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revision 1.2, Wed Sep 27 16:55:38 2006 UTC revision 1.25, Wed Dec 20 20:06:17 2006 UTC
# Line 17  Line 17 
17      use HTML;      use HTML;
18      use BasicLocation;      use BasicLocation;
19      use FeatureQuery;      use FeatureQuery;
20        use URI::Escape;
21        use PageBuilder;
22    
23  =head1 Search Helper Base Class  =head1 Search Helper Base Class
24    
# Line 73  Line 75 
75    
76  List of JavaScript statements to be executed after the form is closed.  List of JavaScript statements to be executed after the form is closed.
77    
78    =item genomeHash
79    
80    Cache of the genome group hash used to build genome selection controls.
81    
82    =item genomeParms
83    
84    List of the parameters that are used to select multiple genomes.
85    
86    =item filtered
87    
88    TRUE if this is a feature-filtered search, else FALSE. B<NOTE> that this
89    field is updated by the B<FeatureQuery> object.
90    
91  =back  =back
92    
93  =head2 Adding a new Search Tool  =head2 Adding a new Search Tool
# Line 98  Line 113 
113    
114  =item 4  =item 4
115    
116  In the C<SearchSkeleton.cgi> script, add a C<use> statement for your search tool  In the C<SearchSkeleton.cgi> script and add a C<use> statement for your search tool.
 and then put the class name in the C<@advancedClasses> list.  
117    
118  =back  =back
119    
# Line 139  Line 153 
153    
154  =item 1  =item 1
155    
156  L</NmpdrGenomeMenu> generates a control for selecting one or more genomes.  L</NmpdrGenomeMenu> generates a control for selecting one or more genomes. Use
157    L</GetGenomes> to retrieve all the genomes passed in for a specified parameter
158    name. Note that as an assist to people working with GET-style links, if no
159    genomes are specified and the incoming request style is GET, all genomes will
160    be returned.
161    
162  =item 2  =item 2
163    
# Line 158  Line 176 
176    
177  =back  =back
178    
179    If you are doing a feature search, you can also change the list of feature
180    columns displayed and their display order by overriding
181    L</DefaultFeatureColumns>.
182    
183  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
184  query parameters as default values so that the search request is persistent.  query parameters as default values so that the search request is persistent.
185    
# Line 195  Line 217 
217                      }                      }
218                  }                  }
219              }              }
         }  
220          # Close the session file.          # Close the session file.
221          $self->CloseSession();          $self->CloseSession();
222            }
223          # Return the result count.          # Return the result count.
224          return $retVal;          return $retVal;
225      }      }
226    
227  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
228  are variations on the above them. For example, you could eschew feature filtering  are variations on the above theme. For example, you could eschew feature filtering
229  entirely in favor of your own custom filtering, you could include extra columns  entirely in favor of your own custom filtering, you could include extra columns
230  in the output, or you could search for something that's not a feature at all. The  in the output, or you could search for something that's not a feature at all. The
231  above code is just a loose framework.  above code is just a loose framework.
# Line 218  Line 240 
240  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
241  the number of items found.  the number of items found.
242    
 =head2 Virtual Methods  
   
 =head3 Form  
   
 C<< my $html = $shelp->Form(); >>  
   
 Generate the HTML for a form to request a new search.  
   
 =head3 Find  
   
 C<< my $resultCount = $shelp->Find(); >>  
   
 Conduct a search based on the current CGI query parameters. The search results will  
 be written to the session cache file and the number of results will be  
 returned. If the search parameters are invalid, a result count of C<undef> will be  
 returned and a result message will be stored in this object describing the problem.  
   
 =head3 Description  
   
 C<< my $htmlText = $shelp->Description(); >>  
   
 Return a description of this search. The description is used for the table of contents  
 on the main search tools page. It may contain HTML, but it should be character-level,  
 not block-level, since the description is going to appear in a list.  
   
243  =cut  =cut
244    
245  # This counter is used to insure every form on the page has a unique name.  # This counter is used to insure every form on the page has a unique name.
246  my $formCount = 0;  my $formCount = 0;
247    # This counter is used to generate unique DIV IDs.
248    my $divCount = 0;
249    
250  =head2 Public Methods  =head2 Public Methods
251    
# Line 258  Line 257 
257    
258  =over 4  =over 4
259    
260  =item query  =item cgi
261    
262  The CGI query object for the current script.  The CGI query object for the current script.
263    
# Line 268  Line 267 
267    
268  sub new {  sub new {
269      # Get the parameters.      # Get the parameters.
270      my ($class, $query) = @_;      my ($class, $cgi) = @_;
271      # Check for a session ID.      # Check for a session ID.
272      my $session_id = $query->param("SessionID");      my $session_id = $cgi->param("SessionID");
273      my $type = "old";      my $type = "old";
274      if (! $session_id) {      if (! $session_id) {
275          # Here we're starting a new session. We create the session ID and          # Here we're starting a new session. We create the session ID and
276          # store it in the query object.          # store it in the query object.
277          $session_id = NewSessionID();          $session_id = NewSessionID();
278          $type = "new";          $type = "new";
279          $query->param(-name => 'SessionID', -value => $session_id);          $cgi->param(-name => 'SessionID', -value => $session_id);
280      }      }
281      # Compute the subclass name.      # Compute the subclass name.
282      $class =~ /SH(.+)$/;      my $subClass;
283      my $subClass = $1;      if ($class =~ /SH(.+)$/) {
284            # Here we have a real search class.
285            $subClass = $1;
286        } else {
287            # Here we have a bare class. The bare class cannot search, but it can
288            # process search results.
289            $subClass = 'SearchHelper';
290        }
291      # Insure everybody knows we're in Sprout mode.      # Insure everybody knows we're in Sprout mode.
292      $query->param(-name => 'SPROUT', -value => 1);      $cgi->param(-name => 'SPROUT', -value => 1);
293      # Generate the form name.      # Generate the form name.
294      my $formName = "$class$formCount";      my $formName = "$class$formCount";
295      $formCount++;      $formCount++;
# Line 291  Line 297 
297      # 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
298      # class name and a placeholder for the Sprout object.      # class name and a placeholder for the Sprout object.
299      my $retVal = {      my $retVal = {
300                    query => $query,                    query => $cgi,
301                    type => $type,                    type => $type,
302                    class => $subClass,                    class => $subClass,
303                    sprout => undef,                    sprout => undef,
304                    orgs => {},                    orgs => {},
305                    name => $formName,                    name => $formName,
306                    scriptQueue => [],                    scriptQueue => [],
307                      genomeList => undef,
308                      genomeParms => [],
309                      filtered => 0,
310                   };                   };
311      # Bless and return it.      # Bless and return it.
312      bless $retVal, $class;      bless $retVal, $class;
# Line 319  Line 328 
328      return $self->{query};      return $self->{query};
329  }  }
330    
331    
332    
333  =head3 DB  =head3 DB
334    
335  C<< my $sprout = $shelp->DB(); >>  C<< my $sprout = $shelp->DB(); >>
# Line 450  Line 461 
461      my ($self, $title) = @_;      my ($self, $title) = @_;
462      # Get the CGI object.      # Get the CGI object.
463      my $cgi = $self->Q();      my $cgi = $self->Q();
464      # Start the form.      # Start the form. Note we use the override option on the Class value, in
465        # case the Advanced button was used.
466      my $retVal = "<div class=\"search\">\n" .      my $retVal = "<div class=\"search\">\n" .
467                   $cgi->start_form(-method => 'POST',                   $cgi->start_form(-method => 'POST',
468                                    -action => $cgi->url(-relative => 1),                                    -action => $cgi->url(-relative => 1),
469                                    -name => $self->FormName()) .                                    -name => $self->FormName()) .
470                   $cgi->hidden(-name => 'Class',                   $cgi->hidden(-name => 'Class',
471                                -value => $self->{class}) .                                -value => $self->{class},
472                                  -override => 1) .
473                   $cgi->hidden(-name => 'SPROUT',                   $cgi->hidden(-name => 'SPROUT',
474                                -value => 1) .                                -value => 1) .
475                   $cgi->h3($title);                   $cgi->h3($title);
# Line 610  Line 623 
623    
624  =head3 PutFeature  =head3 PutFeature
625    
626  C<< $shelp->PutFeature($fquery); >>  C<< $shelp->PutFeature($fdata); >>
627    
628  Store a feature in the result cache. This is the workhorse method for most  Store a feature in the result cache. This is the workhorse method for most
629  searches, since the primary data item in the database is features.  searches, since the primary data item in the database is features.
# Line 621  Line 634 
634  the feature query object using the B<AddExtraColumns> method. For example, the following  the feature query object using the B<AddExtraColumns> method. For example, the following
635  code adds columns for essentiality and virulence.  code adds columns for essentiality and virulence.
636    
637      $fq->AddExtraColumns(essential => $essentialFlag, virulence => $vfactor);      $fd->AddExtraColumns(essential => $essentialFlag, virulence => $vfactor);
638      $shelp->PutFeature($fq);      $shelp->PutFeature($fd);
639    
640  For correct results, all values should be specified for all extra columns in all calls to  For correct results, all values should be specified for all extra columns in all calls to
641  B<PutFeature>. (In particular, the column header names are computed on the first  B<PutFeature>. (In particular, the column header names are computed on the first
# Line 632  Line 645 
645      if (! $essentialFlag) {      if (! $essentialFlag) {
646          $essentialFlag = undef;          $essentialFlag = undef;
647      }      }
648      $fq->AddExtraColumns(essential => $essentialFlag, virulence => $vfactor);      $fd->AddExtraColumns(essential => $essentialFlag, virulence => $vfactor);
649      $shelp->PutFeature($fq);      $shelp->PutFeature($fd);
650    
651  =over 4  =over 4
652    
653  =item fquery  =item fdata
654    
655  FeatureQuery object containing the current feature data.  B<FeatureData> object containing the current feature data.
656    
657  =back  =back
658    
# Line 647  Line 660 
660    
661  sub PutFeature {  sub PutFeature {
662      # Get the parameters.      # Get the parameters.
663      my ($self, $fq) = @_;      my ($self, $fd) = @_;
664        # Get the CGI query object.
665        my $cgi = $self->Q();
666      # Get the feature data.      # Get the feature data.
667      my $record = $fq->Feature();      my $record = $fd->Feature();
668      my $extraCols = $fq->ExtraCols();      my $extraCols = $fd->ExtraCols();
669      # Check for a first-call situation.      # Check for a first-call situation.
670      if (! defined $self->{cols}) {      if (! defined $self->{cols}) {
671          # Here we need to set up the column information. Start with the defaults.          Trace("Setting up the columns.") if T(3);
672          $self->{cols} = $self->DefaultFeatureColumns();          # Here we need to set up the column information. Start with the extras,
673          # Append the extras, sorted by column name.          # sorted by column name.
674            my @colNames = ();
675          for my $col (sort keys %{$extraCols}) {          for my $col (sort keys %{$extraCols}) {
676              push @{$self->{cols}}, "X=$col";              push @colNames, "X=$col";
677          }          }
678            # Add the default columns.
679            push @colNames, $self->DefaultFeatureColumns();
680            # Add any additional columns requested by the feature filter.
681            push @colNames, FeatureQuery::AdditionalColumns($self);
682            Trace("Full column list determined.") if T(3);
683            # Save the full list.
684            $self->{cols} = \@colNames;
685          # Write out the column headers. This also prepares the cache file to receive          # Write out the column headers. This also prepares the cache file to receive
686          # output.          # output.
687            Trace("Writing column headers.") if T(3);
688          $self->WriteColumnHeaders(map { $self->FeatureColumnTitle($_) } @{$self->{cols}});          $self->WriteColumnHeaders(map { $self->FeatureColumnTitle($_) } @{$self->{cols}});
689            Trace("Column headers written.") if T(3);
690      }      }
691      # Get the feature ID.      # Get the feature ID.
