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revision 1.2, Wed Sep 27 16:55:38 2006 UTC revision 1.13, Fri Nov 3 00:40:16 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 139  Line 154 
154    
155  =item 1  =item 1
156    
157  L</NmpdrGenomeMenu> generates a control for selecting one or more genomes.  L</NmpdrGenomeMenu> generates a control for selecting one or more genomes. Use
158    L</GetGenomes> to retrieve all the genomes passed in for a specified parameter
159    name. Note that as an assist to people working with GET-style links, if no
160    genomes are specified and the incoming request style is GET, all genomes will
161    be returned.
162    
163  =item 2  =item 2
164    
# Line 195  Line 214 
214                      }                      }
215                  }                  }
216              }              }
         }  
217          # Close the session file.          # Close the session file.
218          $self->CloseSession();          $self->CloseSession();
219            }
220          # Return the result count.          # Return the result count.
221          return $retVal;          return $retVal;
222      }      }
# Line 218  Line 237 
237  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
238  the number of items found.  the number of items found.
239    
 =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.  
   
240  =cut  =cut
241    
242  # 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.
# Line 298  Line 292 
292                    orgs => {},                    orgs => {},
293                    name => $formName,                    name => $formName,
294                    scriptQueue => [],                    scriptQueue => [],
295                      genomeList => undef,
296                      genomeParms => [],
297                      filtered => 0,
298                   };                   };
299      # Bless and return it.      # Bless and return it.
300      bless $retVal, $class;      bless $retVal, $class;
# Line 319  Line 316 
316      return $self->{query};      return $self->{query};
317  }  }
318    
319    
320    
321  =head3 DB  =head3 DB
322    
323  C<< my $sprout = $shelp->DB(); >>  C<< my $sprout = $shelp->DB(); >>
# Line 610  Line 609 
609    
610  =head3 PutFeature  =head3 PutFeature
611    
612  C<< $shelp->PutFeature($fquery); >>  C<< $shelp->PutFeature($fdata); >>
613    
614  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
615  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 620 
620  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
621  code adds columns for essentiality and virulence.  code adds columns for essentiality and virulence.
622    
623      $fq->AddExtraColumns(essential => $essentialFlag, virulence => $vfactor);      $fd->AddExtraColumns(essential => $essentialFlag, virulence => $vfactor);
624      $shelp->PutFeature($fq);      $shelp->PutFeature($fd);
625    
626  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
627  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 631 
631      if (! $essentialFlag) {      if (! $essentialFlag) {
632          $essentialFlag = undef;          $essentialFlag = undef;
633      }      }
634      $fq->AddExtraColumns(essential => $essentialFlag, virulence => $vfactor);      $fd->AddExtraColumns(essential => $essentialFlag, virulence => $vfactor);
635      $shelp->PutFeature($fq);      $shelp->PutFeature($fd);
636    
637  =over 4  =over 4
638    
639  =item fquery  =item fdata
640    
641  FeatureQuery object containing the current feature data.  B<FeatureData> object containing the current feature data.
642    
643  =back  =back
644    
# Line 647  Line 646 
646    
647  sub PutFeature {  sub PutFeature {
648      # Get the parameters.      # Get the parameters.
649      my ($self, $fq) = @_;      my ($self, $fd) = @_;
650        # Get the CGI query object.
651        my $cgi = $self->Q();
652      # Get the feature data.      # Get the feature data.
653      my $record = $fq->Feature();      my $record = $fd->Feature();
654      my $extraCols = $fq->ExtraCols();      my $extraCols = $fd->ExtraCols();
655      # Check for a first-call situation.      # Check for a first-call situation.
656      if (! defined $self->{cols}) {      if (! defined $self->{cols}) {
657          # Here we need to set up the column information. Start with the defaults.          # Here we need to set up the column information. Start with the defaults.
658          $self->{cols} = $self->DefaultFeatureColumns();          $self->{cols} = $self->DefaultFeatureColumns();
659            # Add any additional columns requested by the feature filter.
660            push @{$self->{cols}}, FeatureQuery::AdditionalColumns($self);
661          # Append the extras, sorted by column name.          # Append the extras, sorted by column name.
662          for my $col (sort keys %{$extraCols}) {          for my $col (sort keys %{$extraCols}) {
663              push @{$self->{cols}}, "X=$col";              push @{$self->{cols}}, "X=$col";
# Line 664  Line 667 
667          $self->WriteColumnHeaders(map { $self->FeatureColumnTitle($_) } @{$self->{cols}});          $self->WriteColumnHeaders(map { $self->FeatureColumnTitle($_) } @{$self->{cols}});
668      }      }
669      # Get the feature ID.      # Get the feature ID.
670      my ($fid) = $record->Value('Feature(id)');      my $fid = $fd->FID();
671      # Loop through the column headers, producing the desired data.      # Loop through the column headers, producing the desired data.
672      my @output = ();      my @output = ();
673      for my $colName (@{$self->{cols}}) {      for my $colName (@{$self->{cols}}) {
674          push @output, $self->FeatureColumnValue($colName, $record, $extraCols);          push @output, $self->FeatureColumnValue($colName, $record, $extraCols);
675      }      }
676      # 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
677      # top of the return list.      # top of the return list.
678      my $group = $self->FeatureGroup($fid);      my $key = $self->SortKey($fd);
     my $key = ($group ? "A$group" : "ZZ");  
679      # Write the feature data.      # Write the feature data.
680      $self->WriteColumnData($key, @output);      $self->WriteColumnData($key, @output);
681  }  }
# Line 754  Line 756 
756      # Check for an open session file.      # Check for an open session file.
757      if (defined $self->{fileHandle}) {      if (defined $self->{fileHandle}) {
758          # We found one, so close it.          # We found one, so close it.
759            Trace("Closing session file.") if T(2);
760          close $self->{fileHandle};          close $self->{fileHandle};
761      }      }
762  }  }
# Line 771  Line 774 
774      my $retVal;      my $retVal;
775      # Get a digest encoder.      # Get a digest encoder.
776      my $md5 = Digest::MD5->new();      my $md5 = Digest::MD5->new();
777      # 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
778      if (open(R, "/dev/urandom")) {      # actually two numbers, and we get them both because we're in list
779          my $b;      # context.
780          read(R, $b, 1024);      $md5->add($$, $ENV{REMOTE_ADDR}, $ENV{REMOTE_PORT}, gettimeofday());
781          $md5->add($b);      # Hash up all this identifying data.
782      }      $retVal = $md5->hexdigest();
783      # Add the PID and the time stamp.      # Return the result.
     $md5->add($$, 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.  
