3 # Copyright (C) 2006-2009 Martin A. Hansen.
5 # This program is free software; you can redistribute it and/or
6 # modify it under the terms of the GNU General Public License
7 # as published by the Free Software Foundation; either version 2
8 # of the License, or (at your option) any later version.
10 # This program is distributed in the hope that it will be useful,
11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 # GNU General Public License for more details.
15 # You should have received a copy of the GNU General Public License
16 # along with this program; if not, write to the Free Software
17 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
19 # http://www.gnu.org/copyleft/gpl.html
21 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
26 use lib $ENV{ 'BP_PERL' };
36 use Maasha::BGB::Session;
37 use Maasha::BGB::Track;
38 use Maasha::BGB::Draw;
40 my ( $cgi, $cookie, @html );
43 $cookie = cookie_default( $cgi );;
45 push @html, Maasha::XHTML::html_header(
47 title => 'Biopieces Genome Browser',
48 css_file => 'bgb.css',
49 author => 'Martin A. Hansen, mail@maasha.dk',
50 description => 'Biopieces Genome Browser',
51 keywords => [ qw( Biopieces biopiece genome browser viewer bacterium bacteria prokaryote prokaryotes ) ],
55 push @html, Maasha::XHTML::h1( txt => "Biopieces Genome Browser", class => 'center' );
56 push @html, Maasha::XHTML::form_beg( action => $cookie->{ 'SCRIPT' }, method => "post", enctype => "multipart/form-data" );
58 push @html, page( $cookie );
60 push @html, Maasha::XHTML::form_end;
61 push @html, Maasha::XHTML::body_end;
62 push @html, Maasha::XHTML::html_end;
64 # push @html, Maasha::XHTML::hdump( [ $cgi->Vars ] ); # DEBUG
65 # push @html, Maasha::XHTML::hdump( \%ENV ); # DEBUG
66 # push @html, Maasha::XHTML::hdump( $cookie ); # DEBUG
68 print "$_\n" foreach @html;
71 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
74 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> COOKIE <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
79 # Martin A. Hansen, November 2009.
81 # Set a cookie with values from the CGI object or defaults.
83 my ( $cgi, # CGI object
92 if ( $cgi->param( 'nav_search' ) )
94 if ( $cgi->param( 'nav_search' ) =~ /([0-9,]+)[ -]([0-9,]+)/ )
96 $cookie->{ 'NAV_START' } = $1;
97 $cookie->{ 'NAV_END' } = $2;
101 $cookie->{ 'SEARCH' } = $cgi->param( 'nav_search' );
103 $cgi->param( 'page', 'search' );
107 $cookie->{ 'SCRIPT' } = Maasha::Common::get_scriptname();
108 $cookie->{ 'DATA_DIR' } = "Data";
109 $cookie->{ 'SESSION_DIR' } = "Sessions";
110 $cookie->{ 'LIST_PAGES' } = [ qw( clade genome assembly contig browse ) ];
112 $cookie->{ 'USER' } = $cgi->param( 'user' ) || '';
113 $cookie->{ 'PASSWORD' } = $cgi->param( 'password' );
114 $cookie->{ 'SESSION_ID' } = $cgi->param( 'session_id' );
116 cookie_session( $cookie );
117 cookie_login( $cookie );
119 $cookie->{ 'PAGE' } ||= $cgi->param( 'page' ) || 'login';
120 $cookie->{ 'CLADE' } = $cgi->param( 'clade' ) || '';
121 $cookie->{ 'GENOME' } = $cgi->param( 'genome' ) || '';
122 $cookie->{ 'ASSEMBLY' } = $cgi->param( 'assembly' ) || '';
123 $cookie->{ 'CONTIG' } = $cgi->param( 'contig' ) || '';
124 $cookie->{ 'Q_ID' } = $cgi->param( 'q_id' );
125 $cookie->{ 'NAV_START' } ||= $cgi->param( 'nav_start' );
126 $cookie->{ 'NAV_END' } ||= $cgi->param( 'nav_end' );
127 $cookie->{ 'NAV_CENTER' } = $cgi->param( 'nav_center' );
128 $cookie->{ 'S_BEG' } = $cgi->param( 's_beg' );
