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| 1 : | parrello | 1.1 | #!/usr/bin/perl -w |
| 2 : | |||
| 3 : | package SHGeneSearch; | ||
| 4 : | |||
| 5 : | use strict; | ||
| 6 : | use Tracer; | ||
| 7 : | use CGI; | ||
| 8 : | use HTML; | ||
| 9 : | use Sprout; | ||
| 10 : | use RHFeatures; | ||
| 11 : | use base 'SearchHelper'; | ||
| 12 : | |||
| 13 : | =head1 Features in Genomes Search Helper | ||
| 14 : | |||
| 15 : | =head2 Introduction | ||
| 16 : | |||
| 17 : | The single feature search finds features from one or more selected organisms | ||
| 18 : | using the full power of the B<RHFeature> filtering. | ||
| 19 : | |||
| 20 : | =over 4 | ||
| 21 : | |||
| 22 : | =item genome | ||
| 23 : | |||
| 24 : | IDs of the relevant genome | ||
| 25 : | |||
| 26 : | =back | ||
| 27 : | |||
| 28 : | =head2 Virtual Methods | ||
| 29 : | |||
| 30 : | =head3 Form | ||
| 31 : | |||
| 32 : | parrello | 1.3 | my $html = $shelp->Form(); |
| 33 : | parrello | 1.1 | |
| 34 : | Generate the HTML for a form to request a new search. | ||
| 35 : | |||
| 36 : | =cut | ||
| 37 : | |||
| 38 : | sub Form { | ||
| 39 : | # Get the parameters. | ||
| 40 : | my ($self) = @_; | ||
| 41 : | # Get the CGI and sprout objects. | ||
| 42 : | my $cgi = $self->Q(); | ||
| 43 : | my $sprout = $self->DB(); | ||
| 44 : | # Get the IDs of the currently-selected genomes (if any). | ||
| 45 : | my @genomeIDs = $cgi->param('genome'); | ||
| 46 : | # Start the form. | ||
| 47 : | my $retVal = $self->FormStart("Gene Search"); | ||
| 48 : | # Get the genome menu. | ||
| 49 : | my $menu = $self->NmpdrGenomeMenu('genome', 'multiple', \@genomeIDs); | ||
| 50 : | # Create a table for the form data. | ||
| 51 : | my @table = (); | ||
| 52 : | push @table, RHFeatures::WordSearchRow($self), | ||
| 53 : | $cgi->Tr($cgi->td("Select one or more genomes"), $cgi->td({colspan => 2}, $menu)), | ||
| 54 : | RHFeatures::FeatureFilterFormRows($self), | ||
| 55 : | $self->SubmitRow(); | ||
| 56 : | $retVal .= $self->MakeTable(\@table); | ||
| 57 : | # Close the form. | ||
| 58 : | $retVal .= $self->FormEnd(); | ||
| 59 : | # Return the result. | ||
| 60 : | return $retVal; | ||
| 61 : | } | ||
| 62 : | |||
| 63 : | =head3 Find | ||
| 64 : | |||
| 65 : | parrello | 1.3 | my $resultCount = $shelp->Find(); |
| 66 : | parrello | 1.1 | |
| 67 : | Conduct a search based on the current CGI query parameters. The search results will | ||
| 68 : | be written to the session cache file and the number of results will be | ||
| 69 : | returned. If the search parameters are invalid, a result count of C<undef> will be | ||
| 70 : | returned and a result message will be stored in this object describing the problem. | ||
| 71 : | |||
| 72 : | =cut | ||
| 73 : | |||
| 74 : | sub Find { | ||
| 75 : | my ($self) = @_; | ||
| 76 : | # Get the CGI and Sprout objects. | ||
| 77 : | my $cgi = $self->Q(); | ||
| 78 : | my $sprout = $self->DB(); | ||
| 79 : | # Declare the return variable. If it remains undefined, the caller will | ||
| 80 : | # know that an error occurred. | ||
| 81 : | my $retVal; | ||
| 82 : | # Get the result helper. | ||
| 83 : | my $rhelp = RHFeatures->new($self); | ||
| 84 : | # Only proceed if the filter parameters are valid. | ||
| 85 : | if ($rhelp->Valid()) { | ||
| 86 : | # Get the genomes. | ||
| 87 : | $self->PrintLine("Retrieving genomes. "); | ||
| 88 : | my @genomes = $self->GetGenomes('genome'); | ||
| 89 : | # If the user specified all genomes, we simply use a single | ||
| 90 : | # undef so that the feature filter knows to act accordingly. | ||
| 91 : | if ($sprout->IsAllGenomes(\@genomes)) { | ||
| 92 : | $self->PrintLine("All genomes selected.<br />"); | ||
| 93 : | @genomes = (undef); | ||
| 94 : | } else { | ||
