use CGI;
use Data::Dumper;
+use Digest::MD5;
use Maasha::Common;
use Maasha::Filesys;
use Maasha::Calc;
use Maasha::XHTML;
use Maasha::KISS;
+use Maasha::BBrowser::Session;
use Maasha::BBrowser::Track;
use Maasha::BBrowser::Draw;
);
push @html, Maasha::XHTML::h1( txt => "Biopieces Genome Browser", class => 'center' );
-push @html, Maasha::XHTML::form_beg( action => $cookie->{ 'SCRIPT' }, method => "get", enctype => "multipart/form-data" );
+push @html, Maasha::XHTML::form_beg( action => $cookie->{ 'SCRIPT' }, method => "post", enctype => "multipart/form-data" );
push @html, page( $cookie );
push @html, Maasha::XHTML::body_end;
push @html, Maasha::XHTML::html_end;
-# push @html, Maasha::XHTML::hdump( $cgi->param ); # DEBUG
-# push @html, Maasha::XHTML::hdump( $cookie ); # DEBUG
+# push @html, Maasha::XHTML::hdump( [ $cgi->Vars ] ); # DEBUG
+# push @html, Maasha::XHTML::hdump( \%ENV ); # DEBUG
+# push @html, Maasha::XHTML::hdump( $cookie ); # DEBUG
print "$_\n" foreach @html;
$cookie = {};
+ if ( $cgi->param( 'nav_search' ) )
+ {
+ if ( $cgi->param( 'nav_search' ) =~ /([0-9,]+)[ -]([0-9,]+)/ )
+ {
+ $cookie->{ 'NAV_START' } = $1;
+ $cookie->{ 'NAV_END' } = $2;
+ }
+ else
+ {
+ $cookie->{ 'SEARCH' } = $cgi->param( 'nav_search' );
+
+ $cgi->param( 'page', 'search' );
+ }
+ }
+
$cookie->{ 'SCRIPT' } = Maasha::Common::get_scriptname();
$cookie->{ 'DATA_DIR' } = "Data";
- $cookie->{ 'LIST_PAGES' } = [ qw( user clade genome assembly contig browse ) ];
- $cookie->{ 'PAGE' } = $cgi->param( 'page' ) || 'user';
- $cookie->{ 'USER' } = $cgi->param( 'user' ) || '';
+ $cookie->{ 'SESSION_DIR' } = "Sessions";
+ $cookie->{ 'LIST_PAGES' } = [ qw( clade genome assembly contig browse ) ];
+
+ $cookie->{ 'USER' } = $cgi->param( 'user' );
+ $cookie->{ 'PASSWORD' } = $cgi->param( 'password' );
+ $cookie->{ 'SESSION_ID' } = $cgi->param( 'session_id' );
+
+ cookie_session( $cookie );
+ cookie_login( $cookie );
+
+ $cookie->{ 'PAGE' } ||= $cgi->param( 'page' ) || 'login';
$cookie->{ 'CLADE' } = $cgi->param( 'clade' ) || '';
$cookie->{ 'GENOME' } = $cgi->param( 'genome' ) || '';
$cookie->{ 'ASSEMBLY' } = $cgi->param( 'assembly' ) || '';
$cookie->{ 'CONTIG' } = $cgi->param( 'contig' ) || '';
- $cookie->{ 'NAV_START' } = $cgi->param( 'nav_start' );
- $cookie->{ 'NAV_END' } = $cgi->param( 'nav_end' );
+ $cookie->{ 'Q_ID' } = $cgi->param( 'q_id' );
+ $cookie->{ 'S_BEG' } = $cgi->param( 's_beg' );
+ $cookie->{ 'S_END' } = $cgi->param( 's_end' );
+ $cookie->{ 'STRAND' } = $cgi->param( 'strand' );
$cookie->{ 'ZOOM_IN1' } = $cgi->param( 'zoom_in1' );
$cookie->{ 'ZOOM_IN2' } = $cgi->param( 'zoom_in2' );
$cookie->{ 'ZOOM_IN3' } = $cgi->param( 'zoom_in3' );
cookie_move( $cookie );
}
+ $cookie->{ 'STRAND' } = '+' if defined $cookie->{ 'STRAND' } and $cookie->{ 'STRAND' } eq ' '; # FIXME ugly HTML fix
+
return wantarray ? %{ $cookie } : $cookie;
}
+sub cookie_session
+{
+ # Martin A. Hansen, December 2009.
