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revision 1.10, Fri Oct 13 21:45:11 2006 UTC revision 1.13, Fri Nov 3 00:40:16 2006 UTC
# Line 609  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 620  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 631  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 646  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.      # Get the CGI query object.
651      my $cgi = $self->Q();      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} = $self->DefaultFeatureColumns();
659          # Add the externals if they were requested.          # Add any additional columns requested by the feature filter.
660          if ($cgi->param('ShowAliases')) {          push @{$self->{cols}}, FeatureQuery::AdditionalColumns($self);
             push @{$self->{cols}}, 'alias';  
         }  
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 669  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}}) {
# Line 677  Line 675 
675      }      }
676      # Compute the sort key. The sort key usually 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 $key = $self->SortKey($record);      my $key = $self->SortKey($fd);
679      # Write the feature data.      # Write the feature data.
680      $self->WriteColumnData($key, @output);      $self->WriteColumnData($key, @output);
681  }  }
# Line 979  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 = $self->DB();
992          # Get the FIG ID. Note that we only use the first feature found. We are not          # Get the FIG ID. Note that we only use the first feature found. We are not
993          # supposed to have redundant aliases, though we may have an ID that doesn't          # supposed to have redundant aliases, though we may have an ID that doesn't
# Line 993  Line 995 
995          my ($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 $incomingType sequence";
# Line 1028  Line 1037 
1037          # we've already prevented a conversion from protein to DNA.          # we've already prevented a conversion from protein to DNA.
1038          if ($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 1146  Line 1163 
1163      if (defined $selected) {      if (defined $selected) {
1164          %selectedHash = map { $_ => 1 } grep { defined($_) } @{$selected};          %selectedHash = map { $_ => 1 } grep { defined($_) } @{$selected};
1165      }      }
1166      # Now it gets complicated. We need a way to mark all the NMPDR genomes.      # 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 1156  Line 1176 
1176      # If multiple selection is supported, create an onChange event.      # If multiple selection is supported, create an onChange event.
1177      my $onChange = "";      my $onChange = "";
1178      if ($cross) {      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)\"";          $onChange = " onChange=\"crossUnSelect($menuName, '$divID', $cross, '${formName}_${cross}_status', 1000)\"";
1182      } elsif ($multiple) {      } 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 $select = "<SELECT name=\"$menuName\"$onChange$multipleTag size=\"$rows\">";      my @lines = ("<SELECT name=\"$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, so we can't use it.  
         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, "    $optionTag";
1206          }          }
1207          # Close the option group.          # Close the option group.
# Line 1194  Line 1215 
1215          push @lines, "<br />";          push @lines, "<br />";
1216          push @lines, "<INPUT type=\"button\" name=\"SelectAll\" class=\"bigButton\" value=\"Select All\" onClick=\"selectAll($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          # Now add the search box. This allows the user to type text and have all genomes containing
1221          # the text selected automatically.          # the text selected automatically.
1222          my $searchThingName = "${menuName}_SearchThing";          my $searchThingName = "${menuName}_SearchThing";
# Line 1354  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 1573  Line 1594 
1594          # a singleton list, but that's okay.          # a singleton list, but that's okay.
1595          my @values = split (/\0/, $parms{$parmKey});          my @values = split (/\0/, $parms{$parmKey});
1596          # Check for special cases.          # Check for special cases.
1597          if ($parmKey eq 'featureTypes') {          if (grep { $_ eq $parmKey } qw(SessionID ResultCount Page PageSize Trace TF ShowURL)) {
             # Here we need to see if the user wants all the feature types. If he  
             # does, we erase all the values so that the parameter is not output.  
             my %valueCheck = map { $_ => 1 } @values;  
             my @list = FeatureQuery::AllFeatureTypes();  
             my $okFlag = 1;  
             for (my $i = 0; $okFlag && $i <= $#list; $i++) {  
                 if (! $valueCheck{$list[$i]}) {  
                     $okFlag = 0;  
                 }  
             }  
             if ($okFlag) {  
                 @values = ();  
             }  
         } elsif (grep { $_ eq $parmKey } qw(SessionID ResultCount Page PageSize Trace TF ShowURL)) {  
1598              # These are bookkeeping parameters we don't need to start a search.              # These are bookkeeping parameters we don't need to start a search.
1599              @values = ();              @values = ();
1600          } elsif ($parmKey =~ /_SearchThing$/) {          } elsif ($parmKey =~ /_SearchThing$/) {
# Line 1649  Line 1656 
1656      return $retVal;      return $retVal;
1657  }  }
1658    
 =head3 FeatureTypeMap  
   
 C<< my %features = SearchHelper::FeatureTypeMap(); >>  
   
 Return a map of feature types to descriptions. The feature type data is stored  
 in the B<FIG_Config> file. Currently, it only contains a space-delimited list of  
 feature types. The map returned by this method is a hash mapping the type codes to  
 descriptive names.  
   