784      return $retVal;      return $retVal;
785  }  }
786    
# Line 827  Line 824 
824                                                      ['Genome(genus)', 'Genome(species)',                                                      ['Genome(genus)', 'Genome(species)',
825                                                       'Genome(unique-characterization)',                                                       'Genome(unique-characterization)',
826                                                       'Genome(primary-group)']);                                                       'Genome(primary-group)']);
827          # Null out the supporting group.          # Format and cache the name and display group.
828          $group = "" if ($group eq $FIG_Config::otherGroup);          ($orgName, $group) = $self->SaveOrganismData($group, $genomeID, $genus, $species,
829          # 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, $group];  
830      }      }
831      # Return the result.      # Return the result.
832      return ($orgName, $group);      return ($orgName, $group);
# Line 942  Line 928 
928      } else {      } else {
929          # Here we can get its genome data.          # Here we can get its genome data.
930          $retVal = $self->Organism($genomeID);          $retVal = $self->Organism($genomeID);
931          # Append the type and number.          # Append the FIG ID.
932          $retVal .= " [$type $num]";          $retVal .= " [$fid]";
933      }      }
934      # Return the result.      # Return the result.
935      return $retVal;      return $retVal;
# Line 991  Line 977 
977      my ($self, $incomingType, $desiredType, $sequence) = @_;      my ($self, $incomingType, $desiredType, $sequence) = @_;
978      # Declare the return variable. If an error occurs, it will remain undefined.      # Declare the return variable. If an error occurs, it will remain undefined.
979      my $retVal;      my $retVal;
980        # This variable will be cleared if an error is detected.
981        my $okFlag = 1;
982      # Create variables to hold the FASTA label and data.      # Create variables to hold the FASTA label and data.
983      my ($fastaLabel, $fastaData);      my ($fastaLabel, $fastaData);
984        Trace("FASTA incoming type is $incomingType, desired type is $desiredType.") if T(4);
985      # Check for a feature specification.      # Check for a feature specification.
986      if ($sequence =~ /^\s*(\w+\|\S+)\s*$/) {      if ($sequence =~ /^\s*(\w+\|\S+)\s*$/) {
987          # 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
988          # it.          # it.
989          my $fid = $1;          my $fid = $1;
990            Trace("Feature ID for fasta is $fid.") if T(3);
991          my $sprout = $self->DB();          my $sprout = $self->DB();
992          # Get the FIG ID. Note that we only use the first feature found. We are not          # Get the FIG ID. Note that we only use the first feature found. We are not
993          # supposed to have redundant aliases, though we may have an ID that doesn't          # supposed to have redundant aliases, though we may have an ID that doesn't
# Line 1005  Line 995 
995          my ($figID) = $sprout->FeaturesByAlias($fid);          my ($figID) = $sprout->FeaturesByAlias($fid);
996          if (! $figID) {          if (! $figID) {
997              $self->SetMessage("No feature found with the ID \"$fid\".");              $self->SetMessage("No feature found with the ID \"$fid\".");
998                $okFlag = 0;
999          } else {          } else {
1000              # Set the FASTA label.              # Set the FASTA label.
1001              my $fastaLabel = $fid;              my $fastaLabel = $fid;
1002              # Now proceed according to the sequence type.              # Now proceed according to the sequence type.
1003              if ($desiredType =~ /prot/i) {              if ($desiredType eq 'prot') {
1004                  # We want protein, so get the translation.                  # We want protein, so get the translation.
1005                  $fastaData = $sprout->FeatureTranslation($figID);                  $fastaData = $sprout->FeatureTranslation($figID);
1006                    Trace(length $fastaData . " characters returned for translation of $fastaLabel.") if T(3);
1007              } else {              } else {
1008                  # 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.
1009                  my @locList = $sprout->FeatureLocation($figID);                  my @locList = $sprout->FeatureLocation($figID);
1010                  $fastaData = $sprout->DNASeq(\@locList);                  $fastaData = $sprout->DNASeq(\@locList);
1011                    Trace(length $fastaData . " characters returned for DNA of $fastaLabel.") if T(3);
1012              }              }
1013          }          }
1014      } elsif ($incomingType =~ /prot/ && $desiredType =~ /dna/) {      } elsif ($incomingType eq 'prot' && $desiredType eq 'dna') {
1015          # Here we're being asked to do an impossible conversion.          # Here we're being asked to do an impossible conversion.
1016          $self->SetMessage("Cannot convert a protein sequence to DNA.");          $self->SetMessage("Cannot convert a protein sequence to DNA.");
1017            $okFlag = 0;
1018      } else {      } else {
1019            Trace("Analyzing FASTA sequence.") if T(4);
1020          # Here we are expecting a FASTA. We need to see if there's a label.          # Here we are expecting a FASTA. We need to see if there's a label.
1021          if ($sequence =~ /^>\s*(\S.*)\s*\n(.+)$/) {          if ($sequence =~ /^>[\n\s]*(\S[^\n]*)\n(.+)$/s) {
1022                Trace("Label \"$1\" found in match to sequence:\n$sequence") if T(4);
1023              # Here we have a label, so we split it from the data.              # Here we have a label, so we split it from the data.
1024              $fastaLabel = $1;              $fastaLabel = $1;
1025              $fastaData = $2;              $fastaData = $2;
1026          } else {          } else {
1027                Trace("No label found in match to sequence:\n$sequence") if T(4);
1028              # 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
1029              # as data.              # as data.
1030              $fastaLabel = "User-specified $incomingType sequence";              $fastaLabel = "User-specified $incomingType sequence";
# Line 1040  Line 1037 
1037          # we've already prevented a conversion from protein to DNA.          # we've already prevented a conversion from protein to DNA.
1038          if ($incomingType ne $desiredType) {          if ($incomingType ne $desiredType) {
1039              $fastaData = Sprout::Protein($fastaData);              $fastaData = Sprout::Protein($fastaData);
1040                # Check for bad characters.
1041                if ($fastaData =~ /X/) {
1042                    $self->SetMessage("Invalid characters detected. Is the input really of type $incomingType?");
1043                    $okFlag = 0;
1044                }
1045            } elsif ($desiredType eq 'dna' && $fastaData =~ /[^agct]/i) {
1046                $self->SetMessage("Invaid characters detected. Is the input really a DNA sequence?");
1047                $okFlag = 0;
1048          }          }
1049      }      }
1050      # At this point, either "$fastaLabel" and "$fastaData" have values or an error is      Trace("FASTA data sequence: $fastaData") if T(4);
1051      # in progress.      # Only proceed if no error was detected.
