BioMart::Formatter HTML_36
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
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Summary
BioMart::Formatter::HTML_36
Package variables
Privates (from "my" definitions)
$current_rowcount = 0
Included modules
EnsEMBL::Web::DBSQL::DBConnection
EnsEMBL::Web::RegObj
Readonly
Inherit
BioMart::FormatterI
Synopsis
The HTML_36 Formatter returns data formatted into a HTML_36 table
for a BioMart query's ResultTable
Description
When given a BioMart::ResultTable containing the results of
a BioMart::Query the HTML_36 Formatter will return HTML_36 formatted tabular
output. The getDisplayNames and getFooterText can be used to return
appropiately formatted headers and footers respectively. If hyperlink
templates are defined for the attributes in the Dataset's ConfigurationTree
then appropiate hyperlinks will be calculated for each cell of the table.
Addition of any extra attributes to the Query that may be required for this
hyperlink formatting is handled in this Formatter
Methods
_new
No description
Code
getDisplayNames
No description
Code
getFooterText
No description
Code
getFormatterDisplayName
No description
Code
getMimeType
No description
Code
nextRow
No description
Code
processQuery
No description
Code
Methods description
None available.
Methods code
_newdescriptionprevnextTop
sub _new {
    my ($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);
}
getDisplayNamesdescriptionprevnextTop
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).
}
getFooterTextdescriptionprevnextTop
sub getFooterText {
       return q{
</table>
</body>
</html>
}
;
}
getFormatterDisplayNamedescriptionprevnextTop
sub getFormatterDisplayName {
    return 'Mouse 36 assembly (HTML)';
}
getMimeTypedescriptionprevnextTop
sub getMimeType {
    return 'text/html';
}


1;
}
nextRowdescriptionprevnextTop
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 . $ROW_END_TMPL;
}
processQuerydescriptionprevnextTop
sub processQuery {
    my ($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
AUTHORSTop
    *(1)
    *(2)
CONTACTTop
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