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Summary

BioMart::Formatter::HTML_36

Package variables

Included modules

Inherit

BioMart::FormatterI

Synopsis

The HTML_36 Formatter returns data formatted into a HTML_36 table
for a BioMart query's ResultTable

Description

When given a BioMart::ResultTable containing the results of
a BioMart::Query the HTML_36 Formatter will return HTML_36 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();

    # connect to database and get adaptors
    my $db = EnsEMBL::Web::DBSQL::DBConnection->new( 'Mus_musculus', $ENSEMBL_WEB_REGISTRY->species_defs
      )->get_DBAdaptor( 'core', 'Mus_musculus' );
    $self->attr('db_adaptor',$db);

}

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;
    }

    # 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 HTML valid).

}

sub getFooterText {

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

}

sub getFormatterDisplayName {

    return 'Mouse 36 assembly (HTML)';

}

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;
   }





   my $chromosome = $$row[-1];
   my $strand = $$row[-2];

   # convert coordinates to NCBI36 assembly
   my @atts_to_convert = qw(
                             start_position
                             end_position
                             transcript_start
                             transcript_end
                             feat_chr_start
                             feat_chr_end
                             gene_chrom_start
                             gene_chrom_end
                             transcript_chrom_start
                             transcript_chrom_end
                             exon_chrom_start
                             exon_coding_end
                             exon_chrom_end
                             exon_coding_start
                             chromosome_location
                             );
   my $attribute_order = $self->get('original_attributes');
   my $attribute_number = 0;
   my ($orig_attribute,$position,$new_position);
   foreach (@$attribute_order){
       $orig_attribute = $_->name;
       foreach (@atts_to_convert){
	   if ($orig_attribute eq $_){
                # covert coordinates
	       $position = $$row[$attribute_number];
	       
	       next if (!$position);
	       my $db = $self->get('db_adaptor');
	       my $sa = $db->get_SliceAdaptor();

               # create an analysis for the type of feature you wish to store
                my $analysis = new Bio::EnsEMBL::Analysis(
                                                          -LOGIC_NAME => 'your_analysis'
                                                          );
                my $slice_oldasm = $sa->fetch_by_region('chromosome', $chromosome, undef, undef,
                                                        undef, $current_assembly);



                # create a new feature on the old assembly
                my $feat = Bio::EnsEMBL::SimpleFeature->new(
                                                            -DISPLAY_LABEL  => '',
                                                            -START          => $position,
                                                            -END            => $position,
                                                            -STRAND         => $strand,
                                                            -SLICE          => $slice_oldasm,
                                                            -ANALYSIS       => $analysis,
							    );

                # project feature to new assembly
	       my $feat_slice = $feat->feature_Slice;
	       my @segments;
	       if ($feat_slice){
		   @segments = @{ $feat->feature_Slice->project('chromosome', $new_assembly) };
	       }


                # do some sanity checks on the projection results:
                # discard the projected feature if
                #   1. it doesn't project at all (no segments returned)
                #   2. the projection is fragmented (more than one segment)
                #   3. the projection doesn't have the same length as the original
                #      feature

	       if (scalar(@segments) != 1){
		   $new_position = '-';
	       }
	       elsif ($segments[0]->to_Slice()->length != $feat->length){
		   $new_position = '-';
	       }
	       elsif ($segments[0]->to_Slice()->seq_region_name ne $feat->slice->seq_region_name){
		   $new_position = '-';
	       }
	       else{
		   $new_position = $segments[0]->to_Slice()->start;
	       }

	       $$row[$attribute_number] = $new_position;
	   }
       }
       $attribute_number++;
   }
   my $new_row_length = @$row - 3;
   $row = [@$row[0..$new_row_length]];


   


   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');

   for (my $i = 0; $i < @{$attribute_positions}; $i++){
       # superscripting for emma mart
       $$row[$$attribute_positions[$i]] =~ s/\<(.*)\>/<span style="vertical-align:super;font-size:0.8em">$1<\/span>/;
	   


       if ($$attribute_url[$i]){
	   my @url_data = map {$$row[$_]} @{$$attribute_url_positions[$i]};
	   my $url_string = sprintf($$attribute_url[$i],@url_data);
	   push @{$new_row}, '<a href="'.$url_string.'" target="_blank">'.
	       $$row[$$attribute_positions[$i]]."</a>";
       }
       else{
	   push @{$new_row},$$row[$$attribute_positions[$i]];
       }
   }

   $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;

}

sub processQuery {

    my ($self, $query) = @_;
    $self->set('original_attributes',[@{$query->getAllAttributes()}]) 
	if ($query->getAllAttributes());
    $query = $self->setHTMLAttributes($query);
    $query->addAttribute('strand');
    $query->addAttribute('chromosome_name');
    $self->set('query',$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