#!/usr/bin/env perl

# Copyright (C) 2006-2009 Martin A. Hansen.

# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.

# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.

# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.

# http://www.gnu.org/copyleft/gpl.html

# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

use strict;
use warnings;

use lib "/Users/maasha/biopieces/code_perl/";

use CGI;
use Cairo;
use Pango;
use Data::Dumper;
use Time::HiRes;
use Maasha::Common;
use Maasha::Filesys;
use Maasha::Calc;
use Maasha::XHTML;
use Maasha::Biopieces;
use Maasha::KISS::IO;
use Maasha::KISS::Track;
use Maasha::KISS::Draw;

my ( $cgi, $database, $user, $password, $dbh, $script, @html );

$cgi = new CGI;

$database = 'S_aur_COL';
$user     = Maasha::Biopieces::biopiecesrc( "MYSQL_USER" );
$password = Maasha::Biopieces::biopiecesrc( "MYSQL_PASSWORD" );

$dbh = Maasha::SQL::connect( $database, $user, $password );

$script = Maasha::Common::get_scriptname();

push @html, Maasha::XHTML::html_header(
    cgi_header  => 1,
    title       => "KISS Genome Browser",
#    css_file    => "test.css",
    author      => "Martin A. Hansen, mail\@maasha.dk",
    description => "Biopieces bacterial genome browser - KISS",
    keywords    => [ qw( KISS Biopieces biopiece genome browser viewer bacterium bacteria prokaryote prokaryotes ) ],
    no_cache    => 1,
);

push @html, Maasha::XHTML::h1( txt => "KISS Genome Browser", class => "center" );
push @html, Maasha::XHTML::form_beg( action => $script, method => "get", enctype => "multipart/form-data" );

push @html, sec_navigate( $cgi );
push @html, sec_browse( $dbh, $cgi->param( 'nav_start' ), $cgi->param( 'nav_end' ) );

push @html, Maasha::XHTML::form_end;
push @html, Maasha::XHTML::body_end;
push @html, Maasha::XHTML::html_end;

print "$_\n" foreach @html;


# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<


sub sec_navigate
{
    my ( $cgi,   # CGI object
       ) = @_;

    # Returns a list.

    my ( $list_clade, $list_genome, $list_assembly, $list_contig, $def_clade, $def_genome, $def_assembly, $def_contig, $def_start, $def_end, @html );

    $list_clade    = nav_list_clade();
    $list_genome   = nav_list_genome();
    $list_assembly = nav_list_assembly();
    $list_contig   = nav_list_contig();

    nav_zoom( $cgi );
    nav_move( $cgi, 2_800_000 ); # FIXME

    $def_clade     = nav_def_clade( $cgi );
    $def_genome    = nav_def_genome( $cgi );
    $def_assembly  = nav_def_assembly( $cgi );
    $def_contig    = nav_def_contig( $cgi );
    $def_start     = nav_def_start( $cgi );
    $def_end       = nav_def_end( $cgi );

    push @html, Maasha::XHTML::table_beg( summary => "Navigation table" );
    push @html, Maasha::XHTML::table_row_simple( tr => [ qw( Clade Genome Assembly Contig Start End ) ], align => 'center' );
    push @html, Maasha::XHTML::table_row_simple( tr => [
        Maasha::XHTML::menu( name => "nav_clade",    options => $list_clade,    selected => $def_clade ),
        Maasha::XHTML::menu( name => "nav_genome",   options => $list_genome,   selected => $def_genome ),
        Maasha::XHTML::menu( name => "nav_assembly", options => $list_assembly, selected => $def_assembly ),
        Maasha::XHTML::menu( name => "nav_contig",   options => $list_contig,   selected => $def_contig ),
        Maasha::XHTML::text( name => "nav_start", value => Maasha::Calc::commify( $def_start ), size => 20 ),
        Maasha::XHTML::text( name => "nav_end",   value => Maasha::Calc::commify( $def_end ),   size => 20 ), 
        Maasha::XHTML::submit( name => "nav_submit", value => "Submit" ),
    ] );
    push @html, Maasha::XHTML::table_end;