129 $cookie->{ 'S_END' } = $cgi->param( 's_end' );
130 $cookie->{ 'STRAND' } = $cgi->param( 'strand' );
131 $cookie->{ 'ZOOM_IN1' } = $cgi->param( 'zoom_in1' );
132 $cookie->{ 'ZOOM_IN2' } = $cgi->param( 'zoom_in2' );
133 $cookie->{ 'ZOOM_IN3' } = $cgi->param( 'zoom_in3' );
134 $cookie->{ 'ZOOM_OUT1' } = $cgi->param( 'zoom_out1' );
135 $cookie->{ 'ZOOM_OUT2' } = $cgi->param( 'zoom_out2' );
136 $cookie->{ 'ZOOM_OUT3' } = $cgi->param( 'zoom_out3' );
137 $cookie->{ 'MOVE_LEFT1' } = $cgi->param( 'move_left1' );
138 $cookie->{ 'MOVE_LEFT2' } = $cgi->param( 'move_left2' );
139 $cookie->{ 'MOVE_LEFT3' } = $cgi->param( 'move_left3' );
140 $cookie->{ 'MOVE_RIGHT1' } = $cgi->param( 'move_right1' );
141 $cookie->{ 'MOVE_RIGHT2' } = $cgi->param( 'move_right2' );
142 $cookie->{ 'MOVE_RIGHT3' } = $cgi->param( 'move_right3' );
144 $cookie->{ 'IMG_WIDTH' } = 1200; # Width of browser image in pixels
145 $cookie->{ 'IMG_HEIGHT' } = 800; # Height of browser image in pixels
146 $cookie->{ 'WIGGLE_HEIGHT' } = 75; # Height of Wiggle tracks in pixels
147 $cookie->{ 'TRACK_OFFSET' } = 20;
148 $cookie->{ 'TRACK_SPACE' } = 20;
149 $cookie->{ 'RULER_FONT_SIZE' } = 10; # Size of ruler font in pixels
150 $cookie->{ 'RULER_COLOR' } = [ 0, 0, 0 ];
151 $cookie->{ 'SEQ_FONT_SIZE' } = 10;
152 $cookie->{ 'SEQ_COLOR' } = [ 0, 0, 0, ];
153 $cookie->{ 'FEAT_WIDTH' } = 5;
154 $cookie->{ 'FEAT_COLOR' } = [ 0, 0, 0 ];
155 $cookie->{ 'FEAT_MAX' } = 5000; # TODO: Reduntant?
157 $cookie->{ 'LIST_USER' } = Maasha::BGB::Track::list_users();
158 $cookie->{ 'LIST_CLADE' } = Maasha::BGB::Track::list_clades( $cookie->{ 'USER' } );
159 $cookie->{ 'LIST_GENOME' } = Maasha::BGB::Track::list_genomes( $cookie->{ 'USER' }, $cookie->{ 'CLADE' } );
160 $cookie->{ 'LIST_ASSEMBLY' } = Maasha::BGB::Track::list_assemblies( $cookie->{ 'USER' }, $cookie->{ 'CLADE' }, $cookie->{ 'GENOME' } );
161 $cookie->{ 'LIST_CONTIG' } = Maasha::BGB::Track::list_contigs( $cookie->{ 'USER' }, $cookie->{ 'CLADE' }, $cookie->{ 'GENOME' }, $cookie->{ 'ASSEMBLY' } );
163 if ( $cookie->{ 'CONTIG' } )
165 cookie_start( $cookie );
166 cookie_end( $cookie );
167 cookie_zoom( $cookie );
168 cookie_move( $cookie );
169 cookie_center( $cookie );
172 $cookie->{ 'STRAND' } = '+' if defined $cookie->{ 'STRAND' } and $cookie->{ 'STRAND' } eq ' '; # FIXME ugly HTML fix
174 return wantarray ? %{ $cookie } : $cookie;
180 # Martin A. Hansen, December 2009.
182 # Check cookie information against session information.
184 my ( $cookie, # cookie hash
191 $session = Maasha::BGB::Session::session_restore( "$cookie->{ 'SESSION_DIR' }/sessions.txt" );
193 # if ( $cookie->{ 'SESSION_ID' } )
195 # if ( $cookie->{ 'SESSION_ID' } ne $ENV{ 'SSL_SESSION_ID' } ) {
196 # $cookie->{ 'PAGE' } = 'login';
197 # print STDERR "HER1"; # DEBUG
202 # $cookie->{ 'PAGE' } = 'login';
204 # print STDERR "HER2"; # DEBUG
207 if ( exists $session->{ $cookie->{ 'USER' } } and $cookie->{ 'SESSION_ID' } )
209 if ( $session->{ $cookie->{ 'USER' } }->{ 'SESSION_ID' } ne $cookie->{ 'SESSION_ID' } ) {
210 $cookie->{ 'PAGE' } = 'login';
211 print STDERR "HER3"; # DEBUG
216 $cookie->{ 'PAGE' } = 'login';
217 print STDERR "HER4"; # DEBUG
218 print STDERR "NO COOKIE SESSION ID\n" if not $cookie->{ 'SESSION_ID' }; # DEBUG
219 print STDERR "NO COOKIE USER\n" if not $cookie->{ 'USER' }; # DEBUG
220 print STDERR "NO SESSION USER\n" if not exists $session->{ $cookie->{ 'USER' } }; # DEBUG
227 # Martin A. Hansen, December 2009.