692      my ($fid) = $record->Value('Feature(id)');      my $fid = $fd->FID();
693      # Loop through the column headers, producing the desired data.      # Loop through the column headers, producing the desired data.
694      my @output = ();      my @output = ();
695      for my $colName (@{$self->{cols}}) {      for my $colName (@{$self->{cols}}) {
696          push @output, $self->FeatureColumnValue($colName, $record, $extraCols);          push @output, $self->FeatureColumnValue($colName, $record, $extraCols);
697      }      }
698      # Compute the sort key. The sort key floats NMPDR organism features to the      # Compute the sort key. The sort key usually floats NMPDR organism features to the
699      # top of the return list.      # top of the return list.
700      my $group = $self->FeatureGroup($fid);      my $key = $self->SortKey($fd);
     my $key = ($group ? "A$group" : "ZZ");  
701      # Write the feature data.      # Write the feature data.
702      $self->WriteColumnData($key, @output);      $self->WriteColumnData($key, @output);
703  }  }
# Line 754  Line 778 
778      # Check for an open session file.      # Check for an open session file.
779      if (defined $self->{fileHandle}) {      if (defined $self->{fileHandle}) {
780          # We found one, so close it.          # We found one, so close it.
781            Trace("Closing session file.") if T(2);
782          close $self->{fileHandle};          close $self->{fileHandle};
783      }      }
784  }  }
# Line 771  Line 796 
796      my $retVal;      my $retVal;
797      # Get a digest encoder.      # Get a digest encoder.
798      my $md5 = Digest::MD5->new();      my $md5 = Digest::MD5->new();
799      # If we have a randomization file, use it to seed the digester.      # Add the PID, the IP, and the time stamp. Note that the time stamp is
800      if (open(R, "/dev/urandom")) {      # actually two numbers, and we get them both because we're in list
801          my $b;      # context.
802          read(R, $b, 1024);      $md5->add($$, $ENV{REMOTE_ADDR}, $ENV{REMOTE_PORT}, gettimeofday());
803          $md5->add($b);      # Hash up all this identifying data.
804      }      $retVal = $md5->hexdigest();
805      # Add the PID and the time stamp.      # Return the result.
     $md5->add($$, gettimeofday);  
     # Hash it up and clean the result so that it works as a file name.  
     $retVal = $md5->b64digest();  
     $retVal =~ s,/,\$,g;  
     $retVal =~ s,\+,@,g;  
     # Return it.  
806      return $retVal;      return $retVal;
807  }  }
808    
# Line 827  Line 846 
846                                                      ['Genome(genus)', 'Genome(species)',                                                      ['Genome(genus)', 'Genome(species)',
847                                                       'Genome(unique-characterization)',                                                       'Genome(unique-characterization)',
848                                                       'Genome(primary-group)']);                                                       'Genome(primary-group)']);
849          # Null out the supporting group.          # Format and cache the name and display group.
850          $group = "" if ($group eq $FIG_Config::otherGroup);          ($orgName, $group) = $self->SaveOrganismData($group, $genomeID, $genus, $species,
851          # If the organism does not exist, format an unknown name.                                                              $strain);
         if (! defined($genus)) {  
             $orgName = "Unknown Genome $genomeID";  
         } else {  
             # It does exist, so format the organism name.  
             $orgName = "$genus $species";  
             if ($strain) {  
                 $orgName .= " $strain";  
             }  
         }  
         # Save this organism in the cache.  
         $cache->{$genomeID} = [$orgName, $group];  
852      }      }
853      # Return the result.      # Return the result.
854      return ($orgName, $group);      return ($orgName, $group);
# Line 942  Line 950 
950      } else {      } else {
951          # Here we can get its genome data.          # Here we can get its genome data.
952          $retVal = $self->Organism($genomeID);          $retVal = $self->Organism($genomeID);
953          # Append the type and number.          # Append the FIG ID.
954          $retVal .= " [$type $num]";          $retVal .= " [$fid]";
955      }      }
956      # Return the result.      # Return the result.
957      return $retVal;      return $retVal;
# Line 951  Line 959 
959    
960  =head3 ComputeFASTA  =head3 ComputeFASTA
961    
962  C<< my $fasta = $shelp->ComputeFASTA($incomingType, $desiredType, $sequence); >>  C<< my $fasta = $shelp->ComputeFASTA($desiredType, $sequence); >>
963    
964  Parse a sequence input and convert it into a FASTA string of the desired type. Note  Parse a sequence input and convert it into a FASTA string of the desired type.
 that it is possible to convert a DNA sequence into a protein sequence, but the reverse  
 is not possible.  
965    
966  =over 4  =over 4
967    
 =item incomingType  
   
 C<dna> if this is a DNA sequence, C<prot> if this is a protein sequence.  
   
968  =item desiredType  =item desiredType
969    
970  C<dna> to return a DNA sequence, C<prot> to return a protein sequence. If the  C<dna> to return a DNA sequence, C<prot> to return a protein sequence.
 I<$incomingType> is C<prot> and this value is C<dna>, an error will be thrown.  
971    
972  =item sequence  =item sequence
973    
# Line 988  Line 989 
989    
990  sub ComputeFASTA {  sub ComputeFASTA {
991      # Get the parameters.      # Get the parameters.
992      my ($self, $incomingType, $desiredType, $sequence) = @_;      my ($self, $desiredType, $sequence) = @_;
993      # Declare the return variable. If an error occurs, it will remain undefined.      # Declare the return variable. If an error occurs, it will remain undefined.
994      my $retVal;      my $retVal;
995        # This variable will be cleared if an error is detected.
996        my $okFlag = 1;
997      # Create variables to hold the FASTA label and data.      # Create variables to hold the FASTA label and data.
998      my ($fastaLabel, $fastaData);      my ($fastaLabel, $fastaData);
999        Trace("FASTA desired type is $desiredType.") if T(4);
1000      # Check for a feature specification.      # Check for a feature specification.
1001      if ($sequence =~ /^\s*(\w+\|\S+)\s*$/) {      if ($sequence =~ /^\s*(\w+\|\S+)\s*$/) {
1002          # 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
1003          # it.          # it.
1004          my $fid = $1;          my $fid = $1;
1005            Trace("Feature ID for fasta is $fid.") if T(3);
1006          my $sprout = $self->DB();          my $sprout = $self->DB();
1007          # Get the FIG ID. Note that we only use the first feature found. We are not          # Get the FIG ID. Note that we only use the first feature found. We are not
1008          # supposed to have redundant aliases, though we may have an ID that doesn't          # supposed to have redundant aliases, though we may have an ID that doesn't
1009          # exist.          # exist.
1010          my ($figID) = $sprout->FeaturesByAlias($fid);          my ($figID) = $sprout->FeaturesByAlias($fid);
1011          if (! $figID) {          if (! $figID) {
1012              $self->SetMessage("No feature found with the ID \"$fid\".");              $self->SetMessage("No gene found with the ID \"$fid\".");
1013                $okFlag = 0;
1014          } else {          } else {
1015              # Set the FASTA label.              # Set the FASTA label.
1016              my $fastaLabel = $fid;              my $fastaLabel = $fid;
1017              # Now proceed according to the sequence type.              # Now proceed according to the sequence type.
1018              if ($desiredType =~ /prot/i) {              if ($desiredType eq 'prot') {
1019                  # We want protein, so get the translation.                  # We want protein, so get the translation.
1020                  $fastaData = $sprout->FeatureTranslation($figID);                  $fastaData = $sprout->FeatureTranslation($figID);
1021                    Trace(length $fastaData . " characters returned for translation of $fastaLabel.") if T(3);
1022              } else {              } else {
1023                  # 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.
1024                  my @locList = $sprout->FeatureLocation($figID);                  my @locList = $sprout->FeatureLocation($figID);
1025                  $fastaData = $sprout->DNASeq(\@locList);                  $fastaData = $sprout->DNASeq(\@locList);
1026                    Trace(length $fastaData . " characters returned for DNA of $fastaLabel.") if T(3);
1027              }              }
1028          }          }
     } elsif ($incomingType =~ /prot/ && $desiredType =~ /dna/) {  
         # Here we're being asked to do an impossible conversion.  
         $self->SetMessage("Cannot convert a protein sequence to DNA.");  
1029      } else {      } else {
1030            Trace("Analyzing FASTA sequence.") if T(4);
1031          # Here we are expecting a FASTA. We need to see if there's a label.          # Here we are expecting a FASTA. We need to see if there's a label.
1032          if ($sequence =~ /^>\s*(\S.*)\s*\n(.+)$/) {          if ($sequence =~ /^>[\n\s]*(\S[^\n]*)\n(.+)$/s) {
1033                Trace("Label \"$1\" found in match to sequence:\n$sequence") if T(4);
1034              # Here we have a label, so we split it from the data.              # Here we have a label, so we split it from the data.
1035              $fastaLabel = $1;              $fastaLabel = $1;
1036              $fastaData = $2;              $fastaData = $2;
1037          } else {          } else {
1038                Trace("No label found in match to sequence:\n$sequence") if T(4);
1039              # 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
1040              # as data.              # as data.
1041              $fastaLabel = "User-specified $incomingType sequence";              $fastaLabel = "User-specified $desiredType sequence";
1042              $fastaData = $sequence;              $fastaData = $sequence;
1043          }          }
1044          # The next step is to clean the junk out of the sequence.          # The next step is to clean the junk out of the sequence.
1045          $fastaData =~ s/\n//g;          $fastaData =~ s/\n//g;
1046          $fastaData =~ s/\s+//g;          $fastaData =~ s/\s+//g;
1047          # Finally, if the user wants to convert to protein, we do it here. Note that          # Finally, verify that it's DNA if we're doing DNA stuff.
1048          # we've already prevented a conversion from protein to DNA.          if ($desiredType eq 'dna' && $fastaData =~ /[^agctxn]/i) {
1049          if ($incomingType ne $desiredType) {              $self->SetMessage("Invalid characters detected. Is the input really a DNA sequence?");
1050              $fastaData = Sprout::Protein($fastaData);              $okFlag = 0;
1051          }          }
1052      }      }
1053      # At this point, either "$fastaLabel" and "$fastaData" have values or an error is      Trace("FASTA data sequence: $fastaData") if T(4);
1054      # in progress.      # Only proceed if no error was detected.
1055      if (defined $fastaLabel) {      if ($okFlag) {
1056          # 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
1057          # grep-split trick. The split, because of the presence of the parentheses,          # grep-split trick. The split, because of the presence of the parentheses,
1058          # includes the matched delimiters in the output list. The grep strips out          # includes the matched delimiters in the output list. The grep strips out
1059          # the empty list items that appear between the so-called delimiters, since          # the empty list items that appear between the so-called delimiters, since
1060          # the delimiters are what we want.          # the delimiters are what we want.
1061          my @chunks = grep { $_ } split /(.{1,60})/, $fastaData;          my @chunks = grep { $_ } split /(.{1,60})/, $fastaData;
1062          my $retVal = join("\n", ">$fastaLabel", @chunks, "");          $retVal = join("\n", ">$fastaLabel", @chunks, "");
1063      }      }
1064      # Return the result.      # Return the result.
1065      return $retVal;      return $retVal;
1066  }  }
1067    
1068    =head3 SubsystemTree
1069    
1070    C<< my $tree = SearchHelper::SubsystemTree($sprout, %options); >>
1071    
1072    This method creates a subsystem selection tree suitable for passing to
1073    L</SelectionTree>. Each leaf node in the tree will have a link to the
1074    subsystem display page. In addition, each node can have a radio button. The
1075    radio button alue is either C<classification=>I<string>, where I<string> is
1076    a classification string, or C<id=>I<string>, where I<string> is a subsystem ID.
1077    Thus, it can either be used to filter by a group of related subsystems or a
1078    single subsystem.