+
+ # Check cookie information against session information.
+
+ my ( $cookie, # cookie hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $session );
+
+ $session = Maasha::BBrowser::Session::session_restore( "$cookie->{ 'SESSION_DIR' }/sessions.txt" );
+
+ $cookie->{ 'PAGE' } = 'login' if not $cookie->{ 'SESSION_ID' };
+ $cookie->{ 'PAGE' } = 'login' if $cookie->{ 'SESSION_ID' } ne $ENV{ 'SSL_SESSION_ID' };
+ $cookie->{ 'PAGE' } = 'login' if not exists $session->{ $cookie->{ 'USER' } };
+ $cookie->{ 'PAGE' } = 'login' if $session->{ $cookie->{ 'USER' } }->{ 'SESSION_ID' } ne $cookie->{ 'SESSION_ID' };
+}
+
+
+sub cookie_login
+{
+ # Martin A. Hansen, December 2009.
+
+ # Check a user and password from CGI against the password file and
+ # set the session ID, if found, in the cookie.
+
+ my ( $cookie, # cookie hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $session );
+
+ $session = Maasha::BBrowser::Session::session_restore( "$cookie->{ 'SESSION_DIR' }/sessions.txt" );
+
+ if ( $cookie->{ 'USER' } and $cookie->{ 'PASSWORD' } )
+ {
+ if ( exists $session->{ $cookie->{ 'USER' } } and
+ $session->{ $cookie->{ 'USER' } }->{ 'PASSWORD' } eq Digest::MD5::md5_hex( $cookie->{ 'PASSWORD' } ) )
+ {
+ # $session->{ $cookie->{ 'USER' } }->{ 'SESSION_ID' } ||= Maasha::BBrowser::Session::session_new();
+ $session->{ $cookie->{ 'USER' } }->{ 'SESSION_ID' } = $ENV{ 'SSL_SESSION_ID' };
+ $session->{ $cookie->{ 'USER' } }->{ 'TIME' } = Maasha::Common::time_stamp();
+
+ $cookie->{ 'SESSION_ID' } = $session->{ $cookie->{ 'USER' } }->{ 'SESSION_ID' };
+ $cookie->{ 'LOGIN' } = "OK";
+ $cookie->{ 'USER' } = $cookie->{ 'USER' };
+ $cookie->{ 'PAGE' } = 'clade';
+
+ Maasha::BBrowser::Session::session_store( "$cookie->{ 'SESSION_DIR' }/sessions.txt", $session );
+ }
+ else
+ {
+ $cookie->{ 'LOGIN' } = "ERROR";
+ }
+ }
+}
+
+
sub cookie_start
{
# Martin A. Hansen, November 2009.
if ( defined $cookie->{ 'NAV_START' } )
{
$cookie->{ 'NAV_START' } =~ tr/,//d;
- $cookie->{ 'NAV_START' } = 1 if $cookie->{ 'NAV_START' } <= 0;
+ $cookie->{ 'NAV_START' } = 0 if $cookie->{ 'NAV_START' } < 0;
}
else
{
- $cookie->{ 'NAV_START' } = 1;
+ $cookie->{ 'NAV_START' } = 0;
}
}
$cookie->{ 'NAV_START' } = int( $cookie->{ 'NAV_START' } + ( $dist_diff / 2 ) );
$cookie->{ 'NAV_END' } = int( $cookie->{ 'NAV_END' } - ( $dist_diff / 2 ) );
- $cookie->{ 'NAV_START' } = 1 if $cookie->{ 'NAV_START' } <= 0;
+ $cookie->{ 'NAV_START' } = 0 if $cookie->{ 'NAV_START' } < 0;
$cookie->{ 'NAV_END' } = $max if $cookie->{ 'NAV_END' } > $max;