229 # Check a user and password from CGI against the password file and
230 # set the session ID, if found, in the cookie.
232 my ( $cookie, # cookie hash
239 if ( $cookie->{ 'USER' } and $cookie->{ 'PASSWORD' } )
241 $session = Maasha::BGB::Session::session_restore( "$cookie->{ 'SESSION_DIR' }/sessions.txt" );
243 if ( exists $session->{ $cookie->{ 'USER' } } and
244 $session->{ $cookie->{ 'USER' } }->{ 'PASSWORD' } eq Digest::MD5::md5_hex( $cookie->{ 'PASSWORD' } ) )
246 $session->{ $cookie->{ 'USER' } }->{ 'SESSION_ID' } ||= Maasha::BGB::Session::session_new();
247 # $session->{ $cookie->{ 'USER' } }->{ 'SESSION_ID' } = $ENV{ 'SSL_SESSION_ID' };
248 $session->{ $cookie->{ 'USER' } }->{ 'TIME' } = Maasha::Common::time_stamp();
250 $cookie->{ 'SESSION_ID' } = $session->{ $cookie->{ 'USER' } }->{ 'SESSION_ID' };
251 $cookie->{ 'LOGIN' } = "OK";
252 $cookie->{ 'PAGE' } = 'clade';
254 Maasha::BGB::Session::session_store( "$cookie->{ 'SESSION_DIR' }/sessions.txt", $session );
258 $cookie->{ 'LOGIN' } = "ERROR";
266 # Martin A. Hansen, November 2009.
268 # Decommify the cookie value for NAV_START and adjust it to
269 # to prevent negative values.
271 my ( $cookie, # cookie hash
276 if ( defined $cookie->{ 'NAV_START' } )
278 $cookie->{ 'NAV_START' } =~ tr/,//d;
279 $cookie->{ 'NAV_START' } = 0 if $cookie->{ 'NAV_START' } < 0;
283 $cookie->{ 'NAV_START' } = 0;
290 # Martin A. Hansen, November 2009.
292 # Decommify the cookie value for NAV_END and adjust it to prevent
293 # overshooting the max value for the contig size as determined
296 my ( $cookie, # cookie hash
303 $max = Maasha::Filesys::file_size( Maasha::BGB::Track::path_seq( $cookie ) );
305 if ( defined $cookie->{ 'NAV_END' } )
307 $cookie->{ 'NAV_END' } =~ tr/,//d;
308 $cookie->{ 'NAV_END' } = $max if $cookie->{ 'NAV_END' } > $max;
312 $cookie->{ 'NAV_END' } = $max;
319 # Martin A. Hansen, November 2009.
321 # Adjust the cookie values for NAV_START and NAV_END based
322 # on cookie ZOOM values.
324 my ( $cookie, # cookie hash
329 my ( $max, $dist, $new_dist, $dist_diff );
331 $max = Maasha::Filesys::file_size( Maasha::BGB::Track::path_seq( $cookie ) );
333 $dist = $cookie->{ 'NAV_END' } - $cookie->{ 'NAV_START' };
335 if ( defined $cookie->{ 'ZOOM_IN1' } ) {
336 $new_dist = $dist / 1.5;
337 } elsif ( defined $cookie->{ 'ZOOM_IN2' } ) {
338 $new_dist = $dist / 3;
339 } elsif ( defined $cookie->{ 'ZOOM_IN3' } ) {
340 $new_dist = $dist / 10;
341 } elsif ( defined $cookie->{ 'ZOOM_OUT1' } ) {
342 $new_dist = $dist * 1.5;
343 } elsif ( defined $cookie->{ 'ZOOM_OUT2' } ) {
344 $new_dist = $dist * 3;
345 } elsif ( defined $cookie->{ 'ZOOM_OUT3' } ) {
346 $new_dist = $dist * 10;
351 $dist_diff = $dist - $new_dist;
353 $cookie->{ 'NAV_START' } = int( $cookie->{ 'NAV_START' } + ( $dist_diff / 2 ) );
354 $cookie->{ 'NAV_END' } = int( $cookie->{ 'NAV_END' } - ( $dist_diff / 2 ) );
356 $cookie->{ 'NAV_START' } = 0 if $cookie->{ 'NAV_START' } < 0;
357 $cookie->{ 'NAV_END' } = $max if $cookie->{ 'NAV_END' } > $max;
364 # Martin A. Hansen, November 2009.
366 # Adjust the cookie values for NAV_START and NAV_END based
367 # on cookie MOVE values.
