use URI::Escape;
use Data::Dumper;
use Digest::MD5;
+use Time::HiRes;
use Maasha::Common;
use Maasha::Filesys;
use Maasha::Calc;
push @html, Maasha::XHTML::html_end;
# push @html, Maasha::XHTML::hdump( { $cgi->Vars } ); # DEBUG
-# push @html, Maasha::XHTML::hdump( \%ENV ); # DEBUG
# push @html, Maasha::XHTML::hdump( $cookie ); # DEBUG
+# push @html, Maasha::XHTML::hdump( \%ENV ); # DEBUG
print "$_\n" foreach @html;
-
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
# Returns a hash.
- my ( $cookie );
+ my ( $cookie, $session );
$cookie = {};
}
}
- $cookie->{ 'SCRIPT' } = Maasha::Common::get_scriptname();
- $cookie->{ 'DATA_DIR' } = "Data";
- $cookie->{ 'SESSION_DIR' } = "Sessions";
- $cookie->{ 'LIST_PAGES' } = [ qw( clade genome assembly contig browse ) ];
+ $cookie->{ 'SCRIPT' } = Maasha::Common::get_scriptname();
+ $cookie->{ 'DATA_DIR' } = "Data";
+ $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->{ 'USER' } = $cgi->param( 'user' ) || '';
- $cookie->{ 'PASSWORD' } = $cgi->param( 'password' );
- $cookie->{ 'SESSION_ID' } = $cgi->param( 'session_id' );
+ $session = session_restore( $cookie );
- cookie_session( $cookie );
cookie_login( $cookie );
- $cookie->{ 'PAGE' } ||= $cgi->param( 'page' ) || 'login';
+ # session_id_check( $cookie, $session );
- if ( $cookie->{ 'LOGIN' } eq 'OK' )
+ if ( $cookie->{ 'LOGIN_ERROR' } or $cookie->{ 'SESSION_ERROR' } )
+ {
+ $cookie->{ 'PAGE' } = 'login';
+ }
+ elsif ( $cookie->{ 'LOGIN' } )
{
if ( $cgi->param( 'genome' ) ) {
$cookie->{ 'PAGE' } = 'browse';
} else {
- $cookie->{ 'PAGE' } = 'clade';
+ $cookie->{ 'PAGE' } = $session->{ 'PAGE' } || 'clade';
}
}
+ elsif ( not defined $cookie->{ 'USER' } )
+ {
+ $cookie->{ 'PAGE' } = 'login';
+ }
+ else
+ {
+ $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->{ 'Q_ID' } = $cgi->param( 'q_id' );
- $cookie->{ 'NAV_START' } ||= $cgi->param( 'nav_start' );
- $cookie->{ 'NAV_END' } ||= $cgi->param( 'nav_end' );
+ $cookie->{ 'TRACK_STATUS' } = $session->{ 'TRACK_STATUS' };
+ $cookie->{ 'CLADE' } = $cgi->param( 'clade' ) || $session->{ 'CLADE' };
+ $cookie->{ 'GENOME' } = $cgi->param( 'genome' ) || $session->{ 'GENOME' };
+ $cookie->{ 'ASSEMBLY' } = $cgi->param( 'assembly' ) || $session->{ 'ASSEMBLY' };
+ $cookie->{ 'CONTIG' } = $cgi->param( 'contig' ) || $session->{ 'CONTIG' };
+ $cookie->{ 'Q_ID' } = $cgi->param( 'q_id' ) || $session->{ 'Q_ID' };
+ $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' );
- $cookie->{ 'S_END' } = $cgi->param( 's_end' );
- $cookie->{ 'STRAND' } = $cgi->param( 'strand' );
+ $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->{ 'ZOOM_IN2' } = $cgi->param( 'zoom_in2' );
$cookie->{ 'ZOOM_IN3' } = $cgi->param( 'zoom_in3' );
$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;
$cookie->{ 'SEQ_COLOR' } = [ 0, 0, 0, ];
$cookie->{ 'FEAT_WIDTH' } = 5;
$cookie->{ 'FEAT_COLOR' } = [ 0, 0, 0 ];
- $cookie->{ 'FEAT_MAX' } = 5000; # TODO: Reduntant?
+# $cookie->{ 'FEAT_MAX' } = 5000; # TODO: Reduntant?