}
}
# Returns a string.
- my ( @href );
+ my ( @href_list, %href_hash, $href );
+
+ $href_hash{ "user" } = $cookie->{ 'USER' } if $cookie->{ 'USER' };
while ( 1 )
{
- push @href, "$cookie->{ 'SCRIPT' }?page=$page";
- push @href, "user=$cookie->{ 'USER' }" if $cookie->{ 'USER' };
- last if $page eq 'user';
- push @href, "clade=$cookie->{ 'CLADE' }" if $cookie->{ 'CLADE' };
+ $href_hash{ "clade" } = $cookie->{ 'CLADE' } if $cookie->{ 'CLADE' };
last if $page eq 'clade';
- push @href, "genome=$cookie->{ 'GENOME' }" if $cookie->{ 'GENOME' };
+ $href_hash{ "genome" } = $cookie->{ 'GENOME' } if $cookie->{ 'GENOME' };
last if $page eq 'genome';
- push @href, "assembly=$cookie->{ 'ASSEMBLY' }" if $cookie->{ 'ASSEMBLY' };
+ $href_hash{ "assembly" } = $cookie->{ 'ASSEMBLY' } if $cookie->{ 'ASSEMBLY' };
last if $page eq 'assembly';
- push @href, "contig=$cookie->{ 'CONTIG' }" if $cookie->{ 'CONTIG' };
+ $href_hash{ "contig" } = $cookie->{ 'CONTIG' } if $cookie->{ 'CONTIG' };
last if $page eq 'contig';
last;
}
- return join "&", @href;
+ if ( defined $cookie->{ 'NAV_START' } and defined $cookie->{ 'NAV_END' } ) {
+ $href_hash{ "nav_search" } = "$cookie->{ 'NAV_START' }-$cookie->{ 'NAV_END' }";
+ }
+
+ $href_hash{ "s_beg" } = $cookie->{ 'S_BEG' } if defined $cookie->{ 'S_BEG' };
+ $href_hash{ "s_end" } = $cookie->{ 'S_END' } if defined $cookie->{ 'S_END' };
+ $href_hash{ "q_id" } = $cookie->{ 'Q_ID' } if defined $cookie->{ 'Q_ID' };
+ $href_hash{ "strand" } = $cookie->{ 'STRAND' } if defined $cookie->{ 'STRAND' };
+ $href_hash{ "session_id" } = $cookie->{ 'SESSION_ID' } if defined $cookie->{ 'SESSION_ID' };
+
+ push @href_list, "$cookie->{ 'SCRIPT' }?page=$page";
+
+ foreach $href ( keys %href_hash ) {
+ push @href_list, "$href=$href_hash{ $href }";
+ }
+
+ return join "&", @href_list;
}
my ( @html );
- if ( $cookie->{ 'PAGE' } eq 'export' ) {
- push @html, page_export( $cookie );
+ if ( $cookie->{ 'PAGE' } eq 'login' ) {
+ push @html, page_login( $cookie );
+ } elsif ( $cookie->{ 'PAGE' } eq 'search' ) {
+ push @html, page_search( $cookie );
} elsif ( $cookie->{ 'PAGE' } eq 'browse' ) {
push @html, page_browse( $cookie );
+ } elsif ( $cookie->{ 'PAGE' } eq 'dna' ) {
+ push @html, page_dna( $cookie );
+ } elsif ( $cookie->{ 'PAGE' } eq 'export' ) {
+ push @html, page_export( $cookie );
} else {
push @html, page_taxonomy( $cookie );
}
+ push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "session_id", value => "$cookie->{ 'SESSION_ID' }" ) );
+
return wantarray ? @html : \@html;
}
-sub page_export
+sub page_login
{
- # Martin A. Hansen, November 2009.
+ # Martin A. Hansen, December 2009.
- # Renders the export page.
+ # Renders the login page.
+
+ my ( $cookie,
+ ) = @_;
+
+ # Returns a list.
+
+ my ( @html );
+
+ push @html, section_login( $cookie );
+
+ return wantarray ? @html : \@html;
+}
+
+
+sub page_search
+{
+ # Martin A. Hansen, December 2009.
+
+ # Renders the search page.
my ( $cookie,
) = @_;
my ( @html );
push @html, section_taxonomy_table( $cookie );
- push @html, section_export( $cookie );
+ push @html, section_search( $cookie );
return wantarray ? @html : \@html;
}
}
+sub page_dna
+{
+ # Martin A. Hansen, November 2009.
+
+ # Renders the DNA page.
