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revision 1.1, Tue Sep 26 13:46:03 2006 UTC revision 1.6, Mon Oct 2 07:31:46 2006 UTC
# Line 16  Line 16 
16      use FIGRules;      use FIGRules;
17      use HTML;      use HTML;
18      use BasicLocation;      use BasicLocation;
19        use FeatureQuery;
20        use URI::Escape;
21        use PageBuilder;
22    
23  =head1 Search Helper Base Class  =head1 Search Helper Base Class
24    
# Line 72  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
92    
93    =head2 Adding a new Search Tool
94    
95    To add a new search tool to the system, you must
96    
97    =over 4
98    
99    =item 1
100    
101    Choose a class name for your search tool.
102    
103    =item 2
104    
105    Create a new subclass of this object and implement each of the virtual methods. The
106    name of the subclass must be C<SH>I<className>.
107    
108    =item 3
109    
110    Create an include file among the web server pages that describes how to use
111    the search tool. The include file must be in the B<includes> directory, and
112    its name must be C<SearchHelp_>I<className>C<.inc>.
113    
114    =item 4
115    
116    In the C<SearchSkeleton.cgi> script, add a C<use> statement for your search tool
117    and then put the class name in the C<@advancedClasses> list.
118    
119    =back
120    
121    =head3 Building a Search Form
122    
123    All search forms are three-column tables. In general, you want one form
124    variable per table row. The first column should contain the label and
125    the second should contain the form control for specifying the variable
126    value. If the control is wide, you should use C<colspan="2"> to give it
127    extra room. B<Do not> specify a width in any of your table cells, as
128    width management is handled by this class.
129    
130    The general code for creating the form should be
131    
132        sub Form {
133            my ($self) = @_;
134            # Get the CGI object.
135            my $cgi = @self->Q();
136            # Start the form.
137            my $retVal = $self->FormStart("form title");
138            # Assemble the table rows.
139            my @rows = ();
140            ... push table row Html into @rows ...
141            push @rows, $self->SubmitRow();
142            ... push more Html into @rows ...
143            # Build the table from the rows.
144            $retVal .= $self->MakeTable(\@rows);
145            # Close the form.
146            $retVal .= $self->FormEnd();
147            # Return the form Html.
148            return $retVal;
149        }
150    
151    Several helper methods are provided for particular purposes.
152    
153    =over 4
154    
155    =item 1
156    
157    L</NmpdrGenomeMenu> generates a control for selecting one or more genomes. Use
158    L</GetGenomes> to retrieve all the genomes passed in for a specified parameter
159    name. Note that as an assist to people working with GET-style links, if no
160    genomes are specified and the incoming request style is GET, all genomes will
161    be returned.
162    
163    =item 2
164    
165    L</FeatureFilterRow> formats several rows of controls for filtering features.
166    When you start building the code for the L</Find> method, you can use a
167    B<FeatureQuery> object to automatically filter each genome's features using
168    the values from the filter controls.
169    
170    =item 3
171    
172    L</QueueFormScript> allows you to queue JavaScript statements for execution
173    after the form is fully generated. If you are using very complicated
174    form controls, the L</QueueFormScript> method allows you to perform
175    JavaScript initialization. The L</NmpdrGenomeMenu> control uses this
176    facility to display a list of the pre-selected genomes.
177    
178  =back  =back
179    
180    Finally, when generating the code for your controls, be sure to use any incoming
181    query parameters as default values so that the search request is persistent.
182    
183    =head3 Finding Search Results
184    
185    The L</Find> method is used to create the search results. For a search that
186    wants to return features (which is most of them), the basic code structure
187    would work as follows. It is assumed that the L</FeatureFilterRows> method
188    has been used to create feature filtering parameters.
189    
190        sub Find {
191            my ($self) = @_;
192            # Get the CGI and Sprout objects.
193            my $cgi = $self->Q();
194            my $sprout = $self->DB();
195            # Declare the return variable. If it remains undefined, the caller will
196            # know that an error occurred.
197            my $retVal;
198            ... validate the parameters ...
199            if (... invalid parameters...) {
200                $self->SetMessage(...appropriate message...);
201            } elsif (FeatureQuery::Valid($self)) {
202                # Initialize the session file.
203                $self->OpenSession();
204                # Initialize the result counter.
205                $retVal = 0;
206                ... get a list of genomes ...
207                for my $genomeID (... each genome ...) {
208                    my $fq = FeatureQuery->new($self, $genomeID);
209                    while (my $feature = $fq->Fetch()) {
210                        ... examine the feature ...
211                        if (... we want to keep it ...) {
212                            $self->PutFeature($fq);
213                            $retVal++;
214                        }
215                    }
216                }
217            }
218            # Close the session file.
219            $self->CloseSession();
220            # Return the result count.
221            return $retVal;
222        }
223    
224    A Find method is of course much more complicated than generating a form, and there
225    are variations on the above them. For example, you could eschew feature filtering
226    entirely in favor of your own custom filtering, you could include extra columns
227    in the output, or you could search for something that's not a feature at all. The
228    above code is just a loose framework.
229    
230    If you wish to add your own extra columns to the output, use the B<AddExtraColumns>
231    method of the feature query object.
