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::BBrowser::Session;
37 use Maasha::BBrowser::Track;
38 use Maasha::BBrowser::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 $session = Maasha::BBrowser::Session::session_restore( "$cookie->{ 'SESSION_DIR' }/sessions.txt" );
202 $cookie->{ 'PAGE' } = 'login' if not $cookie->{ 'SESSION_ID' };
203 $cookie->{ 'PAGE' } = 'login' if not exists $session->{ $cookie->{ 'USER' } };
204 $cookie->{ 'PAGE' } = 'login' if $session->{ $cookie->{ 'USER' } }->{ 'SESSION_ID' } ne $cookie->{ 'SESSION_ID' };
210 # Martin A. Hansen, December 2009.
212 # Check a user and password from CGI against the password file and
213 # set the session ID, if found, in the cookie.
215 my ( $cookie, # cookie hash
222 $session = Maasha::BBrowser::Session::session_restore( "$cookie->{ 'SESSION_DIR' }/sessions.txt" );
224 if ( $cookie->{ 'USER' } and $cookie->{ 'PASSWORD' } )
226 if ( exists $session->{ $cookie->{ 'USER' } } and
227 $session->{ $cookie->{ 'USER' } }->{ 'PASSWORD' } eq Digest::MD5::md5_hex( $cookie->{ 'PASSWORD' } ) )
229 $session->{ $cookie->{ 'USER' } }->{ 'SESSION_ID' } ||= Maasha::BBrowser::Session::session_new();
230 $session->{ $cookie->{ 'USER' } }->{ 'TIME' } = Maasha::Common::time_stamp();
232 $cookie->{ 'SESSION_ID' } = $session->{ $cookie->{ 'USER' } }->{ 'SESSION_ID' };
233 $cookie->{ 'LOGIN' } = "OK";
234 $cookie->{ 'USER' } = $cookie->{ 'USER' };
235 $cookie->{ 'PAGE' } = 'clade';
237 Maasha::BBrowser::Session::session_store( "$cookie->{ 'SESSION_DIR' }/sessions.txt", $session );
241 $cookie->{ 'LOGIN' } = "ERROR";
249 # Martin A. Hansen, November 2009.
251 # Decommify the cookie value for NAV_START and adjust it to
252 # to prevent negative values.
254 my ( $cookie, # cookie hash
259 if ( defined $cookie->{ 'NAV_START' } )
261 $cookie->{ 'NAV_START' } =~ tr/,//d;
262 $cookie->{ 'NAV_START' } = 0 if $cookie->{ 'NAV_START' } < 0;
266 $cookie->{ 'NAV_START' } = 0;
273 # Martin A. Hansen, November 2009.
275 # Decommify the cookie value for NAV_END and adjust it to prevent
276 # overshooting the max value for the contig size as determined
279 my ( $cookie, # cookie hash
286 $max = Maasha::Filesys::file_size( Maasha::BBrowser::Track::path_seq( $cookie ) );
288 if ( defined $cookie->{ 'NAV_END' } )
290 $cookie->{ 'NAV_END' } =~ tr/,//d;
291 $cookie->{ 'NAV_END' } = $max if $cookie->{ 'NAV_END' } > $max;
295 $cookie->{ 'NAV_END' } = $max;
302 # Martin A. Hansen, November 2009.
304 # Adjust the cookie values for NAV_START and NAV_END based
305 # on cookie ZOOM values.
307 my ( $cookie, # cookie hash
312 my ( $max, $dist, $new_dist, $dist_diff );
314 $max = Maasha::Filesys::file_size( Maasha::BBrowser::Track::path_seq( $cookie ) );
316 $dist = $cookie->{ 'NAV_END' } - $cookie->{ 'NAV_START' };
318 if ( defined $cookie->{ 'ZOOM_IN1' } ) {
319 $new_dist = $dist / 1.5;
320 } elsif ( defined $cookie->{ 'ZOOM_IN2' } ) {
321 $new_dist = $dist / 3;
322 } elsif ( defined $cookie->{ 'ZOOM_IN3' } ) {
323 $new_dist = $dist / 10;
324 } elsif ( defined $cookie->{ 'ZOOM_OUT1' } ) {
325 $new_dist = $dist * 1.5;
326 } elsif ( defined $cookie->{ 'ZOOM_OUT2' } ) {
327 $new_dist = $dist * 3;
328 } elsif ( defined $cookie->{ 'ZOOM_OUT3' } ) {
329 $new_dist = $dist * 10;
334 $dist_diff = $dist - $new_dist;
336 $cookie->{ 'NAV_START' } = int( $cookie->{ 'NAV_START' } + ( $dist_diff / 2 ) );
337 $cookie->{ 'NAV_END' } = int( $cookie->{ 'NAV_END' } - ( $dist_diff / 2 ) );
339 $cookie->{ 'NAV_START' } = 0 if $cookie->{ 'NAV_START' } < 0;
340 $cookie->{ 'NAV_END' } = $max if $cookie->{ 'NAV_END' } > $max;
347 # Martin A. Hansen, November 2009.