- $cookie->{ 'LIST_USER' } = Maasha::BGB::Track::list_users();
+# $cookie->{ 'LIST_USER' } = Maasha::BGB::Track::list_users(); # TODO: Redundant?
- if ( $cookie->{ 'USER' } )
+ 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' } )
{
cookie_zoom( $cookie );
cookie_move( $cookie );
cookie_center( $cookie );
+ cookie_track_status( $cookie );
}
}
$cookie->{ 'STRAND' } = '+' if defined $cookie->{ 'STRAND' } and $cookie->{ 'STRAND' } eq ' '; # FIXME ugly HTML fix
+ session_store( $cookie, $session );
+
return wantarray ? %{ $cookie } : $cookie;
}
-sub cookie_session
+sub session_restore
{
- # Martin A. Hansen, December 2009.
+ # Martin A. Hansen, March 2010.
- # Check cookie information against session information.
+ # Restores session and returns this.
my ( $cookie, # cookie hash
) = @_;
- # Returns nothing.
+ # Returns hashref.
my ( $session );
- $session = Maasha::BGB::Session::session_restore( "$cookie->{ 'SESSION_DIR' }/sessions.json" );
-
- # if ( $cookie->{ 'SESSION_ID' } )
- # {
- # if ( $cookie->{ 'SESSION_ID' } ne $ENV{ 'SSL_SESSION_ID' } ) {
- # $cookie->{ 'PAGE' } = 'login';
- # print STDERR "HER1\n"; # DEBUG
- # }
- # }
- # else
- # {
- # $cookie->{ 'PAGE' } = 'login';
- #
- # print STDERR "HER2\n"; # DEBUG
- # }
-
- if ( exists $session->{ $cookie->{ 'USER' } } and $cookie->{ 'SESSION_ID' } )
+ if ( defined $cookie->{ 'USER' } and -d "$cookie->{ 'SESSION_DIR' }/$cookie->{ 'USER' }" ) {
+ $session = Maasha::BGB::Session::session_restore( "$cookie->{ 'SESSION_DIR' }/$cookie->{ 'USER' }/session.json" );
+ }
+
+ return wantarray ? %{ $session } : $session;
+}
+
+
+sub session_store
+{
+ # Martin A. Hansen, March 2010.
+
+ # Store a session updated with cookie information to session file.
+
+ my ( $cookie, # cookie hash
+ $session, # session hash
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $new_session );
+
+ if ( defined $cookie->{ 'USER' } and $cookie->{ 'USER' } ne '' and -d "$cookie->{ 'SESSION_DIR' }/$cookie->{ 'USER' }" )
{
- if ( $session->{ $cookie->{ 'USER' } }->{ 'SESSION_ID' } ne $cookie->{ 'SESSION_ID' } ) {
- $cookie->{ 'PAGE' } = 'login';
- print STDERR "HER3\n"; # DEBUG
+ $new_session->{ 'PASSWORD' } = $session->{ 'PASSWORD' };
+ $new_session->{ 'SESSION_ID' } = $session->{ 'SESSION_ID' };
+ $new_session->{ 'TIME' } = Maasha::Common::time_stamp();
+ $new_session->{ 'PAGE' } = $cookie->{ 'PAGE' };
+
+ if ( $cookie->{ 'PAGE' } =~ /browse|export_pdf|export_svg/ )
+ {
+ $new_session->{ 'CLADE' } = $cookie->{ 'CLADE' };
+ $new_session->{ 'GENOME' } = $cookie->{ 'GENOME' };
+ $new_session->{ 'ASSEMBLY' } = $cookie->{ 'ASSEMBLY' };
+ $new_session->{ 'CONTIG' } = $cookie->{ 'CONTIG' };
+ $new_session->{ 'NAV_START' } = $cookie->{ 'NAV_START' };
+ $new_session->{ 'NAV_END' } = $cookie->{ 'NAV_END' };
+ }
+ elsif ( $cookie->{ 'PAGE' } eq 'contig' )
+ {
+ $new_session->{ 'CLADE' } = $cookie->{ 'CLADE' };
+ $new_session->{ 'GENOME' } = $cookie->{ 'GENOME' };
+ $new_session->{ 'ASSEMBLY' } = $cookie->{ 'ASSEMBLY' };
+ }
+ elsif ( $cookie->{ 'PAGE' } eq 'assembly' )
+ {
