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
88 my ( $cookie, $path );
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->{ 'S_BEG' } = $cgi->param( 's_beg' );
126 $cookie->{ 'S_END' } = $cgi->param( 's_end' );
127 $cookie->{ 'STRAND' } = $cgi->param( 'strand' );
128 $cookie->{ 'ZOOM_IN1' } = $cgi->param( 'zoom_in1' );
129 $cookie->{ 'ZOOM_IN2' } = $cgi->param( 'zoom_in2' );
130 $cookie->{ 'ZOOM_IN3' } = $cgi->param( 'zoom_in3' );
131 $cookie->{ 'ZOOM_OUT1' } = $cgi->param( 'zoom_out1' );
132 $cookie->{ 'ZOOM_OUT2' } = $cgi->param( 'zoom_out2' );
133 $cookie->{ 'ZOOM_OUT3' } = $cgi->param( 'zoom_out3' );
134 $cookie->{ 'MOVE_LEFT1' } = $cgi->param( 'move_left1' );
135 $cookie->{ 'MOVE_LEFT2' } = $cgi->param( 'move_left2' );
136 $cookie->{ 'MOVE_LEFT3' } = $cgi->param( 'move_left3' );
137 $cookie->{ 'MOVE_RIGHT1' } = $cgi->param( 'move_right1' );
138 $cookie->{ 'MOVE_RIGHT2' } = $cgi->param( 'move_right2' );
139 $cookie->{ 'MOVE_RIGHT3' } = $cgi->param( 'move_right3' );
141 $cookie->{ 'IMG_WIDTH' } = 1200;
142 $cookie->{ 'IMG_HEIGHT' } = 800;
143 $cookie->{ 'TRACK_OFFSET' } = 20;
144 $cookie->{ 'TRACK_SPACE' } = 20;
145 $cookie->{ 'RULER_FONT_SIZE' } = 10;
146 $cookie->{ 'RULER_COLOR' } = [ 0, 0, 0 ];
147 $cookie->{ 'SEQ_FONT_SIZE' } = 10;
148 $cookie->{ 'SEQ_COLOR' } = [ 0, 0, 0, ];
149 $cookie->{ 'FEAT_WIDTH' } = 5;
150 $cookie->{ 'FEAT_COLOR' } = [ 0, 0, 0 ];
151 $cookie->{ 'FEAT_MAX' } = 5000;
153 $path = "$cookie->{ 'DATA_DIR' }/Users";
155 $cookie->{ 'LIST_USER' } = Maasha::Filesys::ls_dirs_base( $path ) if -d $path;
157 $path .= "/$cookie->{ 'USER' }";
159 $cookie->{ 'LIST_CLADE' } = Maasha::Filesys::ls_dirs_base( $path ) if -d $path;
161 $path .= "/$cookie->{ 'CLADE' }";
163 $cookie->{ 'LIST_GENOME' } = Maasha::Filesys::ls_dirs_base( $path ) if -d $path;
165 $path .= "/$cookie->{ 'GENOME' }";
167 $cookie->{ 'LIST_ASSEMBLY' } = Maasha::Filesys::ls_dirs_base( $path ) if -d $path;
169 $path .= "/$cookie->{ 'ASSEMBLY' }";
171 $cookie->{ 'LIST_CONTIG' } = Maasha::Filesys::ls_dirs_base( $path ) if -d $path;
173 if ( $cookie->{ 'CONTIG' } )
175 cookie_start( $cookie );
176 cookie_end( $cookie );
177 cookie_zoom( $cookie );
178 cookie_move( $cookie );
181 $cookie->{ 'STRAND' } = '+' if defined $cookie->{ 'STRAND' } and $cookie->{ 'STRAND' } eq ' '; # FIXME ugly HTML fix
183 return wantarray ? %{ $cookie } : $cookie;
189 # Martin A. Hansen, December 2009.
191 # Check cookie information against session information.