| 95 : | my $genomeCount = scalar(@genomes); | ||
| 96 : | $self->PrintLine("Genomes found: $genomeCount.<br />"); | ||
| 97 : | } | ||
| 98 : | # Only proceed if at least one genome is specified. | ||
| 99 : | if (scalar(@genomes) == 0) { | ||
| 100 : | $self->SetMessage("Please specify at least one genome."); | ||
| 101 : | } else { | ||
| 102 : | # Set the column list. | ||
| 103 : | $self->DefaultColumns($rhelp); | ||
| 104 : | # Initialize the session file. | ||
| 105 : | $self->OpenSession($rhelp); | ||
| 106 : | # Initialize the result counter. | ||
| 107 : | $retVal = 0; | ||
| 108 : | # Loop through the selected genomes. | ||
| 109 : | for my $genomeID (@genomes) { | ||
| 110 : | if (defined $genomeID) { | ||
| 111 : | $self->PrintLine("Processing genome $genomeID. "); | ||
| 112 : | } else { | ||
| 113 : | parrello | 1.2 | $self->PrintLine("Processing query."); |
| 114 : | parrello | 1.1 | } |
| 115 : | Trace("Creating query. GenomeID = $genomeID") if T(3); | ||
| 116 : | my $fquery = $rhelp->GetQuery($genomeID); | ||
| 117 : | my $count = 0; | ||
| 118 : | while (my $feature = $rhelp->Fetch($fquery)) { | ||
| 119 : | # Get the feature ID. | ||
| 120 : | my $fid = $feature->PrimaryValue('Feature(id)'); | ||
| 121 : | # Compute the sort key. | ||
| 122 : | my $sortKey = $rhelp->SortKey($feature); | ||
| 123 : | $rhelp->PutData($sortKey, $fid, $feature); | ||
| 124 : | $count++; | ||
| 125 : | } | ||
| 126 : | $self->PrintLine("Results found: $count.<br />"); | ||
| 127 : | $retVal += $count; | ||
| 128 : | } | ||
| 129 : | # Close the session file. | ||
| 130 : | $self->CloseSession(); | ||
| 131 : | } | ||
| 132 : | } | ||
| 133 : | # Return the result count. | ||
| 134 : | return $retVal; | ||
| 135 : | } | ||
| 136 : | |||
| 137 : | =head3 Description | ||
| 138 : | |||
| 139 : | parrello | 1.3 | my $htmlText = $shelp->Description(); |
| 140 : | parrello | 1.1 | |
| 141 : | Return a description of this search. The description is used for the table of contents | ||
| 142 : | on the main search tools page. It may contain HTML, but it should be character-level, | ||
| 143 : | not block-level, since the description is going to appear in a list. | ||
| 144 : | |||
| 145 : | =cut | ||
| 146 : | |||
| 147 : | sub Description { | ||
| 148 : | # Get the parameters. | ||
| 149 : | my ($self) = @_; | ||
| 150 : | # Return the result. | ||
| 151 : | return "Search for genes in selected genomes, filtered by subsystem or search keywords."; | ||
| 152 : | } | ||
| 153 : | |||
| 154 : | =head3 SearchTitle | ||
| 155 : | |||
| 156 : | parrello | 1.3 | my $titleHtml = $shelp->SearchTitle(); |
| 157 : | parrello | 1.1 | |
| 158 : | Return the display title for this search. The display title appears above the search results. | ||
| 159 : | If no result is returned, no title will be displayed. The result should be an html string | ||
| 160 : | that can be legally put inside a block tag such as C<h3> or C<p>. | ||
| 161 : | |||
| 162 : | =cut | ||
| 163 : | |||
| 164 : | sub SearchTitle { | ||
| 165 : | # Get the parameters. | ||
| 166 : | my ($self) = @_; | ||
| 167 : | # Compute the title. We extract the number of genomes from the query parameters. | ||
| 168 : | my $cgi = $self->Q(); | ||
| 169 : | my @genomes = $cgi->param('genome'); | ||
| 170 : | my $count = scalar(@genomes); | ||
| 171 : | if ($count == 1) { | ||
| 172 : | $count = $genomes[0]; | ||
| 173 : | } else { | ||
| 174 : | $count = "$count Genomes"; | ||
| 175 : | } | ||
| 176 : | my $retVal = "Search for Genes in $count"; | ||
| 177 : | # Return it. | ||
| 178 : | return $retVal; | ||
| 179 : | } | ||
| 180 : | |||
| 181 : | |||
| 182 : | parrello | 1.3 | 1; |
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