349 # Adjust the cookie values for NAV_START and NAV_END based
350 # on cookie MOVE values.
352 my ( $cookie, # cookie hash
355 my ( $max, $dist, $shift, $new_start, $new_end );
357 $max = Maasha::Filesys::file_size( Maasha::BBrowser::Track::path_seq( $cookie ) );
359 $dist = $cookie->{ 'NAV_END' } - $cookie->{ 'NAV_START' };
361 if ( defined $cookie->{ 'MOVE_LEFT1' } ) {
362 $shift = -1 * $dist * 0.10;
363 } elsif ( defined $cookie->{ 'MOVE_LEFT2' } ) {
364 $shift = -1 * $dist * 0.475;
365 } elsif ( defined $cookie->{ 'MOVE_LEFT3' } ) {
366 $shift = -1 * $dist * 0.95;
367 } elsif ( defined $cookie->{ 'MOVE_RIGHT1' } ) {
368 $shift = $dist * 0.10;
369 } elsif ( defined $cookie->{ 'MOVE_RIGHT2' } ) {
370 $shift = $dist * 0.475;
371 } elsif ( defined $cookie->{ 'MOVE_RIGHT3' } ) {
372 $shift = $dist * 0.95;
377 $new_start = int( $cookie->{ 'NAV_START' } + $shift );
378 $new_end = int( $cookie->{ 'NAV_END' } + $shift );
380 if ( $new_start > 0 and $new_end < $max )
382 $cookie->{ 'NAV_START' } = $new_start;
383 $cookie->{ 'NAV_END' } = $new_end;
391 # Martin A. Hansen, November 2009.
393 # Returns the href for a taxonomy path terminated at a given
394 # page using information stored in a cookie.
396 my ( $cookie, # cookie hash
402 my ( @href_list, %href_hash, $href );
404 $href_hash{ "user" } = $cookie->{ 'USER' } if $cookie->{ 'USER' };
408 $href_hash{ "clade" } = $cookie->{ 'CLADE' } if $cookie->{ 'CLADE' };
409 last if $page eq 'clade';
410 $href_hash{ "genome" } = $cookie->{ 'GENOME' } if $cookie->{ 'GENOME' };
411 last if $page eq 'genome';
412 $href_hash{ "assembly" } = $cookie->{ 'ASSEMBLY' } if $cookie->{ 'ASSEMBLY' };
413 last if $page eq 'assembly';
414 $href_hash{ "contig" } = $cookie->{ 'CONTIG' } if $cookie->{ 'CONTIG' };
415 last if $page eq 'contig';
419 if ( defined $cookie->{ 'NAV_START' } and defined $cookie->{ 'NAV_END' } ) {
420 $href_hash{ "nav_search" } = "$cookie->{ 'NAV_START' }-$cookie->{ 'NAV_END' }";
423 $href_hash{ "s_beg" } = $cookie->{ 'S_BEG' } if defined $cookie->{ 'S_BEG' };
424 $href_hash{ "s_end" } = $cookie->{ 'S_END' } if defined $cookie->{ 'S_END' };
425 $href_hash{ "q_id" } = $cookie->{ 'Q_ID' } if defined $cookie->{ 'Q_ID' };
426 $href_hash{ "strand" } = $cookie->{ 'STRAND' } if defined $cookie->{ 'STRAND' };
427 $href_hash{ "session_id" } = $cookie->{ 'SESSION_ID' } if defined $cookie->{ 'SESSION_ID' };
429 push @href_list, "$cookie->{ 'SCRIPT' }?page=$page";
431 foreach $href ( keys %href_hash ) {
432 push @href_list, "$href=$href_hash{ $href }";
435 return join "&", @href_list;
441 # Martin A. Hansen, November 2009.