232    
233        $fq->AddExtraColumns(score => $sc);
234    
235    The L</Find> method must return C<undef> if the search parameters are invalid. If this
236    is the case, then a message describing the problem should be passed to the framework
237    by calling L</SetMessage>. If the parameters are valid, then the method must return
238    the number of items found.
239    
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 113  Line 276 
276      # Compute the subclass name.      # Compute the subclass name.
277      $class =~ /SH(.+)$/;      $class =~ /SH(.+)$/;
278      my $subClass = $1;      my $subClass = $1;
     # Create the Sprout object.  
     my $sprout = SFXlate->new_sprout_only();  
279      # Insure everybody knows we're in Sprout mode.      # Insure everybody knows we're in Sprout mode.
280      $query->param(-name => 'SPROUT', -value => 1);      $query->param(-name => 'SPROUT', -value => 1);
281      # Generate the form name.      # Generate the form name.
# Line 122  Line 283 
283      $formCount++;      $formCount++;
284      # Create the shelp object. It contains the query object (with the session ID)      # Create the shelp object. It contains the query object (with the session ID)
285      # as well as an indicator as to whether or not the session is new, plus the      # as well as an indicator as to whether or not the session is new, plus the
286      # class name and the Sprout object.      # class name and a placeholder for the Sprout object.
287      my $retVal = {      my $retVal = {
288                    query => $query,                    query => $query,
289                    type => $type,                    type => $type,
290                    class => $subClass,                    class => $subClass,
291                    sprout => $sprout,                    sprout => undef,
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, $class;
# Line 163  Line 327 
327  sub DB {  sub DB {
328      # Get the parameters.      # Get the parameters.
329      my ($self) = @_;      my ($self) = @_;
330        # Insure we have a database.
331        my $retVal = $self->{sprout};
332        if (! defined $retVal) {
333            $retVal = SFXlate->new_sprout_only();
334            $self->{sprout} = $retVal;
335        }
336      # Return the result.      # Return the result.
337      return $self->{sprout};      return $retVal;
338  }  }
339    
340  =head3 IsNew  =head3 IsNew
# Line 437  Line 607 
607    
608  =head3 PutFeature  =head3 PutFeature
609    
610  C<< $shelp->PutFeature($record, %extraCols); >>  C<< $shelp->PutFeature($fquery); >>
611    
612  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
613  searches, since the primary data item in the database is features.  searches, since the primary data item in the database is features.
614    
615  For each feature, there are certain columns that are standard: the feature name, the  For each feature, there are certain columns that are standard: the feature name, the
616  GBrowse and protein page links, the functional assignment, and so forth. If additional  GBrowse and protein page links, the functional assignment, and so forth. If additional
617  columns are required by a particular search subclass, they should be included in the  columns are required by a particular search subclass, they should be stored in
618  parameters, in key-value form. For example, the following call adds columns for  the feature query object using the B<AddExtraColumns> method. For example, the following
619  essentiality and virulence.  code adds columns for essentiality and virulence.
620    
621      $shelp->PutFeature($record, essential => $essentialFlag, virulence => $vfactor);      $fq->AddExtraColumns(essential => $essentialFlag, virulence => $vfactor);
622        $shelp->PutFeature($fq);
623    
624  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
625  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 458  Line 629 
629      if (! $essentialFlag) {      if (! $essentialFlag) {
630          $essentialFlag = undef;          $essentialFlag = undef;
631      }      }
632      $shelp->PutFeature($record, essential => $essentialFlag, virulence = $vfactor);      $fq->AddExtraColumns(essential => $essentialFlag, virulence => $vfactor);
633        $shelp->PutFeature($fq);
634    
635  =over 4  =over 4
636    
637  =item record  =item fquery
   
 DBObject record for the feature.  
638    
639  =item extraCols  FeatureQuery object containing the current feature data.
640    
641  =back  =back
642    
643  =cut  =cut
644    
645  sub PutFeature {  sub PutFeature {
646      # Get the parameters. Note that the extra columns are read in as a list      # Get the parameters.
647      # instead of a hash so that the column order is preserved.      my ($self, $fq) = @_;
648      my ($self, $record, @extraColList) = @_;      # Get the CGI query object.
649        my $cgi = $self->Q();
650        # Get the feature data.
651        my $record = $fq->Feature();
652        my $extraCols = $fq->ExtraCols();
653      # Check for a first-call situation.      # Check for a first-call situation.
654      if (! defined $self->{cols}) {      if (! defined $self->{cols}) {
655          # 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.
656          $self->{cols} = $self->DefaultFeatureColumns();          $self->{cols} = $self->DefaultFeatureColumns();
657          # Append the extras. Note we proceed by twos because the columns are          # Add the externals if they were requested.
658          # specified in the form name => value.          if ($cgi->param('ShowAliases')) {
659          for (my $i = 0; $i <= $#extraColList; $i += 2) {              push @{$self->{cols}}, 'alias';
660              push @{$self->{cols}}, "X=$extraColList[$i]";          }
661            # Append the extras, sorted by column name.
662            for my $col (sort keys %{$extraCols}) {
663                push @{$self->{cols}}, "X=$col";
664          }          }
665          # Write out the column headers. This also prepares the cache file to receive          # Write out the column headers. This also prepares the cache file to receive
666          # output.          # output.
# Line 491  Line 668 
668      }      }
669      # Get the feature ID.      # Get the feature ID.