1079    
1080    =over 4
1081    
1082    =item sprout
1083    
1084    Sprout database object used to get the list of subsystems.
1085    
1086    =item options
1087    
1088    Hash containing options for building the tree.
1089    
1090    =item RETURN
1091    
1092    Returns a reference to a tree list suitable for passing to L</SelectionTree>.
1093    
1094    =back
1095    
1096    The supported options are as follows.
1097    
1098    =over 4
1099    
1100    =item radio
1101    
1102    TRUE if the tree should be configured for radio buttons. The default is FALSE.
1103    
1104    =item links
1105    
1106    TRUE if the tree should be configured for links. The default is TRUE.
1107    
1108    =back
1109    
1110    =cut
1111    
1112    sub SubsystemTree {
1113        # Get the parameters.
1114        my ($sprout, %options) = @_;
1115        # Process the options.
1116        my $optionThing = Tracer::GetOptions({ radio => 0, links => 1 }, \%options);
1117        # Read in the subsystems.
1118        my @subs = $sprout->GetAll(['Subsystem'], "ORDER BY Subsystem(classification), Subsystem(id)", [],
1119                                   ['Subsystem(classification)', 'Subsystem(id)']);
1120        # Declare the return variable.
1121        my @retVal = ();
1122        # Each element in @subs represents a leaf node, so as we loop through it we will be
1123        # producing one leaf node at a time. The leaf node is represented as a 2-tuple. The
1124        # first element is a semi-colon-delimited list of the classifications for the
1125        # subsystem. There will be a stack of currently-active classifications, which we will
1126        # compare to the incoming classifications from the end backward. A new classification
1127        # requires starting a new branch. A different classification requires closing an old
1128        # branch and starting a new one. Each classification in the stack will also contain
1129        # that classification's current branch. We'll add a fake classification at the
1130        # beginning that we can use to represent the tree as a whole.
1131        my $rootName = '<root>';
1132        # Create the classification stack. Note the stack is a pair of parallel lists,
1133        # one containing names and the other containing content.
1134        my @stackNames = ($rootName);
1135        my @stackContents = (\@retVal);
1136        # Add a null entry at the end of the subsystem list to force an unrolling.
1137        push @subs, ['', undef];
1138        # Loop through the subsystems.
1139        for my $sub (@subs) {
1140            # Pull out the classification list and the subsystem ID.
1141            my ($classString, $id) = @{$sub};
1142            Trace("Processing class \"$classString\" and subsystem $id.") if T(4);
1143            # Convert the classification string to a list with the root classification in
1144            # the front.
1145            my @classList = ($rootName, split($FIG_Config::splitter, $classString));
1146            # Find the leftmost point at which the class list differs from the stack.
1147            my $matchPoint = 0;
1148            while ($matchPoint <= $#stackNames && $matchPoint <= $#classList &&
1149                   $stackNames[$matchPoint] eq $classList[$matchPoint]) {
1150                $matchPoint++;
1151            }
1152            Trace("Match point is $matchPoint. Stack length is " . scalar(@stackNames) .
1153                  ". Class List length is " . scalar(@classList) . ".") if T(4);
1154            # Unroll the stack to the matchpoint.
1155            while ($#stackNames >= $matchPoint) {
1156                my $popped = pop @stackNames;
1157                pop @stackContents;
1158                Trace("\"$popped\" popped from stack.") if T(4);
1159            }
1160            # Start branches for any new classifications.
1161            while ($#stackNames < $#classList) {
1162                # The branch for a new classification contains its radio button
1163                # data and then a list of children. So, at this point, if radio buttons
1164                # are desired, we put them into the content.
1165                my $newLevel = scalar(@stackNames);
1166                my @newClassContent = ();
1167                if ($optionThing->{radio}) {
1168                    my $newClassString = join($FIG_Config::splitter, @classList[1..$newLevel]);
1169                    push @newClassContent, { value => "classification=$newClassString%" };
1170                }
1171                # The new classification node is appended to its parent's content
1172                # and then pushed onto the stack. First, we need the node name.
1173                my $nodeName = $classList[$newLevel];
1174                # Add the classification to its parent. This makes it part of the
1175                # tree we'll be returning to the user.
1176                push @{$stackContents[$#stackNames]}, $nodeName, \@newClassContent;
1177                # Push the classification onto the stack.
1178                push @stackContents, \@newClassContent;
1179                push @stackNames, $nodeName;
1180                Trace("\"$nodeName\" pushed onto stack.") if T(4);
1181            }
1182            # Now the stack contains all our parent branches. We add the subsystem to
1183            # the branch at the top of the stack, but only if it's NOT the dummy node.
1184            if (defined $id) {
1185                # Compute the node name from the ID.
1186                my $nodeName = $id;
1187                $nodeName =~ s/_/ /g;
1188                # Create the node's leaf hash. This depends on the value of the radio
1189                # and link options.
1190                my $nodeContent = {};
1191                if ($optionThing->{links}) {
1192                    # Compute the link value.
1193                    my $linkable = uri_escape($id);
1194                    $nodeContent->{link} = "../FIG/display_subsys.cgi?ssa_name=$linkable;request=show_ssa;sort=by_phylo;SPROUT=1";
1195                }
1196                if ($optionThing->{radio}) {
1197                    # Compute the radio value.
1198                    $nodeContent->{value} = "id=$id";
1199                }
1200                # Push the node into its parent branch.
1201                Trace("\"$nodeName\" added to node list.") if T(4);
1202                push @{$stackContents[$#stackNames]}, $nodeName, $nodeContent;
1203            }
1204        }
1205        # Return the result.
1206        return \@retVal;
1207    }
1208    
1209    
1210  =head3 NmpdrGenomeMenu  =head3 NmpdrGenomeMenu
1211    
1212  C<< my $htmlText = $shelp->NmpdrGenomeMenu($menuName, \%options, \@selected); >>  C<< my $htmlText = $shelp->NmpdrGenomeMenu($menuName, $multiple, \@selected, $rows); >>
1213    
1214  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
1215  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 1071  Line 1221 
1221    
1222  Name to give to the menu.  Name to give to the menu.
1223    
1224  =item options  =item multiple
1225    
1226  Reference to a hash containing the options to be applied to the C<SELECT> tag form the menu.  TRUE if the user is allowed to select multiple genomes, else FALSE.
 Typical options would include C<multiple> to specify  
 that multiple selections are allowed and C<size> to set the number of rows to display  
 in the menu.  
1227    
1228  =item selected  =item selected
1229    
# Line 1084  Line 1231 
1231  is not intended to allow multiple selections, the list should be a singleton. If the  is not intended to allow multiple selections, the list should be a singleton. If the
1232  list is empty, nothing will be pre-selected.  list is empty, nothing will be pre-selected.
1233    
1234    =item rows (optional)
1235    
1236    Number of rows to display. If omitted, the default is 1 for a single-select list
1237    and 10 for a multi-select list.
1238    
1239    =item crossMenu (optional)
1240    
1241    If specified, is presumed to be the name of another genome menu whose contents
1242    are to be mutually exclusive with the contents of this menu. As a result, instead
1243    of the standard onChange event, the onChange event will deselect any entries in
1244    the other menu.
1245    
1246  =item RETURN  =item RETURN
1247    
1248  Returns the HTML text to generate a C<SELECT> menu inside a form.  Returns the HTML text to generate a C<SELECT> menu inside a form.
# Line 1094  Line 1253 
1253    
1254  sub NmpdrGenomeMenu {  sub NmpdrGenomeMenu {
1255      # Get the parameters.      # Get the parameters.
1256      my ($self, $menuName, $options, $selected) = @_;      my ($self, $menuName, $multiple, $selected, $rows, $cross) = @_;
1257      # Get the Sprout and CGI objects.      # Get the Sprout and CGI objects.
1258      my $sprout = $self->DB();      my $sprout = $self->DB();
1259      my $cgi = $self->Q();      my $cgi = $self->Q();
1260        # Compute the row count.
1261        if (! defined $rows) {
1262            $rows = ($multiple ? 10 : 1);
1263        }
1264        # Create the multiple tag.
1265        my $multipleTag = ($multiple ? " multiple" : "");
1266      # Get the form name.      # Get the form name.
1267      my $formName = $self->FormName();      my $formName = $self->FormName();
1268        # Check to see if we already have a genome list in memory.
1269        my $genomes = $self->{genomeList};
1270        my $groupHash;
1271        if (defined $genomes) {
1272            # We have a list ready to use.
1273            $groupHash = $genomes;
1274        } else {
1275      # 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
1276      # 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
1277      # take advantage of an existing index.      # take advantage of an existing index.
# Line 1111  Line 1283 
1283      # 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
1284      # 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
1285      # name.      # name.
1286      my %groupHash = ();          my %gHash = ();
1287      for my $genome (@genomeList) {      for my $genome (@genomeList) {
1288          # Get the genome data.          # Get the genome data.
1289          my ($group, $genomeID, $genus, $species, $strain) = @{$genome};          my ($group, $genomeID, $genus, $species, $strain) = @{$genome};
1290          # Form the genome name.              # Compute and cache its name and display group.
1291          my $name = "$genus $species";              my ($name, $displayGroup) = $self->SaveOrganismData($group, $genomeID, $genus, $species,
1292          if ($strain) {                                                                  $strain);
1293              $name .= " $strain";              # Push the genome into the group's list. Note that we use the real group
1294          }              # name here, not the display group name.
1295          # Push the genome into the group's list.              push @{$gHash{$group}}, [$genomeID, $name];
1296          push @{$groupHash{$group}}, [$genomeID, $name];          }
1297            # Save the genome list for future use.
1298            $self->{genomeList} = \%gHash;
1299            $groupHash = \%gHash;
1300      }      }
1301      # Now we are ready to unroll the menu out of the group hash. First, we sort the groups, putting      # Now we are ready to unroll the menu out of the group hash. First, we sort the groups, putting
1302      # the supporting-genome group last.      # the supporting-genome group last.
1303      my @groups = sort grep { $_ ne $FIG_Config::otherGroup } keys %groupHash;      my @groups = sort grep { $_ ne $FIG_Config::otherGroup } keys %{$groupHash};
1304      push @groups, $FIG_Config::otherGroup;      push @groups, $FIG_Config::otherGroup;
1305      # Next, create a hash that specifies the pre-selected entries.      # Next, create a hash that specifies the pre-selected entries. Note that we need to deal
1306      my %selectedHash = map { $_ => 1 } @{$selected};      # with the possibility of undefined values in the incoming list.
1307      # Now it gets complicated. We need a way to mark all the NMPDR genomes.      my %selectedHash = ();
1308        if (defined $selected) {
1309            %selectedHash = map { $_ => 1 } grep { defined($_) } @{$selected};
1310        }
1311        # Now it gets complicated. We need a way to mark all the NMPDR genomes. We take advantage
1312        # of the fact they come first in the list. We'll accumulate a count of the NMPDR genomes
1313        # and use that to make the selections.
1314        my $nmpdrCount = 0;
1315      # Create the type counters.      # Create the type counters.
1316      my $groupCount = 1;      my $groupCount = 1;
1317      # Compute the ID for the status display.      # Compute the ID for the status display.
# Line 1138  Line 1320 
1320      my $showSelect = "showSelected($menuName, '$divID', 1000);";      my $showSelect = "showSelected($menuName, '$divID', 1000);";
1321      # If multiple selection is supported, create an onChange event.      # If multiple selection is supported, create an onChange event.
1322      my $onChange = "";      my $onChange = "";
1323      if ($options->{multiple}) {      if ($cross) {
1324            # Here we have a paired menu. Selecting something in our menu unselects it in the
1325            # other and redisplays the status of both.
1326            $onChange = " onChange=\"crossUnSelect($menuName, '$divID', $cross, '${formName}_${cross}_status', 1000)\"";
1327        } elsif ($multiple) {
1328            # This is an unpaired menu, so all we do is redisplay our status.