1052      if (defined $fastaLabel) {      if ($okFlag) {
1053          # 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
1054          # grep-split trick. The split, because of the presence of the parentheses,          # grep-split trick. The split, because of the presence of the parentheses,
1055          # includes the matched delimiters in the output list. The grep strips out          # includes the matched delimiters in the output list. The grep strips out
1056          # the empty list items that appear between the so-called delimiters, since          # the empty list items that appear between the so-called delimiters, since
1057          # the delimiters are what we want.          # the delimiters are what we want.
1058          my @chunks = grep { $_ } split /(.{1,60})/, $fastaData;          my @chunks = grep { $_ } split /(.{1,60})/, $fastaData;
1059          my $retVal = join("\n", ">$fastaLabel", @chunks, "");          $retVal = join("\n", ">$fastaLabel", @chunks, "");
1060      }      }
1061      # Return the result.      # Return the result.
1062      return $retVal;      return $retVal;
# Line 1059  Line 1064 
1064    
1065  =head3 NmpdrGenomeMenu  =head3 NmpdrGenomeMenu
1066    
1067  C<< my $htmlText = $shelp->NmpdrGenomeMenu($menuName, \%options, \@selected); >>  C<< my $htmlText = $shelp->NmpdrGenomeMenu($menuName, $multiple, \@selected, $rows); >>
1068    
1069  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
1070  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 1076 
1076    
1077  Name to give to the menu.  Name to give to the menu.
1078    
1079  =item options  =item multiple
1080    
1081  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.  
1082    
1083  =item selected  =item selected
1084    
# Line 1084  Line 1086 
1086  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
1087  list is empty, nothing will be pre-selected.  list is empty, nothing will be pre-selected.
1088    
1089    =item rows (optional)
1090    
1091    Number of rows to display. If omitted, the default is 1 for a single-select list
1092    and 10 for a multi-select list.
1093    
1094    =item crossMenu (optional)
1095    
1096    If specified, is presumed to be the name of another genome menu whose contents
1097    are to be mutually exclusive with the contents of this menu. As a result, instead
1098    of the standard onChange event, the onChange event will deselect any entries in
1099    the other menu.
1100    
1101  =item RETURN  =item RETURN
1102    
1103  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 1108 
1108    
1109  sub NmpdrGenomeMenu {  sub NmpdrGenomeMenu {
1110      # Get the parameters.      # Get the parameters.
1111      my ($self, $menuName, $options, $selected) = @_;      my ($self, $menuName, $multiple, $selected, $rows, $cross) = @_;
1112      # Get the Sprout and CGI objects.      # Get the Sprout and CGI objects.
1113      my $sprout = $self->DB();      my $sprout = $self->DB();
1114      my $cgi = $self->Q();      my $cgi = $self->Q();
1115        # Compute the row count.
1116        if (! defined $rows) {
1117            $rows = ($multiple ? 10 : 1);
1118        }
1119        # Create the multiple tag.
1120        my $multipleTag = ($multiple ? " multiple" : "");
1121      # Get the form name.      # Get the form name.
1122      my $formName = $self->FormName();      my $formName = $self->FormName();
1123        # Check to see if we already have a genome list in memory.
1124        my $genomes = $self->{genomeList};
1125        my $groupHash;
1126        if (defined $genomes) {
1127            # We have a list ready to use.
1128            $groupHash = $genomes;
1129        } else {
1130      # 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
1131      # 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
1132      # take advantage of an existing index.      # take advantage of an existing index.
# Line 1111  Line 1138 
1138      # 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
1139      # 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
1140      # name.      # name.
1141      my %groupHash = ();          my %gHash = ();
1142      for my $genome (@genomeList) {      for my $genome (@genomeList) {
1143          # Get the genome data.          # Get the genome data.
1144          my ($group, $genomeID, $genus, $species, $strain) = @{$genome};          my ($group, $genomeID, $genus, $species, $strain) = @{$genome};
1145          # Form the genome name.              # Compute and cache its name and display group.
1146          my $name = "$genus $species";              my ($name, $displayGroup) = $self->SaveOrganismData($group, $genomeID, $genus, $species,
1147          if ($strain) {                                                                  $strain);
1148              $name .= " $strain";              # Push the genome into the group's list. Note that we use the real group
1149          }              # name here, not the display group name.
1150          # Push the genome into the group's list.              push @{$gHash{$group}}, [$genomeID, $name];
1151          push @{$groupHash{$group}}, [$genomeID, $name];          }
1152            # Save the genome list for future use.
1153            $self->{genomeList} = \%gHash;
1154            $groupHash = \%gHash;
1155      }      }
1156      # 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
1157      # the supporting-genome group last.      # the supporting-genome group last.
1158      my @groups = sort grep { $_ ne $FIG_Config::otherGroup } keys %groupHash;      my @groups = sort grep { $_ ne $FIG_Config::otherGroup } keys %{$groupHash};
1159      push @groups, $FIG_Config::otherGroup;      push @groups, $FIG_Config::otherGroup;
1160      # 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
1161      my %selectedHash = map { $_ => 1 } @{$selected};      # with the possibility of undefined values in the incoming list.
1162      # Now it gets complicated. We need a way to mark all the NMPDR genomes.      my %selectedHash = ();
1163        if (defined $selected) {
1164            %selectedHash = map { $_ => 1 } grep { defined($_) } @{$selected};
1165        }
1166        # Now it gets complicated. We need a way to mark all the NMPDR genomes. We take advantage
1167        # of the fact they come first in the list. We'll accumulate a count of the NMPDR genomes
1168        # and use that to make the selections.
1169        my $nmpdrCount = 0;
1170      # Create the type counters.      # Create the type counters.
1171      my $groupCount = 1;      my $groupCount = 1;
1172      # Compute the ID for the status display.      # Compute the ID for the status display.
# Line 1138  Line 1175 
1175      my $showSelect = "showSelected($menuName, '$divID', 1000);";      my $showSelect = "showSelected($menuName, '$divID', 1000);";
1176      # If multiple selection is supported, create an onChange event.      # If multiple selection is supported, create an onChange event.
1177      my $onChange = "";      my $onChange = "";
1178      if ($options->{multiple}) {      if ($cross) {
1179            # Here we have a paired menu. Selecting something in our menu unselects it in the
1180            # other and redisplays the status of both.
1181            $onChange = " onChange=\"crossUnSelect($menuName, '$divID', $cross, '${formName}_${cross}_status', 1000)\"";
1182        } elsif ($multiple) {
1183            # This is an unpaired menu, so all we do is redisplay our status.
