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revision 1.12, Tue Apr 10 06:10:02 2007 UTC revision 1.14, Thu Apr 19 00:07:02 2007 UTC
# Line 96  Line 96 
96      my $statistical = $cgi->param('statistical') || 1;      my $statistical = $cgi->param('statistical') || 1;
97      my $showMatch = $cgi->param('showMatch') || 0;      my $showMatch = $cgi->param('showMatch') || 0;
98      my $useSims = $cgi->param('useSims') || 0;      my $useSims = $cgi->param('useSims') || 0;
99      my $pegsOnly = $cgi->param('pegsOnly') || 0;      my $pegsOnly = $cgi->param('pegsOnly') || 1;
100      # Now we build the table rows.      # Now we build the table rows.
101      my @rows = ();      my @rows = ();
102      # First we have the given genome.      # First we have the given genome.
# Line 126  Line 126 
126                                                   -checked => $showMatch,                                                   -checked => $showMatch,
127                                                   -value => 1,                                                   -value => 1,
128                                                   -label => 'Show Matching Genes'),                                                   -label => 'Show Matching Genes'),
129                                    $cgi->checkbox(-name => 'pegsOnly',  #                                  $cgi->checkbox(-name => 'pegsOnly',
130                                                   -checked => $pegsOnly,  #                                                 -checked => $pegsOnly,
131                                                   -value => 1,  #                                                 -value => 1,
132                                                   -label => 'PEGs Only')))),  #                                                 -label => 'PEGs Only')
133                                      ))),
134                  $cgi->Tr($cgi->td("Cutoff"),                  $cgi->Tr($cgi->td("Cutoff"),
135                           $cgi->td($cgi->textfield(-name => 'cutoff',                           $cgi->td($cgi->textfield(-name => 'cutoff',
136                                                    -value => $cutoff,                                                    -value => $cutoff,
# Line 167  Line 168 
168      # assume there was an error.      # assume there was an error.
169      my $retVal;      my $retVal;
170      # Denote the extra columns go at the end.      # Denote the extra columns go at the end.
171      $self->SetExtraPos(1);      $self->SetExtraPos('score');
172      # Create the timers.      # Create the timers.
173      my ($saveTime, $loopCounter, $bbhTimer, $putTimer, $queryTimer) = (0, 0, 0, 0, 0);      my ($saveTime, $loopCounter, $bbhTimer, $putTimer, $queryTimer) = (0, 0, 0, 0, 0);
174      # Validate the numeric parameters.      # Validate the numeric parameters.
175      my $commonality = $cgi->param('commonality');      my $commonality = $cgi->param('commonality');
176      my $cutoff = $cgi->param('cutoff');      my $cutoff = $cgi->param('cutoff');
177      my $pegsOnly = $cgi->param('pegsOnly');      my $pegsOnly = $cgi->param('pegsOnly') || 1;
178      if ($commonality !~ /^\s*\d(\.\d+)?\s*$/) {      if ($commonality !~ /^\s*\d(\.\d+)?\s*$/) {
179          $self->SetMessage("Commonality value appears invalid, too big, negative, or not a number.");          $self->SetMessage("Commonality value appears invalid, too big, negative, or not a number.");
180      } elsif ($commonality <= 0 || $commonality > 1) {      } elsif ($commonality <= 0 || $commonality > 1) {

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