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revision 1.112, Wed May 28 17:39:38 2008 UTC revision 1.114, Wed Sep 3 20:59:57 2008 UTC
# Line 536  Line 536 
536      # Get the parameters.      # Get the parameters.
537      my ($self, %options) = @_;      my ($self, %options) = @_;
538      # Get the control's name and ID.      # Get the control's name and ID.
539      my $menuName = $options{name} || 'myGenomeControl';      my $menuName = $options{name} || $options{id} || 'myGenomeControl';
540      my $menuID = $options{id} || $menuName;      my $menuID = $options{id} || $menuName;
541        Trace("Genome menu name = $menuName with ID $menuID.") if T(3);
542      # Compute the IDs for the status display.      # Compute the IDs for the status display.
543      my $divID = "${menuID}_status";      my $divID = "${menuID}_status";
544      my $urlID = "${menuID}_url";      my $urlID = "${menuID}_url";
# Line 628  Line 629 
629      # Set up the style class.      # Set up the style class.
630      my $classTag = ($class ? " class=\"$class\"" : "" );      my $classTag = ($class ? " class=\"$class\"" : "" );
631      # Create the SELECT tag and stuff it into the output array.      # Create the SELECT tag and stuff it into the output array.
632      my @lines = ("<SELECT name=\"$menuID\" id=\"$menuID\" $onChangeTag$multipleTag$classTag size=\"$rows\">");      my @lines = ("<SELECT name=\"$menuName\" id=\"$menuID\" $onChangeTag$multipleTag$classTag size=\"$rows\">");
633      # Loop through the groups.      # Loop through the groups.
634      for my $group (@groups) {      for my $group (@groups) {
635          # Get the genomes in the group.          # Get the genomes in the group.
# Line 664  Line 665 
665          my $searchThingLabel = ($multiSelect ? "<INPUT type=\"button\" name=\"MacroSearch\" class=\"button\" value=\"Select genomes containing\" onClick=\"selectShowing('$menuID', '$searchThingName'); $showSelect;\" />"          my $searchThingLabel = ($multiSelect ? "<INPUT type=\"button\" name=\"MacroSearch\" class=\"button\" value=\"Select genomes containing\" onClick=\"selectShowing('$menuID', '$searchThingName'); $showSelect;\" />"
666                                               : "Show genomes containing");                                               : "Show genomes containing");
667          push @lines, "<br />$searchThingLabel&nbsp;" .          push @lines, "<br />$searchThingLabel&nbsp;" .
668                       "<INPUT type=\"text\" id=\"$searchThingName\" name=\"$searchThingName\" size=\"30\" onKeyup=\"showTyped('$menuID', '$searchThingName');\" />";                       "<INPUT type=\"text\" id=\"$searchThingName\" name=\"$searchThingName\" size=\"30\" onKeyup=\"showTyped('$menuID', '$searchThingName');\" />" .
669                         Hint("GenomeControl", "Type here to filter the genomes displayed.") . "<br />";
670          # For multi-select mode, we also have buttons to set and clear selections.          # For multi-select mode, we also have buttons to set and clear selections.
671          if ($multiSelect) {          if ($multiSelect) {
672              push @lines, "<INPUT type=\"button\" name=\"ClearAll\" class=\"bigButton\"  value=\"Clear All\" onClick=\"clearAll('$menuID'); $showSelect\" />";              push @lines, "<INPUT type=\"button\" name=\"ClearAll\" class=\"bigButton\"  value=\"Clear All\" onClick=\"clearAll('$menuID'); $showSelect\" />";
# Line 672  Line 674 
674              push @lines, "<INPUT type=\"button\" name=\"NMPDROnly\" class=\"bigButton\"  value=\"Select NMPDR\" onClick=\"selectSome('$menuID', $nmpdrCount, true); $showSelect;\" />";              push @lines, "<INPUT type=\"button\" name=\"NMPDROnly\" class=\"bigButton\"  value=\"Select NMPDR\" onClick=\"selectSome('$menuID', $nmpdrCount, true); $showSelect;\" />";
675          }          }
676          # Add a hidden field we can use to generate organism page hyperlinks.          # Add a hidden field we can use to generate organism page hyperlinks.
677          push @lines, "<INPUT type=\"hidden\" id=\"$urlID\" value=\"$FIG_Config::cgi_url/seedviewer.cgi?page=Organism;organism=\" />";          push @lines, "<INPUT type=\"hidden\" id=\"$urlID\" value=\"$FIG_Config::cgi_url/wiki/rest.cgi/NmpdrPlugin/SeedViewer?page=Organism;organism=\" />";
678          # Add the status display. This tells the user what's selected no matter where the list is scrolled.          # Add the status display. This tells the user what's selected no matter where the list is scrolled.
679          push @lines, "<DIV id=\"$divID\" class=\"Panel\"></DIV>";          push @lines, "<DIV id=\"$divID\" class=\"Panel\"></DIV>";
680      }      }
# Line 1962  Line 1964 
1964      if ($featureID =~ /^fig\|(\d+\.\d+)/) {      if ($featureID =~ /^fig\|(\d+\.\d+)/) {
1965          $retVal = $1;          $retVal = $1;
1966      } else {      } else {
1967            # Find the feature by alias.
1968            my ($realFeatureID) = $self->FeaturesByAlias($featureID);
1969            if ($realFeatureID && $realFeatureID =~ /^fig\|(\d+\.\d+)/) {
1970                $retVal = $1;
1971            } else {
1972                # Use the external table.
1973                my ($org) = $self->GetFlat(['ExternalAliasOrg'], "ExternalAliasOrg(id) = ?",
1974                                           [$featureID], "ExternalAliasOrg(org)");
1975                if ($org) {
1976                    $retVal = $org;
1977                } else {
1978          Confess("Invalid feature ID $featureID.");          Confess("Invalid feature ID $featureID.");
1979      }      }
1980            }
1981        }
1982      # Return the value found.      # Return the value found.
1983      return $retVal;      return $retVal;
1984  }  }
# Line 2802  Line 2817 
2817      return @retVal;      return @retVal;
2818  }  }
2819    
 =head3 GetProperties  
   
     my @list = $sprout->GetProperties($fid, $key, $value, $url);  
   
 Return a list of the properties with the specified characteristics.  
   