443 # Returns the next page in the taxonomy path.
445 my ( $cookie, # cookie hash
452 for ( $i = 0; $i < @{ $cookie->{ 'LIST_PAGES' } }; $i++ ) {
453 last if $cookie->{ 'PAGE' } eq $cookie->{ 'LIST_PAGES' }->[ $i ];
456 return $cookie->{ 'LIST_PAGES' }->[ $i + 1 ];
460 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PAGES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
465 # Martin A. Hansen, November 2009.
467 # Determines what page to render based on
468 # the cookie's PAGE setting.
470 my ( $cookie, # cookie hash
477 if ( $cookie->{ 'PAGE' } eq 'login' ) {
478 push @html, page_login( $cookie );
479 } elsif ( $cookie->{ 'PAGE' } eq 'search' ) {
480 push @html, page_search( $cookie );
481 } elsif ( $cookie->{ 'PAGE' } eq 'browse' ) {
482 push @html, page_browse( $cookie );
483 } elsif ( $cookie->{ 'PAGE' } eq 'dna' ) {
484 push @html, page_dna( $cookie );
485 } elsif ( $cookie->{ 'PAGE' } eq 'export' ) {
486 push @html, page_export( $cookie );
488 push @html, page_taxonomy( $cookie );
491 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "session_id", value => "$cookie->{ 'SESSION_ID' }" ) );
493 return wantarray ? @html : \@html;
499 # Martin A. Hansen, December 2009.
501 # Renders the login page.
510 push @html, section_login( $cookie );
512 return wantarray ? @html : \@html;
518 # Martin A. Hansen, December 2009.
520 # Renders the search page.
529 push @html, section_taxonomy_table( $cookie );
530 push @html, section_search( $cookie );
532 return wantarray ? @html : \@html;
538 # Martin A. Hansen, November 2009.
540 # Renders the browse page.
549 push @html, section_taxonomy_table( $cookie );
550 push @html, section_navigate( $cookie );
551 push @html, section_browse( $cookie );
553 return wantarray ? @html : \@html;
559 # Martin A. Hansen, November 2009.
561 # Renders the DNA page.
570 push @html, section_taxonomy_table( $cookie );
571 push @html, section_dna( $cookie );
573 return wantarray ? @html : \@html;
579 # Martin A. Hansen, November 2009.
581 # Renders the export page.
590 push @html, section_taxonomy_table( $cookie );
591 push @html, section_export( $cookie );
593 return wantarray ? @html : \@html;
599 # Martin A. Hansen, November 2009.
601 # Renders the browse page.
603 my ( $cookie, # cookie hash
610 push @html, section_taxonomy_table( $cookie );
611 push @html, section_taxonomy_select( $cookie );
613 return wantarray ? @html : \@html;
617 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SECTIONS <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
622 # Martin A. Hansen, December 2009.
624 # Returns a HTML section with a login menu.
626 my ( $cookie, # cookie hash
631 my ( $user, $password, $login, @html );
633 $user = Maasha::XHTML::text( name => "user", value => "", size => 20 );
634 $password = Maasha::XHTML::password( name => "password", value => "", size => 20 );
635 $login = Maasha::XHTML::submit( name => "login_submit", value => "Login" );
637 push @html, Maasha::XHTML::h2( txt => "Login", class => 'center' );
639 push @html, Maasha::XHTML::table_beg( summary => "Login table", align => 'center' );
640 push @html, Maasha::XHTML::table_row_simple( tr => [ "User:", $user ] );
641 push @html, Maasha::XHTML::table_row_simple( tr => [ "Password:", $password ] );
642 push @html, Maasha::XHTML::table_row_simple( tr => [ "", $login ] );
643 push @html, Maasha::XHTML::table_end;
645 if ( $cookie->{ 'LOGIN' } and $cookie->{ 'LOGIN' } eq 'ERROR' ) {
646 push @html, Maasha::XHTML::h3( txt => "Bad user or password - please retry", class => 'error' );
649 return wantarray ? @html : \@html;
653 sub section_taxonomy_table
655 # Martin A. Hansen, November 2009.
657 # Returns a HTML section with a taxonomy table
658 # showing the location in the taxonomy and with
659 # links to browse the taxonomy.