670      my ($fid) = $record->Value('Feature(id)');      my ($fid) = $record->Value('Feature(id)');
     # Now we process the columns themselves. First, convert the extra column list  
     # to a hash.  
     my %extraCols = @extraColList;  
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 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 = $self->SortKey($record);
     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 600  Line 773 
773      my $retVal;      my $retVal;
774      # Get a digest encoder.      # Get a digest encoder.
775      my $md5 = Digest::MD5->new();      my $md5 = Digest::MD5->new();
776      # 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
777      if (open(R, "/dev/urandom")) {      # actually two numbers, and we get them both because we're in list
778          my $b;      # context.
779          read(R, $b, 1024);      $md5->add($$, $ENV{REMOTE_ADDR}, $ENV{REMOTE_PORT}, gettimeofday());
780          $md5->add($b);      # Hash up all this identifying data.
781      }      $retVal = $md5->hexdigest();
782      # Add the PID and the time stamp.      # Return the result.
     $md5->add($$, 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.  
783      return $retVal;      return $retVal;
784  }  }
785    
# Line 771  Line 938 
938      } else {      } else {
939          # Here we can get its genome data.          # Here we can get its genome data.
940          $retVal = $self->Organism($genomeID);          $retVal = $self->Organism($genomeID);
941          # Append the type and number.          # Append the FIG ID.
942          $retVal .= " [$type $num]";          $retVal .= " [$fid]";
943      }      }
944      # Return the result.      # Return the result.
945      return $retVal;      return $retVal;
# Line 888  Line 1055 
1055    
1056  =head3 NmpdrGenomeMenu  =head3 NmpdrGenomeMenu
1057    
1058  C<< my $htmlText = $shelp->NmpdrGenomeMenu($menuName, \%options, \@selected); >>  C<< my $htmlText = $shelp->NmpdrGenomeMenu($menuName, $multiple, \@selected, $rows); >>
1059    
1060  This method creates a hierarchical HTML menu for NMPDR genomes organized by category. The  This method creates a hierarchical HTML menu for NMPDR genomes organized by category. The
1061  category indicates the low-level NMPDR group. Organizing the genomes in this way makes it  category indicates the low-level NMPDR group. Organizing the genomes in this way makes it
# Line 900  Line 1067 
1067    
1068  Name to give to the menu.  Name to give to the menu.
1069    
1070  =item options  =item multiple
1071    
1072  Reference to a hash containing the options to be applied to the C<SELECT> tag form the menu.  TRUE if the user is allowed to select multiple genomes, else FALSE.
 Typical options would include C<multiple> to specify  
 that multiple selections are allowed and C<size> to set the number of rows to display  
 in the menu.  
1073    
1074  =item selected  =item selected
1075    
# Line 913  Line 1077 
1077  is not intended to allow multiple selections, the list should be a singleton. If the  is not intended to allow multiple selections, the list should be a singleton. If the
1078  list is empty, nothing will be pre-selected.  list is empty, nothing will be pre-selected.
1079    
1080    =item rows (optional)
1081    
1082    Number of rows to display. If omitted, the default is 1 for a single-select list
1083    and 10 for a multi-select list.
1084    
1085  =item RETURN  =item RETURN
1086    
1087  Returns the HTML text to generate a C<SELECT> menu inside a form.  Returns the HTML text to generate a C<SELECT> menu inside a form.
# Line 923  Line 1092 
1092    
1093  sub NmpdrGenomeMenu {  sub NmpdrGenomeMenu {
1094      # Get the parameters.      # Get the parameters.
1095      my ($self, $menuName, $options, $selected) = @_;      my ($self, $menuName, $multiple, $selected, $rows) = @_;
1096      # Get the Sprout and CGI objects.      # Get the Sprout and CGI objects.
1097      my $sprout = $self->DB();      my $sprout = $self->DB();
1098      my $cgi = $self->Q();      my $cgi = $self->Q();
1099        # Compute the row count.
1100        if (! defined $rows) {
1101            $rows = ($multiple ? 10 : 1);
1102        }
1103        # Create the multiple tag.
1104        my $multipleTag = ($multiple ? " multiple" : "");
1105      # Get the form name.      # Get the form name.
1106      my $formName = $self->FormName();      my $formName = $self->FormName();
1107        # Check to see if we already have a genome list in memory.
1108        my $genomes = $self->{genomeList};
1109        my $groupHash;
1110        if (defined $genomes) {
1111            # We have a list ready to use.
1112            $groupHash = $genomes;
1113        } else {
1114      # 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
1115      # 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
1116      # take advantage of an existing index.      # take advantage of an existing index.
# Line 940  Line 1122 
1122      # 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
1123      # 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
1124      # name.      # name.
1125      my %groupHash = ();          my %gHash = ();
1126      for my $genome (@genomeList) {      for my $genome (@genomeList) {
1127          # Get the genome data.          # Get the genome data.
1128          my ($group, $genomeID, $genus, $species, $strain) = @{$genome};          my ($group, $genomeID, $genus, $species, $strain) = @{$genome};
# Line 950  Line 1132 
1132              $name .= " $strain";              $name .= " $strain";
1133          }          }
1134          # Push the genome into the group's list.          # Push the genome into the group's list.
1135          push @{$groupHash{$group}}, [$genomeID, $name];              push @{$gHash{$group}}, [$genomeID, $name];
1136            }
1137            # Save the genome list for future use.