+ $new_session->{ 'CLADE' } = $cookie->{ 'CLADE' };
+ $new_session->{ 'GENOME' } = $cookie->{ 'GENOME' };
}
+ elsif ( $cookie->{ 'PAGE' } eq 'genome' )
+ {
+ $new_session->{ 'CLADE' } = $cookie->{ 'CLADE' };
+ }
+ elsif ( $cookie->{ 'PAGE' } =~ /export|dna/ )
+ {
+ $new_session->{ 'CLADE' } = $cookie->{ 'CLADE' };
+ $new_session->{ 'GENOME' } = $cookie->{ 'GENOME' };
+ $new_session->{ 'ASSEMBLY' } = $cookie->{ 'ASSEMBLY' };
+ $new_session->{ 'CONTIG' } = $cookie->{ 'CONTIG' };
+ $new_session->{ 'Q_ID' } = $cookie->{ 'Q_ID' };
+ $new_session->{ 'S_BEG' } = $cookie->{ 'S_BEG' };
+ $new_session->{ 'S_END' } = $cookie->{ 'S_END' };
+ $new_session->{ 'STRAND' } = $cookie->{ 'STRAND' };
+ }
+
+ $new_session->{ 'TRACK_STATUS' } = $cookie->{ 'TRACK_STATUS' };
+
+ Maasha::BGB::Session::session_store( "$cookie->{ 'SESSION_DIR' }/$cookie->{ 'USER' }/session.json", $new_session );
}
- else
+}
+
+
+sub session_id_check
+{
+ # Martin A. Hansen, March 2010.
+
+ # Check that the session id in the cookie and session match.
+ # Sets SESSION_ERROR flag in cookie if not matching.
+
+ my ( $cookie, # cookie hash
+ $session, # session hash
+ ) = @_;
+
+ # Returns nothing.
+
+ if ( defined $cookie->{ 'SESSION_ID' } and defined $session->{ 'SESSION_ID' } )
{
- $cookie->{ 'PAGE' } = 'login';
- print STDERR "HER4\n"; # DEBUG
- print STDERR "NO COOKIE SESSION ID\n" if not $cookie->{ 'SESSION_ID' }; # DEBUG
- print STDERR "NO COOKIE USER\n" if not $cookie->{ 'USER' }; # DEBUG
- print STDERR "NO SESSION USER\n" if not exists $session->{ $cookie->{ 'USER' } }; # DEBUG
+ if ( $cookie->{ 'SESSION_ID' } ne $session->{ 'SESSION_ID' } ) {
+ $cookie->{ 'SESSION_ERROR' } = 1;
+ } else {
+ $cookie->{ 'SESSION_ERROR' } = 0;
+ }
}
}
my ( $session );
- if ( $cookie->{ 'USER' } and $cookie->{ 'PASSWORD' } )
+ if ( defined $cookie->{ 'PASSWORD' } )
{
- $session = Maasha::BGB::Session::session_restore( "$cookie->{ 'SESSION_DIR' }/sessions.json" );
-
- if ( exists $session->{ $cookie->{ 'USER' } } and
- $session->{ $cookie->{ 'USER' } }->{ 'PASSWORD' } eq Digest::MD5::md5_hex( $cookie->{ 'PASSWORD' } ) )
+ if ( defined $cookie->{ 'USER' } and -d "$cookie->{ 'SESSION_DIR' }/$cookie->{ 'USER' }" )
{
- $session->{ $cookie->{ 'USER' } }->{ 'SESSION_ID' } ||= Maasha::BGB::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' };
- $cookie->{ 'LOGIN' } = "OK";
-
- Maasha::BGB::Session::session_store( "$cookie->{ 'SESSION_DIR' }/sessions.json", $session );
+ $session = Maasha::BGB::Session::session_restore( "$cookie->{ 'SESSION_DIR' }/$cookie->{ 'USER' }/session.json" );
+
+ if ( $session->{ 'PASSWORD' } eq Digest::MD5::md5_hex( $cookie->{ 'PASSWORD' } ) )
+ {
+ $cookie->{ 'TIME' } = Maasha::Common::time_stamp();
+ $cookie->{ 'SESSION_ID' } ||= Maasha::BGB::Session::session_new();
+ $cookie->{ 'LOGIN' } = 1;
+ $cookie->{ 'LOGIN_ERROR' } = 0;
+ }
+ else
+ {
+ $cookie->{ 'LOGIN_ERROR' } = 1;
+ }
}
else
{
- $cookie->{ 'LOGIN' } = "ERROR";
+ $cookie->{ 'LOGIN_ERROR' } = 1;
}
}
}
sub cookie_center
{
- # Martin A. Hansen, March 2010
+ # Martin A. Hansen, March 2010.