193 my ( $cookie, # cookie hash
200 $session = Maasha::BGB::Session::session_restore( "$cookie->{ 'SESSION_DIR' }/sessions.txt" );
202 # if ( $cookie->{ 'SESSION_ID' } )
204 # if ( $cookie->{ 'SESSION_ID' } ne $ENV{ 'SSL_SESSION_ID' } ) {
205 # $cookie->{ 'PAGE' } = 'login';
206 # print STDERR "HER1"; # DEBUG
211 # $cookie->{ 'PAGE' } = 'login';
213 # print STDERR "HER2"; # DEBUG
216 if ( exists $session->{ $cookie->{ 'USER' } } and $cookie->{ 'SESSION_ID' } )
218 if ( $session->{ $cookie->{ 'USER' } }->{ 'SESSION_ID' } ne $cookie->{ 'SESSION_ID' } ) {
219 $cookie->{ 'PAGE' } = 'login';
220 print STDERR "HER3"; # DEBUG
225 $cookie->{ 'PAGE' } = 'login';
226 print STDERR "HER4"; # DEBUG
227 print STDERR "NO COOKIE SESSION ID\n" if not $cookie->{ 'SESSION_ID' }; # DEBUG
228 print STDERR "NO COOKIE SESSION ID\n" if not $cookie->{ 'USER' }; # DEBUG
229 print STDERR "NO SESSION USER\n" if not exists $session->{ $cookie->{ 'USER' } }; # DEBUG
236 # Martin A. Hansen, December 2009.
238 # Check a user and password from CGI against the password file and
239 # set the session ID, if found, in the cookie.
241 my ( $cookie, # cookie hash
248 if ( $cookie->{ 'USER' } and $cookie->{ 'PASSWORD' } )
250 $session = Maasha::BGB::Session::session_restore( "$cookie->{ 'SESSION_DIR' }/sessions.txt" );
252 if ( exists $session->{ $cookie->{ 'USER' } } and
253 $session->{ $cookie->{ 'USER' } }->{ 'PASSWORD' } eq Digest::MD5::md5_hex( $cookie->{ 'PASSWORD' } ) )
255 $session->{ $cookie->{ 'USER' } }->{ 'SESSION_ID' } ||= Maasha::BGB::Session::session_new();
256 # $session->{ $cookie->{ 'USER' } }->{ 'SESSION_ID' } = $ENV{ 'SSL_SESSION_ID' };
257 $session->{ $cookie->{ 'USER' } }->{ 'TIME' } = Maasha::Common::time_stamp();
259 $cookie->{ 'SESSION_ID' } = $session->{ $cookie->{ 'USER' } }->{ 'SESSION_ID' };
260 $cookie->{ 'LOGIN' } = "OK";
261 $cookie->{ 'PAGE' } = 'clade';
263 Maasha::BGB::Session::session_store( "$cookie->{ 'SESSION_DIR' }/sessions.txt", $session );
267 $cookie->{ 'LOGIN' } = "ERROR";
275 # Martin A. Hansen, November 2009.
277 # Decommify the cookie value for NAV_START and adjust it to
278 # to prevent negative values.
280 my ( $cookie, # cookie hash
285 if ( defined $cookie->{ 'NAV_START' } )
287 $cookie->{ 'NAV_START' } =~ tr/,//d;
288 $cookie->{ 'NAV_START' } = 0 if $cookie->{ 'NAV_START' } < 0;
292 $cookie->{ 'NAV_START' } = 0;
299 # Martin A. Hansen, November 2009.
301 # Decommify the cookie value for NAV_END and adjust it to prevent
302 # overshooting the max value for the contig size as determined
305 my ( $cookie, # cookie hash
312 $max = Maasha::Filesys::file_size( Maasha::BGB::Track::path_seq( $cookie ) );
314 if ( defined $cookie->{ 'NAV_END' } )
316 $cookie->{ 'NAV_END' } =~ tr/,//d;
317 $cookie->{ 'NAV_END' } = $max if $cookie->{ 'NAV_END' } > $max;
321 $cookie->{ 'NAV_END' } = $max;
328 # Martin A. Hansen, November 2009.