369 my ( $cookie, # cookie hash
374 my ( $max, $dist, $shift, $new_start, $new_end );
376 $max = Maasha::Filesys::file_size( Maasha::BGB::Track::path_seq( $cookie ) );
378 $dist = $cookie->{ 'NAV_END' } - $cookie->{ 'NAV_START' };
380 if ( defined $cookie->{ 'MOVE_LEFT1' } ) {
381 $shift = -1 * $dist * 0.10;
382 } elsif ( defined $cookie->{ 'MOVE_LEFT2' } ) {
383 $shift = -1 * $dist * 0.475;
384 } elsif ( defined $cookie->{ 'MOVE_LEFT3' } ) {
385 $shift = -1 * $dist * 0.95;
386 } elsif ( defined $cookie->{ 'MOVE_RIGHT1' } ) {
387 $shift = $dist * 0.10;
388 } elsif ( defined $cookie->{ 'MOVE_RIGHT2' } ) {
389 $shift = $dist * 0.475;
390 } elsif ( defined $cookie->{ 'MOVE_RIGHT3' } ) {
391 $shift = $dist * 0.95;
396 $new_start = int( $cookie->{ 'NAV_START' } + $shift );
397 $new_end = int( $cookie->{ 'NAV_END' } + $shift );
399 if ( $new_start > 0 and $new_end < $max )
401 $cookie->{ 'NAV_START' } = $new_start;
402 $cookie->{ 'NAV_END' } = $new_end;
410 # Martin A. Hansen, March 2010
412 # Adjust the cookie values for NAV_START and NAV_END based
413 # on cookie CENTER value if defined.
415 my ( $cookie, # cookie hash
420 my ( $l_dist, $r_dist );
422 if ( defined $cookie->{ 'NAV_CENTER' } )
424 $l_dist = $cookie->{ 'NAV_CENTER' } - $cookie->{ 'NAV_START' };
425 $r_dist = $cookie->{ 'NAV_END' } - $cookie->{ 'NAV_CENTER' };
427 if ( $l_dist > $r_dist ) {
428 $cookie->{ 'NAV_START' } = $cookie->{ 'NAV_END' } - 2 * $r_dist;
430 $cookie->{ 'NAV_END' } = $cookie->{ 'NAV_START' } + 2 * $l_dist;
438 # Martin A. Hansen, November 2009.
440 # Returns the next page in the taxonomy path.
442 my ( $cookie, # cookie hash
449 for ( $i = 0; $i < @{ $cookie->{ 'LIST_PAGES' } }; $i++ ) {
450 last if $cookie->{ 'PAGE' } eq $cookie->{ 'LIST_PAGES' }->[ $i ];
453 return $cookie->{ 'LIST_PAGES' }->[ $i + 1 ];
457 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PAGES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
462 # Martin A. Hansen, November 2009.
464 # Determines what page to render based on
465 # the cookie's PAGE setting.
467 my ( $cookie, # cookie hash
474 if ( $cookie->{ 'SESSION_ID' } ) {
475 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "session_id", value => $cookie->{ 'SESSION_ID' } ) );
478 if ( $cookie->{ 'PAGE' } eq 'login' ) {
479 push @html, page_login( $cookie );
480 } elsif ( $cookie->{ 'PAGE' } eq 'search' ) {
481 push @html, page_search( $cookie );
482 } elsif ( $cookie->{ 'PAGE' } eq 'browse' ) {
483 push @html, page_browse( $cookie );
484 } elsif ( $cookie->{ 'PAGE' } eq 'dna' ) {
485 push @html, page_dna( $cookie );
486 } elsif ( $cookie->{ 'PAGE' } eq 'export' ) {
487 push @html, page_export( $cookie );
489 push @html, page_taxonomy( $cookie );
492 return wantarray ? @html : \@html;
498 # Martin A. Hansen, December 2009.
500 # Renders the login page.
509 push @html, section_login( $cookie );
511 return wantarray ? @html : \@html;
517 # Martin A. Hansen, December 2009.
519 # Renders the search page.
528 push @html, section_taxonomy_table( $cookie );
529 push @html, section_search( $cookie );
531 return wantarray ? @html : \@html;
537 # Martin A. Hansen, November 2009.
539 # Renders the browse page.
548 push @html, section_taxonomy_table( $cookie );
549 push @html, section_navigate( $cookie );
550 push @html, section_browse( $cookie );
552 return wantarray ? @html : \@html;
558 # Martin A. Hansen, November 2009.
560 # Renders the DNA page.
569 push @html, section_taxonomy_table( $cookie );
570 push @html, section_dna( $cookie );
572 return wantarray ? @html : \@html;
578 # Martin A. Hansen, November 2009.
580 # Renders the export page.
589 push @html, section_taxonomy_table( $cookie );
590 push @html, section_export( $cookie );
592 return wantarray ? @html : \@html;
598 # Martin A. Hansen, November 2009.