1184          $onChange = " onChange=\"$showSelect\"";          $onChange = " onChange=\"$showSelect\"";
1185      }      }
1186      # Create the SELECT tag and stuff it into the output array.      # Create the SELECT tag and stuff it into the output array.
1187      my $select = "<" . join(" ", "SELECT name=\"$menuName\"$onChange", map { " $_=\"$options->{$_}\"" } keys %{$options}) . ">";      my @lines = ("<SELECT name=\"$menuName\"$onChange$multipleTag size=\"$rows\">");
     my @lines = ($select);  
1188      # Loop through the groups.      # Loop through the groups.
1189      for my $group (@groups) {      for my $group (@groups) {
1190          # Create the option group tag.          # Create the option group tag.
1191          my $tag = "<OPTGROUP label=\"$group\">";          my $tag = "<OPTGROUP label=\"$group\">";
1192          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");  
1193          # Get the genomes in the group.          # Get the genomes in the group.
1194          for my $genome (@{$groupHash{$group}}) {          for my $genome (@{$groupHash->{$group}}) {
1195                # Count this organism if it's NMPDR.
1196                if ($group ne $FIG_Config::otherGroup) {
1197                    $nmpdrCount++;
1198                }
1199                # Get the organism ID and name.
1200              my ($genomeID, $name) = @{$genome};              my ($genomeID, $name) = @{$genome};
1201              # See if it's selected.              # See if it's selected.
1202              my $select = ($selectedHash{$genomeID} ? " selected" : "");              my $select = ($selectedHash{$genomeID} ? " selected" : "");
1203              # Generate the option tag.              # Generate the option tag.
1204              my $optionTag = "<OPTION value=\"$genomeID\" label=\"$label\"$select>$name <em>($genomeID)</em></OPTION>";              my $optionTag = "<OPTION value=\"$genomeID\"$select>$name <em>($genomeID)</em></OPTION>";
1205              push @lines, "    $optionTag";              push @lines, "    $optionTag";
1206          }          }
1207          # Close the option group.          # Close the option group.
# Line 1170  Line 1210 
1210      # Close the SELECT tag.      # Close the SELECT tag.
1211      push @lines, "</SELECT>";      push @lines, "</SELECT>";
1212      # Check for multiple selection.      # Check for multiple selection.
1213      if ($options->{multiple}) {      if ($multiple) {
1214          # Since multi-select is on, we can set up some buttons to set and clear selections.          # Since multi-select is on, we set up some buttons to set and clear selections.
1215          push @lines, "<br />";          push @lines, "<br />";
1216          push @lines, "<INPUT type=\"button\" name=\"SelectAll\" class=\"bigButton\" value=\"Select All\" onClick=\"selectAll($menuName); $showSelect\" />";          push @lines, "<INPUT type=\"button\" name=\"SelectAll\" class=\"bigButton\" value=\"Select All\" onClick=\"selectAll($menuName); $showSelect\" />";
1217          push @lines, "<INPUT type=\"button\" name=\"ClearAll\" class=\"bigButton\"  value=\"Clear All\" onClick=\"clearAll($menuName); $showSelect\" />";          push @lines, "<INPUT type=\"button\" name=\"ClearAll\" class=\"bigButton\"  value=\"Clear All\" onClick=\"clearAll($menuName); $showSelect\" />";
1218          push @lines, "<INPUT type=\"button\" name=\"NMPDROnly\" class=\"bigButton\"  value=\"Select NMPDR\" onClick=\"selectSome($menuName, 'nmpdr'); $showSelect\" />";          push @lines, "<INPUT type=\"button\" name=\"NMPDROnly\" class=\"bigButton\"  value=\"Select NMPDR\" onClick=\"selectSome($menuName, $nmpdrCount, true); $showSelect\" />";
1219          push @lines, "<INPUT type=\"button\" name=\"OtherOnly\" class=\"bigButton\" value=\"Select Supporting\" onClick=\"selectSome($menuName, 'other'); $showSelect\" />";          push @lines, "<INPUT type=\"button\" name=\"OtherOnly\" class=\"bigButton\" value=\"Select Supporting\" onClick=\"selectSome($menuName, $nmpdrCount, false); $showSelect\" />";
1220            # Now add the search box. This allows the user to type text and have all genomes containing
1221            # the text selected automatically.
1222            my $searchThingName = "${menuName}_SearchThing";
1223            push @lines, "<br>Select genomes containing <INPUT type=\"text\" name=\"$searchThingName\" size=\"30\" />&nbsp;" .
1224                         "<INPUT type=\"button\" name=\"Select\" class=\"button\" value=\"Search\" onClick=\"selectViaSearch($menuName, $searchThingName); $showSelect\" />";
1225          # Add the status display, too.          # Add the status display, too.
1226          push @lines, "<DIV id=\"$divID\" class=\"selectStatus\"></DIV>";          push @lines, "<DIV id=\"$divID\" class=\"selectStatus\"></DIV>";
1227          # 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 1230 
1230          # in case we decide to twiddle the parameters.          # in case we decide to twiddle the parameters.
1231          $showSelect =~ s/showSelected\(/showSelected\(thisForm\./;          $showSelect =~ s/showSelected\(/showSelected\(thisForm\./;
1232          $self->QueueFormScript($showSelect);          $self->QueueFormScript($showSelect);
1233            # Finally, add this parameter to the list of genome parameters. This enables us to
1234            # easily find all the parameters used to select one or more genomes.
1235            push @{$self->{genomeParms}}, $menuName;
1236      }      }
1237      # Assemble all the lines into a string.      # Assemble all the lines into a string.
1238      my $retVal = join("\n", @lines, "");      my $retVal = join("\n", @lines, "");
# Line 1192  Line 1240 
1240      return $retVal;      return $retVal;
1241  }  }
1242    
1243    =head3 PropertyMenu
1244    
1245    C<< my $htmlText = $shelp->PropertyMenu($menuName, $selected, $force); >>
1246    
1247    Generate a property name dropdown menu.
1248    
1249    =over 4
1250    
1251    =item menuName
1252    
1253    Name to give to the menu.
1254    
1255    =item selected
1256    
1257    Value of the property name to pre-select.
1258    
1259    =item force (optional)
1260    
1261    If TRUE, then the user will be forced to choose a property name. If FALSE,
1262    then an additional menu choice will be provided to select nothing.
1263    
1264    =item RETURN
1265    
1266    Returns a dropdown menu box that allows the user to select a property name. An additional
1267    selection entry will be provided for selecting no property name
1268    
1269    =back
1270    
1271    =cut
1272    
1273    sub PropertyMenu {
1274        # Get the parameters.