    push @html, Maasha::XHTML::table_beg( summary => "Zoom table" );
    push @html, Maasha::XHTML::table_row_simple( tr => [
        Maasha::XHTML::p( txt => 'Move:' ),
        Maasha::XHTML::submit( name => "move_left3",  value => "<<<", title => "move 95% to the left" ),
        Maasha::XHTML::submit( name => "move_left2",  value => "<<",  title => "move 47.5% to the left" ),
        Maasha::XHTML::submit( name => "move_left1",  value => "<",   title => "move 10% to the left" ),
        Maasha::XHTML::submit( name => "move_right1", value => ">",   title => "move 10% to the rigth" ),
        Maasha::XHTML::submit( name => "move_right2", value => ">>",  title => "move 47.5% to the rigth" ),
        Maasha::XHTML::submit( name => "move_right3", value => ">>>", title => "move 95% to the right" ),
        Maasha::XHTML::p( txt => 'Zoom in:' ),
        Maasha::XHTML::submit( name => "zoom_in1", value => "1.5x" ),
        Maasha::XHTML::submit( name => "zoom_in2", value => "3x" ),
        Maasha::XHTML::submit( name => "zoom_in3", value => "10x" ),
        Maasha::XHTML::p( txt => 'Zoom out:' ),
        Maasha::XHTML::submit( name => "zoom_out1", value => "1.5x" ),
        Maasha::XHTML::submit( name => "zoom_out2", value => "3x" ),
        Maasha::XHTML::submit( name => "zoom_out3", value => "10x" ),
    ] );
    push @html, Maasha::XHTML::table_end;

    return wantarray ? @html : \@html;
}


sub sec_browse
{
    my ( $dbh,     # Database handle
         $start,   # Browse start position
         $end,     # Browse end position
       ) = @_;

    # Returns a list.

    my ( $t0, $t1, $ruler, $index, $index_beg, $index_len, $fh, $seq, $dna, $table, $entries, $features, $surface, $cr, $file, @html );

    $ruler = Maasha::KISS::Track::track_ruler( 1200, 25, $start, $end );

    $index = Maasha::Fasta::index_retrieve( "$ENV{ 'BP_DATA' }/genomes/S_aur_COL/fasta/S_aur_COL.index" );

    ( $index_beg, $index_len ) = @{ $index->{ 'S_aur_COL' } };

    $fh = Maasha::Filesys::file_read_open( "$ENV{ 'BP_DATA' }/genomes/S_aur_COL/fasta/S_aur_COL.fna" );

    $seq = Maasha::Filesys::file_read( $fh, $index_beg + $start, $end - $start + 1 );

    close $fh;

    $dna = Maasha::KISS::Track::track_seq( 1200, 50, $seq ) if length $seq <= 220;

    $table = 'Solexa';

    $t0 = Time::HiRes::gettimeofday();
    $entries = Maasha::KISS::IO::kiss_sql_get( $dbh, $table, $start, $end );
    $t1 = Time::HiRes::gettimeofday();

    push @html, Maasha::XHTML::p( txt => "Feature count: " . Maasha::Calc::commify( scalar @$entries ) );

    push @html, Maasha::XHTML::p( txt => "Time SQL: " . ( $t1 - $t0 ) );

    $t0 = Time::HiRes::gettimeofday();

    my $MAX = 4000;  # FIXME should depend on height of track as well

    if ( @$entries > $MAX ) {
        $features = Maasha::KISS::Track::track_histogram( 1200, 75, $start, $end, $entries );
    } else {
        $features = Maasha::KISS::Track::track_feature( 1200, 75, $start, $end, $entries );
    }