600 # Renders the browse page.
602 my ( $cookie, # cookie hash
609 push @html, section_taxonomy_table( $cookie );
610 push @html, section_taxonomy_select( $cookie );
612 return wantarray ? @html : \@html;
616 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SECTIONS <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
621 # Martin A. Hansen, December 2009.
623 # Returns a HTML section with a login menu.
625 my ( $cookie, # cookie hash
630 my ( $user, $password, $login, @html );
632 $user = Maasha::XHTML::text( name => "user", value => "", size => 20 );
633 $password = Maasha::XHTML::password( name => "password", value => "", size => 20 );
634 $login = Maasha::XHTML::submit( name => "login_submit", value => "Login" );
636 push @html, Maasha::XHTML::h2( txt => "Login", class => 'center' );
638 push @html, Maasha::XHTML::table_beg( summary => "Login table", align => 'center' );
639 push @html, Maasha::XHTML::table_row_simple( tr => [ "User:", $user ] );
640 push @html, Maasha::XHTML::table_row_simple( tr => [ "Password:", $password ] );
641 push @html, Maasha::XHTML::table_row_simple( tr => [ "", $login ] );
642 push @html, Maasha::XHTML::table_end;
644 if ( $cookie->{ 'LOGIN' } and $cookie->{ 'LOGIN' } eq 'ERROR' ) {
645 push @html, Maasha::XHTML::h3( txt => "Bad user or password - please retry", class => 'error' );
648 return wantarray ? @html : \@html;
652 sub section_taxonomy_table
654 # Martin A. Hansen, November 2009.
656 # Returns a HTML section with a taxonomy table
657 # showing the location in the taxonomy and with
658 # links to browse the taxonomy.
660 my ( $cookie, # cookie hash
665 my ( $page, @row, @html, $href, $txt );
667 foreach $page ( @{ $cookie->{ 'LIST_PAGES' } } )
669 last if $page eq $cookie->{ 'PAGE' } or $page eq 'browse';
671 $href = "$cookie->{ 'SCRIPT' }?page=$page";
672 $href .= "&session_id=$cookie->{ 'SESSION_ID' }";
673 $href .= "&user=$cookie->{ 'USER' }";
674 $href .= "&clade=$cookie->{ 'CLADE' }" if $page !~ /clade/;
675 $href .= "&genome=$cookie->{ 'GENOME' }" if $page !~ /clade|genome/;
676 $href .= "&assembly=$cookie->{ 'ASSEMBLY' }" if $page !~ /clade|genome|assembly/;
677 $href .= "&contig=$cookie->{ 'CONTIG' }" if $page !~ /clade|genome|assembly|contig/;
679 $txt = ": $cookie->{ uc $page }";
681 push @row, Maasha::XHTML::ln( txt => $page, href => $href, class => 'inline' );
682 push @row, Maasha::XHTML::p( txt => $txt, class => 'inline' );
685 push @html, Maasha::XHTML::table_beg( summary => "Taxonomy table", align => 'center', cellpadding => '5px' );
686 push @html, Maasha::XHTML::table_row_simple( tr => [ join( "\n", @row ) ], align => 'center' );
687 push @html, Maasha::XHTML::table_end;
689 return wantarray ? @html : \@html;
693 sub section_taxonomy_select
695 # Martin A. Hansen, November 2009.
697 # Returns a HTML section with selection choices
698 # for navigating the taxonomy tree.
700 my ( $cookie, # cookie hash
705 my ( $list, @html, $item, $href );
707 $list = "LIST_" . uc $cookie->{ 'PAGE' };
709 push @html, Maasha::XHTML::h2( txt => "Select $cookie->{ 'PAGE' }", class => 'center' );
711 push @html, Maasha::XHTML::table_beg( summary => "Taxonomy select table", align => 'center', cellpadding => '5px' );
713 foreach $item ( @{ $cookie->{ $list } } )
715 $cookie->{ uc $cookie->{ 'PAGE' } } = $item;
717 $href = "$cookie->{ 'SCRIPT' }?page=" . cookie_page_next( $cookie );
718 $href .= "&session_id=$cookie->{ 'SESSION_ID' }";
719 $href .= "&user=$cookie->{ 'USER' }";
720 $href .= "&clade=$cookie->{ 'CLADE' }";
721 $href .= "&genome=$cookie->{ 'GENOME' }" if $cookie->{ 'GENOME' };
722 $href .= "&assembly=$cookie->{ 'ASSEMBLY' }" if $cookie->{ 'ASSEMBLY' };
723 $href .= "&contig=$cookie->{ 'CONTIG' }" if $cookie->{ 'CONTIG' };
725 push @html, Maasha::XHTML::table_row_simple( tr => [ Maasha::XHTML::ln( txt => $item, href => $href ) ] );
728 push @html, Maasha::XHTML::table_end;
730 return wantarray ? @html : \@html;
736 # Martin A. Hansen, November 2009.