+
+ my ( $cookie,
+ ) = @_;
+
+ # Returns a list.
+
+ my ( @html );
+
+ push @html, section_taxonomy_table( $cookie );
+ push @html, section_dna( $cookie );
+
+ return wantarray ? @html : \@html;
+}
+
+
+sub page_export
+{
+ # Martin A. Hansen, November 2009.
+
+ # Renders the export page.
+
+ my ( $cookie,
+ ) = @_;
+
+ # Returns a list.
+
+ my ( @html );
+
+ push @html, section_taxonomy_table( $cookie );
+ push @html, section_export( $cookie );
+
+ return wantarray ? @html : \@html;
+}
+
+
sub page_taxonomy
{
# Martin A. Hansen, November 2009.
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SECTIONS <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+sub section_login
+{
+ # Martin A. Hansen, December 2009.
+
+ # Returns a HTML section with a login menu.
+
+ my ( $cookie, # cookie hash
+ ) = @_;
+
+ # Returns a list.
+
+ my ( $user, $password, $login, @html );
+
+ $user = Maasha::XHTML::text( name => "user", value => "", size => 20 );
+ $password = Maasha::XHTML::password( name => "password", value => "", size => 20 );
+ $login = Maasha::XHTML::submit( name => "login_submit", value => "Login" );
+
+ push @html, Maasha::XHTML::h2( txt => "Login", class => 'center' );
+
+ push @html, Maasha::XHTML::table_beg( summary => "Login table", align => 'center' );
+ push @html, Maasha::XHTML::table_row_simple( tr => [ "User:", $user ] );
+ push @html, Maasha::XHTML::table_row_simple( tr => [ "Password:", $password ] );
+ push @html, Maasha::XHTML::table_row_simple( tr => [ "", $login ] );
+ push @html, Maasha::XHTML::table_end;
+
+ if ( $cookie->{ 'LOGIN' } and $cookie->{ 'LOGIN' } eq 'ERROR' ) {
+ push @html, Maasha::XHTML::h3( txt => "Bad user or password - please retry", class => 'error' );
+ }
+
+ return wantarray ? @html : \@html;
+}
+
+
sub section_taxonomy_table
{
# Martin A. Hansen, November 2009.
}
push @html, Maasha::XHTML::table_beg( summary => "Taxonomy table", align => 'center', cellpadding => '5px' );
- push @html, Maasha::XHTML::table_row_simple( tr => [ join( " ", @row ) ], align => 'center' );
+ push @html, Maasha::XHTML::table_row_simple( tr => [ join( "\n", @row ) ], align => 'center' );
push @html, Maasha::XHTML::table_end;
return wantarray ? @html : \@html;
push @html, Maasha::XHTML::h2( txt => "Select $cookie->{ 'PAGE' }", class => 'center' );
- push @html, Maasha::XHTML::table_beg( summary => "Select table", align => 'center', cellpadding => '5px' );
+ push @html, Maasha::XHTML::table_beg( summary => "Taxonomy select table", align => 'center', cellpadding => '5px' );
foreach $item ( @{ $cookie->{ $list } } )
{
# Returns a list.
- my ( @html );
+ my ( @html, $nav_val );
+
+ $nav_val = Maasha::Calc::commify( $cookie->{ 'NAV_START' } ) . "-" . Maasha::Calc::commify( $cookie->{ 'NAV_END' } );
push @html, Maasha::XHTML::table_beg( summary => "Navigation table", align => 'center' );
push @html, Maasha::XHTML::table_row_simple( tr => [
- "Start:",
- Maasha::XHTML::text( name => "nav_start", value => Maasha::Calc::commify( $cookie->{ 'NAV_START' } ), size => 20 ),
- "End:",
- Maasha::XHTML::text( name => "nav_end", value => Maasha::Calc::commify( $cookie->{ 'NAV_END' } ), size => 20 ),
+ "Position or search term:",
+ Maasha::XHTML::text( name => "nav_search", value => $nav_val, size => 30 ),
Maasha::XHTML::submit( name => "nav_submit", value => "Submit" ),
] );
push @html, Maasha::XHTML::table_end;