1329          $onChange = " onChange=\"$showSelect\"";          $onChange = " onChange=\"$showSelect\"";
1330      }      }
1331      # Create the SELECT tag and stuff it into the output array.      # Create the SELECT tag and stuff it into the output array.
1332      my $select = "<" . join(" ", "SELECT name=\"$menuName\"$onChange", map { " $_=\"$options->{$_}\"" } keys %{$options}) . ">";      my @lines = ("<SELECT name=\"$menuName\"$onChange$multipleTag size=\"$rows\">");
     my @lines = ($select);  
1333      # Loop through the groups.      # Loop through the groups.
1334      for my $group (@groups) {      for my $group (@groups) {
1335          # Create the option group tag.          # Create the option group tag.
1336          my $tag = "<OPTGROUP label=\"$group\">";          my $tag = "<OPTGROUP label=\"$group\">";
1337          push @lines, "  $tag";          push @lines, "  $tag";
         # Compute the label for this group's options. This is seriously dirty stuff, as the  
         # label option may have functionality in future browsers. If that happens, we'll need  
         # to modify the genome text so that the "selectSome" method can tell which are NMPDR  
         # organisms and which aren't. Sadly, the OPTGROUP tag is invisible in the DOM Javascript  
         # hierarchy.  
         my $label = ($group eq $FIG_Config::otherGroup ? "other" : "nmpdr");  
1338          # Get the genomes in the group.          # Get the genomes in the group.
1339          for my $genome (@{$groupHash{$group}}) {          for my $genome (@{$groupHash->{$group}}) {
1340                # Count this organism if it's NMPDR.
1341                if ($group ne $FIG_Config::otherGroup) {
1342                    $nmpdrCount++;
1343                }
1344                # Get the organism ID and name.
1345              my ($genomeID, $name) = @{$genome};              my ($genomeID, $name) = @{$genome};
1346              # See if it's selected.              # See if it's selected.
1347              my $select = ($selectedHash{$genomeID} ? " selected" : "");              my $select = ($selectedHash{$genomeID} ? " selected" : "");
1348              # Generate the option tag.              # Generate the option tag.
1349              my $optionTag = "<OPTION value=\"$genomeID\" label=\"$label\"$select>$name <em>($genomeID)</em></OPTION>";              my $optionTag = "<OPTION value=\"$genomeID\"$select>$name <em>($genomeID)</em></OPTION>";
1350              push @lines, "    $optionTag";              push @lines, "    $optionTag";
1351          }          }
1352          # Close the option group.          # Close the option group.
# Line 1170  Line 1355 
1355      # Close the SELECT tag.      # Close the SELECT tag.
1356      push @lines, "</SELECT>";      push @lines, "</SELECT>";
1357      # Check for multiple selection.      # Check for multiple selection.
1358      if ($options->{multiple}) {      if ($multiple) {
1359          # Since multi-select is on, we can set up some buttons to set and clear selections.          # Multi-select is on, so we need to add some selection helpers. First is
1360            # the search box. This allows the user to type text and have all genomes containing
1361            # the text selected automatically.
1362            my $searchThingName = "${menuName}_SearchThing";
1363            push @lines, "<br />" .
1364                         "<INPUT type=\"button\" name=\"Search\" class=\"button\" value=\"Select genomes containing\" onClick=\"selectViaSearch($menuName, $searchThingName); $showSelect\" />&nbsp;" .
1365                         "<INPUT type=\"text\" name=\"$searchThingName\" size=\"30\" />";
1366            # Next are the buttons to set and clear selections.
1367          push @lines, "<br />";          push @lines, "<br />";
         push @lines, "<INPUT type=\"button\" name=\"SelectAll\" class=\"bigButton\" value=\"Select All\" onClick=\"selectAll($menuName); $showSelect\" />";  
1368          push @lines, "<INPUT type=\"button\" name=\"ClearAll\" class=\"bigButton\"  value=\"Clear All\" onClick=\"clearAll($menuName); $showSelect\" />";          push @lines, "<INPUT type=\"button\" name=\"ClearAll\" class=\"bigButton\"  value=\"Clear All\" onClick=\"clearAll($menuName); $showSelect\" />";
1369          push @lines, "<INPUT type=\"button\" name=\"NMPDROnly\" class=\"bigButton\"  value=\"Select NMPDR\" onClick=\"selectSome($menuName, 'nmpdr'); $showSelect\" />";          push @lines, "<INPUT type=\"button\" name=\"SelectAll\" class=\"bigButton\" value=\"Select All\" onClick=\"selectAll($menuName); $showSelect\" />";
1370          push @lines, "<INPUT type=\"button\" name=\"OtherOnly\" class=\"bigButton\" value=\"Select Supporting\" onClick=\"selectSome($menuName, 'other'); $showSelect\" />";          push @lines, "<INPUT type=\"button\" name=\"NMPDROnly\" class=\"bigButton\"  value=\"Select NMPDR\" onClick=\"selectSome($menuName, $nmpdrCount, true); $showSelect\" />";
1371            push @lines, "<INPUT type=\"button\" name=\"OtherOnly\" class=\"bigButton\" value=\"Select Supporting\" onClick=\"selectSome($menuName, $nmpdrCount, false); $showSelect\" />";
1372          # Add the status display, too.          # Add the status display, too.
1373          push @lines, "<DIV id=\"$divID\" class=\"selectStatus\"></DIV>";          push @lines, "<DIV id=\"$divID\" class=\"selectStatus\"></DIV>";
1374          # 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 1185  Line 1377 
1377          # in case we decide to twiddle the parameters.          # in case we decide to twiddle the parameters.
1378          $showSelect =~ s/showSelected\(/showSelected\(thisForm\./;          $showSelect =~ s/showSelected\(/showSelected\(thisForm\./;
1379          $self->QueueFormScript($showSelect);          $self->QueueFormScript($showSelect);
1380            # Finally, add this parameter to the list of genome parameters. This enables us to
1381            # easily find all the parameters used to select one or more genomes.
1382            push @{$self->{genomeParms}}, $menuName;
1383      }      }
1384      # Assemble all the lines into a string.      # Assemble all the lines into a string.
1385      my $retVal = join("\n", @lines, "");      my $retVal = join("\n", @lines, "");
# Line 1192  Line 1387 
1387      return $retVal;      return $retVal;
1388  }  }
1389    
1390    =head3 PropertyMenu
1391    
1392    C<< my $htmlText = $shelp->PropertyMenu($menuName, $selected, $force); >>
1393    
1394    Generate a property name dropdown menu.
1395    
1396    =over 4
1397    
1398    =item menuName
1399    
1400    Name to give to the menu.
1401    
1402    =item selected
1403    
1404    Value of the property name to pre-select.
1405    
1406    =item force (optional)
1407    
1408    If TRUE, then the user will be forced to choose a property name. If FALSE,
1409    then an additional menu choice will be provided to select nothing.
1410    
1411    =item RETURN
1412    
1413    Returns a dropdown menu box that allows the user to select a property name. An additional
1414    selection entry will be provided for selecting no property name
1415    
1416    =back
1417    
1418    =cut
1419    
1420    sub PropertyMenu {
1421        # Get the parameters.
1422        my ($self, $menuName, $selected, $force) = @_;
1423        # Get the CGI and Sprout objects.
1424        my $sprout = $self->DB();
1425        my $cgi = $self->Q();
1426        # Create the property name list.
1427        my @propNames = ();
1428        if (! $force) {
1429            push @propNames, "";
1430        }
1431        # Get all the property names, putting them after the null choice if one exists.
1432        push @propNames, $sprout->GetChoices('Property', 'property-name');
1433        # Create a menu from them.
1434        my $retVal = $cgi->popup_menu(-name=> $menuName, -values => \@propNames,
1435                                      -default => $selected);
1436        # Return the result.
1437        return $retVal;
1438    }
1439    
1440  =head3 MakeTable  =head3 MakeTable
1441    
1442  C<< my $htmlText = $shelp->MakeTable(\@rows); >>  C<< my $htmlText = $shelp->MakeTable(\@rows); >>
# Line 1242  Line 1487 
1487    
1488  =head3 SubmitRow  =head3 SubmitRow
1489    
1490  C<< my $htmlText = $shelp->SubmitRow(); >>  C<< my $htmlText = $shelp->SubmitRow($caption); >>
1491    
1492  Returns the HTML text for the row containing the page size control  Returns the HTML text for the row containing the page size control
1493  and the submit button. All searches should have this row somewhere  and the submit button. All searches should have this row somewhere
1494  near the top of the form.  near the top of the form.
1495    
1496    =over 4
1497    
1498    =item caption (optional)
1499    
1500    Caption to be put on the search button. The default is C<Go>.
1501    
1502    =item RETURN
1503    
1504    Returns a table row containing the controls for submitting the search
1505    and tuning the results.
1506    
1507    =back
1508    
1509  =cut  =cut
1510    
1511  sub SubmitRow {  sub SubmitRow {
1512      # Get the parameters.      # Get the parameters.
1513      my ($self) = @_;      my ($self, $caption) = @_;
1514      my $cgi = $self->Q();      my $cgi = $self->Q();
1515      # Declare the return variable.      # Compute the button caption.
1516        my $realCaption = (defined $caption ? $caption : 'Go');
1517        # Get the current page size.
1518        my $pageSize = $cgi->param('PageSize');
1519        # Get the incoming external-link flag.
1520        my $aliases = ($cgi->param('ShowAliases') ? 1 : 0);
1521        # Create the row.
1522      my $retVal = $cgi->Tr($cgi->td("Results/Page"),      my $retVal = $cgi->Tr($cgi->td("Results/Page"),
1523                            $cgi->td($cgi->popup_menu(-name => 'PageSize',                            $cgi->td($cgi->popup_menu(-name => 'PageSize',
1524                                                      -values => [10, 25, 45, 100, 1000],                                                      -values => [10, 25, 50, 100, 1000],
1525                                                      -default => $cgi->param('PageSize'))),                                                      -default => $pageSize)),
1526                            $cgi->td($cgi->submit(-class => 'goButton',                            $cgi->td($cgi->submit(-class => 'goButton',
1527                                                  -name => 'Search',                                                  -name => 'Search',
1528                                                  -value => 'Go')));                                                  -value => $realCaption)));
1529      # Return the result.      # Return the result.
1530      return $retVal;      return $retVal;
1531  }  }
# Line 1270  Line 1534 
1534    
1535  C<< my $htmlText = $shelp->FeatureFilterRows(); >>  C<< my $htmlText = $shelp->FeatureFilterRows(); >>
1536    
1537  This method creates table rows that can be used to filter features. There are  This method creates table rows that can be used to filter features. The form
1538  two rows returned, and the values can be used to select features by genome  values can be used to select features by genome using the B<FeatureQuery>
1539  using the B<FeatureQuery> object.  object.
1540    
1541  =cut  =cut
1542    
# Line 1322  Line 1586 
1586          # Get the feature location string.          # Get the feature location string.
1587          my $loc = $sprout->FeatureLocation($feat);          my $loc = $sprout->FeatureLocation($feat);
1588          # Compute the contig, start, and stop points.          # Compute the contig, start, and stop points.
1589          my($start, $stop, $contig) = BasicLocation::Parse($loc);          my($contig, $start, $stop) = BasicLocation::Parse($loc);
1590            Trace("Start and stop are ($start,$stop) on contig $contig.") if T(3);
1591          # Now we need to do some goofiness to insure that the location is not too          # Now we need to do some goofiness to insure that the location is not too
1592          # big and that we get some surrounding stuff.          # big and that we get some surrounding stuff.