    $t1 = Time::HiRes::gettimeofday();

    # push @html, Maasha::KISS::Draw::hdump( $entries );
    # push @html, Maasha::KISS::Draw::hdump( $features );

    push @html, Maasha::XHTML::p( txt => "Time Track: " . ( $t1 - $t0 ) );

    $file = "fisk.png";

    $surface = Cairo::ImageSurface->create( 'argb32', 1200, 800 );
    $cr      = Cairo::Context->create( $surface );

    $t0 = Time::HiRes::gettimeofday();

    Maasha::KISS::Draw::track_text( $cr, $ruler, "black" ) if $ruler;
    Maasha::KISS::Draw::track_text( $cr, $dna, "black" )   if $dna;

    Maasha::KISS::Draw::track_feature( $cr, $features, 'green' ) if $features;

    Maasha::KISS::Draw::file_png( $surface, $file );

    $t1 = Time::HiRes::gettimeofday();

    push @html, Maasha::XHTML::p( txt => "Time Draw: " . ( $t1 - $t0 ) );

    push @html, Maasha::XHTML::p( txt => Maasha::XHTML::img( src => $file, alt => "Browser Tracks", height => 800, width => 1200, class => "foo", id => "pix_id", usemap => "map"  ) );

    return wantarray ? @html : \@html;
}


sub nav_list_clade
{
    my ( $list_clade );

    $list_clade = [ qw( Eukaryote Bacillus Fish ) ];

    return wantarray ? @{ $list_clade } : $list_clade;
}


sub nav_list_genome
{
    my ( $list_genome );

    $list_genome = [ qw( S.aur_COL E.col B.sub ) ];

    return wantarray ? @{ $list_genome } : $list_genome;
}


sub nav_list_assembly
{
    my ( $list_assembly );

    $list_assembly = [ qw( 2008-02-21 2009-01-23 ) ];

    return wantarray ? @{ $list_assembly } : $list_assembly;
}


sub nav_list_contig
{
    my ( $list_contig );

    $list_contig = [ qw( chr1 chr2 ) ];

    return wantarray ? @{ $list_contig } : $list_contig;
}


sub nav_zoom
{
    my ( $cgi,   # CGI object
       ) = @_;

    my ( $start, $end, $dist, $new_dist, $dist_diff, $new_start, $new_end );

    if ( defined $cgi->param( 'nav_start' ) and $cgi->param( 'nav_end' ) )
    {
        $start = $cgi->param( 'nav_start' );
        $end   = $cgi->param( 'nav_end' );

        $start =~ tr/,//d;
        $end   =~ tr/,//d;

        $dist = $end - $start;

        if ( defined $cgi->param( 'zoom_in1' ) ) {
            $new_dist = $dist / 1.5;
        } elsif ( defined $cgi->param( 'zoom_in2' ) ) {
            $new_dist = $dist / 3;
        } elsif ( defined $cgi->param( 'zoom_in3' ) ) {
            $new_dist = $dist / 10;
        } elsif ( defined $cgi->param( 'zoom_out1' ) ) {
            $new_dist = $dist * 1.5;
        } elsif ( defined $cgi->param( 'zoom_out2' ) ) {
            $new_dist = $dist * 3;
        } elsif ( defined $cgi->param( 'zoom_out3' ) ) {
            $new_dist = $dist * 10;
        }

        if ( $new_dist )
        {
            $dist_diff = $dist - $new_dist;
            $new_start = int( $start + ( $dist_diff / 2 ) );
            $new_end   = int( $end   - ( $dist_diff / 2 ) );

            $cgi->param( 'nav_start', $new_start );
            $cgi->param( 'nav_end',  $new_end );
        }
    }
}


sub nav_move
{
    my ( $cgi,   # CGI object
         $max,   # Max end position
       ) = @_;

    my ( $start, $end, $dist, $shift, $new_start, $new_end );

    if ( defined $cgi->param( 'nav_start' ) and $cgi->param( 'nav_end' ) )
    {
        $start = $cgi->param( 'nav_start' );
        $end   = $cgi->param( 'nav_end' );