# Returns a list.
- my ( @tracks, $i, @features, $feat, $elem, $file, $surface, $cr, @html, @img );
+ my ( @tracks, $i, @features, $feat, $elem, $surface, $cr, $png_data, @html, @img );
push @features, [ Maasha::BBrowser::Track::track_ruler( $cookie ) ];
push @features, [ Maasha::BBrowser::Track::track_seq( $cookie ) ];
push @features, [ Maasha::BBrowser::Track::track_feature( $tracks[ $i ], $cookie ) ];
}
- $file = "fisk.png"; # FIXME
-
$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->rectangle ( 0, 0, $cookie->{ 'IMG_WIDTH' }, $cookie->{ 'TRACK_OFFSET' } );
+ $cr->set_source_rgb ( 1, 1, 1 );
$cr->fill;
foreach $feat ( @features ) {
Maasha::BBrowser::Draw::draw_feature( $cr, $feat ) if $feat;
}
- Maasha::BBrowser::Draw::file_png( $surface, $file );
+ $png_data = Maasha::BBrowser::Draw::base64_png( $surface );
push @img, Maasha::XHTML::img(
- src => $file,
+ src => "data:image/png;base64,$png_data",
alt => "Browser Tracks",
height => $cookie->{ 'TRACK_OFFSET' },
width => $cookie->{ 'IMG_WIDTH' },
{
next if $elem->{ 'type' } eq 'text';
+ #$elem->{ 'strand' } = '+' if $elem->{ 'strand' } eq '+';
+
+ $cookie->{ 'Q_ID' } = $elem->{ 'q_id' };
+ $cookie->{ 'S_BEG' } = $elem->{ 's_beg' };
+ $cookie->{ 'S_END' } = $elem->{ 's_end' };
+ $cookie->{ 'STRAND' } = $elem->{ 'strand' };
+
push @img, Maasha::XHTML::area(
- href => cookie_href( $cookie, "export" ) . "&Q_ID=$elem->{ 'id' }",
+ href => cookie_href( $cookie, "export" ),
+ # href => cookie_href( $cookie, "export" ) . "&q_id=$elem->{ 'q_id' }&s_beg=$elem->{ 's_beg' }&s_end=$elem->{ 's_end' }&strand=$elem->{ 'strand' }",
shape => "rect",
coords => "$elem->{ x1 }, $elem->{ y1 }, $elem->{ x2 }, $elem->{ y2 }", title => "$elem->{ 'title' }",
);
# Returns a list.
- my ( @html );
+ my ( @row_dna_contig, @html );
+
+ push @row_dna_contig, Maasha::XHTML::p( txt => qq(Export Feature: "$cookie->{ 'Q_ID' }" DNA from Contig: ), class => 'inline' );
+ push @row_dna_contig, Maasha::XHTML::p( txt => "$cookie->{ 'CONTIG' } Start: ", class => 'inline' );
+ push @row_dna_contig, Maasha::XHTML::text( name => "s_beg", value => Maasha::Calc::commify( $cookie->{ 'S_BEG' } ), size => 15 );
+ push @row_dna_contig, Maasha::XHTML::p( txt => "End: ", class => 'inline' );
+ push @row_dna_contig, Maasha::XHTML::text( name => "s_end", value => Maasha::Calc::commify( $cookie->{ 'S_END' } ), size => 15 );
+ push @row_dna_contig, Maasha::XHTML::p( txt => "Strand: ", class => 'inline' );
+ push @row_dna_contig, Maasha::XHTML::menu( name => "strand", options => [ qw( + - ) ], selected => $cookie->{ 'STRAND' } );
+ push @row_dna_contig, Maasha::XHTML::submit( name => "export", value => "Export", title => "Fetch DNA from this region" );
+
+ push @html, Maasha::XHTML::h2( txt => "Export", class => 'center' );
+ push @html, Maasha::XHTML::table_beg( summary => "Taxonomy select table", align => 'center' );
+ push @html, Maasha::XHTML::table_row_simple( tr => \@row_dna_contig );
+ push @html, Maasha::XHTML::table_end;
+
+ push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "page", value => "dna" ) );
+ push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "user", value => "$cookie->{ 'USER' }" ) );
+ push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "clade", value => "$cookie->{ 'CLADE' }" ) );
+ push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "genome", value => "$cookie->{ 'GENOME' }" ) );
+ push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "assembly", value => "$cookie->{ 'ASSEMBLY' }" ) );
+ push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "contig", value => "$cookie->{ 'CONTIG' }" ) );
+
+ return wantarray ? @html : \@html;
+}
+
+
+sub section_search
+{
+ # Martin A. Hansen, November 2009.
