use URI::Escape;
use Data::Dumper;
use Digest::MD5;
+use Time::HiRes;
use Maasha::Common;
use Maasha::Filesys;
use Maasha::Calc;
$cookie->{ 'NAV_START' } ||= defined $cgi->param( 'nav_start' ) ? $cgi->param( 'nav_start' ) : $session->{ 'NAV_START' };
$cookie->{ 'NAV_END' } ||= defined $cgi->param( 'nav_end' ) ? $cgi->param( 'nav_end' ) : $session->{ 'NAV_END' };
$cookie->{ 'NAV_CENTER' } = $cgi->param( 'nav_center' );
- $cookie->{ 'S_BEG' } = $cgi->param( 's_beg' ) || $session->{ 'S_BEG' };
- $cookie->{ 'S_END' } = $cgi->param( 's_end' ) || $session->{ 'S_END' };
+ $cookie->{ 'S_BEG' } = defined $cgi->param( 's_beg' ) ? $cgi->param( 's_beg' ) : $session->{ 'S_BEG' };
+ $cookie->{ 'S_END' } = defined $cgi->param( 's_end' ) ? $cgi->param( 's_end' ) : $session->{ 'S_END' };
$cookie->{ 'STRAND' } = $cgi->param( 'strand' ) || $session->{ 'STRAND' };
$cookie->{ 'TRACK' } = $cgi->param( 'track' );
$cookie->{ 'ZOOM_IN1' } = $cgi->param( 'zoom_in1' );
$cookie->{ 'MOVE_RIGHT3' } = $cgi->param( 'move_right3' );
$cookie->{ 'IMG_WIDTH' } = 1200; # Width of browser image in pixels
- $cookie->{ 'IMG_HEIGHT' } = 800; # Height of browser image in pixels
+ $cookie->{ 'IMG_HEIGHT' } = 800; # Height of browser image in pixels # TODO: Redundant?
$cookie->{ 'WIGGLE_HEIGHT' } = 75; # Height of Wiggle tracks in pixels
$cookie->{ 'TRACK_OFFSET' } = 20;
$cookie->{ 'TRACK_SPACE' } = 20;
if ( $cookie->{ 'USER' } and not $cookie->{ 'LOGIN_ERROR' } )
{
$cookie->{ 'LIST_CLADE' } = Maasha::BGB::Track::list_clades( $cookie->{ 'USER' } );
- $cookie->{ 'LIST_GENOME' } = Maasha::BGB::Track::list_genomes( $cookie->{ 'USER' }, $cookie->{ 'CLADE' } );
- $cookie->{ 'LIST_ASSEMBLY' } = Maasha::BGB::Track::list_assemblies( $cookie->{ 'USER' }, $cookie->{ 'CLADE' }, $cookie->{ 'GENOME' } );
- $cookie->{ 'LIST_CONTIG' } = Maasha::BGB::Track::list_contigs( $cookie->{ 'USER' }, $cookie->{ 'CLADE' }, $cookie->{ 'GENOME' }, $cookie->{ 'ASSEMBLY' } );
+
+ if ( $cookie->{ 'CLADE' } )
+ {
+ $cookie->{ 'LIST_GENOME' } = Maasha::BGB::Track::list_genomes( $cookie->{ 'USER' }, $cookie->{ 'CLADE' } );
+
+ if ( $cookie->{ 'GENOME' } )
+ {
+ $cookie->{ 'LIST_ASSEMBLY' } = Maasha::BGB::Track::list_assemblies( $cookie->{ 'USER' }, $cookie->{ 'CLADE' }, $cookie->{ 'GENOME' } );
+
+ if ( $cookie->{ 'ASSEMBLY' } )
+ {
+ $cookie->{ 'LIST_CONTIG' } = Maasha::BGB::Track::list_contigs( $cookie->{ 'USER' }, $cookie->{ 'CLADE' }, $cookie->{ 'GENOME' }, $cookie->{ 'ASSEMBLY' } );
+ }
+ }
+ }
if ( $cookie->{ 'CONTIG' } )
{
$new_session->{ 'TIME' } = Maasha::Common::time_stamp();
$new_session->{ 'PAGE' } = $cookie->{ 'PAGE' };
- if ( $cookie->{ 'PAGE' } eq 'browse' )
+ if ( $cookie->{ 'PAGE' } =~ /browse|export_pdf|export_svg/ )
{
$new_session->{ 'CLADE' } = $cookie->{ 'CLADE' };
$new_session->{ 'GENOME' } = $cookie->{ 'GENOME' };
{
$new_session->{ 'CLADE' } = $cookie->{ 'CLADE' };
}
- elsif ( $cookie->{ 'PAGE' } eq 'export' )
+ elsif ( $cookie->{ 'PAGE' } =~ /export|dna/ )
{
$new_session->{ 'CLADE' } = $cookie->{ 'CLADE' };
$new_session->{ 'GENOME' } = $cookie->{ 'GENOME' };
push @html, page_dna( $cookie );
} elsif ( $cookie->{ 'PAGE' } eq 'export' ) {
push @html, page_export( $cookie );
+ } elsif ( $cookie->{ 'PAGE' } eq 'export_pdf' ) {
+ push @html, page_export_pdf( $cookie );
+ } elsif ( $cookie->{ 'PAGE' } eq 'export_svg' ) {
+ push @html, page_export_svg( $cookie );
} elsif ( $cookie->{ 'PAGE' } eq 'clade' ) {
push @html, page_clade( $cookie );
} elsif ( $cookie->{ 'PAGE' } eq 'genome' ) {
}
+sub page_export_pdf
+{
+ # Martin A. Hansen, March 2010.
