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Summary

BioMart::Formatter::ALL

Package variables

Included modules

Inherit

BioMart::FormatterI

Synopsis

The ALL Formatter returns data formatted into a ALL table
for a BioMart query's ResultTable

Description

When given a BioMart::ResultTable containing the results of
a BioMart::Query the ALL Formatter will return ALL formatted tabular
output. The getDisplayNames and getFooterText can be used to return
appropiately formatted headers and footers respectively. If hyperlink
templates are defined for the attributes in the Dataset's ConfigurationTree
then appropiate hyperlinks will be calculated for each cell of the table.
Addition of any extra attributes to the Query that may be required for this
hyperlink formatting is handled in this Formatter

Methods

Methods description

None available.

Methods code

sub _new {

    my ($self) = @_;

    $self->SUPER::_new();  
    $self->attr('reference',0);

}

sub getDisplayNames {

    my $self = shift;

    my $original_attributes = $self->get('original_attributes');
    my $dataset1_end = $self->get('dataset1_end');
    my $query = $self->get('query');
    my $registry = $query->getRegistry;
    my $final_dataset_order = $query->finalDatasetOrder;
    
    my @attribute_display_names;
    my @original_dataset_attributes;
    foreach my $dataset(reverse @$final_dataset_order){
	foreach (@{$original_attributes}){
	    push @original_dataset_attributes,$_ 
		if ($_->dataSetName eq $dataset);
	}
    }
    foreach my $original_attribute(@original_dataset_attributes){
	push @attribute_display_names, $original_attribute->displayName;
    }

    if ($self->get('reference')){
	$attribute_display_names[-1] .= " (Reference)";
    }
    # print the display names    
    my $header_string = sprintf $HEADER_TMPL, '';
    $header_string .= $ROW_START_TMPL1;
#    map{ $header_string .= 
#	     sprintf $HEADERFIELD_TMPL, $_ } @attribute_display_names;
    map{ $header_string .= sprintf $HEADERFIELD_TMPL1, $_ } @attribute_display_names[0..$dataset1_end];
    map{ $header_string .= sprintf $HEADERFIELD_TMPL2, $_ } @attribute_display_names[$dataset1_end+1..@attribute_display_names-1];
    $header_string .= $ROW_END_TMPL;
    return $header_string;
}

# Override empty-string returning method in superclass, to return proper 
# table- and document-closing tags (to keep ALL valid).

}

sub getFooterText {

       return q{
</table>
</body>
</html>
};

}

sub getFormatterDisplayName {

    return 'All SNPs';

}

sub getMimeType {

    return 'text/html';
}


1;

}

sub nextRow {

   my $self = shift;

   my $rtable = $self->get('result_table');

   # print the data with urls if available
   my $new_row;
   my $row = $rtable->nextRow;
   if (!$row){
       return;
   }
   map { $_ = q{} unless defined ($_); } @$row;
   my $attribute_positions = $self->get('attribute_positions');
   my $attribute_url_positions = $self->get('attribute_url_positions');
   my $attribute_url = $self->get('attribute_url');

   #my $dataset1_end = $self->get('dataset1_end');

   my $reference;
   if ($self->get('reference')){
       $reference= $$row[$$attribute_positions[-1]];
   
       if (!$reference){
	   return "\n";
       }
   }
   my $result_seen;
   for (my $i = 0; $i < @{$attribute_positions}; $i++){


#       if (($i != @{$attribute_positions} - 1) && ($$row[$$attribute_positions[$i]] eq $reference) && $$row[$$attribute_positions[$i]] && $reference){
#          $$row[$$attribute_positions[$i]] = '';
#       }

       if ($reference){
           $result_seen = 1 if ($$row[$$attribute_positions[$i]] =~ /^[ACGT]$/ && ($i != @{$attribute_positions} - 1));
       }
       else{
           $result_seen = 1 if ($$row[$$attribute_positions[$i]] =~ /^[ACGT]$/ );
       }


       if ($$row[$$attribute_positions[$i]] eq 'C'){
	   $$row[$$attribute_positions[$i]] = qw(bgcolor="yellow">).'C';
       }
       elsif ($$row[$$attribute_positions[$i]] eq 'G'){
           $$row[$$attribute_positions[$i]] = qw(bgcolor="green">).'G';
       }
       elsif ($$row[$$attribute_positions[$i]] eq 'A'){
           $$row[$$attribute_positions[$i]] = qw(bgcolor="red">).'A';
       }
       elsif ($$row[$$attribute_positions[$i]] eq 'T'){
           $$row[$$attribute_positions[$i]] = qw(bgcolor="orange">).'T';
       }


       else{
	   $$row[$$attribute_positions[$i]] = qw(>).$$row[$$attribute_positions[$i]];
       }

	   


       if ($$attribute_url[$i]){
	   my @url_data = map {$$row[$_]} @{$$attribute_url_positions[$i]};
	   my $url_string = sprintf($$attribute_url[$i],@url_data);
	   $url_string =~ s/>//g;
	   push @{$new_row}, '<a href="'.$url_string.'" target="_blank"'.
	       $$row[$$attribute_positions[$i]]."</a>";
       }
       else{
	   push @{$new_row},$$row[$$attribute_positions[$i]];
       }
   }
   if ($result_seen){
       $current_rowcount++;
       my $fields_string = '';
       map{ $fields_string .= sprintf ($NORMALFIELD_TMPL1, defined ($_) ? $_ : ''); } @{$new_row};
       return ($current_rowcount % 2 == 0 ? $ROW_START_TMPL1 : $ROW_START_TMPL2)
	                              . $fields_string
                                      . $ROW_END_TMPL;
   }
   else{
       return "\n";
   }

}

sub processQuery {

    my ($self, $query) = @_;

    my $filters = $query->getAllFilters();
    my @filts;
    foreach my $filter(@{$filters}){
	if ($filter->name eq 'reference_strain'){
	    my $rows = $filter->get('attribute_table')->getRows();
	    my $ref_strain = ${$$rows[0]}[0];
	    # remove the filter
	    
	    $ref_strain =~ s/\//\_/g;
            $ref_strain =~ s/ /\_/g;
            $ref_strain =~ s/\+/\_/g;
            $ref_strain =~ s/\./\_/g;
            $ref_strain =~ s/\-/\_/g;
	    $query->addAttribute(lc($ref_strain));
	    $self->set('reference',1);
	}
        else{
	    push @filts,$filter;
	}
    }
    $query->removeAllFilters();
    $query->addFilters(\@filts);


    $self->set('original_attributes',[@{$query->getAllAttributes()}])
          if ($query->getAllAttributes());


    $query = $self->setHTMLAttributes($query);
    $self->set('query',$query);
    return $query;

}

General documentation

This module is part of the BioMart project
http://www.biomart.org
Questions can be posted to the mart-dev mailing list: mart-dev@ebi.ac.uk