330 # Adjust the cookie values for NAV_START and NAV_END based
331 # on cookie ZOOM values.
333 my ( $cookie, # cookie hash
338 my ( $max, $dist, $new_dist, $dist_diff );
340 $max = Maasha::Filesys::file_size( Maasha::BGB::Track::path_seq( $cookie ) );
342 $dist = $cookie->{ 'NAV_END' } - $cookie->{ 'NAV_START' };
344 if ( defined $cookie->{ 'ZOOM_IN1' } ) {
345 $new_dist = $dist / 1.5;
346 } elsif ( defined $cookie->{ 'ZOOM_IN2' } ) {
347 $new_dist = $dist / 3;
348 } elsif ( defined $cookie->{ 'ZOOM_IN3' } ) {
349 $new_dist = $dist / 10;
350 } elsif ( defined $cookie->{ 'ZOOM_OUT1' } ) {
351 $new_dist = $dist * 1.5;
352 } elsif ( defined $cookie->{ 'ZOOM_OUT2' } ) {
353 $new_dist = $dist * 3;
354 } elsif ( defined $cookie->{ 'ZOOM_OUT3' } ) {
355 $new_dist = $dist * 10;
360 $dist_diff = $dist - $new_dist;
362 $cookie->{ 'NAV_START' } = int( $cookie->{ 'NAV_START' } + ( $dist_diff / 2 ) );
363 $cookie->{ 'NAV_END' } = int( $cookie->{ 'NAV_END' } - ( $dist_diff / 2 ) );
365 $cookie->{ 'NAV_START' } = 0 if $cookie->{ 'NAV_START' } < 0;
366 $cookie->{ 'NAV_END' } = $max if $cookie->{ 'NAV_END' } > $max;
373 # Martin A. Hansen, November 2009.
375 # Adjust the cookie values for NAV_START and NAV_END based
376 # on cookie MOVE values.
378 my ( $cookie, # cookie hash
381 my ( $max, $dist, $shift, $new_start, $new_end );
383 $max = Maasha::Filesys::file_size( Maasha::BGB::Track::path_seq( $cookie ) );
385 $dist = $cookie->{ 'NAV_END' } - $cookie->{ 'NAV_START' };
387 if ( defined $cookie->{ 'MOVE_LEFT1' } ) {
388 $shift = -1 * $dist * 0.10;
389 } elsif ( defined $cookie->{ 'MOVE_LEFT2' } ) {
390 $shift = -1 * $dist * 0.475;
391 } elsif ( defined $cookie->{ 'MOVE_LEFT3' } ) {
392 $shift = -1 * $dist * 0.95;
393 } elsif ( defined $cookie->{ 'MOVE_RIGHT1' } ) {
394 $shift = $dist * 0.10;
395 } elsif ( defined $cookie->{ 'MOVE_RIGHT2' } ) {
396 $shift = $dist * 0.475;
397 } elsif ( defined $cookie->{ 'MOVE_RIGHT3' } ) {
398 $shift = $dist * 0.95;
403 $new_start = int( $cookie->{ 'NAV_START' } + $shift );
404 $new_end = int( $cookie->{ 'NAV_END' } + $shift );
406 if ( $new_start > 0 and $new_end < $max )
408 $cookie->{ 'NAV_START' } = $new_start;
409 $cookie->{ 'NAV_END' } = $new_end;
417 # Martin A. Hansen, November 2009.
419 # Returns the href for a taxonomy path terminated at a given
420 # page using information stored in a cookie.