        $start =~ tr/,//d;
        $end   =~ tr/,//d;

        $dist = $end - $start;

        if ( defined $cgi->param( 'move_left1' ) ) {
            $shift = -1 * $dist * 0.10;
        } elsif ( defined $cgi->param( 'move_left2' ) ) {
            $shift = -1 * $dist * 0.475;
        } elsif ( defined $cgi->param( 'move_left3' ) ) {
            $shift = -1 * $dist * 0.95;
        } elsif ( defined $cgi->param( 'move_right1' ) ) {
            $shift = $dist * 0.10;
        } elsif ( defined $cgi->param( 'move_right2' ) ) {
            $shift = $dist * 0.475;
        } elsif ( defined $cgi->param( 'move_right3' ) ) {
            $shift = $dist * 0.95;
        }

        if ( $shift )
        {
            $new_start = int( $start + $shift );
            $new_end   = int( $end   + $shift );

            print "HERRRR: shift: $shift    start: $new_start    end: $new_end\n";

            if ( $new_start > 0 and $new_end < $max )
            {
                $cgi->param( 'nav_start', $new_start );
                $cgi->param( 'nav_end',  $new_end );
            }
        }
    }
}


sub nav_def_clade
{
    my ( $cgi,   # CGI object
       ) = @_;

    my ( $def_clade );

    if ( defined $cgi->param( 'nav_clade' ) )
    {
        $def_clade = $cgi->param( 'nav_clade' );
    }
    else
    {
        $def_clade = "Bacteria";
    }

    return $def_clade;
}


sub nav_def_genome
{
    my ( $cgi,   # CGI object
       ) = @_;

    my ( $def_genome );

    if ( defined $cgi->param( 'nav_genome' ) )
    {
        $def_genome = $cgi->param( 'nav_genome' );
    }
    else
    {
        $def_genome = "S.aur_COL";
    }

    return $def_genome;
}


sub nav_def_assembly
{
    my ( $cgi,   # CGI object
       ) = @_;

    my ( $def_assembly );

    if ( defined $cgi->param( 'nav_assembly' ) )
    {
        $def_assembly = $cgi->param( 'nav_assembly' );
    }
    else
    {
        $def_assembly = "2009-01-23";
    }

    return $def_assembly;
}


sub nav_def_contig
{
    my ( $cgi,   # CGI object
       ) = @_;

    my ( $def_contig );

    if ( defined $cgi->param( 'nav_contig' ) )
    {
        $def_contig = $cgi->param( 'nav_contig' );
    }
    else
    {
        $def_contig = "chr1";
    }

    return $def_contig;
}


sub nav_def_start
{
    my ( $cgi,   # CGI object
       ) = @_;

    my ( $def_start );

    if ( defined $cgi->param( 'nav_start' ) ) {
        $def_start = $cgi->param( 'nav_start' );
    } else {
        $def_start = 1;
    }

    $def_start =~ tr/,//d;

    if ( $def_start <= 0 ) {
        $def_start = 1;
    }

    $cgi->param( 'nav_start', $def_start );

    return $def_start;
}


sub nav_def_end
{
    my ( $cgi,   # CGI object
       ) = @_;

    my ( $def_end );
    
    if ( defined $cgi->param( 'nav_end' ) ) {
        $def_end = $cgi->param( 'nav_end' );
    } else {
        $def_end = 2809422;
        $def_end = 2000;
    }

    $def_end =~ tr/,//d;

    if ( $def_end > 2809422 ) {
        $def_end = 2809422;
    }

    $cgi->param( 'nav_end', $def_end );

    return $def_end;
}


# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<


END
{
    Maasha::SQL::disconnect( $dbh ) if $dbh;
}


__END__