661 my ( $cookie, # cookie hash
666 my ( $page, @row, @html, $href, $txt );
668 foreach $page ( @{ $cookie->{ 'LIST_PAGES' } } )
670 last if $page eq $cookie->{ 'PAGE' } or $page eq 'browse';
672 $href = cookie_href( $cookie, $page );
674 $txt = ": $cookie->{ uc $page }";
676 push @row, Maasha::XHTML::ln( txt => $page, href => $href, class => 'inline' );
677 push @row, Maasha::XHTML::p( txt => $txt, class => 'inline' );
680 push @html, Maasha::XHTML::table_beg( summary => "Taxonomy table", align => 'center', cellpadding => '5px' );
681 push @html, Maasha::XHTML::table_row_simple( tr => [ join( "\n", @row ) ], align => 'center' );
682 push @html, Maasha::XHTML::table_end;
684 return wantarray ? @html : \@html;
688 sub section_taxonomy_select
690 # Martin A. Hansen, November 2009.
692 # Returns a HTML section with selection choices
693 # for navigating the taxonomy tree.
695 my ( $cookie, # cookie hash
700 my ( $list, @html, $item, $href );
702 $list = "LIST_" . uc $cookie->{ 'PAGE' };
704 push @html, Maasha::XHTML::h2( txt => "Select $cookie->{ 'PAGE' }", class => 'center' );
706 push @html, Maasha::XHTML::table_beg( summary => "Taxonomy select table", align => 'center', cellpadding => '5px' );
708 foreach $item ( @{ $cookie->{ $list } } )
710 $cookie->{ uc $cookie->{ 'PAGE' } } = $item;
712 $href = cookie_href( $cookie, cookie_page_next( $cookie ) );
714 push @html, Maasha::XHTML::table_row_simple( tr => [ Maasha::XHTML::ln( txt => $item, href => $href ) ] );
717 push @html, Maasha::XHTML::table_end;
719 return wantarray ? @html : \@html;
725 # Martin A. Hansen, November 2009.
727 # Returns a HTML section for navigating in the browser window.
729 my ( $cookie, # cookie hash
734 my ( @html, $nav_val );
736 $nav_val = Maasha::Calc::commify( $cookie->{ 'NAV_START' } ) . "-" . Maasha::Calc::commify( $cookie->{ 'NAV_END' } );
738 push @html, Maasha::XHTML::table_beg( summary => "Navigation table", align => 'center' );
739 push @html, Maasha::XHTML::table_row_simple( tr => [
740 "Position or search term:",
741 Maasha::XHTML::text( name => "nav_search", value => $nav_val, size => 30 ),
742 Maasha::XHTML::submit( name => "nav_submit", value => "Submit" ),
744 push @html, Maasha::XHTML::table_end;
746 push @html, Maasha::XHTML::table_beg( summary => "Zoom table", align => 'center' );
747 push @html, Maasha::XHTML::table_row_simple( tr => [
748 Maasha::XHTML::p( txt => 'Move:' ),
749 Maasha::XHTML::submit( name => "move_left3", value => "<<<", title => "move 95% to the left" ),
750 Maasha::XHTML::submit( name => "move_left2", value => "<<", title => "move 47.5% to the left" ),
751 Maasha::XHTML::submit( name => "move_left1", value => "<", title => "move 10% to the left" ),
752 Maasha::XHTML::submit( name => "move_right1", value => ">", title => "move 10% to the rigth" ),
753 Maasha::XHTML::submit( name => "move_right2", value => ">>", title => "move 47.5% to the rigth" ),
754 Maasha::XHTML::submit( name => "move_right3", value => ">>>", title => "move 95% to the right" ),
755 Maasha::XHTML::p( txt => 'Zoom in:' ),
756 Maasha::XHTML::submit( name => "zoom_in1", value => "1.5x" ),
757 Maasha::XHTML::submit( name => "zoom_in2", value => "3x" ),