# Adjust the cookie values for NAV_START and NAV_END based
# on cookie CENTER value if defined.
}
-sub cookie_page_next
+sub cookie_track_status
{
- # Martin A. Hansen, November 2009.
-
- # Returns the next page in the taxonomy path.
+ # Martin A. Hansen, March 2010.
+ #
+
my ( $cookie, # cookie hash
) = @_;
- # Returns a string.
+ # Returns nothing.
+
+ my ( $clade, $genome, $assembly, $track );
- my ( $i );
+ $clade = $cookie->{ 'CLADE' };
+ $genome = $cookie->{ 'GENOME' };
+ $assembly = $cookie->{ 'ASSEMBLY' };
+ $track = $cookie->{ 'TRACK' };
- for ( $i = 0; $i < @{ $cookie->{ 'LIST_PAGES' } }; $i++ ) {
- last if $cookie->{ 'PAGE' } eq $cookie->{ 'LIST_PAGES' }->[ $i ];
+ if ( $track )
+ {
+ if ( $cookie->{ 'TRACK_STATUS' }->{ $clade }->{ $genome }->{ $assembly }->{ $track } ) {
+ $cookie->{ 'TRACK_STATUS' }->{ $clade }->{ $genome }->{ $assembly }->{ $track } = 0;
+ } else {
+ $cookie->{ 'TRACK_STATUS' }->{ $clade }->{ $genome }->{ $assembly }->{ $track } = 1;
+ }
}
-
- return $cookie->{ 'LIST_PAGES' }->[ $i + 1 ];
}
push @html, page_dna( $cookie );
} elsif ( $cookie->{ 'PAGE' } eq 'export' ) {
push @html, page_export( $cookie );
- } else {
- push @html, page_taxonomy( $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' ) {
+ push @html, page_genome( $cookie );
+ } elsif ( $cookie->{ 'PAGE' } eq 'assembly' ) {
+ push @html, page_assembly( $cookie );
+ } elsif ( $cookie->{ 'PAGE' } eq 'contig' ) {
+ push @html, page_contig( $cookie );
}
return wantarray ? @html : \@html;
}
-sub page_taxonomy
+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.
+
+ # Renders the clade selection page.
+
+ my ( $cookie, # cookie hash
+ ) = @_;
+
+ # Returns a list.
+
+ my ( @html );
+
+ push @html, section_taxonomy_table( $cookie );
+ push @html, section_clade( $cookie );
+
+ return wantarray ? @html : \@html;
+}
+
+
+sub page_genome
+{
+ # Martin A. Hansen, March 2010.
+
+ # Renders the genome selection page.
+
+ my ( $cookie, # cookie hash
+ ) = @_;
+
+ # Returns a list.
+
+ my ( @html );
+
+ push @html, section_taxonomy_table( $cookie );
+ push @html, section_genome( $cookie );
+
+ return wantarray ? @html : \@html;
+}
+
+
+sub page_assembly
+{
+ # Martin A. Hansen, March 2010.
+
+ # Renders the clade selection page.
+
+ my ( $cookie, # cookie hash
+ ) = @_;
+
+ # Returns a list.
+
+ my ( @html );
+
+ push @html, section_taxonomy_table( $cookie );
+ push @html, section_assembly( $cookie );
+
+ return wantarray ? @html : \@html;
+}
+
+
+sub page_contig
{
# Martin A. Hansen, November 2009.
my ( @html );
push @html, section_taxonomy_table( $cookie );
- push @html, section_taxonomy_select( $cookie );
+ push @html, section_contig( $cookie );
return wantarray ? @html : \@html;
}
push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "nav_end", value => $cookie->{ 'NAV_END' } ) );
}
- if ( $cookie->{ 'LOGIN' } and $cookie->{ 'LOGIN' } eq 'ERROR' ) {
+ if ( $cookie->{ 'LOGIN_ERROR' } ) {
push @html, Maasha::XHTML::h3( txt => "Bad user or password - please retry", class => 'error' );
}
}
-sub section_taxonomy_select
+sub section_clade
{
- # Martin A. Hansen, November 2009.
