub SearchTitle {
2420        # Get the parameters.
2421        my ($self) = @_;
2422        # Declare the return variable.
2423        my $retVal = "";
2424        # Return it.
2425        return $retVal;
2426    }
2427    
2428    =head3 DefaultColumns
2429    
2430  C<< my $key = $shelp->SortKey($fdata); >>  C<< $shelp->DefaultColumns($rhelp); >>
2431    
2432  Return the sort key for the specified feature data. The default is to sort by feature name,  Store the default columns in the result helper. The default action is just to ask
2433  floating NMPDR organisms to the top. If a full-text search is used, then the default  the result helper for its default columns, but this may be changed by overriding
2434  sort is by relevance followed by feature name. This sort may be overridden by the  this method.
 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.  
2435    
2436  =over 4  =over 4
2437    
2438  =item record  =item rhelp
2439    
2440    Result helper object in which the column list should be stored.
2441    
2442    =back
2443    
2444    =cut
2445    
2446    sub DefaultColumns {
2447        # Get the parameters.
2448        my ($self, $rhelp) = @_;
2449        # Get the default columns from the result helper.
2450        my @cols = $rhelp->DefaultResultColumns();
2451        # Store them back.
2452        $rhelp->SetColumns(@cols);
2453    }
2454    
2455  The C<FeatureData> containing the current feature.  =head3 Hint
2456    
2457    C<< my $htmlText = SearchHelper::Hint($wikiPage, $hintText); >>
2458    
2459    Return the HTML for a small question mark that displays the specified hint text when it is clicked.
2460    This HTML can be put in forms to provide a useful hinting mechanism.
2461    
2462    =over 4
2463    
2464    =item wikiPage
2465    
2466    Name of the wiki page to be popped up when the hint maek is clicked.
2467    
2468    =item hintText
2469    
2470    Text to display for the hint. It is raw html, but may not contain any double quotes.
2471    
2472  =item RETURN  =item RETURN
2473    
2474  Returns a key field that can be used to sort this row in among the results.  Returns the html for the hint facility. The resulting html shows a small button-like thing that
2475    uses the standard FIG popup technology.
2476    
2477  =back  =back
2478    
2479  =cut  =cut
2480    
2481  sub SortKey {  sub Hint {
2482      # Get the parameters.      # Get the parameters.
2483      my ($self, $fdata) = @_;      my ($wikiPage, $hintText) = @_;
2484      # Get the feature ID from the record.      # Escape the single quotes in the hint text.
2485      my $fid = $fdata->FID();      my $quotedText = $hintText;
2486      # Get the group from the feature ID.      $quotedText =~ s/'/\\'/g;
2487      my $group = $self->FeatureGroup($fid);      # Convert the wiki page name to a URL.
2488      # Ask the feature query object to form the sort key.      my $wikiURL = ucfirst $wikiPage;
2489      my $retVal = $fdata->SortKey($self, $group);      $wikiURL =~ s/ /_/g;
2490      # Return the result.      $wikiURL = "../wiki/index.php/$wikiURL";
2491        # Create the html.
2492        my $retVal = "&nbsp;<input type=\"button\" class=\"hintbutton\" onMouseOver=\"javascript:if (!this.tooltip) { " .
2493                     "this.tooltip = new Popup_Tooltip(this, 'Search Hint', '$quotedText', '', 1); this.tooltip.addHandler(); } " .
2494                     "return false;\" value=\"?\" onClick=\"javascript:window.open('$wikiURL', 'nmpdrHelp');\" />";
2495        # Return it.
2496      return $retVal;      return $retVal;
2497  }  }
2498    
2499    
2500  1;  1;

Legend:
Removed from v.1.26  
changed lines
  Added in v.1.37

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3