 The reason we have to convert the list from a string is that the B<NMPDRSetup.pl>  
 script is only able to insert strings into the generated B<FIG_Config> file.  
   
 =cut  
   
 sub FeatureTypeMap {  
     my @list = split /\s+/, $FIG_Config::feature_types;  
     my %retVal = map { $_ => $_ } @list;  
     return %retVal;  
 }  
   
1659  =head3 AdvancedClassList  =head3 AdvancedClassList
1660    
1661  C<< my @classes = SearchHelper::AdvancedClassList(); >>  C<< my @classes = SearchHelper::AdvancedClassList(); >>
# Line 1750  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 1819  Line 1811 
1811          if (defined $extraCols->{$1}) {          if (defined $extraCols->{$1}) {
1812              $retVal = $extraCols->{$1};              $retVal = $extraCols->{$1};
1813          }          }
     } elsif ($colName eq 'orgName') {  
         # Here we want the formatted organism name and feature number.  
         $retVal = $self->FeatureName($fid);  
     } elsif ($colName eq 'fid') {  
         # Here we have the raw feature ID. We hyperlink it to the protein page.  
         $retVal = HTML::set_prot_links($fid);  
1814      } elsif ($colName eq 'alias') {      } elsif ($colName eq 'alias') {
1815          # In this case, the user wants a list of external aliases for the feature.          # In this case, the user wants a list of external aliases for the feature.
1816          # These are very expensive, so we compute them when the row is displayed.          # These are very expensive, so we compute them when the row is displayed.
1817          $retVal = "%%aliases=$fid";          $retVal = "%%alias=$fid";
1818        } elsif ($colName eq 'fid') {
1819            # Here we have the raw feature ID. We hyperlink it to the protein page.
1820            $retVal = HTML::set_prot_links($fid);
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 1839  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 1853  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.      # Return the result.
1857      return $retVal;      return $retVal;
# Line 1892  Line 1891 
1891      my $sprout = $self->DB();      my $sprout = $self->DB();
1892      my $cgi = $self->Q();      my $cgi = $self->Q();
1893      # Separate the text into a type and data.      # Separate the text into a type and data.
1894      if ($type eq 'aliases') {      if ($type eq 'alias') {
1895          # Here the caller wants external alias links for a feature. The text          # Here the caller wants external alias links for a feature. The text
1896          # is the feature ID.          # is the feature ID.
1897          my $fid = $text;          my $fid = $text;
# Line 1907  Line 1906 
1906              # Ask the HTML processor to hyperlink them.              # Ask the HTML processor to hyperlink them.
1907              $retVal = HTML::set_prot_links($cgi, $aliasList);              $retVal = HTML::set_prot_links($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;
# Line 2006  Line 2028 
2028    
2029  =head3 SortKey  =head3 SortKey
2030    
2031  C<< my $key = $shelp->SortKey($record); >>  C<< my $key = $shelp->SortKey($fdata); >>
2032    
2033  Return the sort key for the specified record. The default is to sort by feature name,  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  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  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  search class to provide fancier functionality. This method is called by
# Line 2019  Line 2041 
2041    
2042  =item record  =item record
2043    
2044  The C<DBObject> from which the current row of data is derived.  The C<FeatureData> containing the current feature.
2045    
2046  =item RETURN  =item RETURN
2047    
# Line 2031  Line 2053 
2053    
2054  sub SortKey {  sub SortKey {
2055      # Get the parameters.      # Get the parameters.
2056      my ($self, $record) = @_;      my ($self, $fdata) = @_;
2057      # Get the feature ID from the record.      # Get the feature ID from the record.
2058      my ($fid) = $record->Value('Feature(id)');      my $fid = $fdata->FID();
2059      # Get the group from the feature ID.      # Get the group from the feature ID.
2060      my $group = $self->FeatureGroup($fid);      my $group = $self->FeatureGroup($fid);
2061      # Ask the feature query object to form the sort key.      # Ask the feature query object to form the sort key.
2062      my $retVal = FeatureQuery::SortKey($self, $group, $record);      my $retVal = $fdata->SortKey($self, $group);
2063      # Return the result.      # Return the result.
2064      return $retVal;      return $retVal;
2065  }  }

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