use Time::HiRes;
use Maasha::Common;
use Maasha::Filesys;
+use Maasha::Calc;
use Maasha::XHTML;
-use Maasha::Biopieces;
use Maasha::KISS::IO;
use Maasha::KISS::Track;
use Maasha::KISS::Draw;
-my ( $cgi, $database, $user, $password, $dbh, $script, @html );
+my ( $cgi, $cookie, @html );
-$cgi = new CGI;
-
-$database = 'S_aur_COL';
-$user = Maasha::Biopieces::biopiecesrc( "MYSQL_USER" );
-$password = Maasha::Biopieces::biopiecesrc( "MYSQL_PASSWORD" );
-
-$dbh = Maasha::SQL::connect( $database, $user, $password );
-
-
-$script = Maasha::Common::get_scriptname();
+$cgi = new CGI;
+$cookie = cookie_default( $cgi );;
push @html, Maasha::XHTML::html_header(
cgi_header => 1,
title => "KISS Genome Browser",
-# css_file => "test.css",
+ css_file => "kiss.css",
author => "Martin A. Hansen, mail\@maasha.dk",
description => "Biopieces bacterial genome browser - KISS",
keywords => [ qw( KISS Biopieces biopiece genome browser viewer bacterium bacteria prokaryote prokaryotes ) ],
no_cache => 1,
);
-push @html, Maasha::XHTML::h1( txt => "KISS Genome Browser", class => "center" );
-push @html, Maasha::XHTML::form_beg( action => $script, method => "get", enctype => "multipart/form-data" );
+push @html, Maasha::XHTML::h1( txt => "KISS Genome Browser", class => 'center' );
+push @html, Maasha::XHTML::form_beg( action => $cookie->{ 'SCRIPT' }, method => "get", enctype => "multipart/form-data" );
-push @html, sec_navigate( $cgi );
-push @html, sec_browse( $dbh, $cgi->param( 'nav_start' ), $cgi->param( 'nav_end' ) );
+push @html, page( $cookie );
push @html, Maasha::XHTML::form_end;
push @html, Maasha::XHTML::body_end;
push @html, Maasha::XHTML::html_end;
+# push @html, Maasha::KISS::Draw::hdump( $cgi->param );
+# push @html, Maasha::KISS::Draw::hdump( $cookie );
+
print "$_\n" foreach @html;
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-sub sec_navigate
+sub cookie_default
{
my ( $cgi, # CGI object
) = @_;
- # Returns a list.
+ # Returns a hash
- my ( $list_clade, $list_genome, $list_assembly, $list_contig, $def_clade, $def_genome, $def_assembly, $def_contig, $def_start, $def_end, @html );
+ my ( $cookie, $path );
- $list_clade = nav_list_clade();
- $list_genome = nav_list_genome();
- $list_assembly = nav_list_assembly();
- $list_contig = nav_list_contig();
+ $cookie = {};
- nav_zoom( $cgi );
- nav_move( $cgi, 2_800_000 ); # FIXME
+ $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->{ '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->{ 'ZOOM_IN1' } = $cgi->param( 'zoom_in1' );
+ $cookie->{ 'ZOOM_IN2' } = $cgi->param( 'zoom_in2' );
+ $cookie->{ 'ZOOM_IN3' } = $cgi->param( 'zoom_in3' );
+ $cookie->{ 'ZOOM_OUT1' } = $cgi->param( 'zoom_out1' );
+ $cookie->{ 'ZOOM_OUT2' } = $cgi->param( 'zoom_out2' );
+ $cookie->{ 'ZOOM_OUT3' } = $cgi->param( 'zoom_out3' );
+ $cookie->{ 'MOVE_LEFT1' } = $cgi->param( 'move_left1' );
+ $cookie->{ 'MOVE_LEFT2' } = $cgi->param( 'move_left2' );
+ $cookie->{ 'MOVE_LEFT3' } = $cgi->param( 'move_left3' );
+ $cookie->{ 'MOVE_RIGHT1' } = $cgi->param( 'move_right1' );
+ $cookie->{ 'MOVE_RIGHT2' } = $cgi->param( 'move_right2' );
+ $cookie->{ 'MOVE_RIGHT3' } = $cgi->param( 'move_right3' );
- $def_clade = nav_def_clade( $cgi );
- $def_genome = nav_def_genome( $cgi );
- $def_assembly = nav_def_assembly( $cgi );