1593          my $mid = int(($start + $stop) / 2);          my $mid = int(($start + $stop) / 2);
# Line 1352  Line 1617 
1617          }          }
1618          my $seg_id = $contig;          my $seg_id = $contig;
1619          $seg_id =~ s/:/--/g;          $seg_id =~ s/:/--/g;
1620            Trace("Show limits are ($show_start,$show_stop) in genome $genomeID with ref $seg_id.") if T(3);
1621          # Assemble all the pieces.          # Assemble all the pieces.
1622          $retVal = "gbrowse.cgi/GB_$genomeID?ref=$seg_id&start=$show_start&stop=$show_stop";          $retVal = "gbrowse.cgi/GB_$genomeID?ref=$seg_id;start=$show_start;stop=$show_stop";
1623      }      }
1624      # Return the result.      # Return the result.
1625      return $retVal;      return $retVal;
1626  }  }
1627    
1628  =head2 Feature Column Methods  =head3 GetGenomes
1629    
1630  The methods in this column manage feature column data. If you want to provide the  C<< my @genomeList = $shelp->GetGenomes($parmName); >>
 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.  
1631    
1632  There is one special column name syntax for extra columns (that is, nonstandard  Return the list of genomes specified by the specified CGI query parameter.
1633  feature columns). If the column name begins with C<X=>, then it is presumed to be  If the request method is POST, then the list of genome IDs is returned
1634  an extra column. The column title is the text after the C<X=>, and its value is  without preamble. If the request method is GET and the parameter is not
1635  pulled from the extra column hash.  specified, then it is treated as a request for all genomes. This makes it
1636    easier for web pages to link to a search that wants to specify all genomes.
1637    
1638  =head3 DefaultFeatureColumns  =over 4
1639    
1640    =item parmName
1641    
1642    Name of the parameter containing the list of genomes. This will be the
1643    first parameter passed to the L</NmpdrGenomeMenu> call that created the
1644    genome selection control on the form.
1645    
1646    =item RETURN
1647    
1648  C<< my $colNames = $shelp->DefaultFeatureColumns(); >>  Returns a list of the genomes to process.
1649    
1650  Return a reference to a list of the default feature column identifiers. These  =back
 identifiers can be passed to L</FeatureColumnTitle> and L</FeatureColumnValue> in  
 order to produce the column titles and row values.  
1651    
1652  =cut  =cut
1653    
1654  sub DefaultFeatureColumns {  sub GetGenomes {
1655        # Get the parameters.
1656        my ($self, $parmName) = @_;
1657        # Get the CGI query object.
1658        my $cgi = $self->Q();
1659        # Get the list of genome IDs in the request header.
1660        my @retVal = $cgi->param($parmName);
1661        Trace("Genome list for $parmName is (" . join(", ", @retVal) . ") with method " . $cgi->request_method() . ".") if T(3);
1662        # Check for the special GET case.
1663        if ($cgi->request_method() eq "GET" && ! @retVal) {
1664            # Here the caller wants all the genomes.
1665            my $sprout = $self->DB();
1666            @retVal = $sprout->Genomes();
1667        }
1668        # Return the result.
1669        return @retVal;
1670    }
1671    
1672    =head3 GetHelpText
1673    
1674    C<< my $htmlText = $shelp->GetHelpText(); >>
1675    
1676    Get the help text for this search. The help text is stored in files on the template
1677    server. The help text for a specific search is taken from a file named
1678    C<SearchHelp_>I<class>C<.inc> in the template directory C<$FIG_Config::template_url>.
1679    There are also three standard help files: C<SearchHelp1_Filtering.inc> describes the
1680    feature filtering performed by the B<FeatureQuery> object, C<SearchHelp1_GenomeControl.inc>
1681    describes how to use a multiple-selection genome control, and C<SearchHelp1_Standard.inc>
1682    describes the standard controls for a search, such as page size, URL display, and
1683    external alias display.
1684    
1685    =cut
1686    
1687    sub GetHelpText {
1688      # Get the parameters.      # Get the parameters.
1689      my ($self) = @_;      my ($self) = @_;
1690        # Create a list to hold the pieces of the help.
1691        my @helps = ();
1692        # Get the template directory URL.
1693        my $urlBase = $FIG_Config::template_url;
1694        # Start with the specific help.
1695        my $class = $self->{class};
1696        push @helps, PageBuilder::GetPage("$urlBase/SearchHelp_$class.inc");
1697        # Add the genome control help if needed.
1698        if (scalar @{$self->{genomeParms}}) {
1699            push @helps, PageBuilder::GetPage("$urlBase/SearchHelp1_GenomeControl.inc");
1700        }
1701        # Next the filter help.
1702        if ($self->{filtered}) {
1703            push @helps, PageBuilder::GetPage("$urlBase/SearchHelp1_Filtering.inc");
1704        }
1705        # Finally, the standard help.
1706        push @helps, PageBuilder::GetPage("$urlBase/SearchHelp1_Standard.inc");
1707        # Assemble the pieces.
1708        my $retVal = join("\n<p>&nbsp;</p>\n", @helps);
1709      # Return the result.      # Return the result.
1710      return ['orgName', 'function', 'gblink', 'protlink'];      return $retVal;
1711  }  }
1712    
1713  =head3 FeatureColumnTitle  =head3 ComputeSearchURL
1714    
1715  C<< my $title = $shelp->FeatureColumnTitle($colName); >>  C<< my $url = $shelp->ComputeSearchURL(%overrides); >>
1716    
1717  Return the column heading title to be used for the specified feature column.  Compute the GET-style URL for the current search. In order for this to work, there
1718    must be a copy of the search form on the current page. This will always be the
1719    case if the search is coming from C<SearchSkeleton.cgi>.
1720    
1721    A little expense is involved in order to make the URL as smart as possible. The
1722    main complication is that if the user specified all genomes, we'll want to
1723    remove the parameter entirely from a get-style URL.
1724    
1725  =over 4  =over 4
1726    
1727  =item name  =item overrides
1728    
1729  Name of the desired feature column.  Hash containing override values for the parameters, where the parameter name is
1730    the key and the parameter value is the override value. If the override value is
1731    C<undef>, the parameter will be deleted from the result.
1732    
1733  =item RETURN  =item RETURN
1734    
1735  Returns the title to be used as the column header for the named feature column.  Returns a GET-style URL for invoking the search with the specified overrides.
1736    
1737  =back  =back
1738    
1739  =cut  =cut
1740    
1741  sub FeatureColumnTitle {  sub ComputeSearchURL {
1742      # Get the parameters.      # Get the parameters.
1743      my ($self, $colName) = @_;      my ($self, %overrides) = @_;
1744      # Declare the return variable. We default to a blank column name.      # Get the database and CGI query object.
1745      my $retVal = "&nbsp;";      my $cgi = $self->Q();
1746      # Process the column name.      my $sprout = $self->DB();
1747      if ($colName =~ /^X=(.+)$/) {      # Start with the full URL.
1748          # Here we have an extra column.      my $retVal = $cgi->url(-full => 1);
1749          $retVal = $1;      # Get all the query parameters in a hash.
1750      } elsif ($colName eq 'orgName') {      my %parms = $cgi->Vars();
1751          $retVal = "Name";      # Now we need to do some fixing. Each multi-valued parameter is encoded as a string with null
1752      } elsif ($colName eq 'fid') {      # characters separating the individual values. We have to convert those to lists. In addition,
1753          $retVal = "FIG ID";      # the multiple-selection genome parameters and the feature type parameter must be checked to
1754      } elsif ($colName eq 'alias') {      # determine whether or not they can be removed from the URL. First, we get a list of the
1755          $retVal = "External Aliases";      # genome parameters and a list of all genomes. Note that we only need the list if a
1756      } elsif ($colName eq 'function') {      # multiple-selection genome parameter has been found on the form.
1757          $retVal = "Functional Assignment";      my %genomeParms = map { $_ => 1 } @{$self->{genomeParms}};
1758      } elsif ($colName eq 'gblink') {      my @genomeList;
1759          $retVal = "GBrowse";      if (keys %genomeParms) {
1760      } elsif ($colName eq 'protlink') {          @genomeList = $sprout->Genomes();
1761          $retVal = "NMPDR Protein Page";      }
1762      } elsif ($colName eq 'group') {      # Create a list to hold the URL parameters we find.
1763          $retVal = "NMDPR Group";      my @urlList = ();
1764        # Now loop through the parameters in the hash, putting them into the output URL.
1765        for my $parmKey (keys %parms) {
1766            # Get a list of the parameter values. If there's only one, we'll end up with
1767            # a singleton list, but that's okay.
1768            my @values = split (/\0/, $parms{$parmKey});
1769            # Check for special cases.
1770            if (grep { $_ eq $parmKey } qw(SessionID ResultCount Page PageSize Trace TF ShowURL)) {
1771                # These are bookkeeping parameters we don't need to start a search.
1772                @values = ();
1773            } elsif ($parmKey =~ /_SearchThing$/) {
1774                # Here the value coming in is from a genome control's search thing. It does
1775                # not affect the results of the search, so we clear it.
1776                @values = ();
1777            } elsif ($genomeParms{$parmKey}) {
1778                # Here we need to see if the user wants all the genomes. If he does,
1779                # we erase all the values just like with features.
1780                my $allFlag = $sprout->IsAllGenomes(\@values, \@genomeList);
1781                if ($allFlag) {
1782                    @values = ();
1783                }
1784            } elsif (exists $overrides{$parmKey}) {
1785                # Here the value is being overridden, so we skip it for now.
1786                @values = ();
1787            }
1788            # If we still have values, create the URL parameters.
1789            if (@values) {
1790                push @urlList, map { "$parmKey=" . uri_escape($_) } @values;
1791            }
1792        }
1793        # Now do the overrides.
1794        for my $overKey (keys %overrides) {
1795            # Only use this override if it's not a delete marker.
1796            if (defined $overrides{$overKey}) {
1797                push @urlList, "$overKey=" . uri_escape($overrides{$overKey});
1798            }
1799      }      }
1800        # Add the parameters to the URL.
1801        $retVal .= "?" . join(";", @urlList);
1802      # Return the result.      # Return the result.
1803      return $retVal;      return $retVal;
1804  }  }
1805    
1806  =head3 FeatureColumnValue  =head3 GetRunTimeValue
1807    
1808  C<< my $value = $shelp->FeatureColumnValue($colName, $fid, \%extraCols); >>  C<< my $htmlText = $shelp->GetRunTimeValue($text); >>
1809    
1810  Return the value to be displayed in the specified feature column.  Compute a run-time column value.
1811    
1812  =over 4  =over 4
1813    
1814  =item colName  =item text
1815    
1816  Name of the column to be displayed.  The run-time column text. It consists of 2 percent signs, a column type, an equal
1817    sign, and the data for the current row.
1818    
1819  =item record  =item RETURN
1820    
1821  DBObject record for the feature being displayed in the current row.  Returns the fully-formatted HTML text to go into the current column of the current row.
1822    
1823  =item extraCols  =back
1824    
1825  Reference to a hash of extra column names to values. If the incoming column name  =cut
 begins with C<X=>, its value will be taken from this hash.  
1826    
1827  =item RETURN  sub GetRunTimeValue {
1828        # Get the parameters.
1829        my ($self, $text) = @_;
1830        # Declare the return variable.
1831        my $retVal;
1832        # Parse the incoming text.
1833        if ($text =~ /^%%([^=]+)=(.*)$/) {
1834            $retVal = $self->RunTimeColumns($1, $2);
1835        } else {
1836            Confess("Invalid run-time column string \"$text\" encountered in session file.");
1837        }
1838        # Return the result.
1839        return $retVal;
1840    }
1841    
1842  Returns the HTML to be displayed in the named column for the specified feature.  =head3 AdvancedClassList
1843    
1844  =back  C<< my @classes = SearchHelper::AdvancedClassList(); >>
1845    
1846    Return a list of advanced class names. This list is used to generate the directory
1847    of available searches on the search page.