+ # Martin A. Hansen, March 2010.
- # Returns a HTML section with selection choices
+ # Returns a HTML section with clade selection choices
# for navigating the taxonomy tree.
my ( $cookie, # cookie hash
# Returns a list.
- my ( $list, @html, $item, $href );
+ my ( @html, $clade, $href );
+
+ push @html, Maasha::XHTML::h2( txt => "Select clade", class => 'center' );
- $list = "LIST_" . uc $cookie->{ 'PAGE' };
+ push @html, Maasha::XHTML::table_beg( summary => "Taxonomy select table", align => 'center', cellpadding => '5px' );
- push @html, Maasha::XHTML::h2( txt => "Select $cookie->{ 'PAGE' }", class => 'center' );
+ foreach $clade ( @{ $cookie->{ 'LIST_CLADE' } } )
+ {
+ $href = "$cookie->{ 'SCRIPT' }?page=genome";
+ $href .= "&session_id=$cookie->{ 'SESSION_ID' }";
+ $href .= "&user=$cookie->{ 'USER' }";
+ $href .= "&clade=$clade";
+
+ push @html, Maasha::XHTML::table_row_simple( tr => [ Maasha::XHTML::ln( txt => $clade, href => $href ) ] );
+ }
+
+ push @html, Maasha::XHTML::table_end;
+
+ return wantarray ? @html : \@html;
+}
+
+
+sub section_genome
+{
+ # Martin A. Hansen, March 2010.
+
+ # Returns a HTML section with genome selection choices
+ # for navigating the taxonomy tree.
+
+ my ( $cookie, # cookie hash
+ ) = @_;
+
+ # Returns a list.
+
+ my ( @html, $genome, $href );
+
+ push @html, Maasha::XHTML::h2( txt => "Select genome", class => 'center' );
push @html, Maasha::XHTML::table_beg( summary => "Taxonomy select table", align => 'center', cellpadding => '5px' );
- foreach $item ( @{ $cookie->{ $list } } )
+ foreach $genome ( @{ $cookie->{ 'LIST_GENOME' } } )
{
- $cookie->{ uc $cookie->{ 'PAGE' } } = $item;
+ $href = "$cookie->{ 'SCRIPT' }?page=assembly";
+ $href .= "&session_id=$cookie->{ 'SESSION_ID' }";
+ $href .= "&user=$cookie->{ 'USER' }";
+ $href .= "&clade=$cookie->{ 'CLADE' }";
+ $href .= "&genome=$genome";
+
+ push @html, Maasha::XHTML::table_row_simple( tr => [ Maasha::XHTML::ln( txt => $genome, href => $href ) ] );
+ }
- $href = "$cookie->{ 'SCRIPT' }?page=" . cookie_page_next( $cookie );
+ push @html, Maasha::XHTML::table_end;
+
+ return wantarray ? @html : \@html;
+}
+
+
+sub section_assembly
+{
+ # Martin A. Hansen, March 2010.
+
+ # Returns a HTML section with assembly selection choices
+ # for navigating the taxonomy tree.
+
+ my ( $cookie, # cookie hash
+ ) = @_;
+
+ # Returns a list.
+
+ my ( @html, $assembly, $href );
+
+ push @html, Maasha::XHTML::h2( txt => "Select assembly", class => 'center' );
+
+ push @html, Maasha::XHTML::table_beg( summary => "Taxonomy select table", align => 'center', cellpadding => '5px' );
+
+ foreach $assembly ( @{ $cookie->{ 'LIST_ASSEMBLY' } } )
+ {
+ $href = "$cookie->{ 'SCRIPT' }?page=contig";
+ $href .= "&session_id=$cookie->{ 'SESSION_ID' }";
+ $href .= "&user=$cookie->{ 'USER' }";
+ $href .= "&clade=$cookie->{ 'CLADE' }";
+ $href .= "&genome=$cookie->{ 'GENOME' }";
+ $href .= "&assembly=$assembly";
+
+ push @html, Maasha::XHTML::table_row_simple( tr => [ Maasha::XHTML::ln( txt => $assembly, href => $href ) ] );
+ }
+
+ push @html, Maasha::XHTML::table_end;
+
+ return wantarray ? @html : \@html;
+}
+
+
+sub section_contig
+{
+ # Martin A. Hansen, March 2010.