 Properties are the Sprout analog of the FIG attributes. The call is  
 passed directly to the CustomAttributes or RemoteCustomAttributes object  
 contained in this object.  
   
 This method returns a series of tuples that match the specified criteria. Each tuple  
 will contain an object ID, a key, and one or more values. The parameters to this  
 method therefore correspond structurally to the values expected in each tuple. In  
 addition, you can ask for a generic search by suffixing a percent sign (C<%>) to any  
 of the parameters. So, for example,  
   
     my @attributeList = $sprout->GetProperties('fig|100226.1.peg.1004', 'structure%', 1, 2);  
   
 would return something like  
   
     ['fig}100226.1.peg.1004', 'structure', 1, 2]  
     ['fig}100226.1.peg.1004', 'structure1', 1, 2]  
     ['fig}100226.1.peg.1004', 'structure2', 1, 2]  
     ['fig}100226.1.peg.1004', 'structureA', 1, 2]  
   
 Use of C<undef> in any position acts as a wild card (all values). You can also specify  
 a list reference in the ID column. Thus,  
   
     my @attributeList = $sprout->GetProperties(['100226.1', 'fig|100226.1.%'], 'PUBMED');  
   
 would get the PUBMED attribute data for Streptomyces coelicolor A3(2) and all its  
 features.  
   
 In addition to values in multiple sections, a single attribute key can have multiple  
 values, so even  
   
     my @attributeList = $sprout->GetProperties($peg, 'virulent');  
   
 which has no wildcard in the key or the object ID, may return multiple tuples.  
   
 =over 4  
   
 =item objectID  
   
 ID of object whose attributes are desired. If the attributes are desired for multiple  
 objects, this parameter can be specified as a list reference. If the attributes are  
 desired for all objects, specify C<undef> or an empty string. Finally, you can specify  
 attributes for a range of object IDs by putting a percent sign (C<%>) at the end.  
   
 =item key  
   
 Attribute key name. A value of C<undef> or an empty string will match all  
 attribute keys. If the values are desired for multiple keys, this parameter can be  
 specified as a list reference. Finally, you can specify attributes for a range of  
 keys by putting a percent sign (C<%>) at the end.  
   
 =item values  
   
 List of the desired attribute values, section by section. If C<undef>  
 or an empty string is specified, all values in that section will match. A  
 generic match can be requested by placing a percent sign (C<%>) at the end.  
 In that case, all values that match up to and not including the percent sign  
 will match. You may also specify a regular expression enclosed  
 in slashes. All values that match the regular expression will be returned. For  
 performance reasons, only values have this extra capability.  
   
 =item RETURN  
   
 Returns a list of tuples. The first element in the tuple is an object ID, the  
 second is an attribute key, and the remaining elements are the sections of  
 the attribute value. All of the tuples will match the criteria set forth in  
 the parameter list.  
   
 =back  
   
 =cut  
   
 sub GetProperties {  
     # Get the parameters.  
     my ($self, @parms) = @_;  
     # Declare the return variable.  
     my @retVal = $self->{_ca}->GetAttributes(@parms);  
     # Return the result.  
     return @retVal;  
 }  
   
2820  =head3 FeatureProperties  =head3 FeatureProperties
2821    
2822      my @properties = $sprout->FeatureProperties($featureID);      my @properties = $sprout->FeatureProperties($featureID);
# Line 4237  Line 4166 
4166  }  }
4167    
4168    
4169    =head3 Hint
4170    
4171        my $htmlText = SearchHelper::Hint($wikiPage, $hintText);
4172    
4173    Return the HTML for a small question mark that displays the specified hint text when it is clicked.
4174    This HTML can be put in forms to provide a useful hinting mechanism.
4175    
4176    =over 4
4177    
4178    =item wikiPage
4179    
4180    Name of the wiki page to be popped up when the hint mark is clicked.
4181    
4182    =item hintText
4183    
4184    Text to display for the hint. It is raw html, but may not contain any double quotes.
4185    
4186    =item RETURN
4187    
4188    Returns the html for the hint facility. The resulting html shows a small button-like thing that
4189    uses the standard FIG popup technology.
4190    
4191    =back
4192    
4193    =cut
4194    
4195    sub Hint {
4196        # Get the parameters.
4197        my ($wikiPage, $hintText) = @_;
4198        # Escape the single quotes in the hint text.
4199        my $quotedText = $hintText;
4200        $quotedText =~ s/'/\\'/g;
4201        # Convert the wiki page name to a URL.
4202        my $wikiURL = join("", map { ucfirst $_ } split /\s+/, $wikiPage);
4203        $wikiURL = "$FIG_Config::cgi_url/wiki/view.cgi/FIG/$wikiURL";
4204        # Compute the mouseover script.
4205        my $mouseOver = "doTooltip(this, '$quotedText')";
4206        # Create the html.
4207        my $retVal = "&nbsp;<a href=\"$wikiURL\"><img src=\"$FIG_Config::cgi_url/Html/button-h.png\" class=\"helpicon\" onmouseover=\"$mouseOver\"/></a>";
4208        # Return it.
4209        return $retVal;
4210    }
4211    
4212  1;  1;

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