1138            $self->{genomeList} = \%gHash;
1139            $groupHash = \%gHash;
1140      }      }
1141      # 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
1142      # the supporting-genome group last.      # the supporting-genome group last.
1143      my @groups = sort grep { $_ ne $FIG_Config::otherGroup } keys %groupHash;      my @groups = sort grep { $_ ne $FIG_Config::otherGroup } keys %{$groupHash};
1144      push @groups, $FIG_Config::otherGroup;      push @groups, $FIG_Config::otherGroup;
1145      # 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
1146      my %selectedHash = map { $_ => 1 } @{$selected};      # with the possibility of undefined values in the incoming list.
1147        my %selectedHash = ();
1148        if (defined $selected) {
1149            %selectedHash = map { $_ => 1 } grep { defined($_) } @{$selected};
1150        }
1151      # 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.
1152      # Create the type counters.      # Create the type counters.
1153      my $groupCount = 1;      my $groupCount = 1;
# Line 967  Line 1157 
1157      my $showSelect = "showSelected($menuName, '$divID', 1000);";      my $showSelect = "showSelected($menuName, '$divID', 1000);";
1158      # If multiple selection is supported, create an onChange event.      # If multiple selection is supported, create an onChange event.
1159      my $onChange = "";      my $onChange = "";
1160      if ($options->{multiple}) {      if ($multiple) {
1161          $onChange = " onChange=\"$showSelect\"";          $onChange = " onChange=\"$showSelect\"";
1162      }      }
1163      # Create the SELECT tag and stuff it into the output array.      # Create the SELECT tag and stuff it into the output array.
1164      my $select = "<" . join(" ", "SELECT name=\"$menuName\"$onChange", map { " $_=\"$options->{$_}\"" } keys %{$options}) . ">";      my $select = "<SELECT name=\"$menuName\"$onChange$multipleTag size=\"$rows\">";
1165      my @lines = ($select);      my @lines = ($select);
1166      # Loop through the groups.      # Loop through the groups.
1167      for my $group (@groups) {      for my $group (@groups) {
# Line 982  Line 1172 
1172          # label option may have functionality in future browsers. If that happens, we'll need          # label option may have functionality in future browsers. If that happens, we'll need
1173          # to modify the genome text so that the "selectSome" method can tell which are NMPDR          # to modify the genome text so that the "selectSome" method can tell which are NMPDR
1174          # organisms and which aren't. Sadly, the OPTGROUP tag is invisible in the DOM Javascript          # organisms and which aren't. Sadly, the OPTGROUP tag is invisible in the DOM Javascript
1175          # hierarchy.          # hierarchy, so we can't use it.
1176          my $label = ($group eq $FIG_Config::otherGroup ? "other" : "nmpdr");          my $label = ($group eq $FIG_Config::otherGroup ? "other" : "nmpdr");
1177          # Get the genomes in the group.          # Get the genomes in the group.
1178          for my $genome (@{$groupHash{$group}}) {          for my $genome (@{$groupHash->{$group}}) {
1179              my ($genomeID, $name) = @{$genome};              my ($genomeID, $name) = @{$genome};
1180              # See if it's selected.              # See if it's selected.
1181              my $select = ($selectedHash{$genomeID} ? " selected" : "");              my $select = ($selectedHash{$genomeID} ? " selected" : "");
# Line 999  Line 1189 
1189      # Close the SELECT tag.      # Close the SELECT tag.
1190      push @lines, "</SELECT>";      push @lines, "</SELECT>";
1191      # Check for multiple selection.      # Check for multiple selection.
1192      if ($options->{multiple}) {      if ($multiple) {
1193          # Since multi-select is on, we can set up some buttons to set and clear selections.          # Since multi-select is on, we set up some buttons to set and clear selections.
1194          push @lines, "<br />";          push @lines, "<br />";
1195          push @lines, "<INPUT type=\"button\" name=\"SelectAll\" class=\"bigButton\" value=\"Select All\" onClick=\"selectAll($menuName); $showSelect\" />";          push @lines, "<INPUT type=\"button\" name=\"SelectAll\" class=\"bigButton\" value=\"Select All\" onClick=\"selectAll($menuName); $showSelect\" />";
1196          push @lines, "<INPUT type=\"button\" name=\"ClearAll\" class=\"bigButton\"  value=\"Clear All\" onClick=\"clearAll($menuName); $showSelect\" />";          push @lines, "<INPUT type=\"button\" name=\"ClearAll\" class=\"bigButton\"  value=\"Clear All\" onClick=\"clearAll($menuName); $showSelect\" />";
1197          push @lines, "<INPUT type=\"button\" name=\"NMPDROnly\" class=\"bigButton\"  value=\"Select NMPDR\" onClick=\"selectSome($menuName, 'nmpdr'); $showSelect\" />";          push @lines, "<INPUT type=\"button\" name=\"NMPDROnly\" class=\"bigButton\"  value=\"Select NMPDR\" onClick=\"selectSome($menuName, 'nmpdr'); $showSelect\" />";
1198          push @lines, "<INPUT type=\"button\" name=\"OtherOnly\" class=\"bigButton\" value=\"Select Supporting\" onClick=\"selectSome($menuName, 'other'); $showSelect\" />";          push @lines, "<INPUT type=\"button\" name=\"OtherOnly\" class=\"bigButton\" value=\"Select Supporting\" onClick=\"selectSome($menuName, 'other'); $showSelect\" />";
1199            # Now add the search box. This allows the user to type text and have all genomes containing
1200            # the text selected automatically.