422 my ( $cookie, # cookie hash
428 my ( @href_list, %href_hash, $href );
430 $href_hash{ "user" } = $cookie->{ 'USER' } if $cookie->{ 'USER' };
434 $href_hash{ "clade" } = $cookie->{ 'CLADE' } if $cookie->{ 'CLADE' };
435 last if $page eq 'clade';
436 $href_hash{ "genome" } = $cookie->{ 'GENOME' } if $cookie->{ 'GENOME' };
437 last if $page eq 'genome';
438 $href_hash{ "assembly" } = $cookie->{ 'ASSEMBLY' } if $cookie->{ 'ASSEMBLY' };
439 last if $page eq 'assembly';
440 $href_hash{ "contig" } = $cookie->{ 'CONTIG' } if $cookie->{ 'CONTIG' };
441 last if $page eq 'contig';
445 if ( defined $cookie->{ 'NAV_START' } and defined $cookie->{ 'NAV_END' } and $page !~ /clade|genome|assembly|contig|browse/ ) {
446 $href_hash{ "nav_search" } = "$cookie->{ 'NAV_START' }-$cookie->{ 'NAV_END' }";
449 $href_hash{ "s_beg" } = $cookie->{ 'S_BEG' } if defined $cookie->{ 'S_BEG' };
450 $href_hash{ "s_end" } = $cookie->{ 'S_END' } if defined $cookie->{ 'S_END' };
451 $href_hash{ "q_id" } = $cookie->{ 'Q_ID' } if defined $cookie->{ 'Q_ID' };
452 $href_hash{ "strand" } = $cookie->{ 'STRAND' } if defined $cookie->{ 'STRAND' };
453 $href_hash{ "session_id" } = $cookie->{ 'SESSION_ID' } if defined $cookie->{ 'SESSION_ID' };
455 push @href_list, "$cookie->{ 'SCRIPT' }?page=$page";
457 foreach $href ( keys %href_hash ) {
458 push @href_list, "$href=$href_hash{ $href }";
461 return join "&", @href_list;
467 # Martin A. Hansen, November 2009.
469 # Returns the next page in the taxonomy path.
471 my ( $cookie, # cookie hash
478 for ( $i = 0; $i < @{ $cookie->{ 'LIST_PAGES' } }; $i++ ) {
479 last if $cookie->{ 'PAGE' } eq $cookie->{ 'LIST_PAGES' }->[ $i ];
482 return $cookie->{ 'LIST_PAGES' }->[ $i + 1 ];
486 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PAGES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
491 # Martin A. Hansen, November 2009.
493 # Determines what page to render based on
494 # the cookie's PAGE setting.
496 my ( $cookie, # cookie hash
503 if ( $cookie->{ 'PAGE' } eq 'login' ) {
504 push @html, page_login( $cookie );
505 } elsif ( $cookie->{ 'PAGE' } eq 'search' ) {
506 push @html, page_search( $cookie );
507 } elsif ( $cookie->{ 'PAGE' } eq 'browse' ) {
508 push @html, page_browse( $cookie );
509 } elsif ( $cookie->{ 'PAGE' } eq 'dna' ) {
510 push @html, page_dna( $cookie );
511 } elsif ( $cookie->{ 'PAGE' } eq 'export' ) {
512 push @html, page_export( $cookie );
514 push @html, page_taxonomy( $cookie );
517 if ( $cookie->{ 'SESSION_ID' } ) {
518 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "session_id", value => "$cookie->{ 'SESSION_ID' }" ) );
521 return wantarray ? @html : \@html;
527 # Martin A. Hansen, December 2009.
529 # Renders the login page.
538 push @html, section_login( $cookie );
540 return wantarray ? @html : \@html;
546 # Martin A. Hansen, December 2009.
548 # Renders the search page.
557 push @html, section_taxonomy_table( $cookie );
558 push @html, section_search( $cookie );
560 return wantarray ? @html : \@html;
566 # Martin A. Hansen, November 2009.
568 # Renders the browse page.
