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revision 1.60, Fri Jun 20 16:08:32 2008 UTC revision 1.62, Wed Jul 9 19:55:31 2008 UTC
# Line 374  Line 374 
374    
375  }  }
376    
377    =head
378        provides layer of abstraction between tools and underlying access method to Attribute Server
379    =cut
380    
381    sub get_attributes{
382        my ($self,$fig,$search_set,$search_term,$value_array_ref) = @_;
383        my @attributes = $fig->get_attributes($search_set,$search_term,@$value_array_ref);
384        return @attributes;
385    }
386    
387  =head3 get_sims_objects()  =head3 get_sims_objects()
388    
389  This is the B<REAL WORKHORSE> method of this Package.  This is the B<REAL WORKHORSE> method of this Package.
# Line 695  Line 705 
705  sub get_sims_observations{  sub get_sims_observations{
706      my ($fid,$datasets_ref,$fig,$parameters) = (@_);      my ($fid,$datasets_ref,$fig,$parameters) = (@_);
707    
708      my ($max_sims, $max_expand, $max_eval, $sim_order, $db_filter);      my ($max_sims, $max_expand, $max_eval, $sim_order, $db_filter, $sim_filters);
709      if ($parameters->{flag}){      if ($parameters->{flag}){
710        $max_sims = $parameters->{max_sims};        $max_sims = $parameters->{max_sims};
711        $max_expand = $parameters->{max_expand};        $max_expand = $parameters->{max_expand};
712        $max_eval = $parameters->{max_eval};        $max_eval = $parameters->{max_eval};
713        $db_filter = $parameters->{db_filter};        $db_filter = $parameters->{db_filter};
714        $sim_order = $parameters->{sim_order};        $sim_filters->{ sort_by } = $parameters->{sim_order};
715          #$sim_order = $parameters->{sim_order};
716        $group_by_genome = 1 if (defined ($parameters->{group_genome}));        $group_by_genome = 1 if (defined ($parameters->{group_genome}));
717      }      }
718      else{      else{
# Line 709  Line 720 
720        $max_expand = 5;        $max_expand = 5;
721        $max_eval = 1e-5;        $max_eval = 1e-5;
722        $db_filter = "figx";        $db_filter = "figx";
723        $sim_order = "id";        $sim_filters->{ sort_by } = 'id';
724          #$sim_order = "id";
725      }      }
726    
727      my($id, $genome, @genomes, %sims);      my($id, $genome, @genomes, %sims);
728      my @tmp= $fig->sims($fid,$max_sims,$max_eval,$db_filter,$max_expand);      my @tmp= $fig->sims($fid,$max_sims,$max_eval,$db_filter,$max_expand,$sim_filters);
729      @tmp = grep { !($_->id2 =~ /^fig\|/ and $fig->is_deleted_fid($_->id2)) } @tmp;      @tmp = grep { !($_->id2 =~ /^fig\|/ and $fig->is_deleted_fid($_->id2)) } @tmp;
730      my ($dataset);      my ($dataset);
731    
# Line 2227  Line 2239 
2239          $white = '#999966' if ($id eq $query_fid);          $white = '#999966' if ($id eq $query_fid);
2240          $org_color = '#999966' if ($id eq $query_fid);          $org_color = '#999966' if ($id eq $query_fid);
2241          my $anchor_name = "anchor_". $replace_id;          my $anchor_name = "anchor_". $replace_id;
2242            my $checked = ""; $checked = "checked" if ($id eq $query_fid);
2243          if ($id =~ /^fig\|/){          if ($id =~ /^fig\|/){
2244            my $box = qq(<a name="$anchor_name"></a><input type="checkbox" name="seq" value="$id" id="$field_name" onClick="VisualCheckPair('$field_name', '$pair_name','$cell_name');">);            my $box = qq(<a name="$anchor_name"></a><input type="checkbox" name="seq" value="$id" id="$field_name" onClick="VisualCheckPair('$field_name', '$pair_name','$cell_name');" $checked>);
2245            my $radio = qq(<input type="radio" name="function_select" value="$id" id="$field_name" >);            my $radio = qq(<input type="radio" name="function_select" value="$id" id="$field_name" >);
2246            $box_cell = { 'data'=>$box, 'highlight'=>$org_color};            $box_cell = { 'data'=>$box, 'highlight'=>$org_color};
2247            $radio_cell = { 'data'=>$radio, 'highlight'=>$white};            $radio_cell = { 'data'=>$radio, 'highlight'=>$white};

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