1848    
1849    We use the %INC variable to accomplish this.
1850    
1851  =cut  =cut
1852    
1853  sub FeatureColumnValue {  sub AdvancedClassList {
1854      # Get the parameters.      my @retVal = map { $_ =~ /^SH(\w+)\.pm/; $1 } grep { $_ =~ /^SH/ } keys %INC;
1855      my ($self, $colName, $record, $extraCols) = @_;      return @retVal;
     # 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->{$1};  
1856          }          }
1857      } elsif ($colName eq 'orgName') {  
1858          # Here we want the formatted organism name and feature number.  =head3 SelectionTree
1859          $retVal = $self->FeatureName($fid);  
1860      } elsif ($colName eq 'fid') {  C<< my $htmlText = SearchHelper::SelectionTree($cgi, \%tree, %options); >>
1861          # Here we have the raw feature ID. We hyperlink it to the protein page.  
1862          $retVal = HTML::set_prot_links($fid);  Display a selection tree.
1863    
1864    This method creates the HTML for a tree selection control. The tree is implemented as a set of
1865    nested HTML unordered lists. Each selectable element of the tree will contain a radio button. In
1866    addition, some of the tree nodes can contain hyperlinks.
1867    
1868    The tree itself is passed in as a multi-level list containing node names followed by
1869    contents. Each content element is a reference to a similar list. The first element of
1870    each list may be a hash reference. If so, it should contain one or both of the following
1871    keys.
1872    
1873    =over 4
1874    
1875    =item link
1876    
1877    The navigation URL to be popped up if the user clicks on the node name.
1878    
1879    =item value
1880    
1881    The form value to be returned if the user selects the tree node.
1882    
1883    =back
1884    
1885    The presence of a C<link> key indicates the node name will be hyperlinked. The presence of
1886    a C<value> key indicates the node name will have a radio button. If a node has no children,
1887    you may pass it a hash reference instead of a list reference.
1888    
1889    The following example shows the hash for a three-level tree with links on the second level and
1890    radio buttons on the third.
1891    
1892        [   Objects => [
1893                Entities => [
1894                    {link => "../docs/WhatIsAnEntity.html"},
1895                    Genome => {value => 'GenomeData'},
1896                    Feature => {value => 'FeatureData'},
1897                    Contig => {value => 'ContigData'},
1898                ],
1899                Relationships => [
1900                    {link => "../docs/WhatIsARelationShip.html"},
1901                    HasFeature => {value => 'GenomeToFeature'},
1902                    IsOnContig => {value => 'FeatureToContig'},
1903                ]
1904            ]
1905        ]
1906    
1907    Note how each leaf of the tree has a hash reference for its value, while the branch nodes
1908    all have list references.
1909    
1910    This next example shows how to set up a taxonomy selection field. The value returned
1911    by the tree control will be the taxonomy string for the selected node ready for use
1912    in a LIKE-style SQL filter. Only the single branch ending in campylobacter is shown for
1913    reasons of space.
1914    
1915        [   All => [
1916                {value => "%"},
1917                Bacteria => [
1918                    {value => "Bacteria%"},
1919                    Proteobacteria => [
1920                        {value => "Bacteria; Proteobacteria%"},
1921                        Epsilonproteobacteria => [
1922                            {value => "Bacteria; Proteobacteria;Epsilonproteobacteria%"},
1923                            Campylobacterales => [
1924                                {value => "Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales%"},
1925                                Campylobacteraceae =>
1926                                    {value => "Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales; Campylobacteraceae%"},
1927                                ...
1928                            ]
1929                            ...
1930                        ]
1931                        ...
1932                    ]
1933                    ...
1934                ]
1935                ...
1936            ]
1937        ]
1938    
1939    
1940    This method of tree storage allows the caller to control the order in which the tree nodes
1941    are displayed and to completely control value selection and use of hyperlinks. It is, however
1942    a bit complicated. Eventually, tree-building classes will be provided to simplify things.
1943    
1944    The parameters to this method are as follows.
1945    
1946    =over 4
1947    
1948    =item cgi
1949    
1950    CGI object used to generate the HTML.
1951    
1952    =item tree
1953    
1954    Reference to a hash describing a tree. See the description above.
1955    
1956    =item options
1957    
1958    Hash containing options for the tree display.
1959    
1960    =back
1961    
1962    The allowable options are as follows
1963    
1964    =over 4
1965    
1966    =item nodeImageClosed
1967    
1968    URL of the image to display next to the tree nodes when they are collapsed. Clicking
1969    on the image will expand a section of the tree. The default is C<../FIG/Html/plus.gif>.
1970    
1971    =item nodeImageOpen
1972    
1973    URL of the image to display next to the tree nodes when they are expanded. Clicking
1974    on the image will collapse a section of the tree. The default is C<../FIG/Html/minus.gif>.
1975    
1976    =item style
1977    
1978    Style to use for the tree. The default is C<tree>. Because the tree style is implemented
1979    as nested lists, the key components of this style are the definitions for the C<ul> and
1980    C<li> tags. The default style file contains the following definitions.
1981    
1982        .tree ul {
1983           margin-left: 0; padding-left: 22px
1984        }
1985        .tree li {
1986            list-style-type: none;
1987        }
1988    
1989    The default image is 22 pixels wide, so in the above scheme each tree level is indented from its
1990    parent by the width of the node image. This use of styles limits the things we can do in formatting
1991    the tree, but it has the advantage of vastly simplifying the tree creation.
1992    
1993    =item name
1994    
1995    Field name to give to the radio buttons in the tree. The default is C<selection>.
1996    
1997    =item target
1998    
1999    Frame target for links. The default is C<_self>.
2000    
2001    =item selected
2002    
2003    If specified, the value of the radio button to be pre-selected.
2004    
2005    =back
2006    
2007    =cut
2008    
2009    sub SelectionTree {
2010        # Get the parameters.
2011        my ($cgi, $tree, %options) = @_;
2012        # Get the options.
2013        my $optionThing = Tracer::GetOptions({ name => 'selection',
2014                                               nodeImageClosed => '../FIG/Html/plus.gif',
2015                                               nodeImageOpen => '../FIG/Html/minus.gif',
2016                                               style => 'tree',
2017                                               target => '_self',
2018                                               selected => undef},
2019                                             \%options);
2020        # Declare the return variable. We'll do the standard thing with creating a list
2021        # of HTML lines and rolling them together at the end.
2022        my @retVal = ();
2023        # Only proceed if the tree is present.
2024        if (defined($tree)) {
2025            # Validate the tree.
2026            if (ref $tree ne 'ARRAY') {
2027                Confess("Selection tree is not a list reference.");
2028            } elsif (scalar @{$tree} == 0) {
2029                # The tree is empty, so we do nothing.
2030            } elsif ($tree->[0] eq 'HASH') {
2031                Confess("Hash reference found at start of selection tree. The tree as a whole cannot have attributes, only tree nodes.");
2032            } else {
2033                # Here we have a real tree. Apply the tree style.
2034                push @retVal, $cgi->start_div({ class => $optionThing->{style} });
2035                # Give us a DIV ID.
2036                my $divID = GetDivID($optionThing->{name});
2037                # Show the tree.
2038                push @retVal, ShowBranch($cgi, "(root)", $divID, $tree, $optionThing, 'block');
2039                # Close the DIV block.
2040                push @retVal, $cgi->end_div();
2041            }
2042        }
2043        # Return the result.
2044        return join("\n", @retVal, "");
2045    }
2046    
2047    =head3 ShowBranch
2048    
2049    C<< my @htmlLines = SearchHelper::ShowBranch($cgi, $label, $id, $branch, $options, $displayType); >>
2050    
2051    This is a recursive method that displays a branch of the tree.
2052    
2053    =over 4
2054    
2055    =item cgi
2056    
2057    CGI object used to format HTML.
2058    
2059    =item label
2060    
2061    Label of this tree branch. It is only used in error messages.
2062    
2063    =item id
2064    
2065    ID to be given to this tree branch. The ID is used in the code that expands and collapses
2066    tree nodes.
2067    
2068    =item branch
2069    
2070    Reference to a list containing the content of the tree branch. The list contains an optional
2071    hash reference that is ignored and the list of children, each child represented by a name
2072    and then its contents. The contents could by a hash reference (indicating the attributes
2073    of a leaf node), or another tree branch.
2074    
2075    =item options
2076    
2077    Options from the original call to L</SelectionTree>.
2078    
2079    =item displayType
2080    
2081    C<block> if the contents of this list are to be displayed, C<none> if they are to be
2082    hidden.
2083    
2084    =item RETURN
2085    
2086    Returns one or more HTML lines that can be used to display the tree branch.
2087    
2088    =back
2089    
2090    =cut
2091    
2092    sub ShowBranch {
2093        # Get the parameters.
2094        my ($cgi, $label, $id, $branch, $options, $displayType) = @_;
2095        # Declare the return variable.
2096        my @retVal = ();
2097        # Start the branch.
2098        push @retVal, $cgi->start_ul({ id => $id, style => "display:$displayType" });
2099        # Check for the hash and choose the start location accordingly.
2100        my $i0 = (ref $branch->[0] eq 'HASH' ? 1 : 0);
2101        # Get the list length.
2102        my $i1 = scalar(@{$branch});
2103        # Verify we have an even number of elements.
2104        if (($i1 - $i0) % 2 != 0) {
2105            Trace("Branch elements are from $i0 to $i1.") if T(3);
2106            Confess("Odd number of elements in tree branch $label.");
2107        } else {
2108            # Loop through the elements.
2109            for (my $i = $i0; $i < $i1; $i += 2) {
2110                # Get this node's label and contents.
2111                my ($myLabel, $myContent) = ($branch->[$i], $branch->[$i+1]);
2112                # Get an ID for this node's children (if any).
2113                my $myID = GetDivID($options->{name});
2114                # Now we need to find the list of children and the options hash.
2115                # This is a bit ugly because we allow the shortcut of a hash without an
2116                # enclosing list. First, we need some variables.
2117                my $attrHash = {};
2118                my @childHtml = ();
2119                my $hasChildren = 0;
2120                if (! ref $myContent) {
2121                    Confess("Invalid tree definition. Scalar found as content of node \"$myLabel\".");
2122                } elsif (ref $myContent eq 'HASH') {
2123                    # Here the node is a leaf and its content contains the link/value hash.
2124                    $attrHash = $myContent;
2125                } elsif (ref $myContent eq 'ARRAY') {
2126                    # Here the node may be a branch. Its content is a list.
2127                    my $len = scalar @{$myContent};
2128                    if ($len >= 1) {
2129                        # Here the first element of the list could by the link/value hash.
2130                        if (ref $myContent->[0] eq 'HASH') {
2131                            $attrHash = $myContent->[0];
2132                            # If there's data in the list besides the hash, it's our child list.
2133                            # We can pass the entire thing as the child list, because the hash
2134                            # is ignored.
2135                            if ($len > 1) {
2136                                $hasChildren = 1;
2137                            }
2138                        } else {
2139                            $hasChildren = 1;
2140                        }
2141                        # If we have children, create the child list with a recursive call.
2142                        if ($hasChildren) {
2143                            Trace("Processing children of $myLabel.") if T(4);
2144                            push @childHtml, ShowBranch($cgi, $myLabel, $myID, $myContent, $options, 'none');
2145                        }
2146                    }
2147                }
2148                # Okay, it's time to pause and take stock. We have the label of the current node
2149                # in $myLabel, its attributes in $attrHash, and if it is NOT a leaf node, we
2150                # have a child list in @childHtml. If it IS a leaf node, $hasChildren is 0.
2151                # Compute the image HTML. It's tricky, because we have to deal with the open and
2152                # closed images.