1275        my ($self, $menuName, $selected, $force) = @_;
1276        # Get the CGI and Sprout objects.
1277        my $sprout = $self->DB();
1278        my $cgi = $self->Q();
1279        # Create the property name list.
1280        my @propNames = ();
1281        if (! $force) {
1282            push @propNames, "";
1283        }
1284        # Get all the property names, putting them after the null choice if one exists.
1285        push @propNames, $sprout->GetChoices('Property', 'property-name');
1286        # Create a menu from them.
1287        my $retVal = $cgi->popup_menu(-name=> $menuName, -values => \@propNames,
1288                                      -default => $selected);
1289        # Return the result.
1290        return $retVal;
1291    }
1292    
1293  =head3 MakeTable  =head3 MakeTable
1294    
1295  C<< my $htmlText = $shelp->MakeTable(\@rows); >>  C<< my $htmlText = $shelp->MakeTable(\@rows); >>
# Line 1254  Line 1352 
1352      # Get the parameters.      # Get the parameters.
1353      my ($self) = @_;      my ($self) = @_;
1354      my $cgi = $self->Q();      my $cgi = $self->Q();
1355      # Declare the return variable.      # Get the current page size.
1356        my $pageSize = $cgi->param('PageSize');
1357        # Get the incoming external-link flag.
1358        my $aliases = ($cgi->param('ShowAliases') ? 1 : 0);
1359        # Create the row.
1360      my $retVal = $cgi->Tr($cgi->td("Results/Page"),      my $retVal = $cgi->Tr($cgi->td("Results/Page"),
1361                            $cgi->td($cgi->popup_menu(-name => 'PageSize',                            $cgi->td($cgi->popup_menu(-name => 'PageSize',
1362                                                      -values => [10, 25, 45, 100, 1000],                                                      -values => [10, 25, 50, 100, 1000],
1363                                                      -default => $cgi->param('PageSize'))),                                                      -default => $pageSize) . " " .
1364                                       $cgi->checkbox(-name => 'ShowURL',
1365                                                      -value => 1,
1366                                                      -label => 'Show URL')),
1367                            $cgi->td($cgi->submit(-class => 'goButton',                            $cgi->td($cgi->submit(-class => 'goButton',
1368                                                  -name => 'Search',                                                  -name => 'Search',
1369                                                  -value => 'Go')));                                                  -value => 'Go')));
# Line 1270  Line 1375 
1375    
1376  C<< my $htmlText = $shelp->FeatureFilterRows(); >>  C<< my $htmlText = $shelp->FeatureFilterRows(); >>
1377    
1378  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
1379  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>
1380  using the B<FeatureQuery> object.  object.
1381    
1382  =cut  =cut
1383    
# Line 1322  Line 1427 
1427          # Get the feature location string.          # Get the feature location string.
1428          my $loc = $sprout->FeatureLocation($feat);          my $loc = $sprout->FeatureLocation($feat);
1429          # Compute the contig, start, and stop points.          # Compute the contig, start, and stop points.
1430          my($start, $stop, $contig) = BasicLocation::Parse($loc);          my($contig, $start, $stop) = BasicLocation::Parse($loc);
1431            Trace("Start and stop are ($start,$stop) on contig $contig.") if T(3);
1432          # 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
1433          # big and that we get some surrounding stuff.          # big and that we get some surrounding stuff.
1434          my $mid = int(($start + $stop) / 2);          my $mid = int(($start + $stop) / 2);
# Line 1352  Line 1458 
1458          }          }
1459          my $seg_id = $contig;          my $seg_id = $contig;
1460          $seg_id =~ s/:/--/g;          $seg_id =~ s/:/--/g;
1461            Trace("Show limits are ($show_start,$show_stop) in genome $genomeID with ref $seg_id.") if T(3);
1462          # Assemble all the pieces.          # Assemble all the pieces.
1463          $retVal = "gbrowse.cgi/GB_$genomeID?ref=$seg_id&start=$show_start&stop=$show_stop";          $retVal = "gbrowse.cgi/GB_$genomeID?ref=$seg_id&start=$show_start&stop=$show_stop";
1464      }      }
# Line 1359  Line 1466 
1466      return $retVal;      return $retVal;
1467  }  }
1468    
1469    =head3 GetGenomes
1470    
1471    C<< my @genomeList = $shelp->GetGenomes($parmName); >>
1472    
1473    Return the list of genomes specified by the specified CGI query parameter.
1474    If the request method is POST, then the list of genome IDs is returned
1475    without preamble. If the request method is GET and the parameter is not
1476    specified, then it is treated as a request for all genomes. This makes it
1477    easier for web pages to link to a search that wants to specify all genomes.
1478    
1479    =over 4
1480    
1481    =item parmName
1482    
1483    Name of the parameter containing the list of genomes. This will be the
1484    first parameter passed to the L</NmpdrGenomeMenu> call that created the
1485    genome selection control on the form.
1486    
1487    =item RETURN
1488    
1489    Returns a list of the genomes to process.
1490    
1491    =back
1492    
1493    =cut
1494    
1495    sub GetGenomes {
1496        # Get the parameters.
1497        my ($self, $parmName) = @_;
1498        # Get the CGI query object.
1499        my $cgi = $self->Q();
1500        # Get the list of genome IDs in the request header.
1501        my @retVal = $cgi->param($parmName);
1502        Trace("Genome list for $parmName is (" . join(", ", @retVal) . ") with method " . $cgi->request_method() . ".") if T(3);
1503        # Check for the special GET case.
1504        if ($cgi->request_method() eq "GET" && ! @retVal) {
1505            # Here the caller wants all the genomes.
1506            my $sprout = $self->DB();
1507            @retVal = $sprout->Genomes();
1508        }
1509        # Return the result.
1510        return @retVal;
1511    }
1512    
1513    =head3 GetHelpText
1514    
1515    C<< my $htmlText = $shelp->GetHelpText(); >>
1516    
1517    Get the help text for this search. The help text is stored in files on the template
1518    server. The help text for a specific search is taken from a file named
1519    C<SearchHelp_>I<class>C<.inc> in the template directory C<$FIG_Config::template_url>.
1520    There are also three standard help files: C<SearchHelp1_Filtering.inc> describes the
1521    feature filtering performed by the B<FeatureQuery> object, C<SearchHelp1_GenomeControl.inc>
1522    describes how to use a multiple-selection genome control, and C<SearchHelp1_Standard.inc>
1523    describes the standard controls for a search, such as page size, URL display, and
1524    external alias display.
1525    
1526    =cut
1527    
1528    sub GetHelpText {
1529        # Get the parameters.