738 # Returns a HTML section for navigating in the browser window.
740 my ( $cookie, # cookie hash
745 my ( @html, $nav_val );
747 $nav_val = Maasha::Calc::commify( $cookie->{ 'NAV_START' } ) . "-" . Maasha::Calc::commify( $cookie->{ 'NAV_END' } );
749 push @html, Maasha::XHTML::table_beg( summary => "Navigation table", align => 'center' );
750 push @html, Maasha::XHTML::table_row_simple( tr => [
751 "Position or search term:",
752 Maasha::XHTML::text( name => "nav_search", value => $nav_val, size => 30 ),
753 Maasha::XHTML::submit( name => "nav_submit", value => "Submit" ),
755 push @html, Maasha::XHTML::table_end;
757 push @html, Maasha::XHTML::table_beg( summary => "Zoom table", align => 'center' );
758 push @html, Maasha::XHTML::table_row_simple( tr => [
759 Maasha::XHTML::p( txt => 'Move:' ),
760 Maasha::XHTML::submit( name => "move_left3", value => "<<<", title => "move 95% to the left" ),
761 Maasha::XHTML::submit( name => "move_left2", value => "<<", title => "move 47.5% to the left" ),
762 Maasha::XHTML::submit( name => "move_left1", value => "<", title => "move 10% to the left" ),
763 Maasha::XHTML::submit( name => "move_right1", value => ">", title => "move 10% to the rigth" ),
764 Maasha::XHTML::submit( name => "move_right2", value => ">>", title => "move 47.5% to the rigth" ),
765 Maasha::XHTML::submit( name => "move_right3", value => ">>>", title => "move 95% to the right" ),
766 Maasha::XHTML::p( txt => 'Zoom in:' ),
767 Maasha::XHTML::submit( name => "zoom_in1", value => "1.5x" ),
768 Maasha::XHTML::submit( name => "zoom_in2", value => "3x" ),
769 Maasha::XHTML::submit( name => "zoom_in3", value => "10x" ),
770 Maasha::XHTML::p( txt => 'Zoom out:' ),
771 Maasha::XHTML::submit( name => "zoom_out1", value => "1.5x" ),
772 Maasha::XHTML::submit( name => "zoom_out2", value => "3x" ),
773 Maasha::XHTML::submit( name => "zoom_out3", value => "10x" ),
775 push @html, Maasha::XHTML::table_end;
777 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "page", value => "browse" ) );
778 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "user", value => $cookie->{ 'USER' } ) );
779 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "clade", value => $cookie->{ 'CLADE' } ) );
780 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "genome", value => $cookie->{ 'GENOME' } ) );
781 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "assembly", value => $cookie->{ 'ASSEMBLY' } ) );
782 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "contig", value => $cookie->{ 'CONTIG' } ) );
784 return wantarray ? @html : \@html;
795 my ( @tracks, $i, @features, $feat, $elem, $surface, $cr, $png_data, @html, @img, $x1, $y1, $x2, $y2, $factor, $center );
797 push @features, [ Maasha::BGB::Track::track_ruler( $cookie ) ];
798 push @features, [ Maasha::BGB::Track::track_seq( $cookie ) ];
800 @tracks = Maasha::BGB::Track::path_tracks( $cookie );
802 for ( $i = 0; $i < @tracks; $i++ )
804 $cookie->{ 'FEAT_COLOR' } = Maasha::BGB::Draw::palette( $i );
806 push @features, [ Maasha::BGB::Track::track_feature( $tracks[ $i ], $cookie ) ];
809 $surface = Cairo::ImageSurface->create( 'argb32', $cookie->{ 'IMG_WIDTH' }, $cookie->{ 'TRACK_OFFSET' } );
810 $cr = Cairo::Context->create( $surface );
812 $cr->rectangle ( 0, 0, $cookie->{ 'IMG_WIDTH' }, $cookie->{ 'TRACK_OFFSET' } );
813 $cr->set_source_rgb ( 1, 1, 1 );
816 foreach $feat ( @features ) {
817 Maasha::BGB::Draw::draw_feature( $cr, $feat ) if $feat;
820 $png_data = Maasha::BGB::Draw::base64_png( $surface );
822 push @img, Maasha::XHTML::img(
823 src => "data:image/png;base64,$png_data",
824 alt => "Browser Tracks",
825 height => $cookie->{ 'TRACK_OFFSET' },
826 width => $cookie->{ 'IMG_WIDTH' },
828 usemap => "#browser_map"
831 push @img, Maasha::XHTML::map_beg( name => "browser_map", id => "browser_map" );
833 $factor = ( $cookie->{ 'NAV_END' } - $cookie->{ 'NAV_START' } + 1 ) / $cookie->{ 'IMG_WIDTH' };