758 Maasha::XHTML::submit( name => "zoom_in3", value => "10x" ),
759 Maasha::XHTML::p( txt => 'Zoom out:' ),
760 Maasha::XHTML::submit( name => "zoom_out1", value => "1.5x" ),
761 Maasha::XHTML::submit( name => "zoom_out2", value => "3x" ),
762 Maasha::XHTML::submit( name => "zoom_out3", value => "10x" ),
764 push @html, Maasha::XHTML::table_end;
766 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "page", value => "browse" ) );
767 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "user", value => "$cookie->{ 'USER' }" ) );
768 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "clade", value => "$cookie->{ 'CLADE' }" ) );
769 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "genome", value => "$cookie->{ 'GENOME' }" ) );
770 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "assembly", value => "$cookie->{ 'ASSEMBLY' }" ) );
771 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "contig", value => "$cookie->{ 'CONTIG' }" ) );
773 return wantarray ? @html : \@html;
784 my ( @tracks, $i, @features, $feat, $elem, $surface, $cr, $png_data, @html, @img );
786 push @features, [ Maasha::BBrowser::Track::track_ruler( $cookie ) ];
787 push @features, [ Maasha::BBrowser::Track::track_seq( $cookie ) ];
789 @tracks = Maasha::BBrowser::Track::path_tracks( $cookie );
791 for ( $i = 0; $i < @tracks; $i++ )
793 $cookie->{ 'FEAT_COLOR' } = Maasha::BBrowser::Draw::palette( $i );
795 push @features, [ Maasha::BBrowser::Track::track_feature( $tracks[ $i ], $cookie ) ];
798 $surface = Cairo::ImageSurface->create( 'argb32', $cookie->{ 'IMG_WIDTH' }, $cookie->{ 'TRACK_OFFSET' } );
799 $cr = Cairo::Context->create( $surface );
801 $cr->rectangle ( 0, 0, $cookie->{ 'IMG_WIDTH' }, $cookie->{ 'TRACK_OFFSET' } );
802 $cr->set_source_rgb ( 1, 1, 1 );
805 foreach $feat ( @features ) {
806 Maasha::BBrowser::Draw::draw_feature( $cr, $feat ) if $feat;
809 $png_data = Maasha::BBrowser::Draw::base64_png( $surface );
811 push @img, Maasha::XHTML::img(
812 src => "data:image/png;base64,$png_data",
813 alt => "Browser Tracks",
814 height => $cookie->{ 'TRACK_OFFSET' },
815 width => $cookie->{ 'IMG_WIDTH' },
817 usemap => "#browser_map"
820 push @img, Maasha::XHTML::map_beg( name => "browser_map", id => "browser_map" );
822 foreach $feat ( @features )
824 foreach $elem ( @{ $feat } )
826 next if $elem->{ 'type' } eq 'text';
828 #$elem->{ 'strand' } = '+' if $elem->{ 'strand' } eq '+';
830 $cookie->{ 'Q_ID' } = $elem->{ 'q_id' };
831 $cookie->{ 'S_BEG' } = $elem->{ 's_beg' };
832 $cookie->{ 'S_END' } = $elem->{ 's_end' };
833 $cookie->{ 'STRAND' } = $elem->{ 'strand' };
835 push @img, Maasha::XHTML::area(
836 href => cookie_href( $cookie, "export" ),
837 # href => cookie_href( $cookie, "export" ) . "&q_id=$elem->{ 'q_id' }&s_beg=$elem->{ 's_beg' }&s_end=$elem->{ 's_end' }&strand=$elem->{ 'strand' }",
839 coords => "$elem->{ x1 }, $elem->{ y1 }, $elem->{ x2 }, $elem->{ y2 }", title => "$elem->{ 'title' }",
844 push @img, Maasha::XHTML::map_end();
846 push @html, Maasha::XHTML::p( txt => join( "\n", @img ) );
848 @html = Maasha::XHTML::div( txt => join( "\n", @html ), class => 'browse' );
850 return wantarray ? @html : \@html;
856 # Martin A. Hansen, November 2009.
858 # Returns a HTML section with export table.