1201            my $searchThingName = "${menuName}_SearchThing";
1202            push @lines, "<br>Select genomes containing <INPUT type=\"text\" name=\"$searchThingName\" size=\"30\" />&nbsp;" .
1203                         "<INPUT type=\"button\" name=\"Select\" class=\"button\" value=\"Search\" onClick=\"selectViaSearch($menuName, $searchThingName); $showSelect\" />";
1204          # Add the status display, too.          # Add the status display, too.
1205          push @lines, "<DIV id=\"$divID\" class=\"selectStatus\"></DIV>";          push @lines, "<DIV id=\"$divID\" class=\"selectStatus\"></DIV>";
1206          # 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 1014  Line 1209 
1209          # in case we decide to twiddle the parameters.          # in case we decide to twiddle the parameters.
1210          $showSelect =~ s/showSelected\(/showSelected\(thisForm\./;          $showSelect =~ s/showSelected\(/showSelected\(thisForm\./;
1211          $self->QueueFormScript($showSelect);          $self->QueueFormScript($showSelect);
1212            # Finally, add this parameter to the list of genome parameters. This enables us to
1213            # easily find all the parameters used to select one or more genomes.
1214            push @{$self->{genomeParms}}, $menuName;
1215      }      }
1216      # Assemble all the lines into a string.      # Assemble all the lines into a string.
1217      my $retVal = join("\n", @lines, "");      my $retVal = join("\n", @lines, "");
# Line 1021  Line 1219 
1219      return $retVal;      return $retVal;
1220  }  }
1221    
1222    =head3 PropertyMenu
1223    
1224    C<< my $htmlText = $shelp->PropertyMenu($menuName, $selected, $force); >>
1225    
1226    Generate a property name dropdown menu.
1227    
1228    =over 4
1229    
1230    =item menuName
1231    
1232    Name to give to the menu.
1233    
1234    =item selected
1235    
1236    Value of the property name to pre-select.
1237    
1238    =item force (optional)
1239    
1240    If TRUE, then the user will be forced to choose a property name. If FALSE,
1241    then an additional menu choice will be provided to select nothing.
1242    
1243    =item RETURN
1244    
1245    Returns a dropdown menu box that allows the user to select a property name. An additional
1246    selection entry will be provided for selecting no property name
1247    
1248    =back
1249    
1250    =cut
1251    
1252    sub PropertyMenu {
1253        # Get the parameters.
1254        my ($self, $menuName, $selected, $force) = @_;
1255        # Get the CGI and Sprout objects.
1256        my $sprout = $self->DB();
1257        my $cgi = $self->Q();
1258        # Create the property name list.
1259        my @propNames = ();
1260        if (! $force) {
1261            push @propNames, "";
1262        }
1263        # Get all the property names, putting them after the null choice if one exists.
1264        push @propNames, $sprout->GetChoices('Property', 'property-name');
1265        # Create a menu from them.
1266        my $retVal = $cgi->popup_menu(-name=> $menuName, -values => \@propNames,
1267                                      -default => $selected);
1268        # Return the result.
1269        return $retVal;
1270    }
1271    
1272  =head3 MakeTable  =head3 MakeTable
1273    
1274  C<< my $htmlText = $shelp->MakeTable(\@rows); >>  C<< my $htmlText = $shelp->MakeTable(\@rows); >>
# Line 1083  Line 1331 
1331      # Get the parameters.      # Get the parameters.
1332      my ($self) = @_;      my ($self) = @_;
1333      my $cgi = $self->Q();      my $cgi = $self->Q();
1334      # Declare the return variable.      # Get the current page size.
1335        my $pageSize = $cgi->param('PageSize');
1336        # Get the incoming external-link flag.
1337        my $aliases = ($cgi->param('ShowAliases') ? 1 : 0);
1338        # Create the row.
1339      my $retVal = $cgi->Tr($cgi->td("Results/Page"),      my $retVal = $cgi->Tr($cgi->td("Results/Page"),
1340                            $cgi->td($cgi->popup_menu(-name => 'PageSize',                            $cgi->td($cgi->popup_menu(-name => 'PageSize',
1341                                                      -values => [10, 25, 45, 100, 1000],                                                      -values => [10, 25, 45, 100, 1000],
1342                                                      -default => $cgi->param('PageSize'))),                                                      -default => $pageSize) . " " .
1343                                       $cgi->checkbox(-name => 'ShowURL',
1344                                                      -value => 1,
1345                                                      -label => 'Show URL')),
1346                            $cgi->td($cgi->submit(-class => 'goButton',                            $cgi->td($cgi->submit(-class => 'goButton',
1347                                                  -name => 'Search',                                                  -name => 'Search',
1348                                                  -value => 'Go')));                                                  -value => 'Go')));
1349      # Return the result.      # Return the result.
1350      return $retVal;      return $retVal;
1351  }  }
1352    
1353    =head3 FeatureFilterRows
1354    
1355    C<< my $htmlText = $shelp->FeatureFilterRows(); >>
1356    
1357    This method creates table rows that can be used to filter features. There are
1358    two rows returned, and the values can be used to select features by genome
1359    using the B<FeatureQuery> object.