835 for ( $i = 0; $i < $cookie->{ 'IMG_WIDTH' }; $i += 5 )
842 $center = int( $cookie->{ 'NAV_START' } + $factor * $i );
844 push @img, Maasha::XHTML::area(
845 href => join( "&", "$cookie->{ 'SCRIPT' }?page=browse",
846 "session_id=$cookie->{ 'SESSION_ID' }",
847 "user=$cookie->{ 'USER' }",
848 "clade=$cookie->{ 'CLADE' }",
849 "genome=$cookie->{ 'GENOME' }",
850 "contig=$cookie->{ 'CONTIG' }",
851 "assembly=$cookie->{ 'ASSEMBLY' }",
852 "nav_start=$cookie->{ 'NAV_START' }",
853 "nav_end=$cookie->{ 'NAV_END' }",
854 "nav_center=$center",
857 coords => "$x1, $y1, $x2, $y2",
858 title => "Center on " . Maasha::Calc::commify( $center ),
862 foreach $feat ( @features )
864 foreach $elem ( @{ $feat } )
866 next if $elem->{ 'type' } eq 'text';
867 next if $elem->{ 'type' } eq 'wiggle';
869 #$elem->{ 'strand' } = '+' if $elem->{ 'strand' } eq '+';
871 $cookie->{ 'Q_ID' } = $elem->{ 'q_id' };
872 $cookie->{ 'S_BEG' } = $elem->{ 's_beg' };
873 $cookie->{ 'S_END' } = $elem->{ 's_end' };
874 $cookie->{ 'STRAND' } = $elem->{ 'strand' };
876 push @img, Maasha::XHTML::area(
877 href => join( "&", "$cookie->{ 'SCRIPT' }?page=export",
878 "session_id=$cookie->{ 'SESSION_ID' }",
879 "user=$cookie->{ 'USER' }",
880 "clade=$cookie->{ 'CLADE' }",
881 "genome=$cookie->{ 'GENOME' }",
882 "contig=$cookie->{ 'CONTIG' }",
883 "assembly=$cookie->{ 'ASSEMBLY' }",
884 "s_beg=$cookie->{ 'S_BEG' }",
885 "s_end=$cookie->{ 'S_END' }",
886 "strand=$cookie->{ 'STRAND' }",
889 coords => "$elem->{ x1 }, $elem->{ y1 }, $elem->{ x2 }, $elem->{ y2 }",
890 title => "$elem->{ 'title' }",
895 push @img, Maasha::XHTML::map_end();
897 push @html, Maasha::XHTML::p( txt => join( "\n", @img ) );
899 @html = Maasha::XHTML::div( txt => join( "\n", @html ), class => 'browse' );
901 return wantarray ? @html : \@html;
907 # Martin A. Hansen, November 2009.
909 # Returns a HTML section with export table.
911 my ( $cookie, # cookie hash
916 my ( $feat, @row_dna_contig, @html );
918 $feat = $cookie->{ 'Q_ID' } || "[no name]";
920 push @row_dna_contig, Maasha::XHTML::p( txt => qq(Export Feature: "$feat" DNA from Contig: ), class => 'inline' );
921 push @row_dna_contig, Maasha::XHTML::p( txt => "$cookie->{ 'CONTIG' } Start: ", class => 'inline' );
922 push @row_dna_contig, Maasha::XHTML::text( name => "s_beg", value => Maasha::Calc::commify( $cookie->{ 'S_BEG' } ), size => 15 );
923 push @row_dna_contig, Maasha::XHTML::p( txt => "End: ", class => 'inline' );
924 push @row_dna_contig, Maasha::XHTML::text( name => "s_end", value => Maasha::Calc::commify( $cookie->{ 'S_END' } ), size => 15 );
925 push @row_dna_contig, Maasha::XHTML::p( txt => "Strand: ", class => 'inline' );
926 push @row_dna_contig, Maasha::XHTML::menu( name => "strand", options => [ qw( + - ) ], selected => $cookie->{ 'STRAND' } );
927 push @row_dna_contig, Maasha::XHTML::submit( name => "export", value => "Export", title => "Fetch DNA from this region" );
929 push @html, Maasha::XHTML::h2( txt => "Export", class => 'center' );
930 push @html, Maasha::XHTML::table_beg( summary => "Taxonomy select table", align => 'center' );
931 push @html, Maasha::XHTML::table_row_simple( tr => \@row_dna_contig );
932 push @html, Maasha::XHTML::table_end;
934 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "page", value => "dna" ) );
935 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "user", value => $cookie->{ 'USER' } ) );
936 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "clade", value => $cookie->{ 'CLADE' } ) );
937 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "genome", value => $cookie->{ 'GENOME' } ) );
938 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "assembly", value => $cookie->{ 'ASSEMBLY' } ) );
939 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "contig", value => $cookie->{ 'CONTIG' } ) );
941 return wantarray ? @html : \@html;
947 # Martin A. Hansen, November 2009.