+
+ # Returns a HTML section with export table.
+
+ my ( $cookie, # cookie hash
+ ) = @_;
+
+ # Returns a list.
+
+ my ( $results, $result, $count, @html, $export, $browse );
+
+ $results = Maasha::BBrowser::Track::search_tracks( $cookie );
+
+ $count = scalar @{ $results };
+
+ push @html, Maasha::XHTML::h2( txt => "Search", class => 'center' );
+ push @html, Maasha::XHTML::p( txt => qq(Results for "$cookie->{ 'SEARCH' }": $count), class => 'center' );
+
+ if ( $count > 0 )
+ {
+ push @html, Maasha::XHTML::table_beg( summary => "Search table", align => 'center', cellpadding => '5px' );
+ push @html, Maasha::XHTML::table_row_simple( tr => [ qw( S_ID S_BEG S_END Q_ID SCORE STRAND HITS ALIGN BLOCK_COUNT BLOCK_BEGS BLOCK_LENS BLOCK_TYPE) ] );
+
+ foreach $result ( @{ $results } )
+ {
+ $cookie->{ 'CONTIG' } = $result->{ 'S_ID' };
+ $cookie->{ 'NAV_START' } = $result->{ 'S_BEG' };
+ $cookie->{ 'NAV_END' } = $result->{ 'S_END' };
+ $cookie->{ 'S_BEG' } = $result->{ 'S_BEG' };
+ $cookie->{ 'S_END' } = $result->{ 'S_END' };
+ $cookie->{ 'STRAND' } = $result->{ 'STRAND' };
+ $cookie->{ 'Q_ID' } = $result->{ 'Q_ID' };
+
+ $browse = Maasha::XHTML::ln( txt => "browse", href => cookie_href( $cookie, "browse" ) );
+ $export = Maasha::XHTML::ln( txt => "export", href => cookie_href( $cookie, "export" ) );
+
+ push @html, Maasha::XHTML::table_row_advanced(
+ tr => [ { td => $result->{ 'S_ID' } },
+ { td => $result->{ 'S_BEG' }, align => 'right' },
+ { td => $result->{ 'S_END' }, align => 'right' },
+ { td => $result->{ 'Q_ID' } },
+ { td => $result->{ 'SCORE' }, align => 'right' },
+ { td => $result->{ 'STRAND' } },
+ { td => $result->{ 'HITS' }, align => 'right' },
+ { td => $result->{ 'ALIGN' } },
+ { td => $result->{ 'BLOCK_COUNT' }, align => 'right' },
+ { td => $result->{ 'BLOCK_BEGS' } },
+ { td => $result->{ 'BLOCK_LENS' } },
+ { td => $result->{ 'BLOCK_TYPE' } },
+ { td => $browse },
+ { td => $export },
+ ], class => "monospace"
+ );
+ }
+
+ push @html, Maasha::XHTML::table_end;
+ }
+
+ return wantarray ? @html : \@html;
+}
+
+
+sub section_dna
+{
+ # Martin A. Hansen, November 2009.
+
+ # Returns a HTML section with extracted DNA.
+
+ my ( $cookie, # cookie hash
+ ) = @_;
+
+ # Returns a list.
+
+ my ( @html, $beg, $end, $seq );
+
+ $beg = $cookie->{ 'S_BEG' };
+ $end = $cookie->{ 'S_END' };
+ $beg =~ tr/,//d;
+ $end =~ tr/,//d;
+
+ $seq = ">$cookie->{ 'CONTIG' }_$beg" . "_$end" . "_$cookie->{ 'STRAND' }\n";
+ $seq .= Maasha::BBrowser::Track::dna_get( $cookie );
- push @html, Maasha::XHTML::h2( txt => "Export", class => 'center' ); # TODO section_export!
+ push @html, Maasha::XHTML::h2( txt => "DNA", class => 'center' );
+ push @html, Maasha::XHTML::pre( txt => $seq );
return wantarray ? @html : \@html;
}
projects / biopieces.git / blobdiff