1530        my ($self) = @_;
1531        # Create a list to hold the pieces of the help.
1532        my @helps = ();
1533        # Get the template directory URL.
1534        my $urlBase = $FIG_Config::template_url;
1535        # Start with the specific help.
1536        my $class = $self->{class};
1537        push @helps, PageBuilder::GetPage("$urlBase/SearchHelp_$class.inc");
1538        # Add the genome control help if needed.
1539        if (scalar @{$self->{genomeParms}}) {
1540            push @helps, PageBuilder::GetPage("$urlBase/SearchHelp1_GenomeControl.inc");
1541        }
1542        # Next the filter help.
1543        if ($self->{filtered}) {
1544            push @helps, PageBuilder::GetPage("$urlBase/SearchHelp1_Filtering.inc");
1545        }
1546        # Finally, the standard help.
1547        push @helps, PageBuilder::GetPage("$urlBase/SearchHelp1_Standard.inc");
1548        # Assemble the pieces.
1549        my $retVal = join("\n<p>&nbsp;</p>\n", @helps);
1550        # Return the result.
1551        return $retVal;
1552    }
1553    
1554    =head3 ComputeSearchURL
1555    
1556    C<< my $url = $shelp->ComputeSearchURL(); >>
1557    
1558    Compute the GET-style URL for the current search. In order for this to work, there
1559    must be a copy of the search form on the current page. This will always be the
1560    case if the search is coming from C<SearchSkeleton.cgi>.
1561    
1562    A little expense is involved in order to make the URL as smart as possible. The
1563    main complication is that if the user specified all genomes, we'll want to
1564    remove the parameter entirely from a get-style URL.
1565    
1566    =cut
1567    
1568    sub ComputeSearchURL {
1569        # Get the parameters.
1570        my ($self) = @_;
1571        # Get the database and CGI query object.
1572        my $cgi = $self->Q();
1573        my $sprout = $self->DB();
1574        # Start with the full URL.
1575        my $retVal = $cgi->url(-full => 1);
1576        # Get all the query parameters in a hash.
1577        my %parms = $cgi->Vars();
1578        # Now we need to do some fixing. Each multi-valued parameter is encoded as a string with null
1579        # characters separating the individual values. We have to convert those to lists. In addition,
1580        # the multiple-selection genome parameters and the feature type parameter must be checked to
1581        # determine whether or not they can be removed from the URL. First, we get a list of the
1582        # genome parameters and a list of all genomes. Note that we only need the list if a
1583        # multiple-selection genome parameter has been found on the form.
1584        my %genomeParms = map { $_ => 1 } @{$self->{genomeParms}};
1585        my @genomeList;
1586        if (keys %genomeParms) {
1587            @genomeList = $sprout->Genomes();
1588        }
1589        # Create a list to hold the URL parameters we find.
1590        my @urlList = ();
1591        # Now loop through the parameters in the hash, putting them into the output URL.
1592        for my $parmKey (keys %parms) {
1593            # Get a list of the parameter values. If there's only one, we'll end up with
1594            # a singleton list, but that's okay.
1595            my @values = split (/\0/, $parms{$parmKey});
1596            # Check for special cases.
1597            if (grep { $_ eq $parmKey } qw(SessionID ResultCount Page PageSize Trace TF ShowURL)) {
1598                # These are bookkeeping parameters we don't need to start a search.
1599                @values = ();
1600            } elsif ($parmKey =~ /_SearchThing$/) {
1601                # Here the value coming in is from a genome control's search thing. It does
1602                # not affect the results of the search, so we clear it.
1603                @values = ();
1604            } elsif ($genomeParms{$parmKey}) {
1605                # Here we need to see if the user wants all the genomes. If he does,
1606                # we erase all the values just like with features.
1607                my $allFlag = $sprout->IsAllGenomes(\@values, \@genomeList);
1608                if ($allFlag) {
1609                    @values = ();
1610                }
1611            }
1612            # If we still have values, create the URL parameters.
1613            if (@values) {
1614                push @urlList, map { "$parmKey=" . uri_escape($_) } @values;
1615            }
1616        }
1617        # Add the parameters to the URL.
1618        $retVal .= "?" . join(";", @urlList);
1619        # Return the result.
1620        return $retVal;
1621    }
1622    
1623    =head3 GetRunTimeValue
1624    
1625    C<< my $htmlText = $shelp->GetRunTimeValue($text); >>
1626    
1627    Compute a run-time column value.
1628    
1629    =over 4
1630    
1631    =item text
1632    
1633    The run-time column text. It consists of 2 percent signs, a column type, an equal
1634    sign, and the data for the current row.
1635    
1636    =item RETURN
1637    
1638    Returns the fully-formatted HTML text to go into the current column of the current row.
1639    
1640    =back
1641    
1642    =cut
1643    
1644    sub GetRunTimeValue {
1645        # Get the parameters.
1646        my ($self, $text) = @_;
1647        # Declare the return variable.
1648        my $retVal;
1649        # Parse the incoming text.
1650        if ($text =~ /^%%([^=]+)=(.*)$/) {
1651            $retVal = $self->RunTimeColumns($1, $2);
1652        } else {
1653            Confess("Invalid run-time column string \"$text\" encountered in session file.");
1654        }
1655        # Return the result.
1656        return $retVal;
1657    }
1658    
1659    =head3 AdvancedClassList
1660    
1661    C<< my @classes = SearchHelper::AdvancedClassList(); >>
1662    
1663    Return a list of advanced class names. This list is used to generate the directory
1664    of available searches on the search page.
1665    
1666    The reason we have to convert the list from a string is that the B<NMPDRSetup.pl>
1667    script is only able to insert strings into the generated B<FIG_Config> file.
1668    
1669    =cut
1670    
1671    sub AdvancedClassList {
1672        return split /\s+/, $FIG_Config::advanced_classes;
1673    }
1674    
1675  =head2 Feature Column Methods  =head2 Feature Column Methods
1676    
1677  The methods in this column manage feature column data. If you want to provide the  The methods in this column manage feature column data. If you want to provide the
# Line 1391  Line 1704 
1704      # Get the parameters.      # Get the parameters.
1705      my ($self) = @_;      my ($self) = @_;
1706      # Return the result.      # Return the result.
1707      return ['orgName', 'function', 'gblink', 'protlink'];      return ['orgName', 'function', 'gblink', 'protlink',
1708                FeatureQuery::AdditionalColumns($self)];
1709  }  }
1710    
1711  =head3 FeatureColumnTitle  =head3 FeatureColumnTitle
# Line 1423  Line 1737 
1737      if ($colName =~ /^X=(.+)$/) {      if ($colName =~ /^X=(.+)$/) {
1738          # Here we have an extra column.          # Here we have an extra column.