949 # Returns a HTML section with export table.
951 my ( $cookie, # cookie hash
956 my ( $results, $result, $count, @html, $export, $browse );
958 $results = Maasha::BGB::Track::search_tracks( $cookie );
960 $count = scalar @{ $results };
962 push @html, Maasha::XHTML::h2( txt => "Search", class => 'center' );
963 push @html, Maasha::XHTML::p( txt => qq(Results for "$cookie->{ 'SEARCH' }": $count), class => 'center' );
967 push @html, Maasha::XHTML::table_beg( summary => "Search table", align => 'center', cellpadding => '5px' );
968 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) ] );
970 foreach $result ( @{ $results } )
972 $cookie->{ 'CONTIG' } = $result->{ 'S_ID' };
973 $cookie->{ 'NAV_START' } = $result->{ 'S_BEG' };
974 $cookie->{ 'NAV_END' } = $result->{ 'S_END' };
975 $cookie->{ 'S_BEG' } = $result->{ 'S_BEG' };
976 $cookie->{ 'S_END' } = $result->{ 'S_END' };
977 $cookie->{ 'STRAND' } = $result->{ 'STRAND' };
978 $cookie->{ 'Q_ID' } = $result->{ 'Q_ID' };
980 $browse = Maasha::XHTML::ln(
982 href => join( "&", "$cookie->{ 'SCRIPT' }?page=browse",
983 "session_id=$cookie->{ 'SESSION_ID' }",
984 "user=$cookie->{ 'USER' }",
985 "clade=$cookie->{ 'CLADE' }",
986 "genome=$cookie->{ 'GENOME' }",
987 "contig=$cookie->{ 'CONTIG' }",
988 "assembly=$cookie->{ 'ASSEMBLY' }",
989 "nav_start=$cookie->{ 'NAV_START' }",
990 "nav_end=$cookie->{ 'NAV_END' }",
995 $export = Maasha::XHTML::ln(
997 href => join( "&", "$cookie->{ 'SCRIPT' }?page=export",
998 "session_id=$cookie->{ 'SESSION_ID' }",
999 "user=$cookie->{ 'USER' }",
1000 "clade=$cookie->{ 'CLADE' }",
1001 "genome=$cookie->{ 'GENOME' }",
1002 "contig=$cookie->{ 'CONTIG' }",
1003 "assembly=$cookie->{ 'ASSEMBLY' }",
1004 "s_beg=$cookie->{ 'S_BEG' }",
1005 "s_end=$cookie->{ 'S_END' }",
1006 "strand=$cookie->{ 'STRAND' }",
1010 push @html, Maasha::XHTML::table_row_advanced(
1011 tr => [ { td => $result->{ 'S_ID' } },
1012 { td => $result->{ 'S_BEG' }, align => 'right' },
1013 { td => $result->{ 'S_END' }, align => 'right' },
1014 { td => $result->{ 'Q_ID' } },
1015 { td => $result->{ 'SCORE' }, align => 'right' },
1016 { td => $result->{ 'STRAND' } },
1017 { td => $result->{ 'HITS' }, align => 'right' },
1018 { td => $result->{ 'ALIGN' } },
1019 { td => $result->{ 'BLOCK_COUNT' }, align => 'right' },
1020 { td => $result->{ 'BLOCK_BEGS' } },
1021 { td => $result->{ 'BLOCK_LENS' } },
1022 { td => $result->{ 'BLOCK_TYPE' } },
1025 ], class => "monospace"
1029 push @html, Maasha::XHTML::table_end;
1032 return wantarray ? @html : \@html;
1038 # Martin A. Hansen, November 2009.
1040 # Returns a HTML section with extracted DNA.
1042 my ( $cookie, # cookie hash
1047 my ( @html, $beg, $end, $seq );
1049 $beg = $cookie->{ 'S_BEG' };
1050 $end = $cookie->{ 'S_END' };
1054 $seq = join ";", ">$cookie->{ 'GENOME' }", $cookie->{ 'ASSEMBLY' }, $cookie->{ 'CONTIG' }, $beg, $end, "$cookie->{ 'STRAND' }\n";
1055 $seq .= Maasha::BGB::Track::dna_get( $cookie );
1057 push @html, Maasha::XHTML::h2( txt => "DNA", class => 'center' );
1058 push @html, Maasha::XHTML::pre( txt => $seq );
1060 return wantarray ? @html : \@html;
1064 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<