577 push @html, section_taxonomy_table( $cookie );
578 push @html, section_navigate( $cookie );
579 push @html, section_browse( $cookie );
581 return wantarray ? @html : \@html;
587 # Martin A. Hansen, November 2009.
589 # Renders the DNA page.
598 push @html, section_taxonomy_table( $cookie );
599 push @html, section_dna( $cookie );
601 return wantarray ? @html : \@html;
607 # Martin A. Hansen, November 2009.
609 # Renders the export page.
618 push @html, section_taxonomy_table( $cookie );
619 push @html, section_export( $cookie );
621 return wantarray ? @html : \@html;
627 # Martin A. Hansen, November 2009.
629 # Renders the browse page.
631 my ( $cookie, # cookie hash
638 push @html, section_taxonomy_table( $cookie );
639 push @html, section_taxonomy_select( $cookie );
641 return wantarray ? @html : \@html;
645 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SECTIONS <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
650 # Martin A. Hansen, December 2009.
652 # Returns a HTML section with a login menu.
654 my ( $cookie, # cookie hash
659 my ( $user, $password, $login, @html );
661 $user = Maasha::XHTML::text( name => "user", value => "", size => 20 );
662 $password = Maasha::XHTML::password( name => "password", value => "", size => 20 );
663 $login = Maasha::XHTML::submit( name => "login_submit", value => "Login" );
665 push @html, Maasha::XHTML::h2( txt => "Login", class => 'center' );
667 push @html, Maasha::XHTML::table_beg( summary => "Login table", align => 'center' );
668 push @html, Maasha::XHTML::table_row_simple( tr => [ "User:", $user ] );
669 push @html, Maasha::XHTML::table_row_simple( tr => [ "Password:", $password ] );
670 push @html, Maasha::XHTML::table_row_simple( tr => [ "", $login ] );
671 push @html, Maasha::XHTML::table_end;
673 if ( $cookie->{ 'LOGIN' } and $cookie->{ 'LOGIN' } eq 'ERROR' ) {
674 push @html, Maasha::XHTML::h3( txt => "Bad user or password - please retry", class => 'error' );
677 return wantarray ? @html : \@html;
681 sub section_taxonomy_table
683 # Martin A. Hansen, November 2009.
685 # Returns a HTML section with a taxonomy table
686 # showing the location in the taxonomy and with
687 # links to browse the taxonomy.
689 my ( $cookie, # cookie hash
694 my ( $page, @row, @html, $href, $txt );
696 foreach $page ( @{ $cookie->{ 'LIST_PAGES' } } )
698 last if $page eq $cookie->{ 'PAGE' } or $page eq 'browse';
700 $href = cookie_href( $cookie, $page );
702 $txt = ": $cookie->{ uc $page }";
704 push @row, Maasha::XHTML::ln( txt => $page, href => $href, class => 'inline' );
705 push @row, Maasha::XHTML::p( txt => $txt, class => 'inline' );
708 push @html, Maasha::XHTML::table_beg( summary => "Taxonomy table", align => 'center', cellpadding => '5px' );
709 push @html, Maasha::XHTML::table_row_simple( tr => [ join( "\n", @row ) ], align => 'center' );
710 push @html, Maasha::XHTML::table_end;
712 return wantarray ? @html : \@html;
716 sub section_taxonomy_select
718 # Martin A. Hansen, November 2009.
720 # Returns a HTML section with selection choices
721 # for navigating the taxonomy tree.
723 my ( $cookie, # cookie hash
728 my ( $list, @html, $item, $href );
730 $list = "LIST_" . uc $cookie->{ 'PAGE' };
732 push @html, Maasha::XHTML::h2( txt => "Select $cookie->{ 'PAGE' }", class => 'center' );
734 push @html, Maasha::XHTML::table_beg( summary => "Taxonomy select table", align => 'center', cellpadding => '5px' );
736 foreach $item ( @{ $cookie->{ $list } } )
738 $cookie->{ uc $cookie->{ 'PAGE' } } = $item;
740 $href = cookie_href( $cookie, cookie_page_next( $cookie ) );
742 push @html, Maasha::XHTML::table_row_simple( tr => [ Maasha::XHTML::ln( txt => $item, href => $href ) ] );
745 push @html, Maasha::XHTML::table_end;
747 return wantarray ? @html : \@html;
753 # Martin A. Hansen, November 2009.