+
+ # Renders the export PDF page.
+
+ my ( $cookie,
+ ) = @_;
+
+ # Returns a list.
+
+ my ( @html );
+
+ push @html, section_taxonomy_table( $cookie );
+ push @html, section_export_pdf( $cookie );
+
+ return wantarray ? @html : \@html;
+}
+
+
+sub page_export_svg
+{
+ # Martin A. Hansen, March 2010.
+
+ # Renders the export SVG page.
+
+ my ( $cookie,
+ ) = @_;
+
+ # Returns a list.
+
+ my ( @html );
+
+ push @html, section_taxonomy_table( $cookie );
+ push @html, section_export_svg( $cookie );
+
+ return wantarray ? @html : \@html;
+}
+
+
sub page_clade
{
# Martin A. Hansen, March 2010.
# Returns a list.
- my ( $link, @html );
+ my ( $link_out, $link_pdf, $link_svg, @html );
- $link = Maasha::XHTML::ln(
+ $link_out = Maasha::XHTML::ln(
txt => 'link',
href => join( "&", "$cookie->{ 'SCRIPT' }?page=browse",
"clade=$cookie->{ 'CLADE' }",
title => "Static link to this view",
);
- push @html, Maasha::XHTML::p( txt => $link, class => 'center' );
+ $link_pdf = Maasha::XHTML::ln(
+ txt => 'PDF',
+ href => join( "&", "$cookie->{ 'SCRIPT' }?page=export_pdf",
+ "session_id=$cookie->{ 'SESSION_ID' }",
+ "user=$cookie->{ 'USER' }",
+ "clade=$cookie->{ 'CLADE' }",
+ "genome=$cookie->{ 'GENOME' }",
+ "assembly=$cookie->{ 'ASSEMBLY' }",
+ "contig=$cookie->{ 'CONTIG' }",
+ "nav_start=$cookie->{ 'NAV_START' }",
+ "nav_end=$cookie->{ 'NAV_END' }",
+ ),
+ title => "Export view in PDF",
+ );
+
+ $link_svg = Maasha::XHTML::ln(
+ txt => 'SVG',
+ href => join( "&", "$cookie->{ 'SCRIPT' }?page=export_svg",
+ "session_id=$cookie->{ 'SESSION_ID' }",
+ "user=$cookie->{ 'USER' }",
+ "clade=$cookie->{ 'CLADE' }",
+ "genome=$cookie->{ 'GENOME' }",
+ "assembly=$cookie->{ 'ASSEMBLY' }",
+ "contig=$cookie->{ 'CONTIG' }",
+ "nav_start=$cookie->{ 'NAV_START' }",
+ "nav_end=$cookie->{ 'NAV_END' }",
+ ),
+ title => "Export view in SVG",
+ );
+
+ push @html, Maasha::XHTML::p( txt => "$link_out $link_pdf $link_svg", class => 'center' );
return wantarray ? @html : \@html;