- $def_contig = nav_def_contig( $cgi );
- $def_start = nav_def_start( $cgi );
- $def_end = nav_def_end( $cgi );
+ $path = "$cookie->{ 'DATA_DIR' }/Users";
- Maasha::Calc::commify( \$def_start );
- Maasha::Calc::commify( \$def_end );
+ $cookie->{ 'LIST_USER' } = ls_dir_base( $path ) if -d $path;
- push @html, Maasha::XHTML::table_beg( summary => "Navigation table" );
- push @html, Maasha::XHTML::table_row_simple( tr => [ qw( Clade Genome Assembly Contig Start End ) ], align => 'center' );
- push @html, Maasha::XHTML::table_row_simple( tr => [
- Maasha::XHTML::menu( name => "nav_clade", options => $list_clade, selected => $def_clade ),
- Maasha::XHTML::menu( name => "nav_genome", options => $list_genome, selected => $def_genome ),
- Maasha::XHTML::menu( name => "nav_assembly", options => $list_assembly, selected => $def_assembly ),
- Maasha::XHTML::menu( name => "nav_contig", options => $list_contig, selected => $def_contig ),
- Maasha::XHTML::text( name => "nav_start", value => $def_start, size => 20 ),
- Maasha::XHTML::text( name => "nav_end", value => $def_end, size => 20 ),
- Maasha::XHTML::submit( name => "nav_submit", value => "Submit" ),
- ] );
- push @html, Maasha::XHTML::table_end;
+ $path .= "/$cookie->{ 'USER' }";
- push @html, Maasha::XHTML::table_beg( summary => "Zoom table" );
- push @html, Maasha::XHTML::table_row_simple( tr => [
- Maasha::XHTML::p( txt => 'Move:' ),
- Maasha::XHTML::submit( name => "move_left3", value => "<<<", title => "move 95% to the left" ),
- Maasha::XHTML::submit( name => "move_left2", value => "<<", title => "move 47.5% to the left" ),
- Maasha::XHTML::submit( name => "move_left1", value => "<", title => "move 10% to the left" ),
- Maasha::XHTML::submit( name => "move_right1", value => ">", title => "move 10% to the rigth" ),
- Maasha::XHTML::submit( name => "move_right2", value => ">>", title => "move 47.5% to the rigth" ),
- Maasha::XHTML::submit( name => "move_right3", value => ">>>", title => "move 95% to the right" ),
- Maasha::XHTML::p( txt => 'Zoom in:' ),
- Maasha::XHTML::submit( name => "zoom_in1", value => "1.5x" ),
- Maasha::XHTML::submit( name => "zoom_in2", value => "3x" ),
- Maasha::XHTML::submit( name => "zoom_in3", value => "10x" ),
- Maasha::XHTML::p( txt => 'Zoom out:' ),
- Maasha::XHTML::submit( name => "zoom_out1", value => "1.5x" ),
- Maasha::XHTML::submit( name => "zoom_out2", value => "3x" ),
- Maasha::XHTML::submit( name => "zoom_out3", value => "10x" ),
- ] );
- push @html, Maasha::XHTML::table_end;
+ $cookie->{ 'LIST_CLADE' } = ls_dir_base( $path ) if -d $path;
- return wantarray ? @html : \@html;
+ $path .= "/$cookie->{ 'CLADE' }";
+
+ $cookie->{ 'LIST_GENOME' } = ls_dir_base( $path ) if -d $path;
+
+ $path .= "/$cookie->{ 'GENOME' }";
+
+ $cookie->{ 'LIST_ASSEMBLY' } = ls_dir_base( $path ) if -d $path;
+
+ $path .= "/$cookie->{ 'ASSEMBLY' }";
+
+ $cookie->{ 'LIST_CONTIG' } = ls_dir_base( $path ) if -d $path;
+
+ if ( $cookie->{ 'CONTIG' } )
+ {
+ cookie_start( $cookie );
+ cookie_end( $cookie );
+ cookie_zoom( $cookie );
+ cookie_move( $cookie );
+ }
+
+ return wantarray ? %{ $cookie } : $cookie;
}
-sub sec_browse
+sub ls_dir_base
{
- my ( $dbh, # Database handle
- $start, # Browse start position
- $end, # Browse end position
+ my ( $path,
) = @_;