2153                my @images = ($options->{nodeImageOpen}, $options->{nodeImageClosed});
2154                my $image = $images[$hasChildren];
2155                my $prefixHtml = $cgi->img({src => $image, id => "${myID}img"});
2156                if ($hasChildren) {
2157                    # If there are children, we wrap the image in a toggle hyperlink.
2158                    $prefixHtml = $cgi->a({ onClick => "javascript:treeToggle('$myID','$images[0]', '$images[1]')" },
2159                                          $prefixHtml);
2160                }
2161                # Now the radio button, if any. Note we use "defined" in case the user wants the
2162                # value to be 0.
2163                if (defined $attrHash->{value}) {
2164                    # Due to a glitchiness in the CGI stuff, we have to build the attribute
2165                    # hash for the "input" method. If the item is pre-selected, we add
2166                    # "checked => undef" to the hash. Otherwise, we can't have "checked"
2167                    # at all.
2168                    my $radioParms = { type => 'radio',
2169                                       name => $options->{name},
2170                                       value => $attrHash->{value},
2171                                     };
2172                    if (defined $options->{selected} && $options->{selected} eq $attrHash->{value}) {
2173                        $radioParms->{checked} = undef;
2174                    }
2175                    $prefixHtml .= $cgi->input($radioParms);
2176                }
2177                # Next, we format the label.
2178                my $labelHtml = $myLabel;
2179                Trace("Formatting tree node for $myLabel.") if T(4);
2180                # Apply a hyperlink if necessary.
2181                if (defined $attrHash->{link}) {
2182                    $labelHtml = $cgi->a({ href => $attrHash->{link}, target => $options->{target} },
2183                                         $labelHtml);
2184                }
2185                # Finally, roll up the child HTML. If there are no children, we'll get a null string
2186                # here.
2187                my $childHtml = join("\n", @childHtml);
2188                # Now we have all the pieces, so we can put them together.
2189                push @retVal, $cgi->li("$prefixHtml$labelHtml$childHtml");
2190            }
2191        }
2192        # Close the tree branch.
2193        push @retVal, $cgi->end_ul();
2194        # Return the result.
2195        return @retVal;
2196    }
2197    
2198    =head3 GetDivID
2199    
2200    C<< my $idString = SearchHelper::GetDivID($name); >>
2201    
2202    Return a new HTML ID string.
2203    
2204    =over 4
2205    
2206    =item name
2207    
2208    Name to be prefixed to the ID string.
2209    
2210    =item RETURN
2211    
2212    Returns a hopefully-unique ID string.
2213    
2214    =back
2215    
2216    =cut
2217    
2218    sub GetDivID {
2219        # Get the parameters.
2220        my ($name) = @_;
2221        # Compute the ID.
2222        my $retVal = "elt_$name$divCount";
2223        # Increment the counter to make sure this ID is not re-used.
2224        $divCount++;
2225        # Return the result.
2226        return $retVal;
2227    }
2228    
2229    =head2 Feature Column Methods
2230    
2231    The methods in this section manage feature column data. If you want to provide the
2232    capability to include new types of data in feature columns, then all the changes
2233    are made to this section of the source file. Technically, this should be implemented
2234    using object-oriented methods, but this is simpler for non-programmers to maintain.
2235    To add a new column of feature data, you must first give it a name. For example,
2236    the name for the protein page link column is C<protlink>. If the column is to appear
2237    in the default list of feature columns, add it to the list returned by
2238    L</DefaultFeatureColumns>. Then add code to produce the column title to
2239    L</FeatureColumnTitle> and code to produce its value to L</FeatureColumnValue>, and
2240    everything else will happen automatically.
2241    
2242    There is one special column name syntax for extra columns (that is, nonstandard
2243    feature columns). If the column name begins with C<X=>, then it is presumed to be
2244    an extra column. The column title is the text after the C<X=>, and its value is
2245    pulled from the extra column hash.
2246    
2247    =head3 DefaultFeatureColumns
2248    
2249    C<< my @colNames = $shelp->DefaultFeatureColumns(); >>
2250    
2251    Return a list of the default feature column identifiers. These identifiers can
2252    be passed to L</FeatureColumnTitle> and L</FeatureColumnValue> in order to
2253    produce the column titles and row values.
2254    
2255    =cut
2256    
2257    sub DefaultFeatureColumns {
2258        # Get the parameters.
2259        my ($self) = @_;
2260        # Return the result.
2261        return qw(orgName function gblink protlink);
2262    }
2263    
2264    =head3 FeatureColumnTitle
2265    
2266    C<< my $title = $shelp->FeatureColumnTitle($colName); >>
2267    
2268    Return the column heading title to be used for the specified feature column.
2269    
2270    =over 4
2271    
2272    =item name
2273    
2274    Name of the desired feature column.
2275    
2276    =item RETURN
2277    
2278    Returns the title to be used as the column header for the named feature column.
2279    
2280    =back
2281    
2282    =cut
2283    
2284    sub FeatureColumnTitle {
2285        # Get the parameters.
2286        my ($self, $colName) = @_;
2287        # Declare the return variable. We default to a blank column name.
2288        my $retVal = "&nbsp;";
2289        # Process the column name.
2290        if ($colName =~ /^X=(.+)$/) {
2291            # Here we have an extra column.
2292            $retVal = $1;
2293      } elsif ($colName eq 'alias') {      } elsif ($colName eq 'alias') {
2294          # In this case, the user wants a list of external aliases for the feature.          $retVal = "External Aliases";
2295          # The complicated part is we have to hyperlink them. First, get the      } elsif ($colName eq 'fid') {
2296          # aliases.          $retVal = "FIG ID";
2297          my @aliases = $sprout->FeatureAliases($fid);      } elsif ($colName eq 'function') {
2298          # Only proceed if we found some.          $retVal = "Functional Assignment";
2299          if (@aliases) {      } elsif ($colName eq 'gblink') {
2300              # Join the aliases into a comma-delimited list.          $retVal = "GBrowse";
2301              my $aliasList = join(", ", @aliases);      } elsif ($colName eq 'group') {
2302              # Ask the HTML processor to hyperlink them.          $retVal = "NMDPR Group";
2303              $retVal = HTML::set_prot_links($aliasList);      } elsif ($colName =~ /^keyword:(.+)$/) {
2304            $retVal = ucfirst $1;
2305        } elsif ($colName eq 'orgName') {
2306            $retVal = "Organism and Gene ID";
2307        } elsif ($colName eq 'protlink') {
2308            $retVal = "NMPDR Protein Page";
2309        } elsif ($colName eq 'subsystem') {
2310            $retVal = "Subsystems";
2311          }          }
2312        # Return the result.
2313        return $retVal;
2314    }
2315    
2316    
2317    =head3 FeatureColumnValue
2318    
2319    C<< my $value = $shelp->FeatureColumnValue($colName, $fid, \%extraCols); >>
2320    
2321    Return the value to be displayed in the specified feature column.
2322    
2323    =over 4
2324    
2325    =item colName
2326    
2327    Name of the column to be displayed.
2328    
2329    =item record
2330    
2331    DBObject record for the feature being displayed in the current row.
2332    
2333    =item extraCols
2334    
2335    Reference to a hash of extra column names to values. If the incoming column name
2336    begins with C<X=>, its value will be taken from this hash.
2337    
2338    =item RETURN
2339    
2340    Returns the HTML to be displayed in the named column for the specified feature.
2341    
2342    =back
2343    
2344    =cut
2345    
2346    sub FeatureColumnValue {
2347        # Get the parameters.
2348        my ($self, $colName, $record, $extraCols) = @_;
2349        # Get the sprout and CGI objects.
2350        my $cgi = $self->Q();
2351        my $sprout = $self->DB();
2352        # Get the feature ID.
2353        my ($fid) = $record->Value('Feature(id)');
2354        # Declare the return variable. Denote that we default to a non-breaking space,
2355        # which will translate to an empty table cell (rather than a table cell with no
2356        # interior, which is what you get for a null string).
2357        my $retVal = "&nbsp;";
2358        # Process according to the column name.
2359        if ($colName =~ /^X=(.+)$/) {
2360            # Here we have an extra column. Only update if the value exists. Note that
2361            # a value of C<undef> is treated as a non-existent value, because the
2362            # caller may have put "colName => undef" in the "PutFeature" call in order
2363            # to insure we know the extra column exists.
2364            if (defined $extraCols->{$1}) {
2365                $retVal = $extraCols->{$1};
2366            }
2367        } elsif ($colName eq 'alias') {
2368            # In this case, the user wants a list of external aliases for the feature.
2369            # These are very expensive, so we compute them when the row is displayed.
2370            $retVal = "%%alias=$fid";
2371        } elsif ($colName eq 'fid') {
2372            # Here we have the raw feature ID. We hyperlink it to the protein page.
2373            $retVal = HTML::set_prot_links($fid);
2374      } elsif ($colName eq 'function') {      } elsif ($colName eq 'function') {
2375          # The functional assignment is just a matter of getting some text.          # The functional assignment is just a matter of getting some text.
2376          ($retVal) = $record->Value('Feature(assignment)');          ($retVal) = $record->Value('Feature(assignment)');
2377      } elsif ($colName eq 'gblink') {      } elsif ($colName eq 'gblink') {
2378          # Here we want a link to the GBrowse page using the official GBrowse button.          # Here we want a link to the GBrowse page using the official GBrowse button.
2379          my $gurl = "GetGBrowse.cgi?fid=$fid";          $retVal = FakeButton('GBrowse', "GetGBrowse.cgi", undef,
2380          $retVal = $cgi->a({ href => $gurl, title => "GBrowse for $fid" },                            fid => $fid);
                           $cgi->img({ src => "../images/button-gbrowse.png",  
                                       border => 0 })  
                          );  
     } elsif ($colName eq 'protlink') {  
         # Here we want a link to the protein page using the official NMPDR button.  
         my $hurl = HTML::fid_link($cgi, $fid, 0, 1);  
         $retVal = $cgi->a({ href => $hurl, title => "Protein page for $fid" },  
                           $cgi->img({ src => "../images/button-nmpdr.png",  
                                      border => 0 })  
                          );  
2381      } elsif ($colName eq 'group') {      } elsif ($colName eq 'group') {
2382          # Get the NMPDR group name.          # Get the NMPDR group name.
2383          my (undef, $group) = $self->OrganismData($fid);          my (undef, $group) = $self->OrganismData($fid);
# Line 1534  Line 2385 
2385          my $nurl = $sprout->GroupPageName($group);          my $nurl = $sprout->GroupPageName($group);
2386          $retVal = $cgi->a({ href => $nurl, title => "$group summary" },          $retVal = $cgi->a({ href => $nurl, title => "$group summary" },
2387                            $group);                            $group);
2388        } elsif ($colName =~ /^keyword:(.+)$/) {
2389            # Here we want keyword-related values. This is also expensive, so
2390            # we compute them when the row is displayed.
2391            $retVal = "%%$colName=$fid";
2392        } elsif ($colName eq 'orgName') {
2393            # Here we want the formatted organism name and feature number.
2394            $retVal = $self->FeatureName($fid);
2395        } elsif ($colName eq 'protlink') {
2396            # Here we want a link to the protein page using the official NMPDR button.
2397            $retVal = FakeButton('NMPDR', "protein.cgi", undef,
2398                              prot => $fid, SPROUT => 1, new_framework => 0,
2399                              user => '');
2400        }elsif ($colName eq 'subsystem') {
2401            # Another run-time column: subsystem list.
2402            $retVal = "%%subsystem=$fid";
2403        }
2404        # Return the result.
2405        return $retVal;
2406    }
2407    
2408    =head3 RunTimeColumns
2409    
2410    C<< my $htmlText = $shelp->RunTimeColumns($type, $text); >>
2411    
2412    Return the HTML text for a run-time column. Run-time columns are evaluated when the
2413    list is displayed, rather than when it is generated.