1360    
1361    =cut
1362    
1363    sub FeatureFilterRows {
1364        # Get the parameters.
1365        my ($self) = @_;
1366        # Return the result.
1367        return FeatureQuery::FilterRows($self);
1368    }
1369    
1370  =head3 GBrowseFeatureURL  =head3 GBrowseFeatureURL
1371    
1372  C<< my $url = SearchHelper::GBrowseFeatureURL($sprout, $feat); >>  C<< my $url = SearchHelper::GBrowseFeatureURL($sprout, $feat); >>
# Line 1133  Line 1406 
1406          # Get the feature location string.          # Get the feature location string.
1407          my $loc = $sprout->FeatureLocation($feat);          my $loc = $sprout->FeatureLocation($feat);
1408          # Compute the contig, start, and stop points.          # Compute the contig, start, and stop points.
1409          my($start, $stop, $contig) = BasicLocation::Parse($loc);          my($contig, $start, $stop) = BasicLocation::Parse($loc);
1410            Trace("Start and stop are ($start,$stop) on contig $contig.") if T(3);
1411          # 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
1412          # big and that we get some surrounding stuff.          # big and that we get some surrounding stuff.
1413          my $mid = int(($start + $stop) / 2);          my $mid = int(($start + $stop) / 2);
# Line 1163  Line 1437 
1437          }          }
1438          my $seg_id = $contig;          my $seg_id = $contig;
1439          $seg_id =~ s/:/--/g;          $seg_id =~ s/:/--/g;
1440            Trace("Show limits are ($show_start,$show_stop) in genome $genomeID with ref $seg_id.") if T(3);
1441          # Assemble all the pieces.          # Assemble all the pieces.
1442          $retVal = "gbrowse.cgi/GB_$genomeID?ref=$seg_id&start=$show_start&stop=$show_stop";          $retVal = "gbrowse.cgi/GB_$genomeID?ref=$seg_id&start=$show_start&stop=$show_stop";
1443      }      }
# Line 1170  Line 1445 
1445      return $retVal;      return $retVal;
1446  }  }
1447    
1448    =head3 GetGenomes
1449    
1450    C<< my @genomeList = $shelp->GetGenomes($parmName); >>
1451    
1452    Return the list of genomes specified by the specified CGI query parameter.
1453    If the request method is POST, then the list of genome IDs is returned
1454    without preamble. If the request method is GET and the parameter is not
1455    specified, then it is treated as a request for all genomes. This makes it
1456    easier for web pages to link to a search that wants to specify all genomes.
1457    
1458    =over 4
1459    
1460    =item parmName
1461    
1462    Name of the parameter containing the list of genomes. This will be the
1463    first parameter passed to the L</NmpdrGenomeMenu> call that created the
1464    genome selection control on the form.
1465    
1466    =item RETURN
1467    
1468    Returns a list of the genomes to process.
1469    
1470    =back
1471    
1472    =cut
1473    
1474    sub GetGenomes {
1475        # Get the parameters.
1476        my ($self, $parmName) = @_;
1477        # Get the CGI query object.
1478        my $cgi = $self->Q();
1479        # Get the list of genome IDs in the request header.
1480        my @retVal = $cgi->param($parmName);
1481        Trace("Genome list for $parmName is (" . join(", ", @retVal) . ") with method " . $cgi->request_method() . ".") if T(3);
1482        # Check for the special GET case.
1483        if ($cgi->request_method() eq "GET" && ! @retVal) {
1484            # Here the caller wants all the genomes.
1485            my $sprout = $self->DB();
1486            @retVal = $sprout->Genomes();
1487        }
1488        # Return the result.
1489        return @retVal;
1490    }
1491    
1492    =head3 GetHelpText
1493    
1494    C<< my $htmlText = $shelp->GetHelpText(); >>
1495    
1496    Get the help text for this search. The help text is stored in files on the template
1497    server. The help text for a specific search is taken from a file named
1498    C<SearchHelp_>I<class>C<.inc> in the template directory C<$FIG_Config::template_url>.
1499    There are also three standard help files: C<SearchHelp1_Filtering.inc> describes the
1500    feature filtering performed by the B<FeatureQuery> object, C<SearchHelp1_GenomeControl.inc>
1501    describes how to use a multiple-selection genome control, and C<SearchHelp1_Standard.inc>
1502    describes the standard controls for a search, such as page size, URL display, and
1503    external alias display.
1504    
1505    =cut
1506    
1507    sub GetHelpText {
1508        # Get the parameters.
1509        my ($self) = @_;
1510        # Create a list to hold the pieces of the help.
1511        my @helps = ();
1512        # Get the template directory URL.
1513        my $urlBase = $FIG_Config::template_url;
1514        # Start with the specific help.
1515        my $class = $self->{class};
1516        push @helps, PageBuilder::GetPage("$urlBase/SearchHelp_$class.inc");
1517        # Add the genome control help if needed.
1518        if (scalar @{$self->{genomeParms}}) {
1519            push @helps, PageBuilder::GetPage("$urlBase/SearchHelp1_GenomeControl.inc");
1520        }
1521        # Next the filter help.
