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revision 1.6, Mon Jan 19 21:56:19 2009 UTC revision 1.7, Thu Feb 5 07:25:34 2009 UTC
# Line 345  Line 345 
345      my $outputHits = 0;      my $outputHits = 0;
346      # Create the xml string from the data.      # Create the xml string from the data.
347      my $xmlString = join("", @{$data});      my $xmlString = join("", @{$data});
348        # Only proceed if we got something back.
349      # Parse the XML. The various options help to keep the result more compact and predictable.      # Parse the XML. The various options help to keep the result more compact and predictable.
350      # Note we do some major error-checking here, because XMLin is very delicate.      # Note we do some major error-checking here, because XMLin is very delicate.
351      my $xmlThing;      my $xmlThing;
352      eval {      eval {
353            if ($xmlString) {
354          $xmlThing = XMLin($xmlString, GroupTags =>  { Iteration_hits => 'Hit', Hit_hsps => 'Hsp' },          $xmlThing = XMLin($xmlString, GroupTags =>  { Iteration_hits => 'Hit', Hit_hsps => 'Hsp' },
355                                        ForceArray => ['Hit', 'Hsp']);                                        ForceArray => ['Hit', 'Hsp']);
356            }
357      };      };
358      if ($@) {      if ($@) {
359          Confess("XML parsing error for $genome: $@");          Confess("XML parsing error for $genome: $@");
# Line 655  Line 658 
658      push @rows, CGI::Tr(CGI::td("Tool"), CGI::td($toolMenu));      push @rows, CGI::Tr(CGI::td("Tool"), CGI::td($toolMenu));
659      push @rows, CGI::Tr(CGI::td("Sequence in Raw or FASTA Format"),      push @rows, CGI::Tr(CGI::td("Sequence in Raw or FASTA Format"),
660                           CGI::td({colspan => 2}, CGI::textarea(-name => "sequence", -rows => 5,                           CGI::td({colspan => 2}, CGI::textarea(-name => "sequence", -rows => 5,
661                                                                 -value => $sequence, -cols => 62)));                                                                 -value => $sequence, -cols => 62,
662                                                                   -style => 'font-family: monospace')));
663      push @rows, CGI::Tr(CGI::td("Select one or more genomes"),      push @rows, CGI::Tr(CGI::td("Select one or more genomes"),
664                           CGI::td({colspan => 2}, $menu));                           CGI::td({colspan => 2}, $menu));
665      push @rows, CGI::Tr(CGI::td("Blast Options"),      push @rows, CGI::Tr(CGI::td("Blast Options"),

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