1739          $retVal = $1;          $retVal = $1;
     } elsif ($colName eq 'orgName') {  
         $retVal = "Name";  
     } elsif ($colName eq 'fid') {  
         $retVal = "FIG ID";  
1740      } elsif ($colName eq 'alias') {      } elsif ($colName eq 'alias') {
1741          $retVal = "External Aliases";          $retVal = "External Aliases";
1742        } elsif ($colName eq 'fid') {
1743            $retVal = "FIG ID";
1744      } elsif ($colName eq 'function') {      } elsif ($colName eq 'function') {
1745          $retVal = "Functional Assignment";          $retVal = "Functional Assignment";
1746      } elsif ($colName eq 'gblink') {      } elsif ($colName eq 'gblink') {
1747          $retVal = "GBrowse";          $retVal = "GBrowse";
     } elsif ($colName eq 'protlink') {  
         $retVal = "NMPDR Protein Page";  
1748      } elsif ($colName eq 'group') {      } elsif ($colName eq 'group') {
1749          $retVal = "NMDPR Group";          $retVal = "NMDPR Group";
1750        } elsif ($colName =~ /^keyword:(.+)$/) {
1751            $retVal = ucfirst $1;
1752        } elsif ($colName eq 'orgName') {
1753            $retVal = "Name";
1754        } elsif ($colName eq 'protlink') {
1755            $retVal = "NMPDR Protein Page";
1756        } elsif ($colName eq 'subsystem') {
1757            $retVal = "Subsystems";
1758      }      }
1759      # Return the result.      # Return the result.
1760      return $retVal;      return $retVal;
1761  }  }
1762    
1763    
1764  =head3 FeatureColumnValue  =head3 FeatureColumnValue
1765    
1766  C<< my $value = $shelp->FeatureColumnValue($colName, $fid, \%extraCols); >>  C<< my $value = $shelp->FeatureColumnValue($colName, $fid, \%extraCols); >>
# Line 1492  Line 1811 
1811          if (defined $extraCols->{$1}) {          if (defined $extraCols->{$1}) {
1812              $retVal = $extraCols->{$1};              $retVal = $extraCols->{$1};
1813          }          }
1814      } elsif ($colName eq 'orgName') {      } elsif ($colName eq 'alias') {
1815          # Here we want the formatted organism name and feature number.          # In this case, the user wants a list of external aliases for the feature.
1816          $retVal = $self->FeatureName($fid);          # These are very expensive, so we compute them when the row is displayed.
1817            $retVal = "%%alias=$fid";
1818      } elsif ($colName eq 'fid') {      } elsif ($colName eq 'fid') {
1819          # Here we have the raw feature ID. We hyperlink it to the protein page.          # Here we have the raw feature ID. We hyperlink it to the protein page.
1820          $retVal = HTML::set_prot_links($fid);          $retVal = HTML::set_prot_links($fid);
     } elsif ($colName eq 'alias') {  
         # In this case, the user wants a list of external aliases for the feature.  
         # The complicated part is we have to hyperlink them. First, get the  
         # aliases.  
         my @aliases = $sprout->FeatureAliases($fid);  
         # Only proceed if we found some.  
         if (@aliases) {  
             # Join the aliases into a comma-delimited list.  
             my $aliasList = join(", ", @aliases);  
             # Ask the HTML processor to hyperlink them.  
             $retVal = HTML::set_prot_links($aliasList);  
         }  
1821      } elsif ($colName eq 'function') {      } elsif ($colName eq 'function') {
1822          # The functional assignment is just a matter of getting some text.          # The functional assignment is just a matter of getting some text.
1823          ($retVal) = $record->Value('Feature(assignment)');          ($retVal) = $record->Value('Feature(assignment)');
# Line 1520  Line 1828 
1828                            $cgi->img({ src => "../images/button-gbrowse.png",                            $cgi->img({ src => "../images/button-gbrowse.png",
1829                                        border => 0 })                                        border => 0 })
1830                           );                           );
     } elsif ($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" },  
                           $cgi->img({ src => "../images/button-nmpdr.png",  
                                      border => 0 })  
                          );  
1831      } elsif ($colName eq 'group') {      } elsif ($colName eq 'group') {
1832          # Get the NMPDR group name.          # Get the NMPDR group name.
1833          my (undef, $group) = $self->OrganismData($fid);          my (undef, $group) = $self->OrganismData($fid);
# Line 1534  Line 1835 
1835          my $nurl = $sprout->GroupPageName($group);          my $nurl = $sprout->GroupPageName($group);
1836          $retVal = $cgi->a({ href => $nurl, title => "$group summary" },          $retVal = $cgi->a({ href => $nurl, title => "$group summary" },
1837                            $group);                            $group);
1838        } elsif ($colName =~ /^keyword:(.+)$/) {
1839            # Here we want keyword-related values. This is also expensive, so
1840            # we compute them when the row is displayed.
1841            $retVal = "%%colName=$fid";
1842        } elsif ($colName eq 'orgName') {
1843            # Here we want the formatted organism name and feature number.
1844            $retVal = $self->FeatureName($fid);
1845        } elsif ($colName eq 'protlink') {
1846            # Here we want a link to the protein page using the official NMPDR button.
1847            my $hurl = HTML::fid_link($cgi, $fid, 0, 1);
1848            $retVal = $cgi->a({ href => $hurl, title => "Protein page for $fid" },
1849                              $cgi->img({ src => "../images/button-nmpdr.png",
1850                                         border => 0 })
1851                             );
1852        }elsif ($colName eq 'subsystem') {
1853            # Another run-time column: subsystem list.
1854            $retVal = "%%subsystem=$fid";
1855        }
1856        # Return the result.
1857        return $retVal;
1858    }
1859    
1860    =head3 RunTimeColumns
1861    
1862    C<< my $htmlText = $shelp->RunTimeColumns($type, $text); >>
1863    
1864    Return the HTML text for a run-time column. Run-time columns are evaluated when the
1865    list is displayed, rather than when it is generated.
1866    
1867    =over 4
1868    
1869    =item type
1870    
1871    Type of column.
1872    
1873    =item text
1874    
1875    Data relevant to this row of the column.
1876    
1877    =item RETURN
1878    
1879    Returns the fully-formatted HTML text to go in the specified column.
1880    
1881    =back
1882    
1883    =cut
1884    
1885    sub RunTimeColumns {
1886        # Get the parameters.