2414    
2415    =over 4
2416    
2417    =item type
2418    
2419    Type of column.
2420    
2421    =item text
2422    
2423    Data relevant to this row of the column.
2424    
2425    =item RETURN
2426    
2427    Returns the fully-formatted HTML text to go in the specified column.
2428    
2429    =back
2430    
2431    =cut
2432    
2433    sub RunTimeColumns {
2434        # Get the parameters.
2435        my ($self, $type, $text) = @_;
2436        # Declare the return variable.
2437        my $retVal = "";
2438        # Get the Sprout and CGI objects.
2439        my $sprout = $self->DB();
2440        my $cgi = $self->Q();
2441        Trace("Runtime column $type with text \"$text\" found.") if T(4);
2442        # Separate the text into a type and data.
2443        if ($type eq 'alias') {
2444            # Here the caller wants external alias links for a feature. The text
2445            # is the feature ID.
2446            my $fid = $text;
2447            # The complicated part is we have to hyperlink them. First, get the
2448            # aliases.
2449            Trace("Generating aliases for feature $fid.") if T(4);
2450            my @aliases = $sprout->FeatureAliases($fid);
2451            # Only proceed if we found some.
2452            if (@aliases) {
2453                # Join the aliases into a comma-delimited list.
2454                my $aliasList = join(", ", @aliases);
2455                # Ask the HTML processor to hyperlink them.
2456                $retVal = HTML::set_prot_links($cgi, $aliasList);
2457            }
2458        } elsif ($type eq 'subsystem') {
2459            # Here the caller wants the subsystems in which this feature participates.
2460            # The text is the feature ID. We will list the subsystem names with links
2461            # to the subsystem's summary page.
2462            my $fid = $text;
2463            # Get the subsystems.
2464            Trace("Generating subsystems for feature $fid.") if T(4);
2465            my %subs = $sprout->SubsystemsOf($fid);
2466            # Extract the subsystem names.
2467            my @names = map { HTML::sub_link($cgi, $_) } sort keys %subs;
2468            # String them into a list.
2469            $retVal = join(", ", @names);
2470        } elsif ($type =~ /^keyword:(.+)$/) {
2471            # Here the caller wants the value of the named keyword. The text is the
2472            # feature ID.
2473            my $keywordName = $1;
2474            my $fid = $text;
2475            # Get the attribute values.
2476            Trace("Getting $keywordName values for feature $fid.") if T(4);
2477            my @values = $sprout->GetFlat(['Feature'], "Feature(id) = ?", [$fid],
2478                                          "Feature($keywordName)");
2479            # String them into a list.
2480            $retVal = join(", ", @values);
2481        }
2482        # Return the result.
2483        return $retVal;
2484    }
2485    
2486    =head3 SaveOrganismData
2487    
2488    C<< my ($name, $displayGroup) = $shelp->SaveOrganismData($group, $genomeID, $genus, $species, $strain); >>
2489    
2490    Format the name of an organism and the display version of its group name. The incoming
2491    data should be the relevant fields from the B<Genome> record in the database. The
2492    data will also be stored in the genome cache for later use in posting search results.
2493    
2494    =over 4
2495    
2496    =item group
2497    
2498    Name of the genome's group as it appears in the database.
2499    
2500    =item genomeID
2501    
2502    ID of the relevant genome.
2503    
2504    =item genus
2505    
2506    Genus of the genome's organism. If undefined or null, it will be assumed the genome is not
2507    in the database. In this case, the organism name is derived from the genomeID and the group
2508    is automatically the supporting-genomes group.
2509    
2510    =item species
2511    
2512    Species of the genome's organism.
2513    
2514    =item strain
2515    
2516    Strain of the species represented by the genome.
2517    
2518    =item RETURN
2519    
2520    Returns a two-element list. The first element is the formatted genome name. The second
2521    element is the display name of the genome's group.
2522    
2523    =back
2524    
2525    =cut
2526    
2527    sub SaveOrganismData {
2528        # Get the parameters.
2529        my ($self, $group, $genomeID, $genus, $species, $strain) = @_;
2530        # Declare the return values.
2531        my ($name, $displayGroup);
2532        # If the organism does not exist, format an unknown name and a blank group.
2533        if (! defined($genus)) {
2534            $name = "Unknown Genome $genomeID";
2535            $displayGroup = "";
2536        } else {
2537            # It does exist, so format the organism name.
2538            $name = "$genus $species";
2539            if ($strain) {
2540                $name .= " $strain";
2541            }
2542            # Compute the display group. This is currently the same as the incoming group
2543            # name unless it's the supporting group, which is nulled out.
2544            $displayGroup = ($group eq $FIG_Config::otherGroup ? "" : $group);
2545        }
2546        # Cache the group and organism data.
2547        my $cache = $self->{orgs};
2548        $cache->{$genomeID} = [$name, $displayGroup];
2549        # Return the result.
2550        return ($name, $displayGroup);
2551    }
2552    
2553    =head3 ValidateKeywords
2554    
2555    C<< my $okFlag = $shelp->ValidateKeywords($keywordString, $required); >>
2556    
2557    Insure that a keyword string is reasonably valid. If it is invalid, a message will be
2558    set.
2559    
2560    =over 4
2561    
2562    =item keywordString
2563    
2564    Keyword string specified as a parameter to the current search.
2565    
2566    =item required
2567    
2568    TRUE if there must be at least one keyword specified, else FALSE.
2569    
2570    =item RETURN
2571    
2572    Returns TRUE if the keyword string is valid, else FALSE. Note that a null keyword string
2573    is acceptable if the I<$required> parameter is not specified.
2574    
2575    =back
2576    
2577    =cut
2578    
2579    sub ValidateKeywords {
2580        # Get the parameters.
2581        my ($self, $keywordString, $required) = @_;
2582        # Declare the return variable.
2583        my $retVal = 0;
2584        my @wordList = split /\s+/, $keywordString;
2585        # Right now our only real worry is a list of all minus words. The problem with it is that
2586        # it will return an incorrect result.
2587        my @plusWords = grep { $_ =~ /^[^\-]/ } @wordList;
2588        if (! @wordList) {
2589            if ($required) {
2590                $self->SetMessage("No search words specified.");
2591            } else {
2592                $retVal = 1;
2593            }
2594        } elsif (! @plusWords) {
2595            $self->SetMessage("At least one keyword must be positive. All the keywords entered are preceded by minus signs.");
2596        } else {
2597            $retVal = 1;
2598      }      }
2599      # Return the result.      # Return the result.
2600      return $retVal;      return $retVal;
2601  }  }
2602    
2603    =head3 FakeButton
2604    
2605    C<< my $html = SearchHelper::FakeButton($caption, $url, $target, %parms); >>
2606    
2607    Create a fake button that hyperlinks to the specified URL with the specified parameters.
2608    Unlike a real button, this one won't visibly click, but it will take the user to the
2609    correct place.
2610    
2611    The parameters of this method are deliberately identical to L</Formlet> so that we
2612    can switch easily from real buttons to fake ones in the code.
2613    
2614    =over 4
2615    
2616    =item caption
2617    
2618    Caption to be put on the button.
2619    
2620    =item url
2621    
2622    URL for the target page or script.
2623    
2624    =item target
2625    
2626    Frame or target in which the new page should appear. If C<undef> is specified,
2627    the default target will be used.
2628    
2629    =item parms
2630    
2631    Hash containing the parameter names as keys and the parameter values as values.
2632    These will be appended to the URL.
2633    
2634    =back
2635    
2636    =cut
2637    
2638    sub FakeButton {
2639        # Get the parameters.
2640        my ($caption, $url, $target, %parms) = @_;
2641        # Declare the return variable.
2642        my $retVal;
2643        # Compute the target URL.
2644        my $targetUrl = "$url?" . join(";", map { "$_=" . uri_escape($parms{$_}) } keys %parms);
2645        # Compute the target-frame HTML.
2646        my $targetHtml = ($target ? " target=\"$target\"" : "");
2647        # Assemble the result.
2648        return "<a href=\"$targetUrl\" $targetHtml><div class=\"button2 button\">$caption</div></a>";
2649    }
2650    
2651    =head3 Formlet
2652    
2653    C<< my $html = SearchHelper::Formlet($caption, $url, $target, %parms); >>
2654    
2655    Create a mini-form that posts to the specified URL with the specified parameters. The
2656    parameters will be stored in hidden fields, and the form's only visible control will
2657    be a submit button with the specified caption.
2658    
2659    Note that we don't use B<CGI.pm> services here because they generate forms with extra characters
2660    and tags that we don't want to deal with.
2661    
2662    =over 4
2663    
2664    =item caption
2665    
2666    Caption to be put on the form button.
2667    
2668    =item url
2669    
2670    URL to be put in the form's action parameter.
2671    
2672    =item target
2673    
2674    Frame or target in which the form results should appear. If C<undef> is specified,
2675    the default target will be used.
2676    
2677    =item parms
2678    
2679    Hash containing the parameter names as keys and the parameter values as values.
2680    
2681    =back
2682    
2683    =cut
2684    
2685    sub Formlet {
2686        # Get the parameters.
2687        my ($caption, $url, $target, %parms) = @_;
2688        # Compute the target HTML.
2689        my $targetHtml = ($target ? " target=\"$target\"" : "");
2690        # Start the form.
2691        my $retVal = "<form method=\"POST\" action=\"$url\"$target>";
2692        # Add the parameters.
2693        for my $parm (keys %parms) {
2694            $retVal .= "<input type=\"hidden\" name=\"$parm\" value=\"$parms{$parm}\" />";
2695        }
2696        # Put in the button.
2697        $retVal .= "<input type=\"submit\" name=\"submit\" value=\"$caption\" class=\"button\" />";
2698        # Close the form.
2699        $retVal .= "</form>";
2700        # Return the result.
2701        return $retVal;
2702    }
2703    
2704    =head2 Virtual Methods
2705    
2706    =head3 Form
2707    
2708    C<< my $html = $shelp->Form(); >>
2709    
2710    Generate the HTML for a form to request a new search.
2711    
2712    =head3 Find
2713    
2714    C<< my $resultCount = $shelp->Find(); >>
2715    
2716    Conduct a search based on the current CGI query parameters. The search results will
2717    be written to the session cache file and the number of results will be
2718    returned. If the search parameters are invalid, a result count of C<undef> will be
2719    returned and a result message will be stored in this object describing the problem.
2720    
2721    =head3 Description
2722    
2723    C<< my $htmlText = $shelp->Description(); >>
2724    
2725    Return a description of this search. The description is used for the table of contents
2726    on the main search tools page. It may contain HTML, but it should be character-level,
2727    not block-level, since the description is going to appear in a list.
2728    
2729    =head3 SortKey
2730    
2731    C<< my $key = $shelp->SortKey($fdata); >>
2732    
2733    Return the sort key for the specified feature data. The default is to sort by feature name,
2734    floating NMPDR organisms to the top. If a full-text search is used, then the default
2735    sort is by relevance followed by feature name. This sort may be overridden by the
2736    search class to provide fancier functionality. This method is called by
2737    B<PutFeature>, so it is only used for feature searches. A non-feature search
2738    would presumably have its own sort logic.
2739    
2740    =over 4
2741    
2742    =item record
2743    
2744    The C<FeatureData> containing the current feature.
2745    
2746    =item RETURN
2747    
2748    Returns a key field that can be used to sort this row in among the results.
2749    
2750    =back
2751    
2752    =cut
2753    
2754    sub SortKey {
2755        # Get the parameters.
2756        my ($self, $fdata) = @_;
2757        # Get the feature ID from the record.
2758        my $fid = $fdata->FID();
2759        # Get the group from the feature ID.
2760        my $group = $self->FeatureGroup($fid);
2761        # Ask the feature query object to form the sort key.
2762        my $retVal = $fdata->SortKey($self, $group);
2763        # Return the result.
2764        return $retVal;
2765    }
2766    
2767  1;  1;

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