1522        if ($self->{filtered}) {
1523            push @helps, PageBuilder::GetPage("$urlBase/SearchHelp1_Filtering.inc");
1524        }
1525        # Finally, the standard help.
1526        push @helps, PageBuilder::GetPage("$urlBase/SearchHelp1_Standard.inc");
1527        # Assemble the pieces.
1528        my $retVal = join("\n<p>&nbsp;</p>\n", @helps);
1529        # Return the result.
1530        return $retVal;
1531    }
1532    
1533    =head3 ComputeSearchURL
1534    
1535    C<< my $url = $shelp->ComputeSearchURL(); >>
1536    
1537    Compute the GET-style URL for the current search. In order for this to work, there
1538    must be a copy of the search form on the current page. This will always be the
1539    case if the search is coming from C<SearchSkeleton.cgi>.
1540    
1541    A little expense is involved in order to make the URL as smart as possible. The
1542    main complication is that if the user specified all genomes, we'll want to
1543    remove the parameter entirely from a get-style URL.
1544    
1545    =cut
1546    
1547    sub ComputeSearchURL {
1548        # Get the parameters.
1549        my ($self) = @_;
1550        # Get the database and CGI query object.
1551        my $cgi = $self->Q();
1552        my $sprout = $self->DB();
1553        # Start with the full URL.
1554        my $retVal = $cgi->url(-full => 1);
1555        # Get all the query parameters in a hash.
1556        my %parms = $cgi->Vars();
1557        # Now we need to do some fixing. Each multi-valued parameter is encoded as a string with null
1558        # characters separating the individual values. We have to convert those to lists. In addition,
1559        # the multiple-selection genome parameters and the feature type parameter must be checked to
1560        # determine whether or not they can be removed from the URL. First, we get a list of the
1561        # genome parameters and a list of all genomes. Note that we only need the list if a
1562        # multiple-selection genome parameter has been found on the form.
1563        my %genomeParms = map { $_ => 1 } @{$self->{genomeParms}};
1564        my @genomeList;
1565        if (keys %genomeParms) {
1566            @genomeList = $sprout->Genomes();
1567        }
1568        # Create a list to hold the URL parameters we find.
1569        my @urlList = ();
1570        # Now loop through the parameters in the hash, putting them into the output URL.
1571        for my $parmKey (keys %parms) {
1572            # Get a list of the parameter values. If there's only one, we'll end up with
1573            # a singleton list, but that's okay.
1574            my @values = split (/\0/, $parms{$parmKey});
1575            # Check for special cases.
1576            if ($parmKey eq 'featureTypes') {
1577                # Here we need to see if the user wants all the feature types. If he
1578                # does, we erase all the values so that the parameter is not output.
1579                my %valueCheck = map { $_ => 1 } @values;
1580                my @list = FeatureQuery::AllFeatureTypes();
1581                my $okFlag = 1;
1582                for (my $i = 0; $okFlag && $i <= $#list; $i++) {
1583                    if (! $valueCheck{$list[$i]}) {
1584                        $okFlag = 0;
1585                    }
1586                }
1587                if ($okFlag) {
1588                    @values = ();
1589                }
1590            } elsif (grep { $_ eq $parmKey } qw(SessionID ResultCount Page PageSize Trace TF ShowURL)) {
1591                # These are bookkeeping parameters we don't need to start a search.
1592                @values = ();
1593            } elsif ($parmKey =~ /_SearchThing$/) {
1594                # Here the value coming in is from a genome control's search thing. It does
1595                # not affect the results of the search, so we clear it.
1596                @values = ();
1597            } elsif ($genomeParms{$parmKey}) {
1598                # Here we need to see if the user wants all the genomes. If he does,
1599                # we erase all the values just like with features.
1600                my $allFlag = $sprout->IsAllGenomes(\@values, \@genomeList);
1601                if ($allFlag) {
1602                    @values = ();
1603                }
1604            }
1605            # If we still have values, create the URL parameters.
1606            if (@values) {
1607                push @urlList, map { "$parmKey=" . uri_escape($_) } @values;
1608            }
1609        }
1610        # Add the parameters to the URL.
1611        $retVal .= "?" . join(";", @urlList);
1612        # Return the result.
1613        return $retVal;
1614    }
1615    
1616    =head3 GetRunTimeValue
1617    
1618    C<< my $htmlText = $shelp->GetRunTimeValue($text); >>
1619    
1620    Compute a run-time column value.
1621    
1622    =over 4
1623    
1624    =item text
1625    
1626    The run-time column text. It consists of 2 percent signs, a column type, an equal
1627    sign, and the data for the current row.
1628    
1629    =item RETURN
1630    
1631    Returns the fully-formatted HTML text to go into the current column of the current row.
1632    
1633    =back
1634    
1635    =cut
1636    
1637    sub GetRunTimeValue {
1638        # Get the parameters.
1639        my ($self, $text) = @_;
1640        # Declare the return variable.
1641        my $retVal;
1642        # Parse the incoming text.
1643        if ($text =~ /^%%([^=]+)=(.*)$/) {
1644            $retVal = $self->RunTimeColumns($1, $2);
1645        } else {
1646            Confess("Invalid run-time column string \"$text\" encountered in session file.");
1647        }
1648        # Return the result.