1887        my ($self, $type, $text) = @_;
1888        # Declare the return variable.
1889        my $retVal = "";
1890        # Get the Sprout and CGI objects.
1891        my $sprout = $self->DB();
1892        my $cgi = $self->Q();
1893        # Separate the text into a type and data.
1894        if ($type eq 'alias') {
1895            # Here the caller wants external alias links for a feature. The text
1896            # is the feature ID.
1897            my $fid = $text;
1898            # The complicated part is we have to hyperlink them. First, get the
1899            # aliases.
1900            Trace("Generating aliases for feature $fid.") if T(4);
1901            my @aliases = $sprout->FeatureAliases($fid);
1902            # Only proceed if we found some.
1903            if (@aliases) {
1904                # Join the aliases into a comma-delimited list.
1905                my $aliasList = join(", ", @aliases);
1906                # Ask the HTML processor to hyperlink them.
1907                $retVal = HTML::set_prot_links($cgi, $aliasList);
1908            }
1909        } elsif ($type eq 'subsystem') {
1910            # Here the caller wants the subsystems in which this feature participates.
1911            # The text is the feature ID. We will list the subsystem names with links
1912            # to the subsystem's summary page.
1913            my $fid = $text;
1914            # Get the subsystems.
1915            Trace("Generating subsystems for feature $fid.") if T(4);
1916            my %subs = $sprout->SubsystemsOf($fid);
1917            # Convert them to links.
1918            my @links = map { HTML::sub_link($cgi, $_) } sort keys %subs;
1919            # String them into a list.
1920            $retVal = join(", ", @links);
1921        } elsif ($type =~ /^keyword:(.+)$/) {
1922            # Here the caller wants the value of the named keyword. The text is the
1923            # feature ID.
1924            my $keywordName = $1;
1925            my $fid = $text;
1926            # Get the attribute values.
1927            Trace("Getting $keywordName values for feature $fid.") if T(4);
1928            my @values = $sprout->GetFlat(['Feature'], "Feature(id) = ?", [$fid],
1929                                          "Feature($keywordName)");
1930            # String them into a list.
1931            $retVal = join(", ", @values);
1932      }      }
1933      # Return the result.      # Return the result.
1934      return $retVal;      return $retVal;
1935  }  }
1936    
1937    =head3 SaveOrganismData
1938    
1939    C<< my ($name, $displayGroup) = $shelp->SaveOrganismData($group, $genomeID, $genus, $species, $strain); >>
1940    
1941    Format the name of an organism and the display version of its group name. The incoming
1942    data should be the relevant fields from the B<Genome> record in the database. The
1943    data will also be stored in the genome cache for later use in posting search results.
1944    
1945    =over 4
1946    
1947    =item group
1948    
1949    Name of the genome's group as it appears in the database.
1950    
1951    =item genomeID
1952    
1953    ID of the relevant genome.
1954    
1955    =item genus
1956    
1957    Genus of the genome's organism. If undefined or null, it will be assumed the genome is not
1958    in the database. In this case, the organism name is derived from the genomeID and the group
1959    is automatically the supporting-genomes group.
1960    
1961    =item species
1962    
1963    Species of the genome's organism.
1964    
1965    =item strain
1966    
1967    Strain of the species represented by the genome.
1968    
1969    =item RETURN
1970    
1971    Returns a two-element list. The first element is the formatted genome name. The second
1972    element is the display name of the genome's group.
1973    
1974    =back
1975    
1976    =cut
1977    
1978    sub SaveOrganismData {
1979        # Get the parameters.
1980        my ($self, $group, $genomeID, $genus, $species, $strain) = @_;
1981        # Declare the return values.
1982        my ($name, $displayGroup);
1983        # If the organism does not exist, format an unknown name and a blank group.
1984        if (! defined($genus)) {
1985            $name = "Unknown Genome $genomeID";
1986            $displayGroup = "";
1987        } else {
1988            # It does exist, so format the organism name.
1989            $name = "$genus $species";
1990            if ($strain) {
1991                $name .= " $strain";
1992            }
1993            # Compute the display group. This is currently the same as the incoming group
1994            # name unless it's the supporting group, which is nulled out.
1995            $displayGroup = ($group eq $FIG_Config::otherGroup ? "" : $group);
1996        }
1997        # Cache the group and organism data.
1998        my $cache = $self->{orgs};
1999        $cache->{$genomeID} = [$name, $displayGroup];
2000        # Return the result.
2001        return ($name, $displayGroup);
2002    }
2003    
2004    =head2 Virtual Methods
2005    
2006    =head3 Form
2007    
2008    C<< my $html = $shelp->Form(); >>
2009    
2010    Generate the HTML for a form to request a new search.
2011    
2012    =head3 Find
2013    
2014    C<< my $resultCount = $shelp->Find(); >>
2015    
2016    Conduct a search based on the current CGI query parameters. The search results will
2017    be written to the session cache file and the number of results will be
2018    returned. If the search parameters are invalid, a result count of C<undef> will be
2019    returned and a result message will be stored in this object describing the problem.
2020    
2021    =head3 Description
2022    
2023    C<< my $htmlText = $shelp->Description(); >>
2024    
2025    Return a description of this search. The description is used for the table of contents
2026    on the main search tools page. It may contain HTML, but it should be character-level,
2027    not block-level, since the description is going to appear in a list.
2028    
2029    =head3 SortKey
2030    
2031    C<< my $key = $shelp->SortKey($fdata); >>
2032    
2033    Return the sort key for the specified feature data. The default is to sort by feature name,
2034    floating NMPDR organisms to the top. If a full-text search is used, then the default
2035    sort is by relevance followed by feature name. This sort may be overridden by the
2036    search class to provide fancier functionality. This method is called by
2037    B<PutFeature>, so it is only used for feature searches. A non-feature search
2038    would presumably have its own sort logic.
2039    
2040    =over 4
2041    
2042    =item record
2043    
2044    The C<FeatureData> containing the current feature.
2045    
2046    =item RETURN
2047    
2048    Returns a key field that can be used to sort this row in among the results.
2049    
2050    =back
2051    
2052    =cut
2053    
2054    sub SortKey {
2055        # Get the parameters.
2056        my ($self, $fdata) = @_;
2057        # Get the feature ID from the record.
2058        my $fid = $fdata->FID();
2059        # Get the group from the feature ID.
2060        my $group = $self->FeatureGroup($fid);
2061        # Ask the feature query object to form the sort key.
2062        my $retVal = $fdata->SortKey($self, $group);
2063        # Return the result.
2064        return $retVal;
2065    }
2066    
2067  1;  1;

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