755 # Returns a HTML section for navigating in the browser window.
757 my ( $cookie, # cookie hash
762 my ( @html, $nav_val );
764 $nav_val = Maasha::Calc::commify( $cookie->{ 'NAV_START' } ) . "-" . Maasha::Calc::commify( $cookie->{ 'NAV_END' } );
766 push @html, Maasha::XHTML::table_beg( summary => "Navigation table", align => 'center' );
767 push @html, Maasha::XHTML::table_row_simple( tr => [
768 "Position or search term:",
769 Maasha::XHTML::text( name => "nav_search", value => $nav_val, size => 30 ),
770 Maasha::XHTML::submit( name => "nav_submit", value => "Submit" ),
772 push @html, Maasha::XHTML::table_end;
774 push @html, Maasha::XHTML::table_beg( summary => "Zoom table", align => 'center' );
775 push @html, Maasha::XHTML::table_row_simple( tr => [
776 Maasha::XHTML::p( txt => 'Move:' ),
777 Maasha::XHTML::submit( name => "move_left3", value => "<<<", title => "move 95% to the left" ),
778 Maasha::XHTML::submit( name => "move_left2", value => "<<", title => "move 47.5% to the left" ),
779 Maasha::XHTML::submit( name => "move_left1", value => "<", title => "move 10% to the left" ),
780 Maasha::XHTML::submit( name => "move_right1", value => ">", title => "move 10% to the rigth" ),
781 Maasha::XHTML::submit( name => "move_right2", value => ">>", title => "move 47.5% to the rigth" ),
782 Maasha::XHTML::submit( name => "move_right3", value => ">>>", title => "move 95% to the right" ),
783 Maasha::XHTML::p( txt => 'Zoom in:' ),
784 Maasha::XHTML::submit( name => "zoom_in1", value => "1.5x" ),
785 Maasha::XHTML::submit( name => "zoom_in2", value => "3x" ),
786 Maasha::XHTML::submit( name => "zoom_in3", value => "10x" ),
787 Maasha::XHTML::p( txt => 'Zoom out:' ),
788 Maasha::XHTML::submit( name => "zoom_out1", value => "1.5x" ),
789 Maasha::XHTML::submit( name => "zoom_out2", value => "3x" ),
790 Maasha::XHTML::submit( name => "zoom_out3", value => "10x" ),
792 push @html, Maasha::XHTML::table_end;
794 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "page", value => "browse" ) );
795 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "user", value => "$cookie->{ 'USER' }" ) );
796 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "clade", value => "$cookie->{ 'CLADE' }" ) );
797 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "genome", value => "$cookie->{ 'GENOME' }" ) );
798 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "assembly", value => "$cookie->{ 'ASSEMBLY' }" ) );
799 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "contig", value => "$cookie->{ 'CONTIG' }" ) );
801 return wantarray ? @html : \@html;
812 my ( @tracks, $i, @features, $feat, $elem, $surface, $cr, $png_data, @html, @img );
814 push @features, [ Maasha::BGB::Track::track_ruler( $cookie ) ];
815 push @features, [ Maasha::BGB::Track::track_seq( $cookie ) ];
817 @tracks = Maasha::BGB::Track::path_tracks( $cookie );
819 for ( $i = 0; $i < @tracks; $i++ )
821 $cookie->{ 'FEAT_COLOR' } = Maasha::BGB::Draw::palette( $i );
823 push @features, [ Maasha::BGB::Track::track_feature( $tracks[ $i ], $cookie ) ];
826 $surface = Cairo::ImageSurface->create( 'argb32', $cookie->{ 'IMG_WIDTH' }, $cookie->{ 'TRACK_OFFSET' } );
827 $cr = Cairo::Context->create( $surface );
829 $cr->rectangle ( 0, 0, $cookie->{ 'IMG_WIDTH' }, $cookie->{ 'TRACK_OFFSET' } );
830 $cr->set_source_rgb ( 1, 1, 1 );
833 foreach $feat ( @features ) {