}
# Returns a list.
- my ( @track_list, $i, @tracks, $track, $elem, $surface, $cr, $png_data, @html, @img, $x1, $y1, $x2, $y2, $factor, $center );
+ my ( @track_list, $i, @tracks, $track, $elem, $png_data, @html, @img, $x1, $y1, $x2, $y2, $factor, $center );
push @tracks, [ Maasha::BGB::Track::track_ruler( $cookie ) ];
push @tracks, [ Maasha::BGB::Track::track_seq( $cookie ) ];
push @tracks, [ Maasha::BGB::Track::track_feature( $track_list[ $i ], $cookie ) ];
}
- $surface = Cairo::ImageSurface->create( 'argb32', $cookie->{ 'IMG_WIDTH' }, $cookie->{ 'TRACK_OFFSET' } );
- $cr = Cairo::Context->create( $surface );
-
- $cr->rectangle( 0, 0, $cookie->{ 'IMG_WIDTH' }, $cookie->{ 'TRACK_OFFSET' } );
- $cr->set_source_rgb( 1, 1, 1 );
- $cr->fill;
-
- foreach $track ( @tracks ) {
- Maasha::BGB::Draw::draw_feature( $cr, $track ) if $track;
- }
+ unshift @tracks, [ Maasha::BGB::Track::track_grid( $cookie ) ];
- $png_data = Maasha::BGB::Draw::base64_png( $surface );
+ $png_data = Maasha::BGB::Draw::render_png( $cookie->{ 'IMG_WIDTH' }, $cookie->{ 'TRACK_OFFSET' }, \@tracks );
push @img, Maasha::XHTML::img(
src => "data:image/png;base64,$png_data",
{
foreach $elem ( @{ $track } )
{
- next if $elem->{ 'type' } =~ /text|wiggle/;
+ next if $elem->{ 'type' } =~ /grid|text|wiggle/;
if ( $elem->{ 'type' } eq 'track_name' )
{
}
+sub section_export_pdf
+{
+ # Martin A. Hansen, March 2010.
+
+ # Returns a HTML section with export table.
+
+ my ( $cookie, # cookie hash
+ ) = @_;
+
+ # Returns a list.
+
+ my ( @tracks, @track_list, $i, $file, @html );
+
+ push @tracks, [ Maasha::BGB::Track::track_ruler( $cookie ) ];
+ push @tracks, [ Maasha::BGB::Track::track_seq( $cookie ) ];
+
+ @track_list = Maasha::BGB::Track::list_track_dir( $cookie->{ 'USER' }, $cookie->{ 'CLADE' }, $cookie->{ 'GENOME' }, $cookie->{ 'ASSEMBLY' }, $cookie->{ 'CONTIG' } );
+
+ for ( $i = 0; $i < @track_list; $i++ )
+ {
+ $cookie->{ 'FEAT_COLOR' } = Maasha::BGB::Draw::palette( $i );
+
+ push @tracks, [ Maasha::BGB::Track::track_feature( $track_list[ $i ], $cookie ) ];
+ }
+
+ unshift @tracks, [ Maasha::BGB::Track::track_grid( $cookie ) ];
+
+ $file = "$cookie->{ 'SESSION_DIR' }/$cookie->{ 'USER' }/BGB_export.pdf";
+
+ Maasha::BGB::Draw::render_pdf_file( $file, $cookie->{ 'IMG_WIDTH' }, $cookie->{ 'TRACK_OFFSET' }, \@tracks );
+
+ push @html, Maasha::XHTML::p( txt => Maasha::XHTML::ln( txt => "BGB_export.pdf", href => $file ), class => 'center' );
+
+ return wantarray ? @html : \@html;
+}
+
+
+sub section_export_svg
+{
+ # Martin A. Hansen, March 2010.
+
+ # Export view in SVG format.
+
+ my ( $cookie, # cookie hash
+ ) = @_;
+
+ # Returns a list.
+
+ my ( @tracks, @track_list, $i, $file, @html );
+
+ push @tracks, [ Maasha::BGB::Track::track_ruler( $cookie ) ];
+ push @tracks, [ Maasha::BGB::Track::track_seq( $cookie ) ];
+
+ @track_list = Maasha::BGB::Track::list_track_dir( $cookie->{ 'USER' }, $cookie->{ 'CLADE' }, $cookie->{ 'GENOME' }, $cookie->{ 'ASSEMBLY' }, $cookie->{ 'CONTIG' } );
+
+ for ( $i = 0; $i < @track_list; $i++ )
+ {
+ $cookie->{ 'FEAT_COLOR' } = Maasha::BGB::Draw::palette( $i );
+
+ push @tracks, [ Maasha::BGB::Track::track_feature( $track_list[ $i ], $cookie ) ];
+ }
+
+ unshift @tracks, [ Maasha::BGB::Track::track_grid( $cookie ) ];
+
+ $file = "$cookie->{ 'SESSION_DIR' }/$cookie->{ 'USER' }/BGB_export.svg";
+
+ Maasha::BGB::Draw::render_svg_file( $file, $cookie->{ 'IMG_WIDTH' }, $cookie->{ 'TRACK_OFFSET' }, \@tracks );
+
+ push @html, Maasha::XHTML::p( txt => Maasha::XHTML::ln( txt => "BGB_export.svg", href => $file ), class => 'center' );
+
+ return wantarray ? @html : \@html;
+}
+
+
sub section_search
{
# Martin A. Hansen, November 2009.
__END__
+
+
+ # my $t0 = Time::HiRes::gettimeofday();
+ # my $t1 = Time::HiRes::gettimeofday(); print STDERR "Time: " . ( $t1 - $t0 ) . "\n";
projects / biopieces.git / blobdiff