1649        return $retVal;
1650    }
1651    
1652  =head2 Feature Column Methods  =head2 Feature Column Methods
1653    
1654  The methods in this column manage feature column data. If you want to provide the  The methods in this column manage feature column data. If you want to provide the
# Line 1202  Line 1681 
1681      # Get the parameters.      # Get the parameters.
1682      my ($self) = @_;      my ($self) = @_;
1683      # Return the result.      # Return the result.
1684      return ['orgName', 'function', 'gblink', 'protlink'];      return ['orgName', 'function', 'gblink', 'protlink',
1685                FeatureQuery::AdditionalColumns($self)];
1686  }  }
1687    
1688  =head3 FeatureColumnTitle  =head3 FeatureColumnTitle
# Line 1311  Line 1791 
1791          $retVal = HTML::set_prot_links($fid);          $retVal = HTML::set_prot_links($fid);
1792      } elsif ($colName eq 'alias') {      } elsif ($colName eq 'alias') {
1793          # 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.
1794          # The complicated part is we have to hyperlink them. First, get the          # These are very expensive, so we compute them when the row is displayed.
1795          # aliases.          $retVal = "%%aliases=$fid";
         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);  
         }  
1796      } elsif ($colName eq 'function') {      } elsif ($colName eq 'function') {
1797          # The functional assignment is just a matter of getting some text.          # The functional assignment is just a matter of getting some text.
1798          ($retVal) = $record->Value('Feature(assignment)');          ($retVal) = $record->Value('Feature(assignment)');
# Line 1350  Line 1822 
1822      return $retVal;      return $retVal;
1823  }  }
1824    
1825    =head3 RunTimeColumns
1826    
1827    C<< my $htmlText = $shelp->RunTimeColumns($type, $text); >>
1828    
1829    Return the HTML text for a run-time column. Run-time columns are evaluated when the
1830    list is displayed, rather than when it is generated.
1831    
1832    =over 4
1833    
1834    =item type
1835    
1836    Type of column.
1837    
1838    =item text
1839    
1840    Data relevant to this row of the column.
1841    
1842    =item RETURN
1843    
1844    Returns the fully-formatted HTML text to go in the specified column.
1845    
1846    =back
1847    
1848    =cut
1849    
1850    sub RunTimeColumns {
1851        # Get the parameters.
1852        my ($self, $type, $text) = @_;
1853        # Declare the return variable.
1854        my $retVal = "";
1855        # Get the Sprout and CGI objects.
1856        my $sprout = $self->DB();
1857        my $cgi = $self->Q();
1858        # Separate the text into a type and data.
1859        if ($type eq 'aliases') {
1860            # Here the caller wants external alias links for a feature. The text
1861            # is the feature ID.
1862            my $fid = $text;
1863            # The complicated part is we have to hyperlink them. First, get the
1864            # aliases.
1865            Trace("Generating aliases for feature $fid.") if T(4);
1866            my @aliases = $sprout->FeatureAliases($fid);
1867            # Only proceed if we found some.
1868            if (@aliases) {
1869                # Join the aliases into a comma-delimited list.
1870                my $aliasList = join(", ", @aliases);
1871                # Ask the HTML processor to hyperlink them.
1872                $retVal = HTML::set_prot_links($cgi, $aliasList);
1873            }
1874        }
1875        # Return the result.
1876        return $retVal;
1877    }
1878    
1879    =head2 Virtual Methods
1880    
1881    =head3 Form
1882    
1883    C<< my $html = $shelp->Form(); >>
1884    
1885    Generate the HTML for a form to request a new search.
1886    
1887    =head3 Find
1888    
1889    C<< my $resultCount = $shelp->Find(); >>
1890    
1891    Conduct a search based on the current CGI query parameters. The search results will
1892    be written to the session cache file and the number of results will be
1893    returned. If the search parameters are invalid, a result count of C<undef> will be
1894    returned and a result message will be stored in this object describing the problem.
1895    
1896    =head3 Description
1897    
1898    C<< my $htmlText = $shelp->Description(); >>
1899    
1900    Return a description of this search. The description is used for the table of contents
1901    on the main search tools page. It may contain HTML, but it should be character-level,
1902    not block-level, since the description is going to appear in a list.
1903    
1904    =head3 SortKey
1905    
1906    C<< my $key = $shelp->SortKey($record); >>
1907    
1908    Return the sort key for the specified record. The default is to sort by feature name,
1909    floating NMPDR organisms to the top. This sort may be overridden by the search class
1910    to provide fancier functionality. This method is called by B<PutFeature>, so it
1911    is only used for feature searches. A non-feature search would presumably have its
1912    own sort logic.
1913    
1914    =over 4
1915    
1916    =item record
1917    
1918    The C<DBObject> from which the current row of data is derived.
1919    
1920    =item RETURN
1921    
1922    Returns a key field that can be used to sort this row in among the results.
1923    
1924    =back
1925    
1926    =cut
1927    
1928    sub SortKey {
1929        # Get the parameters.
1930        my ($self, $record) = @_;
1931        # Get the feature ID from the record.
1932        my ($fid) = $record->Value('Feature(id)');
1933        # Get the group from the feature ID.
1934        my $group = $self->FeatureGroup($fid);
1935        # Ask the feature query object to form the sort key.
1936        my $retVal = FeatureQuery::SortKey($self, $group, $record);
1937        # Return the result.
1938        return $retVal;
1939    }
1940  1;  1;

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