834 Maasha::BGB::Draw::draw_feature( $cr, $feat ) if $feat;
837 $png_data = Maasha::BGB::Draw::base64_png( $surface );
839 push @img, Maasha::XHTML::img(
840 src => "data:image/png;base64,$png_data",
841 alt => "Browser Tracks",
842 height => $cookie->{ 'TRACK_OFFSET' },
843 width => $cookie->{ 'IMG_WIDTH' },
845 usemap => "#browser_map"
848 push @img, Maasha::XHTML::map_beg( name => "browser_map", id => "browser_map" );
850 foreach $feat ( @features )
852 foreach $elem ( @{ $feat } )
854 next if $elem->{ 'type' } eq 'text';
856 #$elem->{ 'strand' } = '+' if $elem->{ 'strand' } eq '+';
858 $cookie->{ 'Q_ID' } = $elem->{ 'q_id' };
859 $cookie->{ 'S_BEG' } = $elem->{ 's_beg' };
860 $cookie->{ 'S_END' } = $elem->{ 's_end' };
861 $cookie->{ 'STRAND' } = $elem->{ 'strand' };
863 push @img, Maasha::XHTML::area(
864 href => cookie_href( $cookie, "export" ),
865 # href => cookie_href( $cookie, "export" ) . "&q_id=$elem->{ 'q_id' }&s_beg=$elem->{ 's_beg' }&s_end=$elem->{ 's_end' }&strand=$elem->{ 'strand' }",
867 coords => "$elem->{ x1 }, $elem->{ y1 }, $elem->{ x2 }, $elem->{ y2 }", title => "$elem->{ 'title' }",
872 push @img, Maasha::XHTML::map_end();
874 push @html, Maasha::XHTML::p( txt => join( "\n", @img ) );
876 @html = Maasha::XHTML::div( txt => join( "\n", @html ), class => 'browse' );
878 return wantarray ? @html : \@html;
884 # Martin A. Hansen, November 2009.
886 # Returns a HTML section with export table.
888 my ( $cookie, # cookie hash
893 my ( @row_dna_contig, @html );
895 push @row_dna_contig, Maasha::XHTML::p( txt => qq(Export Feature: "$cookie->{ 'Q_ID' }" DNA from Contig: ), class => 'inline' );
896 push @row_dna_contig, Maasha::XHTML::p( txt => "$cookie->{ 'CONTIG' } Start: ", class => 'inline' );
897 push @row_dna_contig, Maasha::XHTML::text( name => "s_beg", value => Maasha::Calc::commify( $cookie->{ 'S_BEG' } ), size => 15 );
898 push @row_dna_contig, Maasha::XHTML::p( txt => "End: ", class => 'inline' );
899 push @row_dna_contig, Maasha::XHTML::text( name => "s_end", value => Maasha::Calc::commify( $cookie->{ 'S_END' } ), size => 15 );
900 push @row_dna_contig, Maasha::XHTML::p( txt => "Strand: ", class => 'inline' );
901 push @row_dna_contig, Maasha::XHTML::menu( name => "strand", options => [ qw( + - ) ], selected => $cookie->{ 'STRAND' } );
902 push @row_dna_contig, Maasha::XHTML::submit( name => "export", value => "Export", title => "Fetch DNA from this region" );
904 push @html, Maasha::XHTML::h2( txt => "Export", class => 'center' );
905 push @html, Maasha::XHTML::table_beg( summary => "Taxonomy select table", align => 'center' );
906 push @html, Maasha::XHTML::table_row_simple( tr => \@row_dna_contig );
907 push @html, Maasha::XHTML::table_end;
909 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "page", value => "dna" ) );
910 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "user", value => "$cookie->{ 'USER' }" ) );
911 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "clade", value => "$cookie->{ 'CLADE' }" ) );
912 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "genome", value => "$cookie->{ 'GENOME' }" ) );
913 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "assembly", value => "$cookie->{ 'ASSEMBLY' }" ) );
914 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "contig", value => "$cookie->{ 'CONTIG' }" ) );
916 return wantarray ? @html : \@html;
922 # Martin A. Hansen, November 2009.