+
+ # Returns a HTML section with contig selection choices
+ # for navigating the taxonomy tree.
+
+ my ( $cookie, # cookie hash
+ ) = @_;
+
+ # Returns a list.
+
+ my ( @html, $contig, $href );
+
+ push @html, Maasha::XHTML::h2( txt => "Select contig", class => 'center' );
+
+ push @html, Maasha::XHTML::table_beg( summary => "Taxonomy select table", align => 'center', cellpadding => '5px' );
+
+ foreach $contig ( @{ $cookie->{ 'LIST_CONTIG' } } )
+ {
+ $href = "$cookie->{ 'SCRIPT' }?page=browse";
$href .= "&session_id=$cookie->{ 'SESSION_ID' }";
$href .= "&user=$cookie->{ 'USER' }";
$href .= "&clade=$cookie->{ 'CLADE' }";
- $href .= "&genome=$cookie->{ 'GENOME' }" if $cookie->{ 'GENOME' };
- $href .= "&assembly=$cookie->{ 'ASSEMBLY' }" if $cookie->{ 'ASSEMBLY' };
- $href .= "&contig=$cookie->{ 'CONTIG' }" if $cookie->{ 'CONTIG' };
+ $href .= "&genome=$cookie->{ 'GENOME' }";
+ $href .= "&assembly=$cookie->{ 'ASSEMBLY' }";
+ $href .= "&contig=$contig";
- push @html, Maasha::XHTML::table_row_simple( tr => [ Maasha::XHTML::ln( txt => $item, href => $href ) ] );
+ push @html, Maasha::XHTML::table_row_simple( tr => [ Maasha::XHTML::ln( txt => $contig, href => $href ) ] );
}
push @html, Maasha::XHTML::table_end;
# 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 ( @tracks, $i, @features, $feat, $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 @features, [ Maasha::BGB::Track::track_ruler( $cookie ) ];
- push @features, [ Maasha::BGB::Track::track_seq( $cookie ) ];
+ push @tracks, [ Maasha::BGB::Track::track_ruler( $cookie ) ];
+ push @tracks, [ Maasha::BGB::Track::track_seq( $cookie ) ];
- @tracks = Maasha::BGB::Track::path_tracks( $cookie );
+ @track_list = Maasha::BGB::Track::list_track_dir( $cookie->{ 'USER' }, $cookie->{ 'CLADE' }, $cookie->{ 'GENOME' }, $cookie->{ 'ASSEMBLY' }, $cookie->{ 'CONTIG' } );
- for ( $i = 0; $i < @tracks; $i++ )
+ for ( $i = 0; $i < @track_list; $i++ )
{
$cookie->{ 'FEAT_COLOR' } = Maasha::BGB::Draw::palette( $i );
- push @features, [ Maasha::BGB::Track::track_feature( $tracks[ $i ], $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 );
+ unshift @tracks, [ Maasha::BGB::Track::track_grid( $cookie ) ];
- $cr->rectangle ( 0, 0, $cookie->{ 'IMG_WIDTH' }, $cookie->{ 'TRACK_OFFSET' } );
- $cr->set_source_rgb ( 1, 1, 1 );
- $cr->fill;
-
- foreach $feat ( @features ) {
- Maasha::BGB::Draw::draw_feature( $cr, $feat ) if $feat;
- }
-
- $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",
$center = int( $cookie->{ 'NAV_START' } + $factor * $i );
push @img, Maasha::XHTML::area(
- href => join( "&", "$cookie->{ 'SCRIPT' }?page=browse",
- "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' }",
- "nav_center=$center",
+ href => join( "&", "$cookie->{ 'SCRIPT' }?page=browse",
+ "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' }",