860 my ( $cookie, # cookie hash
865 my ( @row_dna_contig, @html );
867 push @row_dna_contig, Maasha::XHTML::p( txt => qq(Export Feature: "$cookie->{ 'Q_ID' }" DNA from Contig: ), class => 'inline' );
868 push @row_dna_contig, Maasha::XHTML::p( txt => "$cookie->{ 'CONTIG' } Start: ", class => 'inline' );
869 push @row_dna_contig, Maasha::XHTML::text( name => "s_beg", value => Maasha::Calc::commify( $cookie->{ 'S_BEG' } ), size => 15 );
870 push @row_dna_contig, Maasha::XHTML::p( txt => "End: ", class => 'inline' );
871 push @row_dna_contig, Maasha::XHTML::text( name => "s_end", value => Maasha::Calc::commify( $cookie->{ 'S_END' } ), size => 15 );
872 push @row_dna_contig, Maasha::XHTML::p( txt => "Strand: ", class => 'inline' );
873 push @row_dna_contig, Maasha::XHTML::menu( name => "strand", options => [ qw( + - ) ], selected => $cookie->{ 'STRAND' } );
874 push @row_dna_contig, Maasha::XHTML::submit( name => "export", value => "Export", title => "Fetch DNA from this region" );
876 push @html, Maasha::XHTML::h2( txt => "Export", class => 'center' );
877 push @html, Maasha::XHTML::table_beg( summary => "Taxonomy select table", align => 'center' );
878 push @html, Maasha::XHTML::table_row_simple( tr => \@row_dna_contig );
879 push @html, Maasha::XHTML::table_end;
881 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "page", value => "dna" ) );
882 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "user", value => "$cookie->{ 'USER' }" ) );
883 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "clade", value => "$cookie->{ 'CLADE' }" ) );
884 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "genome", value => "$cookie->{ 'GENOME' }" ) );
885 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "assembly", value => "$cookie->{ 'ASSEMBLY' }" ) );
886 push @html, Maasha::XHTML::p( txt => Maasha::XHTML::hidden( name => "contig", value => "$cookie->{ 'CONTIG' }" ) );
888 return wantarray ? @html : \@html;
894 # Martin A. Hansen, November 2009.
896 # Returns a HTML section with export table.
898 my ( $cookie, # cookie hash
903 my ( $results, $result, $count, @html, $export, $browse );
905 $results = Maasha::BBrowser::Track::search_tracks( $cookie );
907 $count = scalar @{ $results };
909 push @html, Maasha::XHTML::h2( txt => "Search", class => 'center' );
910 push @html, Maasha::XHTML::p( txt => qq(Results for "$cookie->{ 'SEARCH' }": $count), class => 'center' );
914 push @html, Maasha::XHTML::table_beg( summary => "Search table", align => 'center', cellpadding => '5px' );
915 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) ] );
917 foreach $result ( @{ $results } )
919 $cookie->{ 'CONTIG' } = $result->{ 'S_ID' };
920 $cookie->{ 'NAV_START' } = $result->{ 'S_BEG' };
921 $cookie->{ 'NAV_END' } = $result->{ 'S_END' };
922 $cookie->{ 'S_BEG' } = $result->{ 'S_BEG' };
923 $cookie->{ 'S_END' } = $result->{ 'S_END' };
924 $cookie->{ 'STRAND' } = $result->{ 'STRAND' };
925 $cookie->{ 'Q_ID' } = $result->{ 'Q_ID' };
927 $browse = Maasha::XHTML::ln( txt => "browse", href => cookie_href( $cookie, "browse" ) );
928 $export = Maasha::XHTML::ln( txt => "export", href => cookie_href( $cookie, "export" ) );
930 push @html, Maasha::XHTML::table_row_advanced(
931 tr => [ { td => $result->{ 'S_ID' } },
932 { td => $result->{ 'S_BEG' }, align => 'right' },
933 { td => $result->{ 'S_END' }, align => 'right' },
934 { td => $result->{ 'Q_ID' } },
935 { td => $result->{ 'SCORE' }, align => 'right' },
936 { td => $result->{ 'STRAND' } },
937 { td => $result->{ 'HITS' }, align => 'right' },
938 { td => $result->{ 'ALIGN' } },
939 { td => $result->{ 'BLOCK_COUNT' }, align => 'right' },
940 { td => $result->{ 'BLOCK_BEGS' } },
941 { td => $result->{ 'BLOCK_LENS' } },
942 { td => $result->{ 'BLOCK_TYPE' } },
945 ], class => "monospace"
949 push @html, Maasha::XHTML::table_end;
952 return wantarray ? @html : \@html;
958 # Martin A. Hansen, November 2009.
960 # Returns a HTML section with extracted DNA.
962 my ( $cookie, # cookie hash
967 my ( @html, $beg, $end, $seq );
969 $beg = $cookie->{ 'S_BEG' };
970 $end = $cookie->{ 'S_END' };
974 $seq = ">$cookie->{ 'CONTIG' }_$beg" . "_$end" . "_$cookie->{ 'STRAND' }\n";
975 $seq .= Maasha::BBrowser::Track::dna_get( $cookie );
977 push @html, Maasha::XHTML::h2( txt => "DNA", class => 'center' );
978 push @html, Maasha::XHTML::pre( txt => $seq );
980 return wantarray ? @html : \@html;
984 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<