924 # Returns a HTML section with export table.
926 my ( $cookie, # cookie hash
931 my ( $results, $result, $count, @html, $export, $browse );
933 $results = Maasha::BGB::Track::search_tracks( $cookie );
935 $count = scalar @{ $results };
937 push @html, Maasha::XHTML::h2( txt => "Search", class => 'center' );
938 push @html, Maasha::XHTML::p( txt => qq(Results for "$cookie->{ 'SEARCH' }": $count), class => 'center' );
942 push @html, Maasha::XHTML::table_beg( summary => "Search table", align => 'center', cellpadding => '5px' );
943 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) ] );
945 foreach $result ( @{ $results } )
947 $cookie->{ 'CONTIG' } = $result->{ 'S_ID' };
948 $cookie->{ 'NAV_START' } = $result->{ 'S_BEG' };
949 $cookie->{ 'NAV_END' } = $result->{ 'S_END' };
950 $cookie->{ 'S_BEG' } = $result->{ 'S_BEG' };
951 $cookie->{ 'S_END' } = $result->{ 'S_END' };
952 $cookie->{ 'STRAND' } = $result->{ 'STRAND' };
953 $cookie->{ 'Q_ID' } = $result->{ 'Q_ID' };
955 $browse = Maasha::XHTML::ln( txt => "browse", href => cookie_href( $cookie, "browse" ) );
956 $export = Maasha::XHTML::ln( txt => "export", href => cookie_href( $cookie, "export" ) );
958 push @html, Maasha::XHTML::table_row_advanced(
959 tr => [ { td => $result->{ 'S_ID' } },
960 { td => $result->{ 'S_BEG' }, align => 'right' },
961 { td => $result->{ 'S_END' }, align => 'right' },
962 { td => $result->{ 'Q_ID' } },
963 { td => $result->{ 'SCORE' }, align => 'right' },
964 { td => $result->{ 'STRAND' } },
965 { td => $result->{ 'HITS' }, align => 'right' },
966 { td => $result->{ 'ALIGN' } },
967 { td => $result->{ 'BLOCK_COUNT' }, align => 'right' },
968 { td => $result->{ 'BLOCK_BEGS' } },
969 { td => $result->{ 'BLOCK_LENS' } },
970 { td => $result->{ 'BLOCK_TYPE' } },
973 ], class => "monospace"
977 push @html, Maasha::XHTML::table_end;
980 return wantarray ? @html : \@html;
986 # Martin A. Hansen, November 2009.
988 # Returns a HTML section with extracted DNA.
990 my ( $cookie, # cookie hash
995 my ( @html, $beg, $end, $seq );
997 $beg = $cookie->{ 'S_BEG' };
998 $end = $cookie->{ 'S_END' };
1002 $seq = join ";", ">$cookie->{ 'GENOME' }", $cookie->{ 'ASSEMBLY' }, $cookie->{ 'CONTIG' }, $beg, $end, "$cookie->{ 'STRAND' }\n";
1003 $seq .= Maasha::BGB::Track::dna_get( $cookie );
1005 push @html, Maasha::XHTML::h2( txt => "DNA", class => 'center' );
1006 push @html, Maasha::XHTML::pre( txt => $seq );
1008 return wantarray ? @html : \@html;
1012 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<