+ "nav_center=$center",
),
shape => 'rect',
coords => "$x1, $y1, $x2, $y2",
);
}
- foreach $feat ( @features )
+ foreach $track ( @tracks )
{
- foreach $elem ( @{ $feat } )
+ foreach $elem ( @{ $track } )
{
- next if $elem->{ 'type' } eq 'text';
- next if $elem->{ 'type' } eq 'wiggle';
-
- #$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' } = $elem->{ 'strand' };
-
- push @img, Maasha::XHTML::area(
- href => join( "&", "$cookie->{ 'SCRIPT' }?page=export",
- "session_id=$cookie->{ 'SESSION_ID' }",
- "user=$cookie->{ 'USER' }",
- "clade=$cookie->{ 'CLADE' }",
- "genome=$cookie->{ 'GENOME' }",
- "assembly=$cookie->{ 'ASSEMBLY' }",
- "contig=$cookie->{ 'CONTIG' }",
- "s_beg=$cookie->{ 'S_BEG' }",
- "s_end=$cookie->{ 'S_END' }",
- "strand=$cookie->{ 'STRAND' }",
- ),
- shape => 'rect',
- coords => "$elem->{ x1 }, $elem->{ y1 }, $elem->{ x2 }, $elem->{ y2 }",
- title => "$elem->{ 'title' }",
- );
+ next if $elem->{ 'type' } =~ /grid|text|wiggle/;
+
+ if ( $elem->{ 'type' } eq 'track_name' )
+ {
+ $x1 = $elem->{ 'x1' };
+ $y1 = $elem->{ 'y1' } - 10;
+ $x2 = $elem->{ 'x1' } + 6 * length $elem->{ 'txt' };
+ $y2 = $elem->{ 'y1' };
+
+ if ( Maasha::BGB::Track::track_hide( $cookie, $elem->{ 'track' } ) )
+ {
+ push @img, Maasha::XHTML::area(
+ href => join( "&", "$cookie->{ 'SCRIPT' }?page=browse",
+ "session_id=$cookie->{ 'SESSION_ID' }",
+ "user=$cookie->{ 'USER' }",
+ "clade=$cookie->{ 'CLADE' }",
+ "genome=$cookie->{ 'GENOME' }",
+ "assembly=$cookie->{ 'ASSEMBLY' }",
+ "contig=$cookie->{ 'CONTIG' }",
+ "track=$elem->{ 'track' }",
+ ),
+ shape => 'rect',
+ coords => "$x1, $y1, $x2, $y2",
+ title => qq(Show track: $elem->{ 'txt' }),
+ );
+ }
+ else
+ {
+ push @img, Maasha::XHTML::area(
+ href => join( "&", "$cookie->{ 'SCRIPT' }?page=browse",
+ "session_id=$cookie->{ 'SESSION_ID' }",
+ "user=$cookie->{ 'USER' }",
+ "clade=$cookie->{ 'CLADE' }",
+ "genome=$cookie->{ 'GENOME' }",
+ "assembly=$cookie->{ 'ASSEMBLY' }",
+ "contig=$cookie->{ 'CONTIG' }",
+ "track=$elem->{ 'track' }",
+ ),
+ shape => 'rect',
+ coords => "$x1, $y1, $x2, $y2",
+ title => qq(Hide track: $elem->{ 'txt' }),
+ );
+ }
+ }
+ else
+ {
+ push @img, Maasha::XHTML::area(
+ href => join( "&", "$cookie->{ 'SCRIPT' }?page=export",
+ "session_id=$cookie->{ 'SESSION_ID' }",
+ "user=$cookie->{ 'USER' }",
+ "clade=$cookie->{ 'CLADE' }",
+ "genome=$cookie->{ 'GENOME' }",
+ "assembly=$cookie->{ 'ASSEMBLY' }",
+ "contig=$cookie->{ 'CONTIG' }",
+ "s_beg=$elem->{ 's_beg' }",
+ "s_end=$elem->{ 's_end' }",
+ "strand=$elem->{ 'strand' }",
+ "q_id=$elem->{ 'q_id' }",
+ ),
+ shape => 'rect',
+ coords => "$elem->{ x1 }, $elem->{ y1 }, $elem->{ x2 }, $elem->{ y2 }",
+ title => "$elem->{ 'title' }",
+ );
+ }
}
}
}
+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