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revision 1.3, Thu Aug 16 19:23:38 2007 UTC revision 1.4, Mon Aug 20 23:27:55 2007 UTC
# Line 123  Line 123 
123                                      output => \&blastXML,                                      output => \&blastXML,
124                                      inputType => 'prot',                                      inputType => 'prot',
125                                      extras => [[bsc => 0, title => "Bit Score", style => "rightAlign", download => 'num'],                                      extras => [[bsc => 0, title => "Bit Score", style => "rightAlign", download => 'num'],
126                                                 [queryLoc => 1, title => "Query Location", style => "leftAlign", download => 'text'],                                                 [queryLoc => undef, title => "Query Location", style => "leftAlign", download => 'text'],
127                                                 [hitLoc => 2, title => "Hit Location", style => "leftAlign", download => 'text'],                                                 [hitLoc => undef, title => "Hit Location", style => "leftAlign", download => 'text'],
128                                                 [alignment => undef, title => "Alignment", style => "code", download => 'align']],                                                 [alignment => undef, title => "Alignment", style => "code", download => 'align']],
129                                      buttonName => 'BLAST',                                      buttonName => 'BLAST',
130                                      targetRelationship => 'HasFeature',                                      targetRelationship => 'HasFeature',
# Line 135  Line 135 
135                                      output => \&blastXML,                                      output => \&blastXML,
136                                      inputType => 'prot',                                      inputType => 'prot',
137                                      extras => [[bsc => 0, title => "Bit Score", style => "rightAlign", download => 'num'],                                      extras => [[bsc => 0, title => "Bit Score", style => "rightAlign", download => 'num'],
138                                                 [queryLoc => 1, title => "Query Location", style => "leftAlign", download => 'text'],                                                 [queryLoc => undef, title => "Query Location", style => "leftAlign", download => 'text'],
139                                                 [hitLoc => 2, title => "Hit Location", style => "leftAlign", download => 'text'],                                                 [hitLoc => undef, title => "Hit Location", style => "leftAlign", download => 'text'],
140                                                 [alignment => undef, title => "Alignment", style => "code", download => 'align']],                                                 [alignment => undef, title => "Alignment", style => "code", download => 'align']],
141                                      buttonName => 'BLAST',                                      buttonName => 'BLAST',
142                                      targetRelationship => 'HasFeature',                                      targetRelationship => 'HasFeature',
# Line 147  Line 147 
147                                      output => \&blastXML,                                      output => \&blastXML,
148                                      inputType => 'dna',                                      inputType => 'dna',
149                                      extras => [[bsc => 0, title => "Bit Score", style => "rightAlign", download => 'num'],                                      extras => [[bsc => 0, title => "Bit Score", style => "rightAlign", download => 'num'],
150                                                 [queryLoc => 1, title => "Query Location", style => "leftAlign", download => 'text'],                                                 [queryLoc => undef, title => "Query Location", style => "leftAlign", download => 'text'],
151                                                 [hitLoc => 2, title => "Hit Location", style => "leftAlign", download => 'text'],                                                 [hitLoc => undef, title => "Hit Location", style => "leftAlign", download => 'text'],
152                                                 [alignment => undef, title => "Alignment", style => "code", download => 'align']],                                                 [alignment => undef, title => "Alignment", style => "code", download => 'align']],
153                                      buttonName => 'BLAST',                                      buttonName => 'BLAST',
154                                      targetRelationship => 'HasContig',                                      targetRelationship => 'HasContig',
# Line 376  Line 376 
376                  # We need to create an output tuple for this hit. First, we                  # We need to create an output tuple for this hit. First, we
377                  # create the alignment string.                  # create the alignment string.
378                  my $alignment = join("<br />", $point->{Hsp_qseq}, $point->{Hsp_midline}, $point->{Hsp_hseq});                  my $alignment = join("<br />", $point->{Hsp_qseq}, $point->{Hsp_midline}, $point->{Hsp_hseq});
379                  # Next, we need to create the locations.                  # Convert the spaces to non-breaking so that they aren't mucked up by HTML formatting.
380                    $alignment =~ s/ /&nbsp;/g;
381                    # Next, we need to create the locations. The fields Hsp_query-frame and Hsp_hit-frame indicate
382                    # whether the location is on the plus or minus strand.
383                  my $hitLoc = BasicLocation->new($hitArea, $point->{'Hsp_hit-from'}, "_", $point->{'Hsp_hit-to'});                  my $hitLoc = BasicLocation->new($hitArea, $point->{'Hsp_hit-from'}, "_", $point->{'Hsp_hit-to'});
384                    $hitLoc->Reverse if $point->{'Hsp_hit-frame'} < 0;
385                  my $queryLoc = BasicLocation->new($queryName, $point->{'Hsp_query-from'}, "_", $point->{'Hsp_query-to'});                  my $queryLoc = BasicLocation->new($queryName, $point->{'Hsp_query-from'}, "_", $point->{'Hsp_query-to'});
386                    $queryLoc->Reverse if $point->{'Hsp_query-frame'} < 0;
387                  # Finally, we get the bit score, formatted nicely for the display.                  # Finally, we get the bit score, formatted nicely for the display.
388                  my $bsc = sprintf("%0.3f", $point->{'Hsp_bit-score'});                  my $bsc = sprintf("%0.3f", $point->{'Hsp_bit-score'});
389                  # Now we can build our output tuple.                  # Now we can build our output tuple.

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