# Returns a list.
+
+ my ( @dirs, $dir, @list );
- my ( $t0, $t1, $table, $entries, $features, $svg, $file, $fh, @html );
+ @dirs = Maasha::Filesys::ls_dirs( $path );
- $table = 'Solexa';
+ foreach $dir ( @dirs )
+ {
+ next if $dir =~ /\/\.\.?$/;
- $t0 = Time::HiRes::gettimeofday();
- $entries = Maasha::KISS::IO::kiss_sql_get( $dbh, $table, $start, $end );
- $t1 = Time::HiRes::gettimeofday();
+ push @list, ( split "/", $dir )[ -1 ];
+ }
- push @html, Maasha::XHTML::p( txt => "Feature count: " . scalar @$entries );
+ return wantarray ? @list : \@list;
+}
- push @html, Maasha::XHTML::p( txt => "Time SQL: " . ( $t1 - $t0 ) );
- $t0 = Time::HiRes::gettimeofday();
- Maasha::KISS::Track::entries_sort( $entries );
- $t1 = Time::HiRes::gettimeofday();
+sub cookie_clade
+{
+ my ( $cookie,
+ ) = @_;
- push @html, Maasha::XHTML::p( txt => "Time sort: " . ( $t1 - $t0 ) );
+ # Returns nothing.
+
+ my ( $user, @dirs, $dir );
- $t0 = Time::HiRes::gettimeofday();
+ $user = $cookie->{ 'USER' };
+
+ @dirs = Maasha::Filesys::ls_dirs( "$cookie->{ 'DATA_DIR' }/Users/$user" );
- my $MAX = 4000; # FIXME should depend on hieght of track as well
+ foreach $dir ( @dirs )
+ {
+ next if $dir =~ /\/\.\.?$/;
- if ( @$entries > $MAX ) {
- $features = Maasha::KISS::Track::track_histogram( 1200, 50, $start, $end, $entries );
- } else {
- $features = Maasha::KISS::Track::track_feature( 1200, 50, $start, $end, $entries );
+ push @{ $cookie->{ 'LIST_CLADE' } }, ( split "/", $dir )[ -1 ];
}
+}
- $t1 = Time::HiRes::gettimeofday();
- # push @html, Maasha::KISS::Draw::hdump( $entries );
- # push @html, Maasha::KISS::Draw::hdump( $features );
+sub cookie_genome
+{
+ my ( $cookie,
+ ) = @_;
- push @html, Maasha::XHTML::p( txt => "Time Track: " . ( $t1 - $t0 ) );
+ # Returns nothing.
+
+ my ( $user, $clade, @dirs, $dir );
- $file = "fisk.svg";
+ $user = $cookie->{ 'USER' };
+ $clade = $cookie->{ 'CLADE' };
- $fh = Maasha::Filesys::file_write_open( $file );
+ @dirs = Maasha::Filesys::ls_dirs( "$cookie->{ 'DATA_DIR' }/Users/$user/$clade" );
- $svg = Maasha::KISS::Draw::svg_init( 800, 1200 );
+ foreach $dir ( @dirs )
+ {
+ next if $dir =~ /\/\.\.?$/;
- $t0 = Time::HiRes::gettimeofday();
- Maasha::KISS::Draw::svg_frame( 800, 1200, $svg );
+ push @{ $cookie->{ 'LIST_GENOME' } }, ( split "/", $dir )[ -1 ];
+ }
+}
- Maasha::KISS::Draw::svg_track_dna( 1200, $svg, 'dna', 'ATCG' );
- if ( @$entries > $MAX ) {
- Maasha::KISS::Draw::svg_track_histogram( $svg, $features, 'track id', 'green' ) if $features;
- } else {
- Maasha::KISS::Draw::svg_track_feature( 800, 1200, $svg, $features, 'track id2', 'green' ) if $features;
- }
+sub cookie_assembly
+{
+ my ( $cookie,
+ ) = @_;
- Maasha::KISS::Draw::svg_print( $svg, $fh );
- $t1 = Time::HiRes::gettimeofday();
+ # Returns nothing.
+
+ my ( $user, $clade, $genome, @dirs, $dir );
- push @html, Maasha::XHTML::p( txt => "Time Draw: " . ( $t1 - $t0 ) );
+ $user = $cookie->{ 'USER' };
+ $clade = $cookie->{ 'CLADE' };
+ $genome = $cookie->{ 'GENOME' };
- close $fh;
+ @dirs = Maasha::Filesys::ls_dirs( "$cookie->{ 'DATA_DIR' }/Users/$user/$clade/$genome" );
- push @html, Maasha::XHTML::object( type => "image/svg+xml",
- # data => "/Users/maasha/test.svg",
- data => $file,
- name => "owMain",
- width => "1200",
- height => "800" );
+ foreach $dir ( @dirs )
+ {
+ next if $dir =~ /\/\.\.?$/;
- return wantarray ? @html : \@html;
+ push @{ $cookie->{ 'LIST_ASSEMBLY' } }, ( split "/", $dir )[ -1 ];
+ }
}
-sub nav_list_clade
+sub cookie_contig
{
- my ( $list_clade );
-
- $list_clade = [ qw( Eukaryote Bacillus Fish ) ];
+ my ( $cookie,
+ ) = @_;
- return wantarray ? @{ $list_clade } : $list_clade;
-}
+ # Returns nothing.
+
+ my ( $user, $clade, $genome, $assembly, @dirs, $dir );
+ $user = $cookie->{ 'USER' };
+ $clade = $cookie->{ 'CLADE' };
+ $genome = $cookie->{ 'GENOME' };
+ $assembly = $cookie->{ 'ASSEMBLY' };
-sub nav_list_genome
-{
- my ( $list_genome );
+ @dirs = Maasha::Filesys::ls_dirs( "$cookie->{ 'DATA_DIR' }/Users/$user/$clade/$genome/$assembly" );
- $list_genome = [ qw( S.aur_COL E.col B.sub ) ];
+ foreach $dir ( @dirs )
+ {
+ next if $dir =~ /\/\.\.?$/;
- return wantarray ? @{ $list_genome } : $list_genome;
+ push @{ $cookie->{ 'LIST_CONTIG' } }, ( split "/", $dir )[ -1 ];
+ }
}
-sub nav_list_assembly
+sub cookie_start
{
- my ( $list_assembly );
+ my ( $cookie,
+ ) = @_;
- $list_assembly = [ qw( 2008-02-21 2009-01-23 ) ];
+ # Returns nothing.
- return wantarray ? @{ $list_assembly } : $list_assembly;
+ if ( defined $cookie->{ 'NAV_START' } )
+ {
+ $cookie->{ 'NAV_START' } =~ tr/,//d;
+ $cookie->{ 'NAV_START' } = 1 if $cookie->{ 'NAV_START' } <= 0;
+ }
+ else
+ {
+ $cookie->{ 'NAV_START' } = 1;
+ }
}
-sub nav_list_contig
+sub cookie_end
{
- my ( $list_contig );
+ my ( $cookie,
+ ) = @_;
- $list_contig = [ qw( chr1 chr2 ) ];
+ # Returns nothing.
- return wantarray ? @{ $list_contig } : $list_contig;
+ my ( $max );
+
+ $max = Maasha::Filesys::file_size( Maasha::KISS::Track::path_seq( $cookie ) );
+
+ if ( defined $cookie->{ 'NAV_END' } )
+ {
+ $cookie->{ 'NAV_END' } =~ tr/,//d;
+ $cookie->{ 'NAV_END' } = $max if $cookie->{ 'NAV_END' } > $max;
+ }
+ else
+ {
+ $cookie->{ 'NAV_END' } = $max;
+ }
}
-sub nav_zoom
+sub cookie_zoom
{
- my ( $cgi, # CGI object
+ my ( $cookie,
) = @_;
- my ( $start, $end, $dist, $new_dist, $dist_diff, $new_start, $new_end );
+ # Returns nothing.
+
+ my ( $max, $dist, $new_dist, $dist_diff );
+
+ $max = Maasha::Filesys::file_size( Maasha::KISS::Track::path_seq( $cookie ) );
+
+ $dist = $cookie->{ 'NAV_END' } - $cookie->{ 'NAV_START' };
- if ( defined $cgi->param( 'nav_start' ) and $cgi->param( 'nav_end' ) )
+ if ( defined $cookie->{ 'ZOOM_IN1' } ) {
+ $new_dist = $dist / 1.5;
+ } elsif ( defined $cookie->{ 'ZOOM_IN2' } ) {
+ $new_dist = $dist / 3;
+ } elsif ( defined $cookie->{ 'ZOOM_IN3' } ) {
+ $new_dist = $dist / 10;
+ } elsif ( defined $cookie->{ 'ZOOM_OUT1' } ) {
+ $new_dist = $dist * 1.5;
+ } elsif ( defined $cookie->{ 'ZOOM_OUT2' } ) {
+ $new_dist = $dist * 3;
+ } elsif ( defined $cookie->{ 'ZOOM_OUT3' } ) {
+ $new_dist = $dist * 10;
+ }
+
+ if ( $new_dist )
{
- $start = $cgi->param( 'nav_start' );
- $end = $cgi->param( 'nav_end' );
-
- $start =~ tr/,//d;
- $end =~ tr/,//d;
-
- $dist = $end - $start;
-
- if ( defined $cgi->param( 'zoom_in1' ) ) {
- $new_dist = $dist / 1.5;
- } elsif ( defined $cgi->param( 'zoom_in2' ) ) {
- $new_dist = $dist / 3;
- } elsif ( defined $cgi->param( 'zoom_in3' ) ) {
- $new_dist = $dist / 10;
- } elsif ( defined $cgi->param( 'zoom_out1' ) ) {
- $new_dist = $dist * 1.5;
- } elsif ( defined $cgi->param( 'zoom_out2' ) ) {
- $new_dist = $dist * 3;
- } elsif ( defined $cgi->param( 'zoom_out3' ) ) {
- $new_dist = $dist * 10;
- }
+ $dist_diff = $dist - $new_dist;
- if ( $new_dist )
- {
- $dist_diff = $dist - $new_dist;
- $new_start = int( $start + ( $dist_diff / 2 ) );
- $new_end = int( $end - ( $dist_diff / 2 ) );
+ $cookie->{ 'NAV_START' } = int( $cookie->{ 'NAV_START' } + ( $dist_diff / 2 ) );
+ $cookie->{ 'NAV_END' } = int( $cookie->{ 'NAV_END' } - ( $dist_diff / 2 ) );
- $cgi->param( 'nav_start', $new_start );
- $cgi->param( 'nav_end', $new_end );
- }
+ $cookie->{ 'NAV_START' } = 1 if $cookie->{ 'NAV_START' } <= 0;
+ $cookie->{ 'NAV_END' } = $max if $cookie->{ 'NAV_END' } > $max;
}
}
-sub nav_move
+sub cookie_move
{
- my ( $cgi, # CGI object
- $max, # Max end position
+ my ( $cookie,
) = @_;
- my ( $start, $end, $dist, $shift, $new_start, $new_end );
+ my ( $max, $dist, $shift, $new_start, $new_end );
- if ( defined $cgi->param( 'nav_start' ) and $cgi->param( 'nav_end' ) )
- {
- $start = $cgi->param( 'nav_start' );
- $end = $cgi->param( 'nav_end' );
-
- $start =~ tr/,//d;
- $end =~ tr/,//d;
-
- $dist = $end - $start;
-
- if ( defined $cgi->param( 'move_left1' ) ) {
- $shift = -1 * $dist * 0.10;
- } elsif ( defined $cgi->param( 'move_left2' ) ) {
- $shift = -1 * $dist * 0.475;
- } elsif ( defined $cgi->param( 'move_left3' ) ) {
- $shift = -1 * $dist * 0.95;
- } elsif ( defined $cgi->param( 'move_right1' ) ) {
- $shift = $dist * 0.10;
- } elsif ( defined $cgi->param( 'move_right2' ) ) {
- $shift = $dist * 0.475;
- } elsif ( defined $cgi->param( 'move_right3' ) ) {
- $shift = $dist * 0.95;
- }
+ $max = Maasha::Filesys::file_size( Maasha::KISS::Track::path_seq( $cookie ) );
- if ( $shift )
- {
- $new_start = int( $start + $shift );
- $new_end = int( $end + $shift );
+ $dist = $cookie->{ 'NAV_END' } - $cookie->{ 'NAV_START' };
- print "HERRRR: shift: $shift start: $new_start end: $new_end\n";
+ if ( defined $cookie->{ 'MOVE_LEFT1' } ) {
+ $shift = -1 * $dist * 0.10;
+ } elsif ( defined $cookie->{ 'MOVE_LEFT2' } ) {
+ $shift = -1 * $dist * 0.475;
+ } elsif ( defined $cookie->{ 'MOVE_LEFT3' } ) {
+ $shift = -1 * $dist * 0.95;
+ } elsif ( defined $cookie->{ 'MOVE_RIGHT1' } ) {
+ $shift = $dist * 0.10;
+ } elsif ( defined $cookie->{ 'MOVE_RIGHT2' } ) {
+ $shift = $dist * 0.475;
+ } elsif ( defined $cookie->{ 'MOVE_RIGHT3' } ) {
+ $shift = $dist * 0.95;
+ }
+
+ if ( $shift )
+ {
+ $new_start = int( $cookie->{ 'NAV_START' } + $shift );
+ $new_end = int( $cookie->{ 'NAV_END' } + $shift );
- if ( $new_start > 0 and $new_end < $max )
- {
- $cgi->param( 'nav_start', $new_start );
- $cgi->param( 'nav_end', $new_end );
- }
+ if ( $new_start > 0 and $new_end < $max )
+ {
+ $cookie->{ 'NAV_START' } = $new_start;
+ $cookie->{ 'NAV_END' } = $new_end;
}
}
}
-sub nav_def_clade
+sub page
{
- my ( $cgi, # CGI object
+ my ( $cookie,
) = @_;
- my ( $def_clade );
+ # Returns a list.
+
+ my ( @html, $list, $item, $href );
- if ( defined $cgi->param( 'nav_clade' ) )
+ push @html, breadcrumb( $cookie );
+
+ $list = "LIST_" . uc $cookie->{ 'PAGE' };
+
+ if ( $cookie->{ 'PAGE' } eq 'export' )
{
- $def_clade = $cgi->param( 'nav_clade' );
+ push @html, Maasha::XHTML::h2( txt => "Export", class => 'center' );
+ }
+ elsif ( $cookie->{ 'PAGE' } ne 'browse' )
+ {
+ push @html, Maasha::XHTML::h2( txt => "Select $cookie->{ 'PAGE' }", class => 'center' );
+
+ push @html, Maasha::XHTML::table_beg( summary => "Select table", align => 'center', cellpadding => '5px' );
+
+ foreach $item ( @{ $cookie->{ $list } } )
+ {
+ $cookie->{ uc $cookie->{ 'PAGE' } } = $item;
+
+ $href = page_href( $cookie, page_next( $cookie ) );
+
+ push @html, Maasha::XHTML::table_row_simple( tr => [ Maasha::XHTML::ln( txt => $item, href => $href ) ] );
+ }
+
+ push @html, Maasha::XHTML::table_end;
}
else
{
- $def_clade = "Bacteria";
+ push @html, sec_navigate( $cookie );
+ push @html, sec_browse( $cookie );
}
- return $def_clade;
+ return wantarray ? @html : \@html;
}
-sub nav_def_genome
+sub page_next
{
- my ( $cgi, # CGI object
+ my ( $cookie,
) = @_;
- my ( $def_genome );
+ my ( $i );
- if ( defined $cgi->param( 'nav_genome' ) )
- {
- $def_genome = $cgi->param( 'nav_genome' );
- }
- else
- {
- $def_genome = "S.aur_COL";
+ for ( $i = 0; $i < @{ $cookie->{ 'LIST_PAGES' } }; $i++ ) {
+ last if $cookie->{ 'PAGE' } eq $cookie->{ 'LIST_PAGES' }->[ $i ];
}
- return $def_genome;
+ return $cookie->{ 'LIST_PAGES' }->[ $i + 1 ];
}
-sub nav_def_assembly
+sub breadcrumb
{
- my ( $cgi, # CGI object
+ my ( $cookie,
) = @_;
- my ( $def_assembly );
+ # Returns a list.
- if ( defined $cgi->param( 'nav_assembly' ) )
- {
- $def_assembly = $cgi->param( 'nav_assembly' );
- }
- else
+ my ( @pages, $page, @row1, @row2, @html, $href, $txt );
+
+ @pages = @{ $cookie->{ 'LIST_PAGES' } };
+
+ pop @pages; # remove 'browse'
+
+ foreach $page ( @pages )
{
- $def_assembly = "2009-01-23";
+ $href = page_href( $cookie, $page );
+
+ $txt = $cookie->{ uc $page } || "";
+
+ push @row1, Maasha::XHTML::ln( txt => $page, href => $href, class => 'inline' );
+ push @row2, Maasha::XHTML::p( txt => $txt, class => 'inline' );
+
+ last if $page eq $cookie->{ 'PAGE' };
}
- return $def_assembly;
+ push @html, Maasha::XHTML::table_beg( summary => "Taxonomy table", align => 'center', cellpadding => '5px' );
+ push @html, Maasha::XHTML::table_row_simple( tr => \@row1, align => 'center' );
+ push @html, Maasha::XHTML::table_row_simple( tr => \@row2, align => 'center' );
+ push @html, Maasha::XHTML::table_end;
+
+ return wantarray ? @html : \@html;
}
-sub nav_def_contig
+sub page_href
{
- my ( $cgi, # CGI object
+ my ( $cookie,
+ $page,
) = @_;
- my ( $def_contig );
+ # Returns a string.
- if ( defined $cgi->param( 'nav_contig' ) )
- {
- $def_contig = $cgi->param( 'nav_contig' );
- }
- else
+ my ( @href );
+
+ while ( 1 )
{
- $def_contig = "chr1";
+ push @href, "$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' };
+ last if $page eq 'clade';
+ push @href, "genome=$cookie->{ 'GENOME' }" if $cookie->{ 'GENOME' };
+ last if $page eq 'genome';
+ push @href, "assembly=$cookie->{ 'ASSEMBLY' }" if $cookie->{ 'ASSEMBLY' };
+ last if $page eq 'assembly';
+ push @href, "contig=$cookie->{ 'CONTIG' }" if $cookie->{ 'CONTIG' };
+ last if $page eq 'contig';
+ last;
}
- return $def_contig;
+ return join "&", @href;
}
-sub nav_def_start
+sub sec_navigate
{
- my ( $cgi, # CGI object
+ my ( $cookie,
) = @_;
- my ( $def_start );
+ # Returns a list.
- if ( defined $cgi->param( 'nav_start' ) ) {
- $def_start = $cgi->param( 'nav_start' );
- } else {
- $def_start = 1;
- }
+ my ( @html );
- $def_start =~ tr/,//d;
+ push @html, Maasha::XHTML::table_beg( summary => "Navigation table", align => 'center' );
+ push @html, Maasha::XHTML::table_row_simple( tr => [ qw( Start End ) ], align => 'center' );
+ push @html, Maasha::XHTML::table_row_simple( tr => [
+ Maasha::XHTML::text( name => "nav_start", value => Maasha::Calc::commify( $cookie->{ 'NAV_START' } ), size => 20 ),
+ Maasha::XHTML::text( name => "nav_end", value => Maasha::Calc::commify( $cookie->{ 'NAV_END' } ), size => 20 ),
+ Maasha::XHTML::submit( name => "nav_submit", value => "Submit" ),
+ ] );
+ push @html, Maasha::XHTML::table_end;
- if ( $def_start <= 0 ) {
- $def_start = 1;
- }
+ push @html, Maasha::XHTML::table_beg( summary => "Zoom table", align => 'center' );
+ push @html, Maasha::XHTML::table_row_simple( tr => [
+ Maasha::XHTML::p( txt => 'Move:' ),
+ Maasha::XHTML::submit( name => "move_left3", value => "<<<", title => "move 95% to the left" ),
+ Maasha::XHTML::submit( name => "move_left2", value => "<<", title => "move 47.5% to the left" ),
+ Maasha::XHTML::submit( name => "move_left1", value => "<", title => "move 10% to the left" ),
+ Maasha::XHTML::submit( name => "move_right1", value => ">", title => "move 10% to the rigth" ),
+ Maasha::XHTML::submit( name => "move_right2", value => ">>", title => "move 47.5% to the rigth" ),
+ Maasha::XHTML::submit( name => "move_right3", value => ">>>", title => "move 95% to the right" ),
+ Maasha::XHTML::p( txt => 'Zoom in:' ),
+ Maasha::XHTML::submit( name => "zoom_in1", value => "1.5x" ),
+ Maasha::XHTML::submit( name => "zoom_in2", value => "3x" ),
+ Maasha::XHTML::submit( name => "zoom_in3", value => "10x" ),
+ Maasha::XHTML::p( txt => 'Zoom out:' ),
+ Maasha::XHTML::submit( name => "zoom_out1", value => "1.5x" ),
+ Maasha::XHTML::submit( name => "zoom_out2", value => "3x" ),
+ Maasha::XHTML::submit( name => "zoom_out3", value => "10x" ),
+ ] );
+ push @html, Maasha::XHTML::table_end;
- $cgi->param( 'nav_start', $def_start );
+ push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "page", value => "browse" ) );
+ push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "user", value => "$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 $def_start;
+ return wantarray ? @html : \@html;
}
-sub nav_def_end
+sub sec_browse
{
- my ( $cgi, # CGI object
+ my ( $cookie,
) = @_;
- my ( $def_end );
+ # Returns a list.
+
+ my ( $draw_metrics, @tracks, $i, @features, $feat, $elem, $file, $surface, $cr, @html, @img );
+
+ $draw_metrics = {
+ IMG_WIDTH => 1200,
+ IMG_HEIGHT => 800,
+ TRACK_OFFSET => 20,
+ TRACK_SPACE => 20,
+ RULER_FONT_SIZE => 10,
+ RULER_COLOR => [ 0, 0, 0 ],
+ SEQ_FONT_SIZE => 10,
+ SEQ_COLOR => [ 0, 0, 0, ],
+ FEAT_WIDTH => 5,
+ FEAT_COLOR => [ 0, 1, 0 ],
+ };
- if ( defined $cgi->param( 'nav_end' ) ) {
- $def_end = $cgi->param( 'nav_end' );
- } else {
- $def_end = 2809422;
- $def_end = 2000;
+ push @features, [ Maasha::KISS::Track::track_ruler( $draw_metrics, $cookie ) ];
+ push @features, [ Maasha::KISS::Track::track_seq( $draw_metrics, $cookie ) ];
+
+ @tracks = Maasha::KISS::Track::path_tracks( $cookie );
+
+ for ( $i = 0; $i < @tracks; $i++ )
+ {
+ $draw_metrics->{ 'FEAT_COLOR' } = palette( $i );
+
+ push @features, [ Maasha::KISS::Track::track_feature( $tracks[ $i ], $draw_metrics, $cookie ) ];
}
- $def_end =~ tr/,//d;
+ $file = "fisk.png";
+
+ $surface = Cairo::ImageSurface->create( 'argb32', $draw_metrics->{ 'IMG_WIDTH' }, $draw_metrics->{ 'TRACK_OFFSET' } );
+ $cr = Cairo::Context->create( $surface );
- if ( $def_end > 2809422 ) {
- $def_end = 2809422;
+ foreach $feat ( @features ) {
+ Maasha::KISS::Draw::draw_feature( $cr, $feat ) if $feat;
}
- $cgi->param( 'nav_end', $def_end );
+ Maasha::KISS::Draw::file_png( $surface, $file );
- return $def_end;
-}
+ push @img, Maasha::XHTML::img(
+ src => $file,
+ alt => "Browser Tracks",
+ height => $draw_metrics->{ 'TRACK_OFFSET' },
+ width => $draw_metrics->{ 'IMG_WIDTH' },
+ id => "browser_map",
+ usemap => "#browser_map"
+ );
+ push @img, Maasha::XHTML::map_beg( name => "browser_map", id => "browser_map" );
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+ foreach $feat ( @features )
+ {
+ foreach $elem ( @{ $feat } )
+ {
+ next if $elem->{ 'type' } eq 'text';
+
+ push @img, Maasha::XHTML::area(
+ href => page_href( $cookie, "export" ) . "&Q_ID=$elem->{ 'id' }",
+ shape => "rect",
+ coords => "$elem->{ x1 }, $elem->{ y1 }, $elem->{ x2 }, $elem->{ y2 }", title => "$elem->{ 'title' }",
+ );
+ }
+ }
+
+ push @img, Maasha::XHTML::map_end();
+
+ push @html, Maasha::XHTML::p( txt => join( "\n", @img ) );
+
+ @html = Maasha::XHTML::div( txt => join( "\n", @html ), class => 'browse' );
+
+ return wantarray ? @html : \@html;
+}
-END
+sub palette
{
- Maasha::SQL::disconnect( $dbh ) if $dbh;
+ my ( $i,
+ ) = @_;
+
+ my ( $palette, $color );
+
+ $palette = [
+ [ 30, 130, 130 ],
+ [ 30, 50, 150 ],
+ [ 130, 130, 50 ],
+ [ 130, 90, 130 ],
+ [ 130, 70, 70 ],
+ [ 70, 170, 130 ],
+ [ 130, 170, 50 ],
+ ];
+
+ $color = $palette->[ $i ];
+
+ map { $_ /= 255 } @{ $color };
+
+ return $color;
}
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
__END__
+
+ # push @html, Maasha::KISS::Draw::hdump( $features );
+
+ $t0 = Time::HiRes::gettimeofday();
+ $t1 = Time::HiRes::gettimeofday();